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Year

Author(s) [non member]

Title

Type

Abecasis, Gonçalo R.

2010

[Ellinghaus, Eva]
[Ellinghaus, David]
[Stuart, Philip E.]
[Nair, Rajan P.]
[Debrus, Sophie]
[Raelson, John V.]
[Belouchi, Majid]
[Fournier, Hélène]
[Reinhard, Claudia]
[Ding, Jun]
[Li, Yun]
[Tejasvi, Trilokraj]
[Gudjonsson, Johann]
[Stoll, Stefan W.]
[Voorhees, John J.]
[Lambert, Sylviane]
[Weidinger, Stephan]
[Eberlein, Bernadette]
[Kunz, Manfred]
[Rahman, Proton]
[Gladman, Dafna D.]
[Gieger, Christian]
[Wichmann, H. Erich]
[Karlsen, Tom H.]
Mayr, Gabriele
Albrecht, Mario
[Kabelitz, Dieter]
[Mrowietz, Ulrich]
[Abecasis, Gonçalo R.]
[Elder, James T.]
[Schreiber, Stefan]
[Weichenthal, Michael]
[Franke, Andre]

Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2
In: Nature Genetics [42], 991-995

Journal Article

Abreu, Vinícius A. C.

2012

[Soares, Siomar C.]
[Abreu, Vinícius A. C.]
[Ramos, Rommel T. J.]
[Cerdeira, Louise]
[Silva, Artur]
Baumbach, Jan
[Trost, Eva]
[Tauch, Andreas]
[Hirata, Raphael]
[Mattos-Guaraldi, Ana L.]
[Miyoshi, Anderson]
[Azevedo, Vasco]

PIPS: Pathogenicity Island Prediction Software
In: PLoS One [7], e30848,1-e30848,10

Electronic Journal Article

2011

[Ruiz, Jeronimo C.]
[D'Afonseca, Vivian]
[Silva, Artur]
[Ali, Amjad]
[Pinto, Anne C.]
[Santos, Anderson R.]
[Rocha, Aryanne A. M. C.]
[Lopes, Debora O.]
[Dorella, Fernanda A.]
[Pacheco, Luis G. C.]
[Costa, Marcilia P.]
[Turk, Meritxell Z.]
[Seyffert, Nubia]
[Moraes, Pablo M. R. O.]
[Soares, Siomar C.]
[Almeida, Sintia S.]
[Castro, Thiago L. P.]
[Abreu, Vinicius A. C.]
[Trost, Eva]
Baumbach, Jan
[Tauch, Andreas]
[Schneider, Maria P. C.]
[McCulloch, John]
[Cerdeira, Louise T.]
[Ramos, Rommel T. J.]
[Zerlotini, Adhemar]
[Dominitini, Anderson]
[Resende, Daniela M.]
[Coser, Elisangela M.]
[Oliveira, Luciana M.]
[Pedrosa, Andre L.]
[Vieira, Carlos U.]
[Guimaraes, Claudia T.]
[Bartholomeu, Daniela C.]
[Oliveira, Diana M.]
[Santos, Fabricio R.]
[Rabelo, Elida Mara]
[Lobo, Francisco P.]
[Franco, Gloria R.]
[Costa, Ana Flavia]
[Castro, Ieso M.]
[Dias, Silvia Regina]
[Ferro, Jesus A.]
[Ortega, Jose Miguel]
[Paiva, Luciano V.]
[Goulart, Luiz R.]
[Almeida, Juliana Franco]
[Ferro, Maria Ines]
[Carneiro, Newton P.]
[Falcao, Paula R. K.]
[Grynberg, Priscila]
[Teixeira, Santuza M. R.]
[Brommonschenkel, Sergio]
[Oliveira, Sergio C.]
[Meyer, Roberto]
[Moore, Robert J.]
[Miyoshi, Anderson]
[Oliveira, Guilherme C.]
[Azevedo, Vaco]

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Abril, JF

2013

[Steijger, T]
[Abril, JF]
[Engström,PG]
[Kokocinski, F]
[Abril, JF]
[Akerman, M]
[Alioto, T]
[Ambrosini, G]
[Antonarakis, SE]
[Behr, J]
[Bohnert, R]
[Bucher, P]
[Cloonan, N]
[Derrien, T]
[Djebali, S]
[Du, J]
[Dudoit, S]
[Engström, PG]
[Gerstein, M]
[Gingeras, TR]
[Gonzalez, D]
[Grimmond, SM]
[Habegger, L]
[Iseli, C]
[Jean, G]
[Kahles, A]
[Kokocinski, F]
[Lagarde, J]
[Leng, J]
[Lefebvre, G]
[Lewis, S]
[Mortazavi, A]
[Niermann, P]
[Rätsch, G]
[Reymond, A]
[Ribeca, P]
[Richard, H]
[Rougemont, J]
[Rozowsky, J]
[Sammeth, M]
[Sboner, A]
Schulz, Marcel Holger
[Searle, SM]
[Solorzano, ND]
[Solovyev, V]
[Stanke, M]
[Steijger, T]
[Stevenson, BJ]
[Stockinger, H]
[Valsesia, A]
[Weese, D]
[White, S]
[Wold, BJ]
[Wu, J]
[Wu, TD]
[Zeller, G]
[Zerbino, D]
[Zhang, MQ]
[Hubbard, TJ]
[Guigó, R]
[Harrow, J]
[Bertone, P]

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Achkar, Jean-Paul

2013

[Liu, Jimmy Z.]
[Hov, Johannes Roksund]
[Folseraas, Trine]
[Ellinghaus, Eva]
[Rushbrook, Simon M.]
Doncheva, Nadezhda T.
[Andreassen, Ole A.]
[Weersma, Rinse K.]
[Weismuller, Tobias J.]
[Eksteen, Bertus]
[Invernizzi, Pietro]
[Hirschfield, Gideon M.]
[Gotthardt, Daniel Nils]
[Pares, Albert]
[Ellinghaus, David]
[Shah, Tejas]
[Juran, Brian D.]
[Milkiewicz, Piotr]
[Rust, Christian]
[Schramm, Christoph]
[Muller, Tobias]
[Srivastava, Brijesh]
[Dalekos, Georgios]
[Nothen, Markus M.]
[Herms, Stefan]
[Winkelmann, Juliane]
[Mitrovic, Mitja]
[Braun, Felix]
[Ponsioen, Cyriel Y.]
[Croucher, Peter J. P.]
[Sterneck, Martina]
[Teufel, Andreas]
[Mason, Andrew L.]
[Saarela, Janna]
[Leppa, Virpi]
[Dorfman, Ruslan]
[Alvaro, Domenico]
[Floreani, Annarosa]
[Onengut-Gumuscu, Suna]
[Rich, Stephen S.]
[Thompson, Wesley K.]
[Schork, Andrew J.]
[Naess, Sigrid]
[Thomsen, Ingo]
Mayr, Gabriele
[Konig, Inke R.]
[Hveem, Kristian]
[Cleynen, Isabelle]
[Gutierrez-Achury, Javier]
[Ricano-Ponce, Isis]
[van Heel, David]
[Bjornsson, Einar]
[Sandford, Richard N.]
[Durie, Peter R.]
[Melum, Espen]
[Vatn, Morten H.]
[Silverberg, Mark S.]
[Duerr, Richard H.]
[Padyukov, Leonid]
[Brand, Stephan]
[Sans, Miquel]
[Annese, Vito]
[Achkar, Jean-Paul]
[Boberg, Kirsten Muri]
[Marschall, Hanns-Ulrich]
[Chazouilleres, Olivier]
[Bowlus, Christopher L.]
[Wijmenga, Cisca]
[Schrumpf, Erik]
[Vermeire, Severine]
Albrecht, Mario
[The UK-PSCSC Consortium,]
[The International IBD Genetics Consortium,]
[Rioux, John D.]
[Alexander, Graeme]
[Bergquist, Annika]
[Cho, Judy]
[Schreiber, Stefan]
[Manns, Michael P.]
[Farkkila, Martti]
[Dale, Anders M.]
[Chapman, Roger W.]
[Lazaridis, Konstantinos N.]
[The International PSC Study Group,]
[Franke, Andre]
[Anderson, Carl A.]
[Karlsen, Tom H.]

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Achten, Dominik

2013

[Radivojac, Predrag]
[Clark, Wyatt T]
[Oron, Tal Ronnen]
[Schnoes, Alexandra M]
[Wittkop, Tobias]
[Sokolov, Artem]
[Graim, Kiley]
[Funk, Christopher]
[Verspoor, Karin]
[Ben-Hur, Asa]
[Pandey, Gaurav]
[Yunes, Jeffrey M]
[Talwalkar, Ameet S]
[Repo, Susanna]
[Souza, Michael L]
[Piovesan, Damiano]
[Casadio, Rita]
[Wang, Zheng]
[Cheng, Jianlin]
[Fang, Hai]
[Gough, Julian]
[Koskinen, Patrik]
[T\"{o}r\"{o}nen, Petri]
[Nokso-Koivisto, Jussi]
[Holm, Liisa]
[Cozzetto, Domenico]
[Buchan, Daniel W A]
[Bryson, Kevin]
[Jones, David T]
[Limaye, Bhakti]
[Inamdar, Harshal]
[Datta, Avik]
[Manjari, Sunitha K]
[Joshi, Rajendra]
[Chitale, Meghana]
[Kihara, Daisuke]
[Lisewski, Andreas M]
[Erdin, Serkan]
[Venner, Eric]
[Lichtarge, Olivier]
[Rentzsch, Robert]
[Yang, Haixuan]
[Romero, Alfonso E]
[Bhat, Prajwal]
[Paccanaro, Alberto]
[Hamp, Tobias]
[Ka\ss ner, Rebecca]
[Seemayer, Stefan]
[Vicedo, Esmeralda]
[Schaefer, Christian]
[Achten, Dominik]
[Auer, Florian]
[Boehm, Ariane]
[Braun, Tatjana]
[Hecht, Maximilian]
[Heron, Mark]
[H\"{o}nigschmid, Peter]
[Hopf, Thomas A]
[Kaufmann, Stefanie]
[Kiening, Michael]
[Krompass, Denis]
[Landerer, Cedric]
[Mahlich, Yannick]
[Roos, Manfred]
[Bj\"{o}rne, Jari]
[Salakoski, Tapio]
[Wong, Andrew]
[Shatkay, Hagit]
Gatzmann, Fanny
Sommer, Ingolf
[Wass, Mark N]
[Sternberg, Michael J E]
[Skunca, Nives]
[Supek, Fran]
[Bo\v{s}njak, Matko]
[Panov, Pan\v{c}e]
[D\v{z}eroski, Sa\v{s}o]
[Smuc, Tomislav]
[Kourmpetis, Yiannis A I]
[van Dijk, Aalt D J]
[Braak, Cajo J F Ter]
[Zhou, Yuanpeng]
[Gong, Qingtian]
[Dong, Xinran]
[Tian, Weidong]
[Falda, Marco]
[Fontana, Paolo]
[Lavezzo, Enrico]
[{Di Camillo}, Barbara]
[Toppo, Stefano]
[Lan, Liang]
[Djuric, Nemanja]
[Guo, Yuhong]
[Vucetic, Slobodan]
[Bairoch, Amos]
[Linial, Michal]
[Babbitt, Patricia C]
[Brenner, Steven E]
[Orengo, Christine]
[Rost, Burkhard]
[Mooney, Sean D]
[Friedberg, Iddo]

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Ackermann, Oliver

2009

[Mihm, Ulrike]
[Ackermann, Oliver]
Welsch, Christoph
[Herrmann, Eva]
[Hofmann, Wolf Peter]
[Grigorian, Natalia]
[Welker, Martin Walter]
Lengauer, Thomas
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Clinical relevance of the 2'-5'-oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis C
In: Journal of Hepatology [50], 49-58

Journal Article

Adams, Ben

2009

McHardy, Alice C.
Adams, Ben

The role of genomics in tracking the evolution of influenza A virus
In: PLoS Pathog [5], e1000566

Electronic Journal Article

2009

Adams, Ben
McHardy, Alice
[Lundegaard, C.]
Lengauer, Thomas

Viral Bioinformatics
In: Modern Genome Annotation - The BioSapiens Network, 429-452

Part of a Book

Adams, David

2012

[Adams, David]
[Altucci, Lucia]
[Antonarakis, Stylianos E]
[Ballesteros, Juan]
[Beck, Stephan]
[Bird, Adrian]
Bock, Christoph
[Boehm, Bernhard]
[Campo, Elias]
[Caricasole, Andrea]
[Dahl, Fredrik]
[Dermitzakis, Emmanouil T]
[Enver, Tariq]
[Esteller, Manel]
[Estivill, Xavier]
[Ferguson-Smith, Anne]
[Fitzgibbon, Jude]
[Flicek, Paul]
[Giehl, Claudia]
[Graf, Thomas]
[Grosveld, Frank]
[Guigó, Roderic]
[Gut, Ivo]
[Helin, Kristian]
[Jarvius, Jonas]
[Küppers, Ralf]
[Lehrach, Hans]
Lengauer, Thomas
[Lernmark, Åke]
[Leslie, David]
[Loeffler, Markus]
[Macintyre, Elizabeth]
[Mai, Antonello]
[Martens, Joost H A]
[Minucci, Saverio]
[Ouwehand, Willem H]
[Pelicci, Pier Giuseppe]
[Pendeville, Hèléne]
[Porse, Bo]
[Rakyan, Vardhman]
[Reik, Wolf]
[Schrappe, Martin]
[Schübeler, Dirk]
[Seifert, Martin]
[Siebert, Reiner]
[Simmons, David]
[Soranzo, Nicole]
[Spicuglia, Salvatore]
[Stratton, Michael]
[Stunnenberg, Hendrik G]
[Tanay, Amos]
[Torrents, David]
[Valencia, Alfonso]
[Vellenga, Edo]
[Vingron, Martin]
[Walter, Jörn]
[Willcocks, Spike]

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Adams, Ortwin

2011

[Reuter, Stefan]
[Oette, Mark]
[Wilhelm, Frank Clemens]
Beggel, Bastian
[Kaiser, Rolf]
[Balduin, Melanie]
[Schweitzer, Finja]
[Verheyen, Jens]
[Adams, Ortwin]
Lengauer, Thomas
[Faetkenheuer, Gerd]
[Pfister, Herbert]
[Haeussinger, Dieter]

Erratum to: Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.
In: Medical Microbiology and Immunology [200], 51-51

Journal Article

2011

Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients
In: Medical Microbiology and Immunology [200], 39-49

Journal Article

Adolph, Hans-Werner

2003

[Olsen, Lars]
[Antony, Jens]
[Ryde, Ulf]
Adolph, Hans-Werner
[Hemmingsen, Lars]

Lactam hydrolysis catalyzed by mononuclear metallo-beta-lactamases: a density functional study
In: Journal of Physical Chemistry / B [107], 2366-2375

Journal Article

Agacfidan, Ali

2011

[Schülter, Eugen]
[Oette, Mark]
[Balduin, Melanie]
[Reuter, Stefan]
[Rockstroh, Jürgen]
[Fätkenheuer, Gerd]
[Esser, Stefan]
Lengauer, Thomas
[Agacfidan, Ali]
[Pfister, Herbert]
[Kaiser, Rolf]
[Akgul, Baki]

HIV prevalence and route of transmission in Turkish immigrants
living in North-Rhine Westphalia, Germany
In: Medical Microbiology and Immunology [200], 219-223

Journal Article

Agartz, Ingrid

2009

[Lawyer, Glenn]
[Nesvåg, Ragnar]
[Varnäs, Katarina]
[Okugawa, Gaku]
[Agartz, Ingrid]

Grey and white matter proportional relationships in the cerebellar vermis altered in schizophrenia
In: Cerebellum [8], 52-60

Journal Article

2009

[Lawyer, Glenn]
[Ferkingstad, Egil]
[Nesvåg, Rangan]
[Varnäs, Katarina]
[Agartz, Ingrid]

Local and covariate-modulated false discovery rates applied in neuroimaging
In: NeuroImage [47], 213-219

Journal Article

Agha-Golzadeh, Esmaeil

2011

[Ebrahimi, Mansou]
[Lakizadeh, Amir]
[Agha-Golzadeh, Esmaeil]
Ebrahimi, Mahdi

Prediction of Thermostability from Amino Acid Attributes by Combination of Clustering with Attribute Weighting: A New Vista in Engineering Enzymes
In: PLoS One [6], e23146,1-e23146,11

Electronic Journal Article

Agirre, Xabier

2012

[Fernandez, Agustin F.]
Assenov, Yassen
[Martin-Subero, Jose Ignacio]
[Balint, Balazs]
[Siebert, Reiner]
[Taniguchi, Hiroaki]
[Yamamoto, Hiroyuki]
[Hidalgo, Manuel]
[Tan, Aik-Choon]
[Galm, Oliver]
[Ferrer, Isidre]
[Sanchez-Cespedes, Montse]
[Villanueva, Alberto]
[Carmona, Javier]
[Sanchez-Mut, Jose V.]
[Berdasco, Maria]
[Moreno, Victor]
[Capella, Gabriel]
[Monk, David]
[Ballestar, Esteban]
[Ropero, Santiago]
[Martinez, Ramon]
[Sanchez-Carbayo, Marta]
[Prosper, Felipe]
[Agirre, Xabier]
[Fraga, Mario F.]
[Gran˜a, Osvaldo]
[Perez-Jurado, Luis]
[Mora, Jaume]
[Puig, Susana]
[Prat, Jaime]
[Badimon, Lina]
[Puca, Annibale A.]
[Meltzer, Stephen J.]
Lengauer, Thomas
[Bridgewater, John]
Bock, Christoph
[Esteller, Manel]

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Aharoni, Ehud

2009

[Prosperi, Mattia C. F.]
Altmann, André
[Rosen-Zvi, Michal]
[Aharoni, Ehud]
[Gabor, Borgulya]
[Fulop, Bazso]
[Sonnerborg, Anders]
[Schulter, Eugen]
[Struck, Daniel]
[Ulivi, Giovanni]
[Vandamme, Anne-Mieke]
[Vercauteren, Jurgen]
[Zazzi, Maurizio]

Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment
In: Antiviral Therapy [14], 433-442

Journal Article

2008

Altmann, Andre
[Rosen-Zvi, Michal]
[Prosperi, Mattia]
[Aharoni, Ehud]
[Neuvirth, Hani]
[Sönnerborg, Anders]
[Schülter, Eugen]
Büch, Joachim
[Struck, Daniel]
[Peres, Yardena]
[Incardona, Francesca]
[Kaiser, Rolf]
[Zazzi, Maurizio]
Lengauer, Thomas

Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy
In: PLoS ONE [3], e3470

Journal Article

2008

[Rosen-Zvi, Michal]
Altmann, Andre
[Prosperi, Mattia]
[Aharoni, Ehud]
[Neuvirth, Hani]
[Sönnerborg, Anders]
[Schülter, Eugen]
[Struck, Daniel]
[Peres, Yardena]
[Incardona, Francesca]
[Kaiser, Rolf]
[Zazzi, Maurizio]
Lengauer, Thomas

Selecting anti-HIV therapies based on a variety of genomic and clinical factors
In: Proceedings of the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), i399-406

Proceedings Article

2008

Altmann, Andre
[Rosen-Zvi, Michal]
[Prosperi, Mattia]
[Aharoni, Ehud]
[Neuvirth, Hani]
[Schülter, Eugen]
Büch, Joachim
[Peres, Yardena]
[Incardona, Incardona]
[Sönnerborg, Anders]
[Kaiser, Rolf]
[Zazzi, Maurizio]
Lengauer, Thomas

The EuResist approach for predicting response to anti HIV-1 therapy
In: Reviews in Antiviral Therapy, 107

Poster

2007

[Zazzi, Maurizio]
[Aharoni, Ehud]
[Altmann, Andre]
[Baszó, Fulop]
[Bidgood, Penny]
[Borgulya, Gabór]
[Denholm-Prince, J]
[Fielder, M]
[Kaiser, Rolf]
[Kent, Carmel]
[Lengauer, Thomas]
[Nepusz, T]
[Neuvirth, Hanni]
[Peres, Yardena]
[Petroczi, Andrea]
[Prosperi, Mattia]
[Romano, L]
[Rosen-Zvi, Michal]
[Schülter, Eugen]
Sing, Tobias
[Sonnerborg, Andras]
[Thompson, R]
[Ulivi, G]
[Zalány, L]
[Incardona, Francesca]

EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

Ahlenstiel, G.

2007

[Ahlenstiel, G.]
Roomp, Kirsten
Däumer, Martin
[Nattermann, T.]
[Vogel, M.]
[Rockstroh, J.K.]
Beerenwinkel, Niko
Kaiser, R.
[Nischalke, H.-D.]
[Sauerbruch, T.]
Lengauer, Thomas
[Spengler, U.]

Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level
In: Clinical and Vaccine Immunology [14], 1266-1273

Journal Article

Ahmad, Iqbal

2005

[Das, Ani V.]
[James, Jackson]
Rahnenführer, Jörg
[Thoresona, Wallace B.]
[Bhattacharyaa, Sumitra]
[Zhao, Xing]
[Ahmad, Iqbal]

Retinal properties and potential of the adult mammalian ciliary epithelium stem cells
In: Vision Research [45], 1653-1666

Journal Article

2004

[James, Jackson]
[Das, Ani V.]
Rahnenführer, Jörg
[Ahmad, Iqbal]

Cellular and Molecular Characterization of Early and Late Retinal Stem Cells/Progenitors: Differential Regulation of Proliferation and Context Dependent Role of Notch Signaling
In: Journal of Neurobiology [61], 359-376

Journal Article

2004

[James, Jackson]
[Das, Ani V.]
[Zhao, Xing]
Rahnenführer, Jörg
[Ahmad, Iqbal]

Identification of c-Kit receptor as a regulator of adult neural stem cells in the mammalian eye: interactions with Notch signaling
In: Developmental Biology [273], 87-105

Journal Article

2003

[James, Jackson]
Das, Ani V.
Rahnenführer, Jörg
[Leon, FAS]
[Ahmad, Iqbal]

Identification of rat brahma (rBRM), a subunit of SWI/SNF chromatin remodeling complex: Involvement in the differentiation of retinal stem cells/progenitors

Miscellaneous

Aigner, T.

2001

[Zien, Alexander]
[Aigner, T.]
[Zimmer, Ralf]
Lengauer, Thomas

Centralization: A biologically sensible method for the normalization of gene expression data
In: Bioinformatics [17], 323S-331S

Journal Article

Akerman, M

2013

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Akgul, Baki

2011

HIV prevalence and route of transmission in Turkish immigrants
living in North-Rhine Westphalia, Germany
In: Medical Microbiology and Immunology [200], 219-223

Journal Article

Akutsu, Tatsuya (ed.)

2008

Sander, Oliver
Domingues, Francisco S.
Zhu, Hongbo
Lengauer, Thomas
Sommer, Ingolf

Structural descriptors of protein-protein binding sites
In: Proceedings of 6th Asia-Pacific Bioinformatics Conference, 79-88

Proceedings Article

Albrecht, Felipe

2012

Halachev, Konstantin
[Bast, Hannah]
Albrecht, Felipe
Lengauer, Thomas
Bock, Christoph

EpiExplorer: live exploration and global analysis of large epigenomic datasets
In: Genome Biology [13], R96,1-R96,14

Electronic Journal Article

Albrecht, F.

2012

Halachev, K.
[Bast, H.]
Albrecht, F.
Lengauer, Thomas
Bock, Christoph

EpiExplorer: live exploration and global analysis of large epigenomic datasets
In: Genome Biology [13], R96,1-R96,14

Journal Article

Albrecht, Mario

2013

[Ellinghaus, David]
[Zhang, Hu]
[Zeissig, Sebastian]
[Lipinski, Simone]
[Till, Andreas]
[Jiang, Tao]
[Stade, Björn]
[Bromberg, Yana]
[Ellinghaus, Eva]
[Keller, Andreas]
[Rivas, Manuel A.]
[Skieceviciene, Jurgita]
Doncheva, Nadezhda T.
[Liu, Xiao]
[Liu, Qing]
[Jiang, Fuman]
[Forster, Michael]
Mayr, Gabriele
Albrecht, Mario
[Häsler, Robert]
[Boehm, Bernhard O.]
[Goodall, Jane]
[Berzuini, Carlo R.]
[Lee, James]
[Andersen, Vibeke]
[Vogel, Ulla]
[Kupcinskas, Limas]
[Kayser, Manfred]
[Krawczak, Michael]
[Nikolaus, Susanna]
[Weersma, Rinse K.]
[Ponsioen, Cyriel Y.]
[Sans, Miquel]
[Wijmenga, Cisca]
[Strachan, David P.]
[McArdle, Wendy L.]
[Vermeire, Séverine]
[Rutgeerts, Paul]
[Sanderson, Jeremy D.]
[Mathew, Christopher G.]
[Vatn, Morten H.]
[Wang, Jun]
[Nöthen, Markus M.]
[Duerr, Richard H.]
[Büning, Carsten]
[Brand, Stephan]
[Glas, Jürgen]
[Winkelmann, Juliane]
[Illig, Thomas]
[Latiano, Anna]
[Annese, Vito]
[Halfvarson, Jonas]
[D'Amato, Mauro]
[Daly, Mark J.]
[Nothnagel, Michael]
[Karlsen, Tom H.]
[Subramani, Suresh]
[Rosenstiel, Philip]
[Schreiber, Stefan]
[Parkes, Miles]
[Franke, Andre]

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

2013

Kacprowski, Tim
Doncheva, Nadezhda T.
Albrecht, Mario

NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules
In: Bioinformatics [29], 1471-1473

Journal Article

2013

[Zanon, Alessandra]
[Rakovic, Aleksandar]
[Blankenburg, Hagen]
Doncheva, Nadezhda T.
[Schwienbacher, Christine]
[Serafin, Alice]
Alexa, Adrian
[Weichenberger, Christian X.]
Albrecht, Mario
[Klein, Christine]
[Hicks, Andrew A.]
[Pramstaller, Peter P.]
[Domingues, Francisco S.]
[Pichler, Irene]

Profiling of parkin-binding partners using tandem affinity purification
In: PLoS ONE [8], 1-17

Journal Article

2012

Lengauer, Thomas
Albrecht, Mario
Domingues, Francisco S.

Computational Biology
In: Encyclopedia of Molecular Cell Biology and Molecular Medicine, 1-71

Part of a Book

2012

Emig, Dorothea
Blankenburg, Hagen
Ramírez, Fidel
Albrecht, Mario

Functional characterization of human genes from exon expression and RNA interference results
In: Bioinformatics and Drug Discovery, 33-53

Part of a Book

2012

[Faria, Daniel]
Schlicker, Andreas
[Pesquita, Catia]
[Bastos, Hugo]
[Ferreira, António E N]
Albrecht, Mario
[Falcão, André O]

Mining GO annotations for improving annotation consistency
In: PLoS ONE [7], e40519,1-e40519,7

Electronic Journal Article

2012

Ramírez, Fidel
Lawyer, Glenn
Albrecht, Mario

Novel search method for the discovery of functional relationships
In: Bioinformatics [28], 269-276

Journal Article

2012

Doncheva, Nadezhda T
Kacprowski, Tim
Albrecht, Mario

Recent approaches to the prioritization of candidate disease genes
In: Wiley Interdisciplinary Reviews: Systems Biology and Medicine [4], 429-442

Journal Article

2012

[Garai, Ágnes]
[Zeke, András]
[Gógl, Gergo]
[Töro, Imre]
[Fördos, Ferenc]
Blankenburg, Hagen
[Bárkai, Tünde]
[Varga, János]
[Alexa, Anita]
Emig, Dorothea
Albrecht, Mario
[Reményi, Attila]

Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove
In: Science Signaling [5], ra74,1-ra74,14

Journal Article

2012

Doncheva, Nadezhda T
Assenov, Yassen
[Domingues, Francisco S.]
Albrecht, Mario

Topological analysis and interactive visualization of biological networks and protein structures
In: Nature Protocols [7], 670-685

Journal Article

2011

Doncheva, Nadezhda T.
[Klein, Karsten]
Domingues, Francisco S.
Albrecht, Mario

Analyzing and visualizing residue networks of protein structures
In: Trends in Biochemical Sciences [36], 179-182

Journal Article

2011

[Wittkop, Tobias]
Emig, Dorothea
[Truss, Anke]
Albrecht, Mario
[Böcker, Sebastian]
Baumbach, Jan

Comprehensive cluster analysis with Transitivity Clustering
In: Nature Protocols [6], 285-295

Journal Article

2011

Nebot, Victoria
Ye, Min
Albrecht, Mario
Eom, Jae-Hong
Weikum, Gerhard

DIDO: a disease-determinants ontology from web sources
In: Proceedings of the 20th International Conference on World Wide Web (WWW 2011), 237-240

Proceedings Article

2011

Schelhorn, Sven-Eric
Mestre, Julián
Zotenko, Elena
Albrecht, Mario

Inferring physical protein contacts from large-scale purification data of protein complexes
In: Molecular & Cellular Proteomics [10], M110.004929,1-M110.004929,15

Electronic Journal Article

2011

Emig, Dorothea
Kacprowski, Tim
Albrecht, Mario

Measuring and analyzing tissue specificity of human genes and protein complexes
In: EURASIP Journal on Bioinformatics and Systems Biology [2011], 5,1-5,6

Journal Article

2011

[Aranda, Bruno]
Blankenburg, Hagen
[Kerrien, Samuel]
[Brinkman, Fiona S.]
[Ceol, Arnaud]
[Chautard, Emilie]
[Dana, Jose M.]
[De Las Rivas, Javier]
[Dumousseau, Marine]
[Galeota, Eugenia]
[Gaulton, Anna]
[Goll, Johannes]
[Hancock, Robert E. W.]
[Isserlin, Ruth]
[Jimenez, Rafael C.]
[Kerssemakers, Jules]
[Khadake, Jyoti]
[Lynn, David J.]
[Michaut, Magali]
[O'Kelly, Gavin]
[Ono, Keiichiro]
[Orchard, Sandra]
[Prieto, Carlos]
[Razick, Sabry]
[Rigina, Olga]
[Salwinski, Lukasz]
[Simonovic, Milan]
[Velankar, Sameer]
[Winter, Andrew]
[Wu, Guanming]
[Bader, Gary D.]
[Cesareni, Gianni]
[Donaldson, Ian M.]
[Eisenberg, David]
[Kleywegt, Gerard J.]
[Overington, John]
[Ricard-Blum, Sylvie]
[Tyers, Mike]
Albrecht, Mario
[Hermjakob, Henning]

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

2011

[Reiss, Simon]
[Rebhan, Ilka]
[Backes, Perdita]
[Romero-Brey, Ines]
[Erfle, Holger]
[Matula, Petr]
[Kaderali, Lars]
[Poenisch, Marion]
Blankenburg, Hagen
[Hiet, Marie-Sophie]
[Longerich, Thomas]
Diehl, Sarah
Ramírez, Fidel
[Balla, Tamas]
[Rohr, Karl]
[Kaul, Artur]
[Bühler, Sandra]
[Pepperkok, Rainer]
Lengauer, Thomas
Albrecht, Mario
[Eils, Roland]
[Schirmacher, Peter]
[Lohmann, Volker]
[Bartenschlager, Ralf]

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
In: Cell Host & Microbe [9], 32-45

Journal Article

2011

Emig, Dorothea
Sander, Oliver
Mayr, Gabriele
Albrecht, Mario

Structure collisions between interacting proteins
In: PLoS ONE [6], e19581,1-e19581,7

Electronic Journal Article

2011

Emig, Dorothea
Albrecht, Mario

Tissue-specific proteins and functional implications
In: Journal of Proteome Research [10], 1893-1903

Journal Article

2010

Emig, Dorothea
[Salomonis, Nathan]
[Baumbach, Jan]
Lengauer, Thomas
[Conklin, Bruce R.]
Albrecht, Mario

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
In: Nucleic Acids Research [38], W755-W762

Journal Article

2010

Albrecht, Mario

Color blindness
In: Nature Methods [7], 775

Journal Article

2010

[Welker, Martin-Walter]
[Welsch, Christoph]
[Meyer, Aline]
Antes, Iris
Albrecht, Mario
[Forestier, Nicole]
[Kronenberger, Bernd]
Lengauer, Thomas
[Piiper, Albrecht]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper
In: Protein Science [19], 1327-1336

Journal Article

2010

Ramírez, Fidel
Albrecht, Mario

Finding scaffold proteins in interactomes
In: Trends in Cell Biology [20], 2-4

Journal Article

2010

Schlicker, Andreas
Albrecht, Mario

FunSimMat update: new features for exploring functional similarity
In: Nucleic Acids Research [38], D244-D248

Journal Article

2010

[Franke, Andre]
[Balschun, Tobias]
[Sina, Christian]
[Ellinghaus, David]
[Häsler, Robert]
Mayr, Gabriele
Albrecht, Mario
[Wittig, Michael]
[Buchert, Eva]
[Nikolaus, Susanna]
[Gieger, Christian]
[Wichmann, H. Erich]
[Sventoraityte, Jurgita]
[Kupcinskas, Limas]
[Onnie, Clive M.]
[Gazouli, Maria]
[Anagnou, Nicholas P.]
[Strachan, David]
[McArdle, Wendy L.]
[Mathew, Christopher G.]
[Rutgeerts, Paul]
[Vermeire, Séverine]
[Vatn, Morten H.]
[Krawczak, Michael]
[Rosenstiel, Philip]
[Karlsen, Tom H.]
[Schreiber, Stefan]

Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL)
In: Nature Genetics [42], 292-294

Journal Article

2010

Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2
In: Nature Genetics [42], 991-995

Journal Article

2010

Schlicker, Andreas
Lengauer, Thomas
Albrecht, Mario

Improving disease gene prioritization using the semantic similarity of Gene Ontology terms
In: Bioinformatics [26], i561-i567

Journal Article

2010

[Brunner, Susanne]
[Hurni, Severine]
[Streckeisen, Philipp]
Mayr, Gabriele
Albrecht, Mario
[Yahiaoui, Nabila]
[Keller, Beat]

Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles
In: The Plant Journal [64], 433-445

Journal Article

2010

Emig, Dorothea
Kacprowski, Tim
Albrecht, Mario

Measuring and analyzing tissue specificity of human genes and protein complexes
In: Seventh International Workshop on Computational Systems
Biology, WCSB 2010, 27-30

Proceedings Article

2010

Albrecht, Mario
[Kerren, Andreas]
[Klein, Karsten]
[Kohlbacher, Oliver]
[Mutzel, Petra]
[Paul, Wolfgang]
[Schreiber, Falk]
[Wybrow, Michael]

On open problems in biological network visualization
In: Graph Drawing : 17th International Symposium, GD 2009, 256-267

Proceedings Article

2010

[Wittkop, Tobias]
Emig, Dorothea
[Lange, Sita]
[Rahmann, Sven]
Albrecht, Mario
[Morris, John H.]
[Böcker, Sebastian]
[Stoye, Jens]
Baumbach, Jan

Partitioning biological data with transitivity clustering
In: Nature Methods [7], 419-420

Journal Article

2009

Blankenburg, Hagen
Ramírez, Fidel
Büch, Joachim
Albrecht, Mario

DASMIweb: online integration, analysis and assessment of distributed protein interaction data
In: Nucleic Acids Research [37], W122-W128

Electronic Journal Article

2009

Blankenburg, Hagen
[Finn, Robert D.]
[Prlić, Andreas]
[Jenkinson, Andrew M.]
Ramírez, Fidel
Emig, Dorothea
Schelhorn, Sven-Eric
Büch, Joachim
Lengauer, Thomas
Albrecht, Mario

DASMI: exchanging, annotating and assessing molecular interaction data
In: Bioinformatics [25], 1321-1328

Journal Article

2009

[Frishman, Dmitrij]
Albrecht, Mario
Blankenburg, Hagen
[Bork, Peer]
[Harrington, Eoghan D.]
[Hermjakob, Henning]
[Jensen, Lars J.]
[Juan, David A.]
Lengauer, Thomas
[Pagel, Philipp]
[Schachter, Vincent]
[Valencia, Alfonso]

Protein-protein interactions: analysis and prediction
In: Modern Genome Annotation - The Biosapiens Network, 353-410

Part of a Book

2008

Schelhorn, Sven-Eric
Lengauer, Thomas
Albrecht, Mario

An integrative approach for predicting interactions of protein regions
In: Bioinformatics [24], i35-i41

Journal Article

2008

Assenov, Yassen
Ramírez, Fidel
Schelhorn, Sven-Eric
Lengauer, Thomas
Albrecht, Mario

Computing topological parameters of biological networks
In: Bioinformatics [24], 282-284

Journal Article

2008

Schlicker, Andreas
Albrecht, Mario

FunSimMat: a comprehensive functional similarity database
In: Nucleic Acids Research [36], D434-D439

Journal Article

2008

[Jenkinson, Andrew M.]
Albrecht, Mario
[Birney, Ewan]
Blankenburg, Hagen
[Down, Thomas]
[Finn, Robert D.]
[Hermjakob, Henning]
[Hubbard, Tim J. P.]
[Jimenez, Rafael C.]
[Jones, Philip]
[Kähäri, Andreas]
[Kulesha, Eugene]
[Macías, José R.]
[Reeves, Gabrielle A.]
[Prlić, Andreas]

Integrating biological data - the Distributed Annotation System
In: BMC Bioinformatics [9], S3.1-7

Journal Article

2008

Emig, Dorothea
[Cline, Melissa S.]
Lengauer, Thomas
Albrecht, Mario

Integrating expression data with domain interaction networks
In: Bioinformatics [24], 2546-2548

Journal Article

2008

Emig, Dorothea
[Cline, Melissa S.]
[Klein, Karsten]
[Kunert, Anne]
[Mutzel, Petra]
Lengauer, Thomas
Albrecht, Mario

Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks
In: Journal of Integrative Bioinformatics [5], 101-115

Journal Article

2008

[Welsch, Christoph]
Domingues, Francisco S.
[Susser, Simone]
Antes, Iris
Hartmann, Christoph
Mayr, Gabriele
Schlicker, Andreas
[Sarrazin, Christoph]
Albrecht, Mario
[Zeuzem, Stefan]
Lengauer, Thomas

Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of HCV
In: Genome Biology [9], R16

Journal Article

2008

[Franke, Andre]
[Balschun, Tobias]
[Karlsen, Tom H.]
[Sventoraityte, Jurgita]
[Nikolaus, Susanna]
Mayr, Gabriele
Domingues, Francisco S.
Albrecht, Mario
[Nothnagel, Michael]
[Ellinghaus, David]
[Sina, Christian]
[Onnie, Clive M.]
[Weersma, Rinse K.]
[Stokkers, Pieter C. F.]
[Wijmenga, Cisca]
[Gazouli, Maria]
[Strachan, David]
[McArdle, Wendy L.]
[Vermeire, Séverine]
[Rutgeers, Paul]
[Rosenstiel, Philip]
[Krawczak, Michael]
[Vatn, Morten H.]
[IBSEN study group, the]
[Mathew, Christopher G.]
[Schreiber, Stefan]

Sequence variants in IL10, ARPC2, and multiple other loci contribute to ulcerative colitis
In: Nature Genetics [40], 1319-1323

Journal Article

2008

[Van Ooijen, Gerben]
Mayr, Gabriele
[Kasiem, Mobien M. A.]
Albrecht, Mario
[Cornelissen, Ben J. C.]
[Takken, Frank L. W.]

Structure-function analysis of the NB-ARC domain of plant disease resistance proteins
In: Journal of Experimental Botany [59], 1383-1397

Journal Article

2008

[Van Ooijen, Gerben]
Mayr, Gabriele
Albrecht, Mario
[Cornelissen, Ben J. C.]
[Takken, Frank L. W.]

Transcomplementation, but not physical association of the CC-NB-ARC and LRR domains of tomato R protein Mi-1.2 is altered by mutations in the ARC2 subdomain
In: Molecular Plant [1], 401-410

Journal Article

2008

Emig, Dorothea
[Klein, Karsten]
[Kunert, Anne]
[Mutzel, Petra]
Albrecht, Mario

Visualizing domain interaction networks and the impact of alternative splicing events
In: Proceedings of the 5th International Conference on BioMedical Visualization (MediVis): Information Visualization in Medical and Biomedical Informatics, 36-43

Proceedings Article

2007

[Hampe, Jochen]
[Franke, Andre]
[Rosenstiel, Philip]
[Till, Andreas]
[Teuber, Markus]
[Huse, Klaus]
Albrecht, Mario
Mayr, Gabriele
[De La Vega, Francisco M.]
[Briggs, Jason]
[Günther, Simone]
[Prescott, Natalie J.]
[Onnie, Clive M.]
[Häsler, Robert]
[Sipos, Bence]
[Fölsch, Ulrich R.]
Lengauer, Thomas
[Platzer, Matthias]
[Mathew, Christopher G.]
[Krawczak, Michael]
[Schreiber, Stefan]

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1
In: Nature Genetics [39], 207-211

Journal Article

2007

[Salamat-Miller, Nazila]
[Fang, Jianwen]
[Seidel, Christopher W.]
Assenov, Yassen
Albrecht, Mario
[Middaugh, C. Russell]

A network-based analysis of polyanion-binding proteins utilizing human protein arrays
In: Journal of Biological Chemistry [282], 10153-10163

Journal Article

2007

Ramírez, Fidel
Schlicker, Andreas
Assenov, Yassen
Lengauer, Thomas
Albrecht, Mario

Computational analysis of human protein interaction networks
In: Proteomics [7], 2541-2552

Journal Article

2007

Schlicker, Andreas
Huthmacher, Carola
Ramírez, Fidel
Lengauer, Thomas
Albrecht, Mario

Functional evaluation of domain-domain interactions and human protein interaction networks
In: Bioinformatics [23], 859-865

Journal Article

2007

Schlicker, Andreas
Rahnenführer, Jörg
Albrecht, Mario
Lengauer, Thomas
Domingues, Francisco S.

GOTax: investigating biological processes and biochemical activities along the taxonomic tree
In: Genome Biology [8], R33.1-10

Electronic Journal Article

2007

[Scheller, Nicoletta]
[Resa-Infante, Patricia]
[de la Luna, Susana]
[Galao, Rui Pedro]
Albrecht, Mario
[Kaestner, Lars]
[Lipp, Peter]
Lengauer, Thomas
[Meyerhans, Andreas]
[Díez, Juana]

Identification of PatL1, a human homolog to yeast P body component Pat1
In: Biochimica et Biophysica Acta - Molecular Cell Research [1773], 1786-1792

Journal Article

2007

Welsch, Christoph
Albrecht, Mario
Maydt, Jochen
[Herrmann, E.]
[Welker, M.W.]
[Sarrazin, C.]
[Scheidig, A.]
Lengauer, Thomas
Zeuzem, S.

Structural and functional comparison of the non-structural protein 4B of flaviviridae
In: Journal of Molecular Graphics and Modeling [26], 546-557

Journal Article

2007

[Franke, Andre]
[Hampe, Jochen]
[Rosenstiel, Philip]
[Becker, Christoph]
[Wagner, Florian]
[Häsler, Robert]
[Little, Randall D.]
[Huse, Klaus]
[Ruether, Andreas]
[Balschun, Tobias]
[Wittig, Michael]
[ElSharawy, Abdou]
Mayr, Gabriele
Albrecht, Mario
[Prescott, Natalie J.]
[Onnie, Clive M.]
[Fournier, Hélène]
[Keith, Tim]
[Radelof, Uwe]
[Platzer, Matthias]
[Mathew, Christopher G.]
[Stoll, Monika]
[Krawczak, Michael]
[Nürnberg, Peter]
[Schreiber, Stefan]

Systematic association mapping identifies NELL1 as a novel IBD disease gene
In: PLoS ONE [2], e691.1-13

Journal Article

2007

[Tress, Michael L.]
[Martelli, Pier L.]
[Frankish, Adam]
[Reeves, Gabrielle A.]
[Wesselink, Jan J.]
[Yeats, Corin]
[Ólason, Páll Í.]
Albrecht, Mario
[Hegyi, Hedi]
[Giorgetti, Alejandro]
[Raimondo, Domenico]
[Lagarde, Julien]
[Laskowski, Roman A.]
[López, Gonzalo]
[Sadowski, Michael I.]
[Watson, James D.]
[Fariselli, Piero]
[Rossi, Ivan]
[Nagy, Alinda]
[Kai, Wang]
[Størling, Zenia]
[Orsini, Massimiliano]
Assenov, Yassen
Blankenburg, Hagen
Huthmacher, Carola
Ramírez, Fidel
Schlicker, Andreas
[Denoued, France]
[Jones, Phil]
[Kerrien, Samuel]
[Orchard, Sandra]
[Antonarakis, Stylianos E.]
[Reymond, Alexandre]
[Birney, Ewan]
[Brunak, Søren]
[Casadio, Rita]
[Guigo, Roderic]
[Harrow, Jennifer]
[Hermjakob, Henning]
[Jones, David T.]
Lengauer, Thomas
[Orengo, Christine A.]
[Patthy, László]
[Thornton, Janet M.]
[Tramontano, Anna]
[Valencia, Alfonso]

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

2007

[Söderhäll, Cilla]
[Marenholz, Ingo]
[Kerscher, Tamara]
[Rüschendorf, Franz]
[Esparza-Gordillo, Jorge]
[Worm, Margitta]
[Gruber, Christoph]
Mayr, Gabriele
Albrecht, Mario
[Rohde, Klaus]
[Schulz, Herbert]
[Wahn, Ulrich]
[Hubner, Norbert]
[Lee, Young-Ae]

Variants in a novel epidermal collagen gene (COL29A1) are associated with atopic dermatitis
In: PLoS Biology [5], e242.1952-1961

Journal Article

2006

[Salamat-Miller, Nazila]
[Fang, Jianwen]
[Seidel, Christopher W.]
[Smalter, Aaron M.]
[Assenov, Yassen]
Albrecht, Mario
[Middaugh, C. Russell]

A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays
In: Molecular and Cellular Proteomics [5], 2263-2278

Journal Article

2006

[Mihm, Ulrike]
[Grigorian, Natalia]
[Welsch, Christoph]
[Herrmann, Eva]
[Kronenberger, Bernd]
[Teuber, Gerlinde]
[von Wagner, Michael]
[Hofmann, Wolf-Peter]
Albrecht, Mario
Lengauer, Thomas
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Amino acid variations in hepatitis C virus p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C
In: Antiviral Therapy [11], 507-519

Journal Article

2006

[Boeddrich, Annett]
[Gaumer, Sébastien]
[Haacke, Annette]
[Tzvetkov, Nikolay]
Albrecht, Mario
[Evert, Bernd O.]
[Müller, Eva C.]
[Lurz, Rudi]
[Breuer, Peter]
[Schugardt, Nancy]
[Plaßmann, Stephanie]
[Xu, Kexiang]
[Warrick, John M.]
[Suopanki, Jaana]
[Wüllner, Ullrich]
[Frank, Ronald]
[Hartl, Ulrich F.]
[Bonini, Nancy M.]
[Wanker, Erich E.]

An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis
In: EMBO Journal [25], 1547-1558

Journal Article

2006

Albrecht, Mario

Combining protein structure prediction with experiments and functional information
Universität des Saarlandes

Thesis - PhD thesis

2006

Schlicker, Andreas
Huthmacher, Carola
Ramírez, Fidel
Lengauer, Thomas
Albrecht, Mario

Functional evaluation of domain-domain interactions and human protein interaction networks
In: German Conference on Bioinformatics (GCB 2006), 115-126

Proceedings Article

2006

[Plotz, Guido]
[Welsch, Christoph]
[Giron-Monzon, Luis]
[Friedhoff, Peter]
Albrecht, Mario
[Piiper, Albrecht]
Biondi, Ricardo M.
Lengauer, Thomas
[Zeuzem, Stefan]
[Raedle, Jochen]

Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair
In: Nucleic Acids Research [34], 6574-6586

Journal Article

2006

[Tameling, Wladimir I.]
[Vossen, Jack H.]
Albrecht, Mario
Lengauer, Thomas
[Berden, Jan A.]
[Haring, Michel A.]
[Cornelissen, Ben J.C.]
Takken, Frank L. W.

Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation
In: Plant Physiology [140], 1233-1245

Journal Article

2006

Takken, Frank L. W.
Albrecht, Mario
[Tameling, Wladimir I.]

Resistance proteins: molecular switches of plant defence
In: Current Opinion in Plant Biology [9], 383-390

Journal Article

2006

Albrecht, Mario
[Takken, Frank L. W.]

Update on the domain architectures of NLRs and R proteins
In: Biochemical and Biophysical Research Communications [339], 459-462

Journal Article

2005

[Van Duist, Marjan M.]
Albrecht, Mario
[Podswiadek, Marta]
[Giachino, Daniela]
Lengauer, Thomas
[Punzi, Leonardo]
[De Marchi, Mario]

A new CARD15 mutation in Blau syndrome
In: European Journal of Human Genetics [13], 742-747

Journal Article

2005

[Ralser, Markus]
Albrecht, Mario
[Nonhoff, Ute]
Lengauer, Thomas
[Lehrach, Hans]
[Krobitsch, Sylvia]

An integrative approach to gain insights into the cellular function of human ataxin-2
In: Journal of Molecular Biology [346], 203-214

Journal Article

2005

[Ralser, Markus]
[Nonhoff, Ute]
Albrecht, Mario
Lengauer, Thomas
[Wanker, Erich E.]
[Lehrach, Hans]
[Krobitsch, Sylvia]

Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways
In: Human Molecular Genetics [14], 2893-2909

Journal Article

2005

[Sarrazin, Christoph]
[Mihm, Ulrike]
[Herrmann, Eva]
[Welsch, Christoph]
Albrecht, Mario
[Sarrazin, Ulrike]
[Traver, Stella]
Lengauer, Thomas
[Zeuzem, Stefan]

Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection
In: The Journal of Infectious Diseases [192], 1710-1719

Journal Article

2005

Lengauer, Thomas
Albrecht, Mario
[Sarrazin, C.]
[Mihm, U.]
[Herrmann, E.]
Welsch, Christoph
[Sarrazin, U.]
[Traver, S.]
[Zeuzem, S.]

Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection.
In: Journal of Infectious Diseases [192], 1710-1719

Journal Article

2005

Albrecht, Mario
Huthmacher, Carola
[Tosatto, Silvio C.E.]
Lengauer, Thomas

Decomposing protein networks into domain-domain interactions
In: Bioinformatics [21], ii220-ii221

Journal Article

2005

[Costello, Christine M.]
[Mah, Nancy]
[Häsler, Robert]
[Rosenstiel, Philip]
[Waetzig, Georg H.]
Hahn, Andreas
[Lu, Tim]
[Gurbuz, Yesim]
[Nikolaus, Susanna]
Albrecht, Mario
[Hampe, Jochen]
[Lucius, Ralph]
[Klöppel, Günther]
[Eickhoff, Holger]
[Lehrach, Hans]
Lengauer, Thomas
[Schreiber, Stefan]

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays identifies novel candidate disease genes
In: PLoS Medicine [2], 771-787

Journal Article

2005

[Castellano, Sergi]
[Lobanov, Alexey V.]
[Chapple, Charles]
[Novoselov, Sergey V.]
Albrecht, Mario
[Hua, Deame]
[Lescure, Alain]
Lengauer, Thomas
[Krol, Alain]
[Gladyshev, Vadim N.]
[Guigó, Roderic]

Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family
In: Proceedings of the National Academy of Sciences [102], 16188-16193

Journal Article

2005

[Schreiber, Stefan]
[Rosenstiel, Philip]
Albrecht, Mario
[Hampe, Jochen]
[Krawczak, Michael]

Genetics of Crohn disease, an archetypal inflammatory barrier disease
In: Nature Reviews Genetics [6], 376-388

Journal Article

2005

Albrecht, Mario

LRRK2 mutations and parkinsonism
In: The Lancet [365], 1230

Journal Article

2005

[Valentonyte, Ruta]
[Hampe, Jochen]
[Huse, Klaus]
[Rosenstiel, Philip]
Albrecht, Mario
[Stenzel, Annette]
[Nagy, Marion]
[Gaede, Karoline I.]
[Franke, Andre]
[Haesler, Robert]
[Koch, Andreas]
Lengauer, Thomas
[Seegert, Dirk]
[Reiling, Norbert]
[Ehlers, Stefan]
[Schwinger, Eberhard]
[Platzer, Mathias]
[Krawczak, Michael]
[Müller-Quernheim, Joachim]
[Schürmann, Manfred]
[Schreiber, Stefan]

Sarcoidosis is associated with a truncating splice site mutation in BTNL2
In: Nature Genetics [37], 357-364

Journal Article

2005

[Bojunga, Jörg]
[Welsch, Christoph]
Antes, Iris
Albrecht, Mario
Lengauer, Thomas
[Zeuzem, Stefan]

Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency
In: Human Genetics [117], 558-564

Journal Article

2005

Albrecht, Mario
[Choubey, Divaker]
Lengauer, Thomas

The HIN domain of IFI-200 proteins consists of two OB folds
In: Biochemical and Biophysical Research Communications [327], 679-687

Journal Article

2004

[Stoll, Monika]
[Corneliussen, Brit]
[Costello, Christine M.]
[Waetzig, Georg H.]
[Mellgard, Bjorn]
[Koch, W. Andreas]
[Rosenstiel, Philip]
Albrecht, Mario
[Croucher, Peter J.P.]
[Seegert, Dirk]
[Nikolaus, Susanna]
[Hampe, Jochen]
Lengauer, Thomas
[Pierrou, Stefan]
[Foelsch, Ulrich R.]
[Mathew, Christopher G.]
[Lagerstrom-Fermer, Maria]
[Schreiber, Stefan]

Genetic variation in DLG5 is associated with inflammatory bowel disease
In: Nature Genetics [36], 376-380

Journal Article

2004

Albrecht, Mario
Lengauer, Thomas

Novel Sm-like proteins with long C-terminal tails and associated methyltransferases
In: FEBS Letters [569], 18-26

Journal Article

2004

Albrecht, Mario
[Golatta, Michael]
[Wüllner, Ullrich]
Lengauer, Thomas

Structural and functional analysis of ataxin-2 and ataxin-3
In: European Journal of Biochemistry [271], 3155-3170

Journal Article

2004

Albrecht, Mario
Lengauer, Thomas

Survey on the PABC recognition motif PAM2
In: Biochemical and Biophysical Research Communications [316], 129-138

Journal Article

2003

Albrecht, Mario
Lengauer, Thomas
[Schreiber, Stefan]

Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence
In: Bioinformatics [19], 2171-2175

Journal Article

2003

Albrecht, Mario
Domingues, Francisco S.
[Schreiber, Stefan]
Lengauer, Thomas

Identification of mammalian orthologs associates PYPAF5 with distinct functional roles
In: FEBS Letters [538], 173-177

Journal Article

2003

Albrecht, Mario
Lengauer, Thomas

Pyranose oxidase identified as a member of the GMC oxidoreductase family
In: Bioinformatics [19], 1216-1220

Journal Article

2003

Albrecht, Mario
[Tosatto, Silvio C.E.]
Lengauer, Thomas
[Valle, Giorgio]

Simple consensus procedures are effective and sufficient in secondary structure prediction
In: Protein Engineering [16], 459-462

Journal Article

2003

Albrecht, Mario
Domingues, Francisco S.
[Schreiber, Stefan]
Lengauer, Thomas

Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2
In: FEBS Letters [554], 520-528

Journal Article

2003

Albrecht, Mario
[Hoffmann, Daniel]
[Evert, Bernd O.]
[Schmitt, Ina]
[Wüllner, Ullrich]
Lengauer, Thomas

Structural modeling of ataxin-3 reveals distant homology to adaptins
In: Proteins: Structure, Function, and Genetics [50], 355-370

Journal Article

2002

[Hoffmann, Daniel]
[Schnaible, Volker]
[Wefing, Stephan,]
Albrecht, Mario
[Hanisch, Daniel]
[Zimmer, Ralf]

A new method for the fast solution of protein-3D-structures, combining experiments and bioinformatics
In: Coupling of Biological and Electronic Systems: Proceedings of the 2nd Caesarium, Bonn, 1-3 November 2000, 59-78

Proceedings Article

2002

Albrecht, Mario
[Hanisch, Daniel]
[Zimmer, Ralf]
Lengauer, Thomas

Improving fold recognition of protein threading by experimental distance constraints
In: In Silico Biology [2], 325-337

Journal Article

Alcaraz, Nicolas

2012

Alcaraz, Nicolas
Kucuk, Hande
[Weile, Jochen]
[Wipat, Anil]
Baumbach, Jan

KeyPathwayMiner - Detecting case-specific biological pathways by using expression data
In: Internet Mathematics [7], 299-313

Journal Article

Alcaro, Stefano

2011

[Alcaro, Stefano]
[Alteri, Claudia]
[Artese, Anna]
[Ceccherini-Silberstein, Francesca]
[Costa, Giosuè]
[Ortuso, Francesco]
[Forbici, Federica]
[Santoro, Maria Mercedes]
[Parrotta, Lucia]
[Flandre, Philippe]
[Descamps, Diane]
[Calvez, Vincent]
[Marcelin, Anne-Genevieve]
[Perno, Carlo Federico]
Sing, Tobias
[Svicher, Valentina]

Docking Analysis and Resistance Evaluation of Clinically Relevant Mutations Associated with the HIV-1 Nonnucleoside Reverse Transcriptase Inhibitors Nevirapine, Efavirenz and Etravirine
In: ChemMedChem [6], 2203-2213

Journal Article

2009

[Alcaro, Stefano]
[Artese, Anna]
[Ceccherini-Silberstein, Francesca]
[Ortuso, Francesca]
[Perno, Carlo Federico]
Sing, Tobias
[Svicher, Valentina]

Molecular Dynamics and Free Energy Studies on the Wild-Type and Mutated HIV-1
Protease Complexed with Four Approved Drugs: Mechanism of Binding and
In: Journal of Chemical Information and Modeling [49], 1751-1761

Journal Article

2007

[Ceccherini-Silberstein, Francesca]
[Svicher, Valentina]
Sing, Tobias
[Artese, Anna]
[Santoro, Maria Mercedes]
[Forbici, Federica]
[Bertoli, Ada]
[Alcaro, Stefano]
[Palamara, Guido]
[Monforte, Antonella d'Arminio]
[Balzarini, Jan]
[Antinori, Andrea]
Lengauer, Thomas
[Perno, Carlo Federico]

Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of restistance to nonnucleoside inhibitors
In: Journal of Virology [81], 11507-11519

Journal Article

Alexander, Graeme

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Alexa, Adrian

2013

Profiling of parkin-binding partners using tandem affinity purification
In: PLoS ONE [8], 1-17

Journal Article

2008

[Hornstein, Max]
[Hoffmann, Michele J.]
Alexa, Adrian
[Yamanaka, Masanori]
[Müller, Mirko]
[Jung, Volker]
[Rahnenführer, Jörg]
[Schulz, Wolfgang A.]

Protein phosphatase and TRAIL receptor genes as new candidate tumor genes on chromosome 8p in prostate cancer
In: Cancer Genomics & Proteomics [5], 123-136

Journal Article

2008

Bogojeska, Jasmina
Alexa, Adrian
Altmann, André
Lengauer, Thomas
[Rahnenführer, Jörg]

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
In: Bioinformatics [24], 2391-2392

Journal Article

2007

[Schulz, Wolfgang A.]
Alexa, Adrian
[Jung, Volker]
[Hader, Christiane]
[Hoffmann, Michele J.]
[Yamanaka, Masanori]
[Fritzsche, Sandy]
[Wlazlinski, Agnes]
[Müller, Mirko]
Lengauer, Thomas
[Engers, Rainer]
[Florl, Andrea R.]
[Wullich, Bernd]
Rahnenführer, Jörg

Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer
In: Molecular Cancer [6], 1-16

Journal Article

2006

Alexa, Adrian
Rahnenführer, Jörg
Lengauer, Thomas

Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating GO Graph Structure
In: Bioinformatics [22], 1600-1607

Journal Article

2005

Alexa, Adrian

Integrating the GO graph structure in scoring the
significance of Gene Ontology terms
Universität des Saarlandes

Thesis - Masters thesis

Alexa, Anita

2012

[Garai, Ágnes]
[Zeke, András]
[Gógl, Gergo]
[Töro, Imre]
[Fördos, Ferenc]
Blankenburg, Hagen
[Bárkai, Tünde]
[Varga, János]
[Alexa, Anita]
Emig, Dorothea
Albrecht, Mario
[Reményi, Attila]

Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove
In: Science Signaling [5], ra74,1-ra74,14

Journal Article

Alioto, T

2013

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Ali, Amjad

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Almeida, Juliana Franco

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Almeida, Sintia S.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Alteri, Claudia

2011

Journal Article

Altmann, Andre

2012

[Oette, Mark]
[Schulter, Eugen]
[Rosen-Zvi, Michal]
[Peres, Yardena]
[Zazzi, Maurizio]
[Sonnerborg, Anders]
[Struck, Daniel]
Altmann, Andre
[Kaiser, Rolf]

Efficacy of antiretroviral therapy switch in HIV-infected patients: A 10-year analysis of the EuResist cohort
In: Intervirology [55], 160-166

Journal Article

2012

[Zazzi, Maurizio]
[Incardona, Francesca]
[Rosen-Zvi, Michal]
[Prosperi, Mattia]
Lengauer, Thomas
Altmann, Andre
[Sonnerborg, Anders]
[Lavee, Tamar]
[Schülter, Eugen]
[Kaiser, Rolf]

Predicting Response to Antiretroviral Treatment by Machine Learning:
The EuResist Project
In: Intervirology [55], 123-127

Journal Article

2011

Pironti, Alejandro
Altmann, André
Büch, Joachim
Lengauer, Thomas

A Computational Method for Predicting First-Line Antiretroviral Therapy Success
In: Abstract Book. 9th Workshop on HIV & Hepatitis Treatment Strategies & Antiviral Drug Resistance, 94

Poster

2011

Lawyer, Glenn
Altmann, André
Thielen, Alex
[Zazzi, Maurizio]
[Sönnerborg, Anders]
Lengauer, Thomas

HIV-1 mutational pathways under multidrug therapy
In: AIDS Research and Therapy [8], 1-13

Journal Article

2011

Saigo, Hiroto
Altmann, André
Bogojeska, Jasmina
Müller, Fabian
[Nowozin, Sebastian]
Lengauer, Thomas

Learning from past treatments and their outcome improves prediction of In Vivo response to anti-HIV therapy
In: Statistical Applications in Genetics and Molecular Biology [10], 1-32

Electronic Journal Article

2011

[Zazzi, M.]
[Kaiser, R.]
[Sönnerborg, A.]
[Struck, D]
Altmann, Andre
[Prosperi, M.]
[Rosen-Zvi, M.]
[Petroczi, A.]
[Peres, Y.]
[Schülter, E.]
[Boucher, C.A.]
[Brun-Vezinet, F.]
[Harrigan, R.]
[Morris, L.]
[Obermeier, M.]
[Perno, C.-F.]
[Phanuphak, P.]
[Pillay, D]
[Shafer, R.W.]
[Vandamme, A.-M.]
[Van Laethem, K.]
[Wensing, A.]
Lengauer, Thomas
[Incardona, F.]

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

2010

[Prosperi, Mattia C. F.]
[Rosen-Zvi, Michal]
Altmann, Andre
[Zazzi, Maurizio]
[Di Giambenedetto, Simona]
[Kaiser, Rolf]
[Schülter, Eugen]
[Struck, Daniel]
[Sloot, Peter]
[van de Vijver, David A.]
[Vandamme, Anne-Mieke]
[Sönnerborg, Anders]

Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models
In: PLoS ONE [5], e13753,1-e13753,8

Electronic Journal Article

2010

Altmann, André

Bioinformatical approaches to ranking of anti-HIV combination therapies and planning of treatment schedules
Universität des Saarlandes

Thesis - PhD thesis

2010

Lengauer, Thomas
Altmann, André
Thielen, Alexander
[Kaiser, Rolf]

Chasing the AIDS Virus
In: Communications of the ACM [53], 66-74

Journal Article

2010

Bogojeska, Jasmina
[Bickel, Steffen]
Altmann, André
Lengauer, Thomas

Dealing with sparse data in predicting outcomes of HIV combination therapies
In: Bioinformatics [26], 2085-2092

Journal Article

2010

Altmann, Andre
Pironti, Alejandro
Perner, Juliane
Büch, Joachim
Lengauer, Thomas

Determination of clinically relevant cutoffs for HIV-1 phenotypic resistance estimates through a combined analysis of clinical trial and cohort data
In: Abstract Book. 8th European Drug Resistance Workshop, 46

Poster

2010

Weisser, Hendrik
Altmann, André
[Sierra, Saleta]
[Incardona, Francesca]
[Struck, Daniel]
[Sönnerborg, Anders]
[Kaiser, Rolf]
[Zazzi, Maurizio]
[Tschochner, Monika]
[Walter, Hauke]
Lengauer, Thomas

Only Slight Impact of Predicted Replicative Capacity for Therapy Response Prediction
In: PLoSOne [5], e9044,1-e9044,10

Electronic Journal Article

2010

Altmann, André
Tolosi, Laura
Sander, Oliver
Lengauer, Thomas

Permutation importance: an unbiased feature importance measure
In: Bioinformatics [26], 1340-1347

Journal Article

2010

[Zazzi, Maurizio]
[Kaiser, Rolf]
[Sönnerborg, Anders]
[Struck, Daniel]
Altmann, Andre
[Prosperi, Mattia C. F.]
[Rosen-Zvi, Michal]
[Petroczi, Andrea]
[Peres, Yardena]
[Schülter, Eugen]
[Boucher, Charles]
[Brun-Vezinet, Francoise]
[Harigan, Richard]
[Morris, Lynn]
[Obermeier, Martin]
[Perno, Federico]
[Shafer, Robert]
[Vandamme, Anne-Mieke]
[van Laethem, Kristel]
[Wensing, Annemarie]
Lengauer, Thomas
[Incardona, Francesca]

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
In: HIV Medicine [Early View], 1-8

Electronic Journal Article

2009

Altmann, André
Sing, Tobias
[Vermeiren, Hans]
[Winters, Bart]
[Van Craenenbroeck, Elke]
[Van der Borght, Koen]
[Rhee, Soo-Yon]
Shafer, Robert W.
[Schülter, Eugen]
[Kaiser, Rolf]
[Peres, Yardena]
[Sönnerborg, Anders]
Fessel, W. Jeffrey
[Incardona, Francesca]
[Zazzi, Maurizio]
[Bacheler, Lee]
[Van Vlijmen, Hermann]
Lengauer, Thomas

Advantages of Predicted Phenotypes and Statistical Learning Models in Inferring Virological Response to Antiretroviral Therapy from HIV Genotype
In: Antiviral Therapy [14], 273-283

Journal Article

2009

Lengauer, Thomas
Altmann, André
Thielen, Alexander

Bioinformatische Unterstützung der Auswahl von HIV Therapien
In: Informatik Spektrum [32], 320-331

Journal Article

2009

Thielen, Alexander
Altmann, André
Bogojeska, Jasmina
[Kaiser, Rolf]
Lengauer, Thomas

Estimating evolutionary pathways to 7CXCR4 usage from cross-sectional data
In: Abstracts presented at the XVIII International HIV Drug Resistance Workshop : Basic Principles & Clinical Implications, A16-A16

Poster

2009

[Sichtig, Nadine]
[Sierra, Saleta]
[Kaiser, Rolf]
[Däumer, Martin]
[Reuter, Stefan]
[Schülter, Eugen]
Altmann, André
[Fätkenheuer, Gerd]
[Dittmer, Ulf]
[Pfister, Herbert]
[Esser, Stefan]

Evolution of raltegravir resistance during therapy
In: Journal of antimicrobial chemotherapy [64], 25-32

Journal Article

2009

Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment
In: Antiviral Therapy [14], 433-442

Journal Article

2009

Altmann, André
[Däumer, Martin]
[Beerenwinkel, Niko]
[Peres, Yardena]
[Schülter, Eugen]
Büch, Joachim
[Rhee, Soo-Yon]
[Sönnerborg, Anders]
[Fessel, W. Jeffrey]
[Shafer, Robert W.]
[Zazzi, Maurizio]
[Kaiser, Rolf]
Lengauer, Thomas

Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation of
geno2pheno-THEO on a Large Clinical Database
In: The Journal of Infectious Diseases [199], 999-1006

Journal Article

2008

Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy
In: PLoS ONE [3], e3470

Journal Article

2008

Sander, Oliver
Altmann, Andre
Lengauer, Thomas

Computational analysis of covariation and interactions between HIV-1 reverse transcriptase and Integrase
In: Reviews in Antiviral Therapy, 113-114

Poster

2008

Thielen, Alexander
[Harrigan, P Richard]
Low, Andrew J.
[Moores, A]
Altmann, Andre
Bozek, Kasia
[Heger, Eva]
[Sichtig, Nadine]
[Kaiser, Rolf]
Lengauer, Thomas

Improved genotypic prediction of HIV-1 coreceptor usage by incorporating V2 loop sequence variation
In: Antiviral Therapy, A100

Poster

2008

[Verheyen, Jens]
Altmann, Andre
[Knops, Elena]
[Schülter, Eugen]
[Sichtig, Nadine]
[Reuter, Stefan]
[Fätkenheuer, Gerd]
[Pfister, Herbert]
[Kaiser, Rolf]

Relevance of HIV gag cleavage site mutations in failures of protease inhibitor therapies
In: Antiviral Therapy, A53

Poster

2008

Bogojeska, Jasmina
Alexa, Adrian
Altmann, André
Lengauer, Thomas
[Rahnenführer, Jörg]

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
In: Bioinformatics [24], 2391-2392

Journal Article

2008

Proceedings Article

2008

[Rosen-Zvi, Michal]
[Schülter, Eugen]
Altmann, Andre
[Sierra-Aragon, Saleta]
[Zazzi, Maurizio]
[Sönnerborg, Anders]
[Oette, Mark]
Lengauer, Thomas
[Kaiser, Rolf]

Sustaining lamivudine/emtricitabine, abacavir, zidovudine or atazanavir from a previous treatment shows a clinical benefit
In: Antiviral Therapy, A86

Poster

2008

The EuResist approach for predicting response to anti HIV-1 therapy
In: Reviews in Antiviral Therapy, 107

Poster

2007

EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

2007

Altmann, Andre
[Beerenwinkel, Niko]
Sing, Tobias
Savenkov, Igor
[Däumer, Martin]
[Kaiser, Rolf]
[Rhee, Soo-Yon]
[Fessel, W Jeffrey]
[Shafer, Robert W]
Lengauer, Thomas

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
In: Antiviral Therapy [12], 169-178

Journal Article

2007

Altmann, Andre
Sing, Tobias
[Vermeiren, Hans]
[Winters, Bart]
[Van Craenenbroeck, Elke]
[Van der Borght, Koen]
[Rhee, Soo-Yon]
[Shafer, Robert W]
[Schülter, Eugen]
[Kaiser, Rolf]
[Peres, Yardena]
[Sonnerborg, Anders]
[Fessel, W Jeffrey]
[Incardona, Francesca]
[Zazzi, Maurizio]
[Bacheler, Lee]
[Van Vlijmen, Hermann]
Lengauer, Thomas

Inferring virological response from genotype: with or without predicted phenotypes?
In: Proceedings of the 16th International HIV Drug Resistance Workshop, S169

Poster

2007

Altmann, Andre
[Däumer, Martin]
Sing, Tobias
[Beerenwinkel, Niko]
[Walter, Hauke]
[Kaiser, Rolf]
Lengauer, Thomas

Validation of geno2pheno and THEO on a large independent clinical dataset
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

Altmeier, S.

2006

[Heckmann-Pohl, Dorothee M.]
[Bastian, Sabine]
[Altmeier, S.]
Antes, Iris

Improvement of the fungal enzyme pyranose 2-oxidase using protein engineering
In: Journal of Biotechnology [124], 26-40

Journal Article

Altmüller, J.

2013

Schelhorn, Sven-Eric
[Fischer, M.]
[Tolosi, Laura]
[Altmüller, J.]
[Nürnberg, P.]
[Pfister, H.]
Lengauer, Thomas
Berthold, F.

Sensitive detection of viral transcripts in human tumor transcriptomes
In: PLOS Computational Biology [9], xx

Journal Article

Altucci, Lucia

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

2012

[Simmer, Femke]
[Brinkman, Arie B.]
Assenov, Yassen
[Matarese, Filomena]
[Kaan, Anita]
[Sabatino, Lina]
[Villanueva, Alberto]
[Huertas, Dori]
[Esteller, Manel]
Lengauer, Thomas
Bock, Christoph
[Colantuoni, Vittorio]
[Altucci, Lucia]
[Stunnenberg, Henk G.]

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
In: Epigenetics [7], 1355-1367

Journal Article

Altucci, L.

2013

[Simmer, F.]
[Brinkmann, A.B.]
Assenov, Yassen
[Matarese, F.]
[Kaan, A.]
Lengauer, Thomas
Bock, Christoph
[Colantuoni, V.]
[Altucci, L.]
[Stunnenberg, H.G.]

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched human tissue
In: Epigenetics [7], 1355-1367

Journal Article

Álvarez-Tejado, Miguel

2011

[Codoner, Francisco]
[Pou, Christian]
Thielen, Alexander
[García, Federico]
[Delgado, Rafael]
[Dalmau, David]
[Álvarez-Tejado, Miguel]
[Ruiz, Lidia]
[Clotet, Bonaventura]
[Paredes, Roger]

Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects
In: PLoS One [6], e19461,1-e19461,5

Electronic Journal Article

Alvaro, Domenico

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Ambalavanan,Namasivayam

2013

Schulz, Marcel Holger
[Pandit, Kusum V]
[Lino Cardenas, Christian L]
[Ambalavanan,Namasivayam]
[Kaminski, Naftali]
[Bar-Joseph, Ziv]

Reconstructing dynamic microRNA-regulated interaction networks
In: Proceedings of the National Academy of Sciences of the United States [110], 15686–15691

Journal Article

Ambrosini, G

2013

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Amoroso, MacKenzie W.

2011

Bock, Christoph
[Kiskinis, Evangelos]
[Verstappen, Griet]
[Gu, Hongcang]
[Boulting, Gabriella]
[Smith, Zachary D.]
[Ziller, Michael]
[Croft, Gist F.]
[Amoroso, MacKenzie W.]
[Oakley, Derek H.]
[Gnirke, Andreas]
[Eggan, Kevin]
[Meissner, Alexander]

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
In: Cell [144], 439-452

Journal Article

Anagnou, Nicholas P.

2010

Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL)
In: Nature Genetics [42], 292-294

Journal Article

Anastassi, Zacharias (ed.)

2012

Reppas, Andreas
Lawyer, Glenn

Low k-shells identify bridge elements critical to disease flow in small-world networks
In: Numerical Analysis and Applied Mathematics (ICNAAM 2012), 1426-1429

Proceedings Article

Andersen, Vibeke

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

Anderson, Carl A.

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Andreassen, Ole A.

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Angel-Rodriguez, Melina (ed.)

2004

Ramírez, Fidel

Evolucion de la Evolucionalidad
In: Biologos lejos del equilibrio: Nuevas metaforas evolutivas, 59-87

Part of a Book

Angelicoa, Mario

2011

[Svichera, Valentina]
[Centoa, Valeria]
[Salpinia, Romina]
[Mercurioa, Fabio]
[Fraune, Maria]
Beggel, Bastian
[Hanc, Yue]
[Gorid, Caterina]
[Wittkope, Linda]
[Bertolif, Ada]
[Michelig, Valeria]
[Gubertinig, Guido]
[Longoh, Roberta]
[Romanoh, Sara]
[Viscah, Michela]
[Gallinaroi, Valentina]
[Marinoj, Nicoletta]
[Mazzottaj, Francesco]
[De Sanctisi, Giuseppe Maria]
[Fleurye, Hervè]
[Trimoulete, Pascale]
[Angelicoa, Mario]
[Cappielloh, Giuseppina]
[Zhangc, Xin Xin]
[Verheyenb, Jens]
[Ceccherini-Silbersteina, Francesca]
[Pernoa, Carlo Federico]

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975–983

Journal Article

Angelico, Mario

2011

[Svicher, Valentina]
[Cento, Valeria]
[Salpini, Romina]
[Mercurio, Fabio]
[Fraune, Maria]
Beggel, Bastian
[Han, Yue]
[Gori, Caterina]
[Wittkop, Linda]
[Bertoli, Ada]
[Micheli, Valeria]
[Gubertini, Guido]
[Longo, Roberta]
[Romano, Sara]
[Visca, Michela]
[Gallinaro, Valentina]
[Marino, Nicoletta]
[Mazzotta, Francesco]
[De Sanctis, Giuseppe Maria]
[Fleury, Hervè]
[Trimoulet, Pascale]
[Angelico, Mario]
[Cappiello, Giuseppina]
[Zhang, Xin Xin]
[Verheyen, Jens]
[Ceccherini-Silberstein, Francesca]
[Perno, Carlo Federico]

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975-983

Journal Article

Anisimova, Maria (ed.)

2012

[Feuerbach, Lars]
Halachev, Konstantin
Assenov, Yassen
Mueller, Fabian
Bock, Christoph
Lengauer, Thomas

Analyzing epigenome data in context of genome evolution and human diseases
In: Evolutionary Genomics : Statistical and Computational Methods, Volume 2, 431-467
In: Methods of Molecular Biology [856], 431-467

Part of a Book

Annese, Vito

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Antes, Iris

2012

Welsch, Christoph
[Schweizer, Sabine]
[Shimakami, Testsuro]
[Domingues, Francisco S.]
[Kim, Seungtaek]
[Lemon, Stanley, M.]
[Antes, Iris]

Ketoamide Resistance and Hepatitis C Virus Fitness in Val55 Variants
of the NS3 Serine Protease
In: Antimicrobial Agents and Chemotherapy [56], 1907-1915

Journal Article

2011

[Bleif, Sabrina]
[Hannemann, Frank]
[Lisurek, Michael]
[von Kries, Jens Peter]
[Zapp, Josef]
Dietzen, Matthias
[Antes, Iris]
[Bernhardt, Rita]

Identification of CYP106A2 as a Regioselective Allylic Bacterial Diterpene Hydroxylase
In: ChemBioChem [12], 576-582

Journal Article

2010

Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper
In: Protein Science [19], 1327-1336

Journal Article

2010

Roomp, Kirsten
Antes, Iris
Lengauer, Thomas

Predicting MHC class I epitopes in large datasets
In: BMC Bioinformatics [11], 90,1-90,11

Electronic Journal Article

2009

Antes, Iris

Computational Methods for the Investigation of Protein-Ligand Interactions
Universität des Saarlandes

Thesis - Habilitation thesis

2009

Hartmann, Christoph
Antes, Iris
Lengauer, Thomas

Docking and scoring with alternative side-chain conformations
In: Proteins: Structure, Function, and Bioinformatics [74], 712-726

Journal Article

2008

[Welsch, Christoph]
Domingues, Francisco S.
[Susser, Simone]
Antes, Iris
Hartmann, Christoph
Mayr, Gabriele
Schlicker, Andreas
[Sarrazin, Christoph]
Albrecht, Mario
[Zeuzem, Stefan]
Lengauer, Thomas

Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of HCV
In: Genome Biology [9], R16

Journal Article

2008

[Lucas, Simon]
[Heim, Ralph]
[Negri, Matthias]
Antes, Iris
[Ries, Christina]
[Schewe, Katarzyna E.]
[Bisi, Alessandra]
[Gobbi, Silvia]
[Hartmann, Rolf W.]

Novel Aldosterone Synthase Inhibitors with Extended Carbocyclic Skeleton by a Combined Ligand-Based and Structure-Based Drug Design Approach
In: Journal of Medical Chemistry [51], 6138-6149

Journal Article

2008

[Lisurek, Michael]
[Simgen, Birgit]
Antes, Iris
[Bernhardt, Rita]

Theoretical and Experimental Evaluation of a CYP106A2 Low Homology Model and Production of Mutants with Changed Activity and Selectivity of Hydroxylation
In: ChemBioChem [9], 1439-1449

Journal Article

2007

Hartmann, Christoph
Antes, Iris
Lengauer, Thomas

IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.
In: Protein Science [16], 1294-1307

Journal Article

2006

Antes, Iris
Siu, Shirley Weng-In
Lengauer, Thomas

DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequence and conformations
In: Bioinformatics [22], 16-24

Journal Article

2006

[Heckmann-Pohl, Dorothee M.]
[Bastian, Sabine]
[Altmeier, S.]
Antes, Iris

Improvement of the fungal enzyme pyranose 2-oxidase using protein engineering
In: Journal of Biotechnology [124], 26-40

Journal Article

2006

Antes, Iris
Lengauer, Thomas

Refinement of homology modeled protein structures for molecular docking
In: Proceedings of the 367. WE-Heraeus Seminar on Biomolecular Simulations, 1

Poster

2006

[Voets, Marieke]
Antes, Iris
[Scherer, Christiane]
[Müller-Vieira, Ursula]
[Biemel, Klaus]
[Marchais-Oberwinkler, Sandrine]
[Hartmann, Rolf W.]

Synthesis and evaluation of heteroaryl substituted dihydronaphthalenes and indenes: potent and selective inhibitors of aldosterone synthase (CYP11B2) for the treatment of congestive heart failure and myocardial fibrosis
In: Journal of Medicinal Chemistry [49], 2222-2231

Journal Article

2005

[Gu, Wei]
[Kofler, Michael]
Antes, Iris
[Freund, Christian]
[Helms, Volkhard]

Alternative Binding Modes of Polyproline Peptides Binding to the GYF Domain
In: Biochemistry [44], 6404-6415

Journal Article

2005

[Voets, Marieke]
Antes, Iris
[Scherer, C]
[Mueller-Vieira, U.]
[Biemel, K.]
[Barrassin, C.]
[Marchais-Oberwinkler, S.]
[Hartmann, R. W.]

Heteroaryl-substituted naphthalenes and structurally modified derivatives: selective inhibitors of CYP11B2 for the treatment of congestive heart failure and myocardial fibrosis
In: Journal of Medicinal Chemistry [48], 6632-6642

Journal Article

2005

Antes, Iris
Merkwirth, Christian
Lengauer, Thomas

POEM: Parameter Optimization using Ensemble Methods: Application to target specific scoring functions
In: Journal of Chemical Information and Modeling [45], 1291-1302

Journal Article

2005

[Bojunga, Jörg]
[Welsch, Christoph]
Antes, Iris
Albrecht, Mario
Lengauer, Thomas
[Zeuzem, Stefan]

Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency
In: Human Genetics [117], 558-564

Journal Article

2005

[Ulmschneider, Sarah]
[Mueller-Vieira, Ursula]
[Mitrenga, Markus]
[Hartmann, Rolf W.]
[Oberwinkler-Marchais, S]
[Klein, Christian D.]
[Bureik, M.]
[Bernhardt, R.]
Antes, Iris
Lengauer, Thomas

Synthesis and Evaluation of Imidazolylmethylenetetrahydronaphthalenes and Imidazolylmethyleneindanes: Potent Inhibitors of Aldosterone Synthase
In: Journal of Medicinal Chemistry [48], 1796-1805

Journal Article

2005

[Ulmschneider, Sarah]
[Mueller-Vieira, Ursula]
[Klein, Christian D.]
Antes, Iris
Lengauer, Thomas
[Hartmann, Rolf W.]

Synthesis and Evaluation of Pyridylmethylene-tetrahydronaphthalenes and -indanes: Potent and Selective Inhibitors of Aldosterone Synthase (CYP11B2)
In: Journal of Medicinal Chemistry [48], 4489-4490

Journal Article

2004

[Crass, T.]
Antes, Iris
[Basekow, R.]
[Bork, P.]
Buning, Christian
[Christensen, M.]
[Claußen, H.]
[Ebeling, C.]
[Ernst,P.]
[Gailus-Durner, V.]
[Glatting, K.-H.]
[Gohla, R.]
[Gößling, F.]
[Grote, K.]
[Heidtke, K.]
[Herrmann, A.]
[O Keefe, S.]
[Kießlich, O.]
[Kolibal, S.]
[Korbel, J.O.]
Lengauer, Thomas
[Liebich, I.]
[van der Linden, M.]
[Luz, H.]
[Meissner, K.]
[von Mering, C.]
[Mevissen, T.]
[Mewes, H.-W.]
[Michael, H.]
[Mokrejs, M.]
[Müller, T.]
[Pospisil, H.]
[Rarey, Matthias]
[Reich, J.G.]
[Schneider, R.]
[Schomburg, D.]
[Schulze-Kremer, S.]
[Schwarzer, K.]
Sommer, Ingolf
[Springstubbe, S.]
[Suhai, S.]
[Thoppae, G.]
[Vingron, M.]
[Warfsmann, J.]
[Werner, T.]
[Wetzler, D.]
[Wingender, E.]
[Zimmer, Ralf]

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

2003

Antes, Iris
Lengauer, Thomas
Mueller, Ursula
[Ulmschneider, Sarah]
[Hartmann, Rolf]

Docking into the homology models of CYP11B1 and CYP11B2
In: Proceedings of the German Conference on Bioinformatics 2003, 13

Poster

2003

Antes, Iris
[Wang, Hongyun]
[Chandler, David]
[Oster, George]

The unbinding of ATP from F1-ATPase
In: Biophysical Journal [85], 695-706

Journal Article

2002

Antes, Iris
[Chandler, David]
[Oster, George]

A classical dynamics study of the unbinding of ATP from the F0F1-ATPase
In: Poster book of the European Conference on Computational Biology, Saarbrücken, Germany 2002, -

Poster

2002

Antes, Iris
[Thiel, Walter]
[Gunsteren van, Wilfred F.]

Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation
In: European Biophysics Jounal [31], 504-520

Journal Article

2001

Antes, Iris
[Klein, Michael L.]

The formation of a β-Peptide/DPC-micelle complex studied by MD simulations

Miscellaneous

Antinori, Andrea

2009

[Trignetti, Maria]
Sing, Tobias
[Svicher, Valentina]
[Santoro, Maria Mercedes]
[Forbici, Federica]
[D'Arrigo, Roberta]
[Bellocchi, Maria Concetta]
[Santoro, Mario]
[Marconi, Patrizia]
[Zaccarelli, Mauro]
[Trotta, Maria Paola]
[Bellagamba, Rita]
[Narciso, Pasquale]
[Antinori, Andrea]
Lengauer, Thomas
[Perno, Carlo Federico]
[Ceccherini-Silberstein, Francesca]

Dynamics of NRTI resistance mutations during therapy interruption
In: AIDS Research and Human Retroviruses [25], 57-64

Journal Article

2007

Journal Article

2006

[Svicher, Valentina]
Sing, Tobias
[Santoro, Maria Mercedes]
[Forbici, Federica]
[Rodriguez- Barrios, Fátima]
[Bertoli, Ada]
[Beerenwinkel, Niko]
[Bellocchi, Maria Concetta]
[Gago, Federigo]
[d´Arminio Monforte, Antonella]
[Antinori, Andrea]
Lengauer, Thomas
Ceccherini-Silberstein, Francesca
[Perno, Carlo-Federico]

Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
In: Journal of Virology [80], 7186-7198

Journal Article

Antinori, A.

2005

[Svicher, Valentina]
[Ceccherini-Silberstein, Francesca]
Sing, Tobias
[Santoro, Maria Mercedes]
[Gori, C.]
Beerenwinkel, Niko
[Gago, F.]
[D'Arrigo, R.]
[Bellochi, M.C.]
[Giannella, S.]
[Bertoli, A.]
[D'Arminio Monforte, A.]
[Antinori, A.]
[Perno, Carlo-Federico]

A highly ordered network of HIV-1 RT mutations regulates the continuous escape from antiviral drugs
In: International Workshop in HIV Dynamics and Evolution, -

Proceedings Article

2005

[Svicher, Valentina]
[Ceccherini-Silberstein, Francesca]
Sing, Tobias
[Santoro, Maria Mercedes]
[Gori, C.]
Beerenwinkel, Niko
[Gago, F.]
[D'Arrigo, R.]
[Bellocchi, M. C.]
[Giannella, S.]
[Bertoli, A.]
[D'Arminio Monforte, A.]
[Antinori, A.]
[Perno, Carlo-Federico]

Additional Mutations in HIV-1 Reverse Transcriptase are Involved in the Highly Ordered Regulation of NRTI Resistance
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -

Proceedings Article

Antonarakis, SE

2013

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Antonarakis, Stylianos E

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Antonarakis, Stylianos E.

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Antony, Jens

2003

[Olsen, Lars]
[Antony, Jens]
[Ryde, Ulf]
Adolph, Hans-Werner
[Hemmingsen, Lars]

Lactam hydrolysis catalyzed by mononuclear metallo-beta-lactamases: a density functional study
In: Journal of Physical Chemistry / B [107], 2366-2375

Journal Article

Apeltsin, Leonard

2011

[Morris, John H.]
[Apeltsin, Leonard]
[Newman, Aaron M.]
Baumbach, Jan
[Wittkop, Tobias]
[Su, Gang]
[Bader, Gary D.]
[Ferrin, Thomas E.]

clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape
In: BMC Bioinformatics [12], 436,1-436,14

Journal Article

Apostolakis, Joannis

2007

Steffen, Andreas
[Karasz, Maximilian]
[Thiele, Carolin]
Lengauer, Thomas
Kämper, Andreas
[Wenz, Gerhard]
[Apostolakis, Joannis]

Journal Article

2007

Steffen, Andreas
[Thiele, Carolin]
[Tietze, Simon]
[Strassnig, Christian]
Kämper, Andreas
Lengauer, Thomas
[Wenz, Gerhard]
[Apostolakis, Joannis]

Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening
In: Chemistry [13], 6801-6809

Journal Article

2006

Kämper, Andreas
[Apostolakis, Joannis]
[Rarey, Matthias]
[Marian, Christel Maria]
Lengauer, Thomas

Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies
In: Journal of Chemical Information and Modeling [46], 903-911

Journal Article

2002

Kämper, Andreas
[Apostolakis, Joannis]
Lengauer, Thomas

Docking of Bacterial Cell-Wall Fragments into Glycopeptide Antibiotics
In: From Genes to Drugs via Crystallography: 33rd crytallographic course at the E. Majorana Center, 49

Poster

2001

[Apostolakis, Joannis]
[Hofmann, D.]
Lengauer, Thomas

Derivation of a scoring function for crystal structure prediction
In: Acta Crystallographica [A57], 442-450

Journal Article

2001

Kämper, Andreas
[Apostolakis, Joannis]
[Rarey, Matthias]
[Marian, Christel Maria]
Lengauer, Thomas

Docking of Ligands into Artificial Receptors

Miscellaneous

2001

[Kämper, Andreas]
[Apostolakis, Joannis]
[Rarey, Matthias]
[Marian, Christel Maria]
[Lengauer, Thomas]

Docking of Ligands into Artificial Receptors
In: Electronically Excited Molecules: Structure and Dynamics, 37th Symposium for Theoretical Chemistry, P76

Proceedings Article

Arabnia, H. R. (ed.)

2002

[Bozinov, Daniel]
Rahnenführer, Jörg
[Burson, Cathy]
[Spiegelstein, Ofer]

Automated Grid Alignment for High-Throughput Analysis of Microarray Images (CIIST-02)
In: Proceedings of the 2002 International Conference on Imaging Science, Systems, and Technology, 161-167

Proceedings Article

Aranda, Bruno

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Arand, Julia

2011

[Lutsik, Pavlo]
Feuerbach, Lars
[Arand, Julia]
Lengauer, Thomas
[Walter, Jörn]
Bock, Christoph

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
In: Nucleic Acids Research [39], W551-W556

Journal Article

Artese, Anna

2011

Journal Article

2009

[Alcaro, Stefano]
[Artese, Anna]
[Ceccherini-Silberstein, Francesca]
[Ortuso, Francesca]
[Perno, Carlo Federico]
Sing, Tobias
[Svicher, Valentina]

Journal Article

2007

Journal Article

Ashbourne-Excoffon, K.J.

1999

[Brooks-Wilson, A]
[Marcil, Michel]
[Clee, Susanne M.]
[Zhang, Lin-Hua]
Roomp, Kirsten
[van Dam, M]
[Yu, L]
[Brewer, C]
[Collins, Jennifer A.]
[Molhuizen, H.O.]
[Loubser, O]
[Ouelette, B.F.]
[Fichter, K]
[Ashbourne-Excoffon, K.J.]
[Sensen, C.W.]
[Scherer, S]
[Mott, S]
[Denis, M]
[Martindale, D]
[Frohlich, J]
[Morgan, K]
[Koop, B]
[Pimstone, S]
[Kastelein, J.J.P.]
[Hayden, Michael R.]

Mutations in ABC1 in Tangier disease and familial high-density lipoprotein
In: Nature Genetics [22], 336-45

Journal Article

Assenov, Yassen

2013

[Sandoval, Juan]
[Mendez-Gonzales, Jesus]
[Nadal, Ernest]
[Chen, Guoan]
[Carmona, F. Javier]
[Sayols, Sergi]
[Moran, Sebastian]
[Heyn, Holger]
[Vizoso, Miguel]
[Gomez, Antonio]
[Sanchez-Cespedes, Montse]
Assenov, Yassen
Müller, Fabian
Bock, Christoph
[Taron, Miquel]
[Mora, Josefina]
[Muscarella, Lucia A.]
[Liloglou, Triantafillos]
[Davies, Michael]
[Pollan, Marina]
[Pajares, Maria J.]
[Torre, Wenceslao]
[Montuenga, Luis M.]
[Brambilla, Elisabeth]
[Field, John K.]
[Roz, Luca]
[Lo Iacono, Marco]
[Scagliotti, Giorgio V.]
[Rosell, Rafael]
[Beer, David G.]
[Esteller,Manel]

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

2013

[Simmer, F.]
[Brinkmann, A.B.]
Assenov, Yassen
[Matarese, F.]
[Kaan, A.]
Lengauer, Thomas
Bock, Christoph
[Colantuoni, V.]
[Altucci, L.]
[Stunnenberg, H.G.]

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched human tissue
In: Epigenetics [7], 1355-1367

Journal Article

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

2012

[Calvanese, Vincenzo]
[Fernandez, Agustín F.]
[Urdinguio, Rocío G.]
[Suarez-Álvarez, Beatriz]
[Mangas, Cristina]
[Pérez-García, Vicente]
[Bueno, Clara]
[Montes, Rosa]
[Ramos-Mejía, Verónica]
[Martínez-Camblor, Pablo]
[Ferrero, Cecilia]
Assenov, Yassen
Bock, Christoph
[Menendez, Pablo]
[Carrera, Ana Clara]
[Lopez-Larrea, Carlos]
[Fraga, Mario F.]

A promoter DNA demethylation landscape of human hematopoietic differentiation
In: Nucleic Acids Research [40], 116-131

Journal Article

2012

[Feuerbach, Lars]
Halachev, Konstantin
Assenov, Yassen
Mueller, Fabian
Bock, Christoph
Lengauer, Thomas

Part of a Book

2012

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
In: Epigenetics [7], 1355-1367

Journal Article

2012

Doncheva, Nadezhda T
Assenov, Yassen
[Domingues, Francisco S.]
Albrecht, Mario

Topological analysis and interactive visualization of biological networks and protein structures
In: Nature Protocols [7], 670-685

Journal Article

2008

Assenov, Yassen
Ramírez, Fidel
Schelhorn, Sven-Eric
Lengauer, Thomas
Albrecht, Mario

Computing topological parameters of biological networks
In: Bioinformatics [24], 282-284

Journal Article

2007

[Salamat-Miller, Nazila]
[Fang, Jianwen]
[Seidel, Christopher W.]
Assenov, Yassen
Albrecht, Mario
[Middaugh, C. Russell]

A network-based analysis of polyanion-binding proteins utilizing human protein arrays
In: Journal of Biological Chemistry [282], 10153-10163

Journal Article

2007

Ramírez, Fidel
Schlicker, Andreas
Assenov, Yassen
Lengauer, Thomas
Albrecht, Mario

Computational analysis of human protein interaction networks
In: Proteomics [7], 2541-2552

Journal Article

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

2006

[Salamat-Miller, Nazila]
[Fang, Jianwen]
[Seidel, Christopher W.]
[Smalter, Aaron M.]
[Assenov, Yassen]
Albrecht, Mario
[Middaugh, C. Russell]

A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays
In: Molecular and Cellular Proteomics [5], 2263-2278

Journal Article

2006

Assenov, Yassen

Topological Analysis of Biological
Networks
Universität des Saarlandes

Thesis - Masters thesis

Athanassiadou, Zoi

2009

[Moser, Dirk]
[Ekawardhani, Savira]
[Kumsta, Robert]
[Palmason, Haukur]
Bock, Christoph
[Athanassiadou, Zoi]
[Lesch, Klaus-Peter]
[Meyer, Jobst]

Functional Analysis of a Potassium-Chloride Co-Transporter 3 (SLC12A6) Promoter Polymorphism Leading to an Additional DNA Methylation Site
In: Neuropsychopharmacology [34], 458-467

Journal Article

Auer, Florian

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Awerkiew, Sabine

2010

[Däumer, Martin]
[Awerkiew, Sabine]
[Sierra Aragon, Saleto]
[Kartashev, Vladimir]
[Poplavskaja, Tatjana]
[Klein, Rolf]
[Sichtig, Nadine]
[Thielen, Bernhard]
Lengauer, Thomas
Roomp, Kirsten
[Pfister, Herbert]
[Kaiser, Rolf]

Short Communication: Selection of Thymidine Analogue Resitance Mutational Patterns in Children from a Common HIV Type 1 Subtype G Source
In: AIDS Research and Human Retroviruses [26], 275-278

Journal Article

Azevedo, Vaco

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Azevedo, Vasco

2013

[Röttger, Richard]
Kalaghatgi, Prabhav
[Sun, Peng]
[de Castro Soares, Siomar]
[Azevedo, Vasco]
[Wittkop, Tobias]
[Baumbach, Jan]

Density Parameter Estimation for Finding Clusters of Homologous Proteins - Tracing Actinobacterial Pathogenicity Life Styles
In: Bioinformatics [29], 215-222

Journal Article

2012

Pauling, Josch
Röttger, Richard
[Tauch, Andreas]
[Azevedo, Vasco]
Baumbach, Jan

CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands
In: Nucleic Acids Research [40], D610-D614

Journal Article

2012

Pauling, Josch
Röttger, Richard
[Neuner, Andreas]
[Salgado, Heladia]
[Collado-Vides, Julio]
Kalaghatgi, Prabhav
[Azevedo, Vasco]
[Tauch, Andreas]
[Pühler, Alfred]
Baumbach, Jan

On the trail of EHEC/EAEC - unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
In: Integrative Biology [4], 728-733

Journal Article

2012

PIPS: Pathogenicity Island Prediction Software
In: PLoS One [7], e30848,1-e30848,10

Electronic Journal Article

2011

[Santos, Anderson R]
[Santos, Marcos A]
Baumbach, Jan
[McCulloch, John A]
[Oliveira, Guilherme C]
[Silva, Artur]
[Miyoshi, Anderson]
[Azevedo, Vasco]

A singular value decomposition approach for improved taxonomy classification of biological sequences
In: BMC Genomics [12], S11,1-S11,15

Journal Article

2011

[Ramos, Rommel T.J.]
[Carneiro, Adriana R.]
Baumbach, Jan
[Azevedo, Vasco]
[Schneider, Maria P.C.]
[Silva, Artur]

Analysis of quality raw data of second generation sequencers with Quality Assessment Software
In: BMC Research Notes [4], 130,1-130,6

Journal Article

Azevedo, Vasco Ariston Carvalho

2011

[Cerdeira, Louise Teixeira]
[Carneir, Aadriana Ribeiro]
[Ramos, Rommel Thiago Juca]
[de Almeida, Sintia Silva]
[D'Afonseca, Vivian]
[Schneider, Maria Paula Cruz]
Baumbach, Jan
[Tauch, Andreas]
[McCulloch, John Anthony]
[Azevedo, Vasco Ariston Carvalho]
[Silva, Aartur]

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study
In: Journal of Microbiological Methods [86], 218-223

Journal Article

Babbitt, Patricia C

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Bacheler, Lee

2009

Advantages of Predicted Phenotypes and Statistical Learning Models in Inferring Virological Response to Antiretroviral Therapy from HIV Genotype
In: Antiviral Therapy [14], 273-283

Journal Article

2007

Inferring virological response from genotype: with or without predicted phenotypes?
In: Proceedings of the 16th International HIV Drug Resistance Workshop, S169

Poster

Backes, Perdita

2011

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
In: Cell Host & Microbe [9], 32-45

Journal Article

Bader, Gary D.

2011

[Morris, John H.]
[Apeltsin, Leonard]
[Newman, Aaron M.]
Baumbach, Jan
[Wittkop, Tobias]
[Su, Gang]
[Bader, Gary D.]
[Ferrin, Thomas E.]

clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape
In: BMC Bioinformatics [12], 436,1-436,14

Journal Article

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Bader, Mathias

2012

Bader, Mathias

Clustering epigenetic data using a Dirichlet process prior
Universität des Saarlandes

Thesis - Masters thesis

Badimon, Lina

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Bairoch, Amos

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Balbin, Alejandro (ed.)

2004

Ramírez, Fidel

Evolucion de la Evolucionalidad
In: Biologos lejos del equilibrio: Nuevas metaforas evolutivas, 59-87

Part of a Book

Balduin, Melanie

2011

Erratum to: Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.
In: Medical Microbiology and Immunology [200], 51-51

Journal Article

2011

HIV prevalence and route of transmission in Turkish immigrants
living in North-Rhine Westphalia, Germany
In: Medical Microbiology and Immunology [200], 219-223

Journal Article

2011

Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients
In: Medical Microbiology and Immunology [200], 39-49

Journal Article

2006

[Verheyen, Jens]
[Litau, Elena]
Sing, Tobias
[Däumer, Martin]
[Balduin, Melanie]
[Oette, Mark]
[Fätkenheuer, Gerd]
[Rockstroh, Jürgen K.]
[Schuldenzucker, Ulrike]
[Hoffmann, Daniel]
[Pfister, Herbert]
[Kaiser, Rolf]

Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients
In: Antiviral Therapy [11], 879-887

Journal Article

2005

[Balduin, Melanie]
Beerenwinkel, Niko
[Sierra, Saleta]
[Däumer, Martin]
[Rockstroh, Jürgen]
[Oette, Mark]
[Fätkenheuer, Gerd]
[Kupfer, Bernd]
[Hoffmann, Daniel]
[Selbig, Joachim]
[Pfister, Herbert]
[Kaiser, Rolf]

Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy
In: J Clin Virol [34], 277-287

Journal Article

Balint, Balazs

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Balla, Tamas

2011

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
In: Cell Host & Microbe [9], 32-45

Journal Article

Ballestar, Esteban

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Ballesteros, Juan

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Ballinger, Tracy

2010

[Harris, R. Alan]
[Wang, Ting]
[Coarfa, Cristian]
[Nagarajan, Raman P.]
[Hong, Chibo]
[Downey, Sara L.]
[Johnson, Brett E.]
[Fouse, Shaun D.]
[Delaney, Allen]
[Zhao, Yongjun]
[Olshen, Adam]
[Ballinger, Tracy]
[Zhou, Xin]
[Forsberg, Kevin J.]
[Gu, Junchen]
[Echipare, Lorigail]
[O'Geen, Heriette]
[Lister, Ryan]
[Pelizzola, Mattia]
[Xi, Yuanxin]
[Epstein, Charles B.]
[Bernstein, Bradley E.]
[Hawkins, R. David]
[Ren, Bing]
[Chung, Wen-Yu]
[Gu, Hongcang]
Bock, Christoph
[Gnirke, Andreas]
[Zhang, Michael Q.]
[Haussler, David]
[Ecker, Joseph R.]
[Li, Wei]
[Farnham, Peggy J.]
[Waterland, Robert a.]
[Meissner, Alexander]
[Marra, Marco A.]
[Hirst, Martin]
[Milosavljevic, Aleksandar]
[Costello, Joseph F.]

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
In: Nature Biotechnology [28], 1097-1105

Journal Article

Balschun, Tobias

2010

Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL)
In: Nature Genetics [42], 292-294

Journal Article

2008

Sequence variants in IL10, ARPC2, and multiple other loci contribute to ulcerative colitis
In: Nature Genetics [40], 1319-1323

Journal Article

2007

Systematic association mapping identifies NELL1 as a novel IBD disease gene
In: PLoS ONE [2], e691.1-13

Journal Article

Balzarini, Jan

2007

Journal Article

Bandyopadhyay, Sanghamitra

2012

[Bhattacharyya, Malay]
Feuerbach, Lars
[Bhadra, Tapas]
[Bandyopadhyay, Sanghamitra]

MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection
In: Statistical Applications in Genetics and Molecular Biology [11], 6.1-6.25

Journal Article

Bandyopadhyay, S.

2013

[Bhadra, T.]
[Battacharya, M.]
[Feuerbach, L.]
Lengauer, Thomas
Bandyopadhyay, S.

DNA Methylation Patterns Facilitate the Identification of Transcription Start Sites: A Brain-specofoc Study
In: PLOSONE [8], xx

Journal Article

Bar-Joseph, Ziv

2013

[Le, Hai-Son]
Schulz, Marcel Holger
[McCauley, Brenna MM]
[Hinman, Veronica F]
[Bar-Joseph, Ziv]

Probabilistic error correction for RNA sequencing
In: Nucleic Acids Researcb [41], e109

Journal Article

2013

Schulz, Marcel Holger
[Pandit, Kusum V]
[Lino Cardenas, Christian L]
[Ambalavanan,Namasivayam]
[Kaminski, Naftali]
[Bar-Joseph, Ziv]

Reconstructing dynamic microRNA-regulated interaction networks
In: Proceedings of the National Academy of Sciences of the United States [110], 15686–15691

Journal Article

Bárkai, Tünde

2012

[Garai, Ágnes]
[Zeke, András]
[Gógl, Gergo]
[Töro, Imre]
[Fördos, Ferenc]
Blankenburg, Hagen
[Bárkai, Tünde]
[Varga, János]
[Alexa, Anita]
Emig, Dorothea
Albrecht, Mario
[Reményi, Attila]

Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove
In: Science Signaling [5], ra74,1-ra74,14

Journal Article

Barnes, Michael R. (ed.)

2010

Bock, Christoph
[Von Kuster, Greg]
Halachev, Konstantin
[Taylor, James]
[Nekrutenko, Anton]
Lengauer, Thomas

Web-based analysis of (epi-) genome data using EpiGRAPH and Galaxy.
In: Genetic Variation : Methods and Protocols, 275-296
In: Methods of Molecular Biology [628], 275-296

Part of a Book

Barnett, Melanie J.

2011

[Krol, Elizaveta]
[Blom, Jochen]
[Winnebald, Jörn]
[Berhörster, Alexander]
[Barnett, Melanie J.]
[Goesmann, Alexander]
Baumbach, Jan
[Becker, Anke]

RhizoRegNet - A database of rhizobial transcription factors and regulatory networks.
In: Journal of Biotechnology [155], 127-134

Journal Article

Barrassin, C.

2005

[Voets, Marieke]
Antes, Iris
[Scherer, C]
[Mueller-Vieira, U.]
[Biemel, K.]
[Barrassin, C.]
[Marchais-Oberwinkler, S.]
[Hartmann, R. W.]

Journal Article

Barretina, Jordi

2009

[Sos, Martin L.]
[Michel, Kathrin]
[Zander, Thomas]
[Weiss, Jonathan]
[Frommolt, Peter]
[Pfeifer, Martin]
[Li, Danan]
[Ullrich, Roland]
[Koker, Mirjam]
[Fischer, Florian]
[Shimamura, Takeshi]
[Rauh, Daniel]
[Mermel, Craig]
[Fischer, Stefanie]
[Stückrath, Isabel]
[Heynck, Stefanie]
[Beroukhim, Rameen]
[Lin, William]
[Winckler, Wendy]
[Shah, Kinjal]
[LaFramboise, Thomas]
[Moriarty, Whei F.]
Hanna, megan
Tolosi, Laura
[Rahnenführer, Jörg]
[Verhaak, Roel]
[Chiang, Derek]
[Getz, Gad]
[Hellmich, Martin]
[Wolf, Jürgen]
[Girard, Luc]
[Peyton, Michael]
[Weir, Barbara A.]
[Chen, Tzu-Hsiu]
[Greulich, Heidi]
[Barretina, Jordi]
[Shapiro, Geoffrey I.]
[Garraway, Levi A.]
[Gazdar, Adi F.]
[Minna, John D.]
[Meyerson, Matthew]
[Wong, Kwok-Kin]
[Thomas, Roman K.]

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Bartenschlager, Ralf

2011

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
In: Cell Host & Microbe [9], 32-45

Journal Article

Bartholomeu, Daniela C.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Bartlett, Peter (ed.)

2011

Bogojeska, Jasmina

History distribution matching method for predicting effectiveness of HIV combination therapies
In: Neural Information Processing Systems (NIPS 2011), 424-432

Electronic Proceedings Article

Basekow, R.

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Bastian, Sabine

2006

[Heckmann-Pohl, Dorothee M.]
[Bastian, Sabine]
[Altmeier, S.]
Antes, Iris

Improvement of the fungal enzyme pyranose 2-oxidase using protein engineering
In: Journal of Biotechnology [124], 26-40

Journal Article

Bastos, Hugo

2012

[Faria, Daniel]
Schlicker, Andreas
[Pesquita, Catia]
[Bastos, Hugo]
[Ferreira, António E N]
Albrecht, Mario
[Falcão, André O]

Mining GO annotations for improving annotation consistency
In: PLoS ONE [7], e40519,1-e40519,7

Electronic Journal Article

Bastys, Tomas

2012

Bastys, Tomas

MAP Kinase Docking Motifs in HIV Proteins
Universität des Saarlandes

Thesis - Masters thesis

Bast, Hannah

2012

Halachev, Konstantin
[Bast, Hannah]
Albrecht, Felipe
Lengauer, Thomas
Bock, Christoph

EpiExplorer: live exploration and global analysis of large epigenomic datasets
In: Genome Biology [13], R96,1-R96,14

Electronic Journal Article

Bast, H.

2013

Halachev, Konstantin
Bast, H.
Lengauer, Thomas
Bock, Christoph

Interactive exploration of large genome and epigenome datasets in real time
In: Genome Biology [13], xx

Journal Article

2012

Halachev, K.
[Bast, H.]
Albrecht, F.
Lengauer, Thomas
Bock, Christoph

EpiExplorer: live exploration and global analysis of large epigenomic datasets
In: Genome Biology [13], R96,1-R96,14

Journal Article

Baszó, Fulop

2007

EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

Battacharya, M.

2013

[Bhadra, T.]
[Battacharya, M.]
[Feuerbach, L.]
Lengauer, Thomas
Bandyopadhyay, S.

DNA Methylation Patterns Facilitate the Identification of Transcription Start Sites: A Brain-specofoc Study
In: PLOSONE [8], xx

Journal Article

Baumbach, Jan

2014

[Smolinska, Agnieszka]
Hauschild, Anne-Christin
[Fijten, Rianne]
[Dallinga, Jan]
Baumbach, Jan
[van Schooten, Frederik]

Current breathomics – A review on data pre-processing techniques and machine learning in metabolomics breath analysis

Unpublished/Draft

2014

[Maurer, Felix]
Hauschild, Anne-Christin
[Eisinger, Kathrin]
Baumbach, Jan
[Mayor, Arno]
[Baumbach, Jörg Ingo]

MIMA - A software for analyte identification in MCC/IMS chromatograms by mapping accompanying GC/MS measurements
In: International Journal for Ion Mobility Spectrometry [?], ?

Journal Article

2014

[Eckel, Sandrah]
Baumbach, Jan
Hauschild, Anne-Christin

On the importance of statistics in breath analysis - Hope or curse?

Unpublished/Draft

2013

[Schneider, Till]
Hauschild, Anne-Christin
[Baumbach, Joerg Ingo]
Baumbach, Jan

An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air
In: Journal of Integrative Bioinformatics [10],

Electronic Journal Article

2013

[Röttger, Richard]
Kalaghatgi, Prabhav
[Sun, Peng]
[de Castro Soares, Siomar]
[Azevedo, Vasco]
[Wittkop, Tobias]
[Baumbach, Jan]

Density Parameter Estimation for Finding Clusters of Homologous Proteins - Tracing Actinobacterial Pathogenicity Life Styles
In: Bioinformatics [29], 215-222

Journal Article

2013

Hauschild, Anne-Christin
[Baumbach, Joerg Ingo]
Baumbach, Jan

Paving the Way for Automated Clinical Breath Analysis and Biomarker Detection

Miscellaneous

2013

Hauschild, Anne-Christin
[Kopczynski, Dominik]
[D'Addario, Marianna]
[Baumbach, Joerg Ingo]
[Rahmann, Sven]
Baumbach, Jan

Peak Detection Method Evaluation for Ion Mobility Spectrometry by using Machine Learning Approaches
In: Metabolites [3], 277-293

Electronic Journal Article

2012

Hauschild, Anne-Christin
[Schneider, Till]
Pauling, Josch
[Rupp, Kathrin]
[Jang, Mi]
[Baumbach, Jörg Ingo]
Baumbach, Jan

Computational Methods for Metabolomic Data Analysis of Ion Mobility Spectrometry Data - Reviewing the State of the Art
In: Metabolites [2], 733-755

Electronic Journal Article

2012

Pauling, Josch
Röttger, Richard
[Tauch, Andreas]
[Azevedo, Vasco]
Baumbach, Jan

CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands
In: Nucleic Acids Research [40], D610-D614

Journal Article

2012

Röttger, Richard
[Rueckert, Ulrich]
[Taubert, Jan]
Baumbach, Jan

How Little Do We Actually Know? - On the Size of Gene Regulatory Networks.
In: IEEE/ACM transactions on computational biology and bioinformatics [9], 1293-1300

Journal Article

2012

Hauschild, Anne-Christin
[Baumbach, Jörg Ingo]
Baumbach, Jan

Integrated statistical learning of metabolic ion mobility spectrometry profiles for pulmonary disease identification
In: Genetics and Molecular Research [11], 2733-2744

Electronic Journal Article

2012

Baumbach, Jan

Integrative computational biology
In: Integrative Biology [4], 713-714

Journal Article

2012

Alcaraz, Nicolas
Kucuk, Hande
[Weile, Jochen]
[Wipat, Anil]
Baumbach, Jan

KeyPathwayMiner - Detecting case-specific biological pathways by using expression data
In: Internet Mathematics [7], 299-313

Journal Article

2012

Pauling, Josch
Röttger, Richard
[Neuner, Andreas]
[Salgado, Heladia]
[Collado-Vides, Julio]
Kalaghatgi, Prabhav
[Azevedo, Vasco]
[Tauch, Andreas]
[Pühler, Alfred]
Baumbach, Jan

On the trail of EHEC/EAEC - unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
In: Integrative Biology [4], 728-733

Journal Article

2012

Röttger, Richard
Kreutzer, Christoph
[Duong Vu, Thuy]
[Wittkop, Tobias]
Baumbach, Jan

Online Transitivity Clustering of Biological Data with Missing Values
In: German Conference on Bioinformatics 2012 (GCB 2012), 57-68

Electronic Proceedings Article

2012

PIPS: Pathogenicity Island Prediction Software
In: PLoS One [7], e30848,1-e30848,10

Electronic Journal Article

2011

[Santos, Anderson R]
[Santos, Marcos A]
Baumbach, Jan
[McCulloch, John A]
[Oliveira, Guilherme C]
[Silva, Artur]
[Miyoshi, Anderson]
[Azevedo, Vasco]

A singular value decomposition approach for improved taxonomy classification of biological sequences
In: BMC Genomics [12], S11,1-S11,15

Journal Article

2011

[Ramos, Rommel T.J.]
[Carneiro, Adriana R.]
Baumbach, Jan
[Azevedo, Vasco]
[Schneider, Maria P.C.]
[Silva, Artur]

Analysis of quality raw data of second generation sequencers with Quality Assessment Software
In: BMC Research Notes [4], 130,1-130,6

Journal Article

2011

[Morris, John H.]
[Apeltsin, Leonard]
[Newman, Aaron M.]
Baumbach, Jan
[Wittkop, Tobias]
[Su, Gang]
[Bader, Gary D.]
[Ferrin, Thomas E.]

clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape
In: BMC Bioinformatics [12], 436,1-436,14

Journal Article

2011

[Wittkop, Tobias]
Emig, Dorothea
[Truss, Anke]
Albrecht, Mario
[Böcker, Sebastian]
Baumbach, Jan

Comprehensive cluster analysis with Transitivity Clustering
In: Nature Protocols [6], 285-295

Journal Article

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

2011

[Wittkop, Tobias]
[Rahmann, Sven]
Roettger, Richard
[Boecker, Sebastian]
Baumbach, Jan

Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis
In: Internet Mathematics [7], 255-273

Journal Article

2011

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study
In: Journal of Microbiological Methods [86], 218-223

Journal Article

2011

[Krol, Elizaveta]
[Blom, Jochen]
[Winnebald, Jörn]
[Berhörster, Alexander]
[Barnett, Melanie J.]
[Goesmann, Alexander]
Baumbach, Jan
[Becker, Anke]

RhizoRegNet - A database of rhizobial transcription factors and regulatory networks.
In: Journal of Biotechnology [155], 127-134

Journal Article

2010

Emig, Dorothea
[Salomonis, Nathan]
[Baumbach, Jan]
Lengauer, Thomas
[Conklin, Bruce R.]
Albrecht, Mario

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
In: Nucleic Acids Research [38], W755-W762

Journal Article

2010

[Wittkop, Tobias]
[Rahmann, Sven]
Baumbach, Jan

Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0
In: Special Issue: 6th International Symposium on Integrative Bioinformatics, 117,1-117,11

Electronic Proceedings Article

2010

Baumbach, Jan

On the power and limits of evolutionary conservation - unraveling bacterial gene regulatory networks
In: Nucleic Acids Research [38], 7877-7884

Journal Article

2010

[Wittkop, Tobias]
Emig, Dorothea
[Lange, Sita]
[Rahmann, Sven]
Albrecht, Mario
[Morris, John H.]
[Böcker, Sebastian]
[Stoye, Jens]
Baumbach, Jan

Partitioning biological data with transitivity clustering
In: Nature Methods [7], 419-420

Journal Article

Baumbach, Joerg Ingo

2013

[Schneider, Till]
Hauschild, Anne-Christin
[Baumbach, Joerg Ingo]
Baumbach, Jan

An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air
In: Journal of Integrative Bioinformatics [10],

Electronic Journal Article

2013

Hauschild, Anne-Christin
[Baumbach, Joerg Ingo]
Baumbach, Jan

Paving the Way for Automated Clinical Breath Analysis and Biomarker Detection

Miscellaneous

2013

Hauschild, Anne-Christin
[Kopczynski, Dominik]
[D'Addario, Marianna]
[Baumbach, Joerg Ingo]
[Rahmann, Sven]
Baumbach, Jan

Peak Detection Method Evaluation for Ion Mobility Spectrometry by using Machine Learning Approaches
In: Metabolites [3], 277-293

Electronic Journal Article

Baumbach, Jörg Ingo

2014

[Maurer, Felix]
Hauschild, Anne-Christin
[Eisinger, Kathrin]
Baumbach, Jan
[Mayor, Arno]
[Baumbach, Jörg Ingo]

MIMA - A software for analyte identification in MCC/IMS chromatograms by mapping accompanying GC/MS measurements
In: International Journal for Ion Mobility Spectrometry [?], ?

Journal Article

2012

Hauschild, Anne-Christin
[Schneider, Till]
Pauling, Josch
[Rupp, Kathrin]
[Jang, Mi]
[Baumbach, Jörg Ingo]
Baumbach, Jan

Computational Methods for Metabolomic Data Analysis of Ion Mobility Spectrometry Data - Reviewing the State of the Art
In: Metabolites [2], 733-755

Electronic Journal Article

2012

Hauschild, Anne-Christin
[Baumbach, Jörg Ingo]
Baumbach, Jan

Integrated statistical learning of metabolic ion mobility spectrometry profiles for pulmonary disease identification
In: Genetics and Molecular Research [11], 2733-2744

Electronic Journal Article

Bayjanov, Jumamurat

2004

Bayjanov, Jumamurat

Scoring pathway activity from gene
expression data
Universität des Saarlandes

Thesis - Masters thesis

Becker, Anke

2011

[Krol, Elizaveta]
[Blom, Jochen]
[Winnebald, Jörn]
[Berhörster, Alexander]
[Barnett, Melanie J.]
[Goesmann, Alexander]
Baumbach, Jan
[Becker, Anke]

RhizoRegNet - A database of rhizobial transcription factors and regulatory networks.
In: Journal of Biotechnology [155], 127-134

Journal Article

Becker, Christoph

2007

Systematic association mapping identifies NELL1 as a novel IBD disease gene
In: PLoS ONE [2], e691.1-13

Journal Article

Beck, Stephan

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Beerenwinkel, Niko

2009

Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation of
geno2pheno-THEO on a Large Clinical Database
In: The Journal of Infectious Diseases [199], 999-1006

Journal Article

2007

[Ketter, Ralf]
[Urbschat, Steffi]
[Henn, Wolfram]
[Feiden, Wolfgang]
Beerenwinkel, Niko
Lengauer, Thomas
[Steudel, Wolf-Ingo]
[Zang, Klaus D.]
Rahnenführer, Jörg

Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas
In: International Journal of Cancer [121], 1473-1480

Journal Article

2007

Altmann, Andre
[Beerenwinkel, Niko]
Sing, Tobias
Savenkov, Igor
[Däumer, Martin]
[Kaiser, Rolf]
[Rhee, Soo-Yon]
[Fessel, W Jeffrey]
[Shafer, Robert W]
Lengauer, Thomas

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
In: Antiviral Therapy [12], 169-178

Journal Article

2007

Sing, Tobias
[Beerenwinkel, Niko]

Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype
In: Advances in Neural Information Processing Systems 19, 1-9

Proceedings Article

2007

Sing, Tobias
Low, Andrew J.
Beerenwinkel, Niko
Sander, Oliver
[Cheung, Peter K.]
Domingues, Francisco S.
Büch, Joachim
[Däumer, Martin]
[Kaiser, Rolf]
Lengauer, Thomas
[Harrigan, P. Richard]

Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
In: Antiviral Therapy [12], 1097-1106

Journal Article

2007

[Ahlenstiel, G.]
Roomp, Kirsten
Däumer, Martin
[Nattermann, T.]
[Vogel, M.]
[Rockstroh, J.K.]
Beerenwinkel, Niko
Kaiser, R.
[Nischalke, H.-D.]
[Sauerbruch, T.]
Lengauer, Thomas
[Spengler, U.]

Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level
In: Clinical and Vaccine Immunology [14], 1266-1273

Journal Article

2007

Altmann, Andre
[Däumer, Martin]
Sing, Tobias
[Beerenwinkel, Niko]
[Walter, Hauke]
[Kaiser, Rolf]
Lengauer, Thomas

Validation of geno2pheno and THEO on a large independent clinical dataset
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

2006

Roomp, Kirsten
Beerenwinkel, Niko
Sing, Tobias
[Schülter, Eugen]
Büch, Joachim
[Sierra-Aragon, Saleta]
[Däumer, Martin]
[Hoffmann, Daniel]
[Kaiser, Rolf]
Lengauer, Thomas
[Selbig, Joachim]

Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV
In: Lecture Notes in Computer Science [4075], 185-194

Journal Article

2006

Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
In: Journal of Virology [80], 7186-7198

Journal Article

2006

[Yin, Junming]
[Beerenwinkel, Niko]
Rahnenführer, Jörg
Lengauer, Thomas

Model Selection for Mixtures of Mutagenetic Trees
In: Statistical Applications in Genetics and Molecular Biology [5], Article 17

Journal Article

2006

Sing, Tobias
Sander, Oliver
Beerenwinkel, Niko
Lengauer, Thomas

ROCR: Visualizing classifier performance in R
In: Bioinformatics [21], 3940-3941

Journal Article

2006

[Lehmann, Clara]
[Däumer, Martin]
[Bousaad, Ibrahim]
Sing, Tobias
[Beerenwinkel, Niko]
Lengauer, Thomas
[Schmeisser, Norbert]
[Wyen, Christoph]
[Fätkenheuer, Gerd]
[Kaiser, Rolf]

Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART
In: Journal of Clinical Virology [37], 300-304

Journal Article

2005

A highly ordered network of HIV-1 RT mutations regulates the continuous escape from antiviral drugs
In: International Workshop in HIV Dynamics and Evolution, -

Proceedings Article

2005

Additional Mutations in HIV-1 Reverse Transcriptase are Involved in the Highly Ordered Regulation of NRTI Resistance
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -

Proceedings Article

2005

Sing, Tobias
[Svicher, Valentina]
Beerenwinkel, Niko
[Ceccherini-Silberstein, Francesca]
[Däumer, Martin]
[Kaiser, Rolf]
[Walter, Hauke]
[Korn, Klaus]
[Hoffmann, Daniel]
[Oette, Mark]
[Rockstroh, Jürgen K.]
Fätkenheuer, Gerd
[Perno, Carlo-Federico]
Lengauer, Thomas

Characterization of novel HIV Drug Resistance Mutations using clustering, multidimensional scaling and SVM-based feature ranking
In: Knowledge Discovery in Databases: PKDD 2005., 285-296

Proceedings Article

2005

[Beerenwinkel, Niko]
Sing, Tobias
Lengauer, Thomas
Rahnenführer, Jörg
Roomp, Kirsten
Savenkov, Igor
[Fischer, Roman]
[Hoffmann, Daniel]
[Selbig, Joachim]
[Korn, Klaus]
[Walter, Hauke]
[Berg, Thomas]
[Braun, Patrick]
[Fätkenheuer, Gerd]
[Oette, Mark]
[Rockstroh, Jürgen]
[Kupfer, Bernd]
[Kaiser, Rolf]
[Däumer, Martin]

Computational methods for the design of effective therapies against drug resistant HIV strains
In: Bioinformatics [21], 3943-3950

Journal Article

2005

Rahnenführer, Jörg
Beerenwinkel, Niko
[Schulz, Wolfgang A.]
[Hartmann, Christian]
[von Deimling, Andreas]
[Wullich, Bernd]
Lengauer, Thomas

Estimating cancer survival and clinical outcome based on genetic tumor progression scores
In: Bioinformatics [21], 2438-2446

Journal Article

2005

Beerenwinkel, Niko
[Däumer, Martin]
Sing, Tobias
Rahnenführer, Jörg
Lengauer, Thomas
[Selbig, Joachim]
[Hoffmann, Daniel]
[Kaiser, Rolf]

Estimating HIV evolutionary pathways and the genetic barrier to drug resistance
In: The Journal of Infectious Diseases [191], 1953-1960

Journal Article

2005

Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy
In: J Clin Virol [34], 277-287

Journal Article

2005

Sing, Tobias
Beerenwinkel, Niko
[Kaiser, Rolf]
[Hoffmann, Daniel]
[Däumer, Martin]
Lengauer, Thomas

Geno2pheno[coreceptor]: a tool for predicting coreceptor usage from genotype and for monitoring coreceptor-associated sequence alterations
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -

Poster

2005

Beerenwinkel, Niko
Rahnenführer, Jörg
[Däumer, Martin]
[Hoffmann, Daniel]
[Kaiser, Rolf]
[Selbig, Joachim]
Lengauer, Thomas

Learning multiple evolutionary pathways from cross-sectional data
In: Journal of Computational Biology [12], 584-598

Journal Article

2005

Beerenwinkel, Niko
Rahnenführer, Jörg
[Kaiser, Rolf]
[Hoffmann, Daniel]
[Selbig, Joachim]
Lengauer, Thomas

Mtreemix: a software package for learning and using mixture models of mutagenetic trees
In: Bioinformatics [21], 2106-2107

Journal Article

2005

[Wemmert, Silke]
[Ketter, Ralf]
Rahnenführer, Jörg
Beerenwinkel, Niko
[Strowitzki, Martin]
[Feiden, Wolfgang]
[Hartmann, Christian]
Lengauer, Thomas
[Stockhammer, Florian]
[Zang, Klaus D.]
[Meese, Eckart]
[Steudel, Wolf-Ingo]
[von Deimling, Andreas]
[Urbschat, Steffi]

Patients with high grade gliomas harboring delections of chromosomes 9p and 10q benefit from temozolomide treatment
In: Neoplasia [7], 883-893

Journal Article

2004

Beerenwinkel, Niko

Computational Analysis of HIV Drug resistance Data

Book

2004

Beerenwinkel, Niko
Sing, Tobias
[Däumer, Martin]
[Kaiser, Rolf]
Lengauer, Thomas

Computing the genetic barrier
In: XII International HIV Drug resistance Workshop, S125-S125

Proceedings Article

2004

Beerenwinkel, Niko

Das Arevir-Projekt : neue Wege zur Optimierung von Anti-HIV-Therapien
In: Resistenz in der HIV-Therapie : Diagnostik und Management, 94-98

Part of a Book

2004

Sing, Tobias
Beerenwinkel, Niko
Lengauer, Thomas

Learning mixtures of localized rules by maximizing the area under the ROC curve
In: ROCAI-2004: 1st International Workshop on ROC Analysis in Artificial Intelligence, 89-96

Proceedings Article

2004

Beerenwinkel, Niko
Rahnenführer, Jörg
Däumer, Martin
Hoffmann, Daniel
Kaiser, Rolf
Selbig, Joachim
Lengauer, Thomas

Learning multiple evolutionary pathways from cross-sectional data
In: RECOMB 2004 : proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology, 36-44

Proceedings Article

2004

Beerenwinkel, Niko

Methoden zur Interpretation genotypischer Resistenztests
In: Resistenz in der HIV-Therapie : Diagnostik und Management, 66-68

Part of a Book

2003

Beerenwinkel, Niko
[Däumer, Martin]
[Hoffmann, Daniel]
[Kaiser, Rolf]
[Selbig, Joachim]
Lengauer, Thomas

Bioinformatikmethoden für die Optimierung antiviraler Kombinationstherapien
In: MPG Jahrbuch, 481-486

Part of a Book

2003

Beerenwinkel, Niko

Computational Analysis of HIV Drug Resistance Data
Universität des Saarlandes

Thesis - PhD thesis

2003

Beerenwinkel, Niko
[Däumer, Martin]
[Kaiser, Rolf]
[Walter, Hauke]
[Korn, Klaus]
[Hoffmann, Daniel]
[Selbig, Joachim]
Lengauer, Thomas

Estimating effective drug combinations against drug-resistant mutants from genotypes
In: Proceedings of the 1st European HIV Drug Resistamce Workshop, 18-18

Proceedings Article

2003

Beerenwinkel, Niko
[Däumer, Martin]
[Oette, Mark]
[Korn, Klaus]
[Hoffmann, Daniel]
[Kaiser, Rolf]
Lengauer, Thomas
[Selbig, Joachim]
[Walter, Hauke]

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes
In: Nucleic Acids Research [31], 3850-3855

Journal Article

2003

Beerenwinkel, Niko
Lengauer, Thomas
[Däumer, Martin]
[Kaiser, Rolf]
[Walter, Hauke]
[Korn, Klaus]
[Hoffmann, Daniel]
[Selbig, Joachim]

Methods for optimizing antiviral combination therapies
In: Bioinformatics [19], i16-i25

Journal Article

2003

[Wolf, Katharina]
[Walter, Hauke]
Beerenwinkel, Niko
[Keulen, Wilco]
[Kaiser, Rolf]
[Hoffmann, Daniel]
Lengauer, Thomas
[Selbig, Joachim]
[Vandamme, Anne-Mieke]
[Korn, Klaus]
[Schmidt, Barbara]

Tenofovir resistance and resensitization
In: Antimicrobial Agents and Chemotherapy [47], 3478-3484

Journal Article

2003

Beerenwinkel, Niko
[Kaiser, Rolf]
Rahnenführer, Jörg
[Däumer, Martin]
[Hoffmann, Daniel]
[Selbig, Joachim]
Lengauer, Thomas

Tree models for the evolution of drug resistance
In: XII International HIV Drug resistance Workshop, S107-S107

Proceedings Article

2002

Beerenwinkel, Niko
[Schmidt, Barbara]
[Walter, Hauke]
[Kaiser, Rolf]
Lengauer, Thomas
[Hoffmann, Daniel]
[Korn, Klaus]
[Selbig, Joachim]

Diversity and complexity of HIV-1drug resistance: A bioinformatics approach to predicting phenotype from genotype
In: Proceedings of the National Academy of Sciences [99], 8271-8276

Journal Article

2002

Beerenwinkel, Niko
Lengauer, Thomas
[Däumer, Martin]
[Sierra, S.]
[Schmidt, Barbara]
[Walter, Hauke]
[Korn, Klaus]
[Oette, Mark]
Fätkenheuer, Gerd
[Rockstroh, J.]
[Hoffmann, Daniel]
[Kaiser, Rolf]
[Selbig, Joachim]

Geno2pheno is predictive of short-term virological response
In: Proceedings from the 5th International Workshop on HIV Drug Resistance & Treatment Strategies, 74-74

Proceedings Article

2002

Beerenwinkel, Niko
Lengauer, Thomas
[Schmidt, Barbara]
[Walter, Hauke]
[Kaiser, Rolf]
[Hoffmann, Daniel]
[Korn, Klaus]
[Selbig, Joachim]

Quantitative phenotype prediction by support vector machines
In: Proceedings from the 5th International Workshop on HIV Drug resistance & Treatment Strategies, 97

Proceedings Article

2001

Lengauer, Thomas
[Beerenwinkel, Niko]
[Schmidt, B.]
[Walter, H.]
[Kaiser, R.]
[Hoffmann, D.]
[Korn, K.]
[Selbig, J.]

Geno2pheno: a new machine learning approach to predicting phenotypic drug resistance from genotype
In: Antiviral Therapy [6], 104

Journal Article

2001

Beerenwinkel, Niko
[Schmidt, Barbara]
[Walter, Hauke]
[Kaiser, Rolf]
Lengauer, Thomas
[Hoffmann, Daniel]
[Korn, Klaus]
[Selbig, Joachim]

Geno2pheno: A system for the interpretation of genotypic HIV Drug resistance tests
In: IEEE Intelligent Systems [16], 35-41

Journal Article

2001

Beerenwinkel, Niko
[Däumer, Martin]
[Hoffmann, Daniel]
[Kaiser, Rolf]
[Korn, Klaus]
Lengauer, Thomas
[Schmidt, Barbara]
[Walter, Hauke]
[Selbig, Joachim]

Neue Wege zur Optimierung von Anti-HIV Therapien
In: BIOforum [24], 912-914

Journal Article

Beer, David G.

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Beggel, Bastian

2013

Beggel, Bastian
[Münk, C.]
[Däumer, M.]
[Hauck, K.]
[Häussinger, D.]
Lengauer, Thomas
[Ehrhardt, A.]

Full genome ultra-deep pyrosequencing associates G-to-A-hypermutation of the hepatitis B virus genome with the natural progression of hepatitis B
In: Journal of Viral Hepatitis [12], 882-889

Journal Article

2013

[Neumann-Fraune, Maria]
Beggel, Bastian
[Pfister, Herbert]
[Kaiser, Rolf]
[Verheyen, Jens]

High frequency of complex mutational patterns in lamivudine resistant hepatitis B virus isolates
In: Journal of Medical Virology [200], 39-49

Journal Article

2013

Beggel, Bastian
Lengauer, Thomas

Inferring short-range linkage information from sequencing chromatograms
In: PLoS One,

Electronic Journal Article

2012

Beggel, Bastian
[Neumann-Fraune, Maria]
[Doering, Matthias]
Lawyer, Glenn
[Kaiser, Rolf]
[Verheyen, Jens]
Lengauer, Thomas

Genotyping hepatitis B virus dual infections using population-based sequence data
In: Journal of General Virology [9], 1899-1907

Journal Article

2011

Erratum to: Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.
In: Medical Microbiology and Immunology [200], 51-51

Journal Article

2011

Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients
In: Medical Microbiology and Immunology [200], 39-49

Journal Article

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975-983

Journal Article

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975–983

Journal Article

2010

[Rhee, Soo-Yon]
[Margeridon-Thermet, Severin]
[Nguyen, Mindie]
[Liu, Tommy]
[Kagan, Ron]
Beggel, Bastian
[Verheyen, Jens]
[Kaiser, Rolf]
[Shafer, Robert]

Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery
In: Antiviral Research [88], 269-275

Journal Article

Behr, J

2013

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Bellagamba, Rita

2009

Dynamics of NRTI resistance mutations during therapy interruption
In: AIDS Research and Human Retroviruses [25], 57-64

Journal Article

Bellocchi, Maria Concetta

2009

Dynamics of NRTI resistance mutations during therapy interruption
In: AIDS Research and Human Retroviruses [25], 57-64

Journal Article

2006

Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
In: Journal of Virology [80], 7186-7198

Journal Article

Bellocchi, M. C.

2005

Additional Mutations in HIV-1 Reverse Transcriptase are Involved in the Highly Ordered Regulation of NRTI Resistance
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -

Proceedings Article

Bellochi, M.C.

2005

A highly ordered network of HIV-1 RT mutations regulates the continuous escape from antiviral drugs
In: International Workshop in HIV Dynamics and Evolution, -

Proceedings Article

Belouchi, Majid

2010

Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2
In: Nature Genetics [42], 991-995

Journal Article

Ben-Hur, Asa

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Bennett, David A.

2013

[Ziller, Michael J.]
[Gu, Hongcang]
Müller, Fabian
[Donaghey, Julie]
[Tsai, Linus T.-Y.]
[Kohlbacher, Oliver]
[De Jager, Philip L.]
[Rosen, Evan D.]
[Bennett, David A.]
[Bernstein, Bradley E.]
[Gnirke, Andreas]
[Meissner, Alexander]

Charting a dynamic DNA methylation landscape of the human genome
In: Nature [500], 477–481

Journal Article

Berdasco, Maria

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Berden, Jan A.

2006

[Tameling, Wladimir I.]
[Vossen, Jack H.]
Albrecht, Mario
Lengauer, Thomas
[Berden, Jan A.]
[Haring, Michel A.]
[Cornelissen, Ben J.C.]
Takken, Frank L. W.

Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation
In: Plant Physiology [140], 1233-1245

Journal Article

Bergquist, Annika

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Berg, Thoma

2010

[Lange, Christian Markus]
Roomp, Kirsten
[Dragan, Anette]
[Nattermann, Jacob]
[Michalk, Monika]
[Spengler, Ulrich]
[Weich, Viola]
Lengauer, Thomas
[Zeuzem, Stefan]
[Berg, Thoma]
[Sarrazin, Christoph]

HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection
In: Journal of Hepatology [53], 1022-1028

Journal Article

Berg, Thomas

2012

[Obermeier, Martin]
Pironti, Alejandro
[Berg, Thomas]
[Braun, Patrick]
[Däumer, Martin]
[Eberle, Josef]
[Ehret, Robert]
[Kaiser, Rolf]
[Kleinkauf, Niels]
[Korn, Klaus]
[Kücherer, Claudia]
[Müller, Harm]
[Noah, Christian]
[Stürmer, Martin]
Thielen, Alexander
[Wolf, Eva]
[Walter, Hauke]

HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge
In: Intervirology [55], 102-107

Journal Article

2008

[Obermeier, Martin]
[Berg, Thomas]
[Sichtig, Nadine]
[Braun, Patrick]
[Däumer, Martin]
[Walter, Hauke]
[Noah, Christian]
[Wolf, Eva]
[Müller, Harm]
[Stürmer, Martin]
Thielen, Alexander
[Kaiser, Rolf]

Determination of HIV-1 co-receptor usage in German patients – comparison of genotypic methods with the TROFILE® phenotypic assay
In: Abstracts of the Ninth International Congress on Drug Therapy in HIV Infection, 123

Poster

2005

Computational methods for the design of effective therapies against drug resistant HIV strains
In: Bioinformatics [21], 3943-3950

Journal Article

Berg, T.

2013

[Dietz, J.]
Schelhorn, Sven-Eric
[Fitting, D.]
[Mihm, U.]
[Susser, S.]
[Welker, M.-W.]
[Füller, C.]
[Däumer, M.]
[Teuber, G.]
[Wedemeyer, H.]
[Berg, T.]
Lengauer, Thomas
[Z., Stefan]
[Herrmann, E.]
[Sarrazin, C.]

Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of HCV genotype 1-infected patients
In: Journal of Virology [87], 6172-6181

Journal Article

Berhörster, Alexander

2011

[Krol, Elizaveta]
[Blom, Jochen]
[Winnebald, Jörn]
[Berhörster, Alexander]
[Barnett, Melanie J.]
[Goesmann, Alexander]
Baumbach, Jan
[Becker, Anke]

RhizoRegNet - A database of rhizobial transcription factors and regulatory networks.
In: Journal of Biotechnology [155], 127-134

Journal Article

Bernhardt, Rita

2011

[Bleif, Sabrina]
[Hannemann, Frank]
[Lisurek, Michael]
[von Kries, Jens Peter]
[Zapp, Josef]
Dietzen, Matthias
[Antes, Iris]
[Bernhardt, Rita]

Identification of CYP106A2 as a Regioselective Allylic Bacterial Diterpene Hydroxylase
In: ChemBioChem [12], 576-582

Journal Article

2008

[Lisurek, Michael]
[Simgen, Birgit]
Antes, Iris
[Bernhardt, Rita]

Theoretical and Experimental Evaluation of a CYP106A2 Low Homology Model and Production of Mutants with Changed Activity and Selectivity of Hydroxylation
In: ChemBioChem [9], 1439-1449

Journal Article

Bernhardt, R.

2005

[Ulmschneider, Sarah]
[Mueller-Vieira, Ursula]
[Mitrenga, Markus]
[Hartmann, Rolf W.]
[Oberwinkler-Marchais, S]
[Klein, Christian D.]
[Bureik, M.]
[Bernhardt, R.]
Antes, Iris
Lengauer, Thomas

Synthesis and Evaluation of Imidazolylmethylenetetrahydronaphthalenes and Imidazolylmethyleneindanes: Potent Inhibitors of Aldosterone Synthase
In: Journal of Medicinal Chemistry [48], 1796-1805

Journal Article

Bernstein, Bradley E.

2013

Charting a dynamic DNA methylation landscape of the human genome
In: Nature [500], 477–481

Journal Article

2011

[Ziller, Michael J.]
Müller, Fabian
[Liao, Jing]
[Zhang, Yingying]
[Gu, Hongcang]
Bock, Christoph
[Boyle, Patrick]
[Epstein, Charles B.]
[Bernstein, Bradley E.]
Lengauer, Thomas
[Gnirke, Andreas]
[Meissner, Alexander]

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
In: PLoS Genetics [17], e1002389,1-e1002389,15

Electronic Journal Article

2010

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
In: Nature Biotechnology [28], 1097-1105

Journal Article

Beroukhim, Rameen

2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Berthold, F.

2013

Tolosi, Laura
[Theißen, J.]
Halachev, Konstantin
[Hero, B.]
[Berthold, F.]
Lengauer, Thomas

A method for finding consensus breakpoints in the cancer genome from copy number data
In: Bioinformatics [29], 1793-1800

Journal Article

2013

Schelhorn, Sven-Eric
[Fischer, M.]
[Tolosi, Laura]
[Altmüller, J.]
[Nürnberg, P.]
[Pfister, H.]
Lengauer, Thomas
Berthold, F.

Sensitive detection of viral transcripts in human tumor transcriptomes
In: PLOS Computational Biology [9], xx

Journal Article

Bertolif, Ada

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975–983

Journal Article

Bertoli, Ada

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975-983

Journal Article

2007

Journal Article

2006

Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
In: Journal of Virology [80], 7186-7198

Journal Article

Bertoli, A.

2005

A highly ordered network of HIV-1 RT mutations regulates the continuous escape from antiviral drugs
In: International Workshop in HIV Dynamics and Evolution, -

Proceedings Article

2005

Additional Mutations in HIV-1 Reverse Transcriptase are Involved in the Highly Ordered Regulation of NRTI Resistance
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -

Proceedings Article

Bertone, P

2013

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Berzuini, Carlo R.

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

Betancourt-Morales, Andres (ed.)

2004

Ramírez, Fidel

Evolucion de la Evolucionalidad
In: Biologos lejos del equilibrio: Nuevas metaforas evolutivas, 59-87

Part of a Book

Betschieder, Dirk

2003

[Jose, Joachim]
[Betschieder, Dirk]
Ray, Somak
Lengauer, Thomas
[Zangen, D]

New inhibitors of human cathepsin G identified by surface display library screening and peptide-protein docking
In: 7th International Symposium on Pharmaceutical Sciences (ISOPS-7), 46-49

Proceedings Article

Bhadra, Tapas

2012

[Bhattacharyya, Malay]
Feuerbach, Lars
[Bhadra, Tapas]
[Bandyopadhyay, Sanghamitra]

MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection
In: Statistical Applications in Genetics and Molecular Biology [11], 6.1-6.25

Journal Article

Bhadra, T.

2013

[Bhadra, T.]
[Battacharya, M.]
[Feuerbach, L.]
Lengauer, Thomas
Bandyopadhyay, S.

DNA Methylation Patterns Facilitate the Identification of Transcription Start Sites: A Brain-specofoc Study
In: PLOSONE [8], xx

Journal Article

Bhattacharyaa, Sumitra

2005

[Das, Ani V.]
[James, Jackson]
Rahnenführer, Jörg
[Thoresona, Wallace B.]
[Bhattacharyaa, Sumitra]
[Zhao, Xing]
[Ahmad, Iqbal]

Retinal properties and potential of the adult mammalian ciliary epithelium stem cells
In: Vision Research [45], 1653-1666

Journal Article

Bhattacharyya, Malay

2012

[Bhattacharyya, Malay]
Feuerbach, Lars
[Bhadra, Tapas]
[Bandyopadhyay, Sanghamitra]

MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection
In: Statistical Applications in Genetics and Molecular Biology [11], 6.1-6.25

Journal Article

Bhat, Prajwal

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Bickel, Steffen

2010

Bogojeska, Jasmina
[Bickel, Steffen]
Altmann, André
Lengauer, Thomas

Dealing with sparse data in predicting outcomes of HIV combination therapies
In: Bioinformatics [26], 2085-2092

Journal Article

2008

Bickel, Steffen
Bogojeska, Jasmina
Lengauer, Thomas
Sheffer, Tobias

Multi-Task Learning for HIV Therapy Screening
In: Proceedings, Twenty-Fifth International Conference on Machine Learning, 56-63

Proceedings Article

Bidgood, Penny

2007

EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

Biemel, Klaus

2006

[Voets, Marieke]
Antes, Iris
[Scherer, Christiane]
[Müller-Vieira, Ursula]
[Biemel, Klaus]
[Marchais-Oberwinkler, Sandrine]
[Hartmann, Rolf W.]

Journal Article

Biemel, K.

2005

[Voets, Marieke]
Antes, Iris
[Scherer, C]
[Mueller-Vieira, U.]
[Biemel, K.]
[Barrassin, C.]
[Marchais-Oberwinkler, S.]
[Hartmann, R. W.]

Journal Article

Binsl, Thomas

2006

Binsl, Thomas

Feature Prints: A new method for calculating molecular similarities
Universität des Saarlandes

Thesis - Masters thesis

2004

Binsl, Thomas

Implementation of a Generic Fragment
Based Method for Automated
Calculation of the Octanol-Water
Partition Coefficient
Universität des Saarlandes

Thesis - Bachelor thesis

Biondi, Ricardo M.

2006

[Plotz, Guido]
[Welsch, Christoph]
[Giron-Monzon, Luis]
[Friedhoff, Peter]
Albrecht, Mario
[Piiper, Albrecht]
Biondi, Ricardo M.
Lengauer, Thomas
[Zeuzem, Stefan]
[Raedle, Jochen]

Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair
In: Nucleic Acids Research [34], 6574-6586

Journal Article

Bird, Adrian

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Birney, Ewan

2008

Integrating biological data - the Distributed Annotation System
In: BMC Bioinformatics [9], S3.1-7

Journal Article

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Bisi, Alessandra

2008

[Lucas, Simon]
[Heim, Ralph]
[Negri, Matthias]
Antes, Iris
[Ries, Christina]
[Schewe, Katarzyna E.]
[Bisi, Alessandra]
[Gobbi, Silvia]
[Hartmann, Rolf W.]

Novel Aldosterone Synthase Inhibitors with Extended Carbocyclic Skeleton by a Combined Ligand-Based and Structure-Based Drug Design Approach
In: Journal of Medical Chemistry [51], 6138-6149

Journal Article

"{o}rne, Jari

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Bjornsson, Einar

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Blankenburg, Hagen

2013

Profiling of parkin-binding partners using tandem affinity purification
In: PLoS ONE [8], 1-17

Journal Article

2012

Emig, Dorothea
Blankenburg, Hagen
Ramírez, Fidel
Albrecht, Mario

Functional characterization of human genes from exon expression and RNA interference results
In: Bioinformatics and Drug Discovery, 33-53

Part of a Book

2012

[Garai, Ágnes]
[Zeke, András]
[Gógl, Gergo]
[Töro, Imre]
[Fördos, Ferenc]
Blankenburg, Hagen
[Bárkai, Tünde]
[Varga, János]
[Alexa, Anita]
Emig, Dorothea
Albrecht, Mario
[Reményi, Attila]

Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove
In: Science Signaling [5], ra74,1-ra74,14

Journal Article

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

2011

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
In: Cell Host & Microbe [9], 32-45

Journal Article

2009

Blankenburg, Hagen
Ramírez, Fidel
Büch, Joachim
Albrecht, Mario

DASMIweb: online integration, analysis and assessment of distributed protein interaction data
In: Nucleic Acids Research [37], W122-W128

Electronic Journal Article

2009

Blankenburg, Hagen
[Finn, Robert D.]
[Prlić, Andreas]
[Jenkinson, Andrew M.]
Ramírez, Fidel
Emig, Dorothea
Schelhorn, Sven-Eric
Büch, Joachim
Lengauer, Thomas
Albrecht, Mario

DASMI: exchanging, annotating and assessing molecular interaction data
In: Bioinformatics [25], 1321-1328

Journal Article

2009

Protein-protein interactions: analysis and prediction
In: Modern Genome Annotation - The Biosapiens Network, 353-410

Part of a Book

2008

Integrating biological data - the Distributed Annotation System
In: BMC Bioinformatics [9], S3.1-7

Journal Article

2007

Blankenburg, Hagen

A Distributed Annotation System for Molecular Interactions
Ruprecht Karl Universität Heidelberg; Universität Heilbronn

Thesis - other

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Bleif, Sabrina

2011

[Bleif, Sabrina]
[Hannemann, Frank]
[Lisurek, Michael]
[von Kries, Jens Peter]
[Zapp, Josef]
Dietzen, Matthias
[Antes, Iris]
[Bernhardt, Rita]

Identification of CYP106A2 as a Regioselective Allylic Bacterial Diterpene Hydroxylase
In: ChemBioChem [12], 576-582

Journal Article

Blom, Jochen

2011

[Krol, Elizaveta]
[Blom, Jochen]
[Winnebald, Jörn]
[Berhörster, Alexander]
[Barnett, Melanie J.]
[Goesmann, Alexander]
Baumbach, Jan
[Becker, Anke]

RhizoRegNet - A database of rhizobial transcription factors and regulatory networks.
In: Journal of Biotechnology [155], 127-134

Journal Article

v{s}njak, Matko

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Boberg, Kirsten Muri

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Böcker, Sebastian

2011

[Wittkop, Tobias]
Emig, Dorothea
[Truss, Anke]
Albrecht, Mario
[Böcker, Sebastian]
Baumbach, Jan

Comprehensive cluster analysis with Transitivity Clustering
In: Nature Protocols [6], 285-295

Journal Article

2010

[Wittkop, Tobias]
Emig, Dorothea
[Lange, Sita]
[Rahmann, Sven]
Albrecht, Mario
[Morris, John H.]
[Böcker, Sebastian]
[Stoye, Jens]
Baumbach, Jan

Partitioning biological data with transitivity clustering
In: Nature Methods [7], 419-420

Journal Article

Böcker, Sebastian (ed.)

2012

Röttger, Richard
Kreutzer, Christoph
[Duong Vu, Thuy]
[Wittkop, Tobias]
Baumbach, Jan

Online Transitivity Clustering of Biological Data with Missing Values
In: German Conference on Bioinformatics 2012 (GCB 2012), 57-68

Electronic Proceedings Article

Bock, Christoph

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

2013

[Simmer, F.]
[Brinkmann, A.B.]
Assenov, Yassen
[Matarese, F.]
[Kaan, A.]
Lengauer, Thomas
Bock, Christoph
[Colantuoni, V.]
[Altucci, L.]
[Stunnenberg, H.G.]

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched human tissue
In: Epigenetics [7], 1355-1367

Journal Article

2013

Halachev, Konstantin
Bast, H.
Lengauer, Thomas
Bock, Christoph

Interactive exploration of large genome and epigenome datasets in real time
In: Genome Biology [13], xx

Journal Article

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

2012

A promoter DNA demethylation landscape of human hematopoietic differentiation
In: Nucleic Acids Research [40], 116-131

Journal Article

2012

Bock, Christoph

Analysing and interpreting DNA methylation data
In: Nature Reviews Genetics [13], 705-719

Journal Article

2012

[Feuerbach, Lars]
Halachev, Konstantin
Assenov, Yassen
Mueller, Fabian
Bock, Christoph
Lengauer, Thomas

Part of a Book

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

2012

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
In: Epigenetics [7], 1355-1367

Journal Article

2012

[Mikeska, Thomas]
Bock, Christoph
[Do, Hongdo]
[Dobrovic, Alexander]

DNA methylation biomarkers in cancer: Progress towards clinical implementation
In: Expert Reviews of Molecular Diagnostics [12], 473-487

Journal Article

2012

Halachev, Konstantin
[Bast, Hannah]
Albrecht, Felipe
Lengauer, Thomas
Bock, Christoph

EpiExplorer: live exploration and global analysis of large epigenomic datasets
In: Genome Biology [13], R96,1-R96,14

Electronic Journal Article

2012

Halachev, K.
[Bast, H.]
Albrecht, F.
Lengauer, Thomas
Bock, Christoph

EpiExplorer: live exploration and global analysis of large epigenomic datasets
In: Genome Biology [13], R96,1-R96,14

Journal Article

2012

Bock, Christoph
Lengauer, Thomas

Epigenom-Karten erstellen und nutzen
In: BIOspektrum [18], 138-141

Journal Article

2012

[Mekhubad, Shila]
Bock, Christoph
[de Boer, A. Sophie]
[Kiskinis, Evangelos]
[Meissner, Alexander]
[Eggan, Kevin]

Erosion of dosage compensation impacts human iPSC disease modeling
In: Cell Stem Cell [10], 595-609

Journal Article

2012

Bock, Christoph
Lengauer, Thomas

Managing drug resistance in cancer: lessons from HIV therapy
In: Nature Reviews Cancer [12], 494-501

Journal Article

2012

Lengauer, Thomas
Bock, Christoph

Managing drug resistance in cancer: lessons from HIV therapy
In: Nature Reviews Cancer [12], 494-501

Journal Article

2012

[Xi, Yuanxin]
Bock, Christoph
Müller, Fabian
[Sun, Deqiang]
[Meissner, Alexander]
[Li, Wei]

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
In: Bioinformatics [28], 430-432

Journal Article

2011

[Lutsik, Pavlo]
Feuerbach, Lars
[Arand, Julia]
Lengauer, Thomas
[Walter, Jörn]
Bock, Christoph

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
In: Nucleic Acids Research [39], W551-W556

Journal Article

2011

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
In: PLoS Genetics [17], e1002389,1-e1002389,15

Electronic Journal Article

2011

[Zacharek, Sima J.]
[Fillmore, Christine M.]
[Lau, Allison N.]
[Gludish, David W.]
[Chou, alan]
[Ho, Joshua W. K.]
[Zamponi, Raffaella]
[Gazit, Roi]
Bock, Christoph
[Jäger, Natalie]
[Smith, Zachary D.]
[Kim, Tae-min]
[Saunders, Arven H.]
[Wong, Janice]
[Lee, Joo-Hyeon]
[Roach, Rebecca R.]
[Rossi, Derrick J.]
[Meissner, Alex]
[Gimelbrant, Alexander A.]
[Park, Peter J.]
[Kim, Carla F.]

Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci
In: Cell Stem Cell [9], 272-280

Journal Article

2011

[Gu, Hongcang]
[Smith, Zachary D.]
Bock, Christoph
[Boyle, Patrick]
[Gnirke, Andreas]
[Meissner, Alexander]

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
In: Nature Protocols [6], 468-481

Journal Article

2011

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
In: Cell [144], 439-452

Journal Article

2011

[Xi, Yuanxin]
Bock, Christoph
Müller, Fabian
[Sun, Deqiang]
[Meissner, Alexander]
[Li, Wei]

RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing
In: Bioinformatics [28], 430-432

Journal Article

2010

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
In: Nature Biotechnology [28], 1097-1105

Journal Article

2010

[Gu, Hongcang]
Bock, Christoph
[Mikkelsen, Tarjei S.]
[Jäger, Natalie]
[Smith, Zachary D.]
[Tomazou, Eleni]
[Gnirke, Andreas]
[Lander, Eric S.]
[Meissner, Alexander]

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
In: Nature Methods [7], 133-136

Journal Article

2010

Bock, Christoph
[Tomazou, Eleni M.]
[Brinkman, Arie B.]
Müller, Fabian
[Simmer, Femke]
[Gu, Hongcang]
[Jäger, Natalie]
[Gnirke, Andreas]
[Stunnenberg, Hendrik G.]
[Meissner, Alexander]

Quantitative comparison of genome-wide DNA methylation mapping technologies
In: Nature Biotechnology [28], 1106-1114

Journal Article

2010

Bock, Christoph
[Von Kuster, Greg]
Halachev, Konstantin
[Taylor, James]
[Nekrutenko, Anton]
Lengauer, Thomas

Web-based analysis of (epi-) genome data using EpiGRAPH and Galaxy.
In: Genetic Variation : Methods and Protocols, 275-296
In: Methods of Molecular Biology [628], 275-296

Part of a Book

2009

Feuerbach, Lars
Halachev, Konstantin
Lengauer, Thomas
Bock, Christoph

An exhaustive methode for CpG island annotation
In: Special Issue: Abstracts of the 3rd MC-GARD Meeting, 146-146

Poster

2009

[Zhang, Yingying]
[Rohde, Christian]
[Tierling, Sascha]
[Jurkowski, Tomasz P.]
Bock, Christoph
[Santacruz, Diana]
[Ragozin, Sergey]
[Reinhardt, Richard]
[Groth, Marco]
[Walter, Jörn]
[Jeltsch, Albert]

DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution
In: PLoS Genetics [5], e1000438:1-e1000438:15

Electronic Journal Article

2009

Bock, Christoph

Epigenetic biomarker development
In: Epigenomics [1], 99-110

Journal Article

2009

Bock, Christoph
Halachev, Konstantin
Büch, Joachim
Lengauer, Thomas

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data
In: Genome Biology [10], R14.1-R14.14

Journal Article

2009

[Moser, Dirk]
[Ekawardhani, Savira]
[Kumsta, Robert]
[Palmason, Haukur]
Bock, Christoph
[Athanassiadou, Zoi]
[Lesch, Klaus-Peter]
[Meyer, Jobst]

Functional Analysis of a Potassium-Chloride Co-Transporter 3 (SLC12A6) Promoter Polymorphism Leading to an Additional DNA Methylation Site
In: Neuropsychopharmacology [34], 458-467

Journal Article

2009

Schüffler, Peter
[Mikeska, Thomas]
[Waha, Andreas]
Lengauer, Thomas
Bock, Christoph

MethMarker: User-friendly design and optimization of gene-specific DNA methylation assays
In: Genome Biology [10], R105:1-R105:10

Journal Article

2008

Bock, Christoph
Lengauer, Thomas

Computational epigenetics
In: Bioinformatics [24], 1-10

Journal Article

2008

Bock, Christoph

Computational Epigenetics - Bioinformatic methods for epigenome prediction, DNA methylation mapping and cancer epigenetics
Universität des Saarlandes

Thesis - PhD thesis

2008

Bock, Christoph
[Walter, Jörn]
[Paulsen, Martina]
Lengauer, Thomas

Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping
In: Nucleic Acids Research [36], e55

Journal Article

2008

Bock, Christoph

IVF: stars may have to consider the risk of stolen parenthood
In: Nature [454], 938

Journal Article

2008

Kircher, Martin
Bock, Christoph
Paulsen, Martina

Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region
In: BMC Genomics [9], 346

Journal Article

2007

Bock, Christoph
Lengauer, Thomas

Computational Epigenetics: Bioinformatik für neue Wege in der Krebsforschung
In: Jahrbuch 2007, 271-277

Part of a Book

2007

Bock, Christoph
[Walter, Jörn]
[Paulsen, Martina]
Lengauer, Thomas

CpG Island Mapping by Epigenome Prediction
In: PLoS Computational Biology [3], 1055-1070

Journal Article

2007

[Mikeska, Thomas]
Bock, Christoph
[El-Maarri, Osman]
[Hübner, Anika]
[Ehrentraut, Denise]
[Schramm, Johannes]
[Felsberg, Jörg]
[Kahl, Philip]
[Büttner, Reinhard]
[Pietsch, Torsten]
[Waha, Andreas]

Optimization of Quantitative MGMT Promoter Methylation Analysis Using Pyrosequencing and Combined Bisulfite Restriction Analysis
In: Journal of Molecular Diagnostics [9], 368-381

Journal Article

2007

[Liu, Fang]
[Tostesen, Eivind]
[Sundet, Jostein K.]
[Jenssen, Tor-Kristian]
Bock, Christoph
[Jerstad, Geir Ivar]
[Thilly, William G.]
[Hovig, Eivind]

The human genomic melting map
In: PLoS Computational Biology [3], e93

Journal Article

2006

Bock, Christoph
[Hesser, Jürgen]

Analysis and Prediction of Helix Shift Errors in Homology Modeling
In: In Silico Biology [6], 131-145

Journal Article

2006

Bock, Christoph

Bioinformatik: Neue Strategien gegen Krebs
In: Deutsches Ärzteblatt PRAXiS [103], 10-11

Journal Article

2006

Bock, Christoph
Halachev, Konstantin
Lengauer, Thomas

Bioinformatisches Data Mining erschließt neue Strategien gegen Krebs
In: Aktuelle Trends in der Softwareforschung, 91-99

Part of a Book

2006

Bock, Christoph
[Paulsen, Martina]
[Tierling, Sascha]
[Mikeska, Thomas]
Lengauer, Thomas
[Walter, Jörn]

CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure
In: PLoS Genetics [2], 0243-0252

Electronic Journal Article

2005

Bock, Christoph
Lengauer, Thomas
[Reither, Sabine]
[Mikeska, Thomas]
[Paulsen, Martina]
[Walter, Jörn]

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
In: Bioinformatics [21], 4067-4068

Journal Article

Boecker, Sebastian

2011

[Wittkop, Tobias]
[Rahmann, Sven]
Roettger, Richard
[Boecker, Sebastian]
Baumbach, Jan

Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis
In: Internet Mathematics [7], 255-273

Journal Article

Boeddrich, Annett

2006

An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis
In: EMBO Journal [25], 1547-1558

Journal Article

Boehme, Richard

2010

[Swenson, Luke C.]
[Boehme‌, Richard]
Thielen, Alexander
[McGovern‌, Rachel A.]
[Harrigan, P. Richard]

Genotypic determination of HIV-1 tropism in the clinical setting
In: HIV Therapy [4], 293-303

Journal Article

Boehm, Ariane

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Boehm, Bernhard

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Boehm, Bernhard O.

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

Bogojeska, Jasmina

2012

Bogojeska, Jasmina
Lengauer, Thomas

Hierarchical Bayes Model for Predicting Effectiveness of HIV Combination Therapies
In: Statistical Applications in Genetics and Molecular Biology [11], 11.1-11.19

Journal Article

2012

Bogojeska, Jasmina
[Stöckel, Daniel]
[Zazzi, Maurizio]
[Kaiser, Rolf]
[Incardona, Francesca]
[Rosen-Zvi, Michal]
Lengauer, Thomas

History-alignment models for bias-aware prediction of virological response to HIV combination therapy
In: Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics (AISTATS 2012), 118-126

Proceedings Article

2011

Bogojeska, Jasmina

History distribution matching method for predicting effectiveness of HIV combination therapies
In: Neural Information Processing Systems (NIPS 2011), 424-432

Electronic Proceedings Article

2011

Saigo, Hiroto
Altmann, André
Bogojeska, Jasmina
Müller, Fabian
[Nowozin, Sebastian]
Lengauer, Thomas

Learning from past treatments and their outcome improves prediction of In Vivo response to anti-HIV therapy
In: Statistical Applications in Genetics and Molecular Biology [10], 1-32

Electronic Journal Article

2011

Bogojeska, Jasmina

Statistical Learning Methods for Bias-aware HIV Therapy Screening
Universität des Saarlandes

Thesis - PhD thesis

2010

Bogojeska, Jasmina
[Bickel, Steffen]
Altmann, André
Lengauer, Thomas

Dealing with sparse data in predicting outcomes of HIV combination therapies
In: Bioinformatics [26], 2085-2092

Journal Article

2009

Thielen, Alexander
Altmann, André
Bogojeska, Jasmina
[Kaiser, Rolf]
Lengauer, Thomas

Poster

2008

Bickel, Steffen
Bogojeska, Jasmina
Lengauer, Thomas
Sheffer, Tobias

Multi-Task Learning for HIV Therapy Screening
In: Proceedings, Twenty-Fifth International Conference on Machine Learning, 56-63

Proceedings Article

2008

Bogojeska, Jasmina
Alexa, Adrian
Altmann, André
Lengauer, Thomas
[Rahnenführer, Jörg]

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
In: Bioinformatics [24], 2391-2392

Journal Article

2008

Bogojeska, Jasmina
Lengauer, Thomas
[Rahnenführer, Jörg]

Stability analysis of mixtures of mutagenetic trees
In: BMC Bioinformatics [9], 165-181

Journal Article

2007

Bogojeska, Jasmina

Stability analysis of oncogenetic trees mixture models
Universität des Saarlandes

Thesis - Masters thesis

Bohnert, R

2013

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Bojunga, Jörg

2005

[Bojunga, Jörg]
[Welsch, Christoph]
Antes, Iris
Albrecht, Mario
Lengauer, Thomas
[Zeuzem, Stefan]

Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency
In: Human Genetics [117], 558-564

Journal Article

Bonini, Nancy M.

2006

An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis
In: EMBO Journal [25], 1547-1558

Journal Article

Borgulya, Gabór

2007

EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

Borkakoti, Neera (ed.)

2002

Kämper, Andreas
[Apostolakis, Joannis]
Lengauer, Thomas

Docking of Bacterial Cell-Wall Fragments into Glycopeptide Antibiotics
In: From Genes to Drugs via Crystallography: 33rd crytallographic course at the E. Majorana Center, 49

Poster

Bork, Peer

2009

Protein-protein interactions: analysis and prediction
In: Modern Genome Annotation - The Biosapiens Network, 353-410

Part of a Book

Bork, P.

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Boucher, B

2000

[Clee, Susanne M.]
[Kastelein, J.J.P.]
[van Dam, M]
[Marcil, Michel]
Roomp, Kirsten
[Zwarts, K.Y.]
[Collins, Jennifer A.]
[Roelants, R]
[Tamasawa, N]
[Stulc, T]
[Suda, T]
[Ceska, R]
[Boucher, B]
[Rondeau, C]
[DeSouich, C]
[Brooks-Wilson, A]
[Molhuizen, H.O.]
[Frohlich, J]
[Genest, Jacques Jr]
[Hayden, Michael R.]

Age and residual cholesterol efflux affect HDL cholesterol levels and coronary artery disease in ABCA1 heterozygotes
In: Journal of Clinical Investigation [106], 1263-70

Journal Article

Boucher, B.

1999

[Marcil, Michel]
[Brooks-Wilson, A.]
[Clee, Susanne M.]
Roomp, Kirsten
[Zhang, Lin-Hua]
[Yu, L.]
[Collins, Jennifer A.]
[van Dam, M.]
[Molhuizen, H. O.]
[Loubser, O.]
[Ouelette, B. F.]
[Sensen, C. W.]
[Fichter, K.]
[Mott, S.]
[Denis, M.]
[Boucher, B.]
[Pimstone, S.]
[Genest, Jacques]
[Kastelein, J. J. P.]
[Hayden, Michael R.]

Mutations in the ABC1 gene in familial HDL deficiency with defective cholesterol efflux
In: The Lancet [354], 1341-6

Journal Article

Boucher, Charles

2010

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
In: HIV Medicine [Early View], 1-8

Electronic Journal Article

Boucher, Charles (ed.)

2010

Altmann, Andre
Pironti, Alejandro
Perner, Juliane
Büch, Joachim
Lengauer, Thomas

Poster

2004

Beerenwinkel, Niko
Sing, Tobias
[Däumer, Martin]
[Kaiser, Rolf]
Lengauer, Thomas

Computing the genetic barrier
In: XII International HIV Drug resistance Workshop, S125-S125

Proceedings Article

2003

Beerenwinkel, Niko
[Kaiser, Rolf]
Rahnenführer, Jörg
[Däumer, Martin]
[Hoffmann, Daniel]
[Selbig, Joachim]
Lengauer, Thomas

Tree models for the evolution of drug resistance
In: XII International HIV Drug resistance Workshop, S107-S107

Proceedings Article

Boucher, C.A.

2011

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

Boulting, Gabriella

2011

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
In: Cell [144], 439-452

Journal Article

Bourne, Philip (ed.)

2004

Beerenwinkel, Niko
Rahnenführer, Jörg
Däumer, Martin
Hoffmann, Daniel
Kaiser, Rolf
Selbig, Joachim
Lengauer, Thomas

Learning multiple evolutionary pathways from cross-sectional data
In: RECOMB 2004 : proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology, 36-44

Proceedings Article

Bourne, P. (ed.)

2004

Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computional Biology 2004 (ISMB/ECCB 2004)

Proceedings

Bousaad, Ibrahim

2006

[Lehmann, Clara]
[Däumer, Martin]
[Bousaad, Ibrahim]
Sing, Tobias
[Beerenwinkel, Niko]
Lengauer, Thomas
[Schmeisser, Norbert]
[Wyen, Christoph]
[Fätkenheuer, Gerd]
[Kaiser, Rolf]

Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART
In: Journal of Clinical Virology [37], 300-304

Journal Article

Boussaad, Ibo

2005

[Kaiser, Rolf]
[Boussaad, Ibo]
[Lehmann, C.]
[Däumer, Martin]
Sing, Tobias
[Schmeisser, N.]
[Wyen, C.]
Fätkenheuer, Gerd

Stable coreceptor usage of HIV-1 in patients with ongoing treatment failure on HAART
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -

Proceedings Article

Bowlus, Christopher L.

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Boyle, Patrick

2011

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
In: PLoS Genetics [17], e1002389,1-e1002389,15

Electronic Journal Article

2011

[Gu, Hongcang]
[Smith, Zachary D.]
Bock, Christoph
[Boyle, Patrick]
[Gnirke, Andreas]
[Meissner, Alexander]

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
In: Nature Protocols [6], 468-481

Journal Article

Bozek, Kasia

2009

[Kono, Ken]
Bozek, Kasia
Domingues, Francisco S.
[Shioda, Tatsuo]
[Nakayama, Emi E.]

Impact of a single amino acid in the variable region 2 of the Old World monkey TRIM5alpha SPRY (B30.2) domain on anti-human immunodeficiency virus type 2 activity
In: Virology [388], 160-168

Journal Article

2009

Bozek, Kasia
[Relógio, Angela]
[Kielbasa, Szymon M.]
[Heine, Markus]
[Dame, Christof]
[Kramer, Achim]
[Herzel, Hanspeter]

Regulation of clock-controlled genes in mammals.
In: PLoS One [4], e4882:1-e4882:12

Electronic Journal Article

2009

Bozek, Kasia
Thielen, Alexander
Sierra, Saleta
[Kaiser, Rolf]
Lengauer, Thomas

V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV.
In: PLoS One [4], e7387:1-e.7387:14

Electronic Journal Article

2008

Thielen, Alexander
[Harrigan, P Richard]
Low, Andrew J.
[Moores, A]
Altmann, Andre
Bozek, Kasia
[Heger, Eva]
[Sichtig, Nadine]
[Kaiser, Rolf]
Lengauer, Thomas

Improved genotypic prediction of HIV-1 coreceptor usage by incorporating V2 loop sequence variation
In: Antiviral Therapy, A100

Poster

Bozek, Katarzyna

2012

Bozek, Katarzyna
[Eckhardt, Manon]
[Sierra, Saleta]
[Kaiser, Rolf]
[Kräusslich, Hans-Georg]
[Müller, Barbara]
Lengauer, Thomas

An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data
In: Retrovirology [9], 60.1-60.15

Journal Article

2011

Bozek, Katarzyna

Analysis of HIV-host interaction on different scales.
Universität des Saarlandes

Thesis - PhD thesis

2010

[Kuroishi, Ayumu]
Bozek, Katarzyna
[Shioda, Tatsuo]
[Nakayama, Emi E.]

A single amino acid substitution of the human immunodeficiency virus type 1 capsid protein affects viral sensitivity to TRIM5 alpha.
In: Retrovirology [7], 58,1-58,10

Electronic Journal Article

2010

Bozek, Katarzyna
[Rosahl, A. L.]
[Gaub, S.]
[Lorenzen, S.]
[Herzel, H.]

Circadian transcription in liver
In: Biosystems [102], 61-69

Journal Article

2010

Bozek, Katarzyna
Lengauer, Thomas

Positive selection of HIV host factors and the evolution of lentivirus genes
In: BMC Evolutionary Biology [10], 186,1-186,15

Electronic Journal Article

Bozek, K.

2013

[Bozek, K.]
Lengauer, Thomas
[Sierra, S.]
[Kaiser, Rolf]
[Domingues, F.S.]

Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage
In: PLoS Computational Biology [x], x

Journal Article

Bozinov, Daniel

2004

Rahnenführer, Jörg
[Bozinov, Daniel]

Hybrid clustering for microarray image analysis combining intensity and shape features
In: BMC Bioinformatics [5], 1-11

Journal Article

2003

Rahnenführer, Jörg
Bozinov, Daniel

Comparative quality analyses for hybrid clustering of microarray images
In: Proceedings of the Sventh Annual International Conference on Computational Biology, -

Poster

2002

[Bozinov, Daniel]
Rahnenführer, Jörg
[Burson, Cathy]
[Spiegelstein, Ofer]

Automated Grid Alignment for High-Throughput Analysis of Microarray Images (CIIST-02)
In: Proceedings of the 2002 International Conference on Imaging Science, Systems, and Technology, 161-167

Proceedings Article

2002

Rahnenführer, Jörg
[Bozinov, Daniel]

Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering
In: Bioinformatics [18], 747-756

Journal Article

Braak, Cajo J F Ter

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Brackmann, Hans H.

2007

[Kupfer, Bernd]
Sing, Tobias
Schüffler, Peter
[Hall, Rabea]
[Kurz, Ralf]
[McKeown, Astrid]
[Schneweis, Karl-Eduard]
[Eberl, Wolfgang]
[Oldenburg, Johannes]
[Brackmann, Hans H.]
[Rockstroh, Jürgen K.]
[Spengler, Ulrich]
Däumer, Martin
[Kaiser, Rolf]
Lengauer, Thomas
[Matz, Bertfried]

Fifteen years of env C2V3C3 evolution in six individuals clonally infected with human immunodeficiency virus type 1
In: Journal of Medical Virology [79], 1629-1639

Journal Article

Brambilla, Elisabeth

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Brand, Stephan

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Braun, Felix

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Braun, Patrick

2012

HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge
In: Intervirology [55], 102-107

Journal Article

2009

Thielen, Alexander
[Sichtig, Nadine]
[Braun, Patrick]
[Däumer, Martin]
[Walter, Hauke]
[Noah, Christian]
[Wolf, Eva]
[Müller, Harm]
[Stürmer, Martin]
Lengauer, Thomas
[Kaiser, Rolf]
[Obermeier, Martin]

Performance of genotypic coreceptor measurement using geno2pheno[coreceptor] in B- and non-B HIV subtypes in a large cohort of therapy-experienced patients in Germany
In: Reviews in Antiviral Therapy, 99-99

Poster

2008

Poster

2008

[Obermeier, Martin]
[Sichtig, Nadine]
[Braun, Patrick]
[Däumer, Martin]
[Walter, Hauke]
[Noah, Christian]
[Wolf, Eva]
[Müller, Harm]
[Stürmer, Martin]
[Kaiser, Rolf]
Thielen, Alexander

Determination of HIV-1 coreceptor usage in German patients - comparison of genotypic methods with the TROFILE phenotypic assay
In: Antiviral Therapy, A112

Poster

2005

Computational methods for the design of effective therapies against drug resistant HIV strains
In: Bioinformatics [21], 3943-3950

Journal Article

Braun, Tatjana

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Bravo, Ignacio G

2010

[Kamp, Christel]
[Wolf, Timo]
[Bravo, Ignacio G]
[Kraus, Benjamin]
[Krause, Birgit]
[Neumann, Britta]
[Winskowsky, Gudrun]
Thielen, Alexander
[Werner, Albrecht]
[Schnierle, Barbara S]

Decreased HIV diversity after allogeneic stem cell transplantation of an HIV-1 infected patient: a case report.
In: Virology Journal [7], 55,1-55,9

Electronic Journal Article

Brazdil, P (ed.)

2005

Characterization of novel HIV Drug Resistance Mutations using clustering, multidimensional scaling and SVM-based feature ranking
In: Knowledge Discovery in Databases: PKDD 2005., 285-296

Proceedings Article

Brazma, Alvis (ed.)

2008

Sander, Oliver
Domingues, Francisco S.
Zhu, Hongbo
Lengauer, Thomas
Sommer, Ingolf

Structural descriptors of protein-protein binding sites
In: Proceedings of 6th Asia-Pacific Bioinformatics Conference, 79-88

Proceedings Article

Breen, Gerome (ed.)

2010

Bock, Christoph
[Von Kuster, Greg]
Halachev, Konstantin
[Taylor, James]
[Nekrutenko, Anton]
Lengauer, Thomas

Web-based analysis of (epi-) genome data using EpiGRAPH and Galaxy.
In: Genetic Variation : Methods and Protocols, 275-296
In: Methods of Molecular Biology [628], 275-296

Part of a Book

Brenner, Steven E

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Breuer, Peter

2006

An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis
In: EMBO Journal [25], 1547-1558

Journal Article

Brewer, C

1999

Mutations in ABC1 in Tangier disease and familial high-density lipoprotein
In: Nature Genetics [22], 336-45

Journal Article

Bridgewater, John

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Briggs, Jason

2007

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1
In: Nature Genetics [39], 207-211

Journal Article

Briggs, John A. G.

2012

Kalinina, Olga V.
[Oberwinkler, Heike]
[Glass, Bärbel]
[Kräusslich, Hans-Georg]
[Russell, Robert B.]
[Briggs, John A. G.]

Computational Identification of Novel Amino-Acid Interactions in HIV Gag via Correlated Evolution
In: PLoS ONE [7], e42468,1-e42468,5

Electronic Journal Article

Brinkmann, A.B.

2013

[Simmer, F.]
[Brinkmann, A.B.]
Assenov, Yassen
[Matarese, F.]
[Kaan, A.]
Lengauer, Thomas
Bock, Christoph
[Colantuoni, V.]
[Altucci, L.]
[Stunnenberg, H.G.]

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched human tissue
In: Epigenetics [7], 1355-1367

Journal Article

Brinkman, Arie B.

2012

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
In: Epigenetics [7], 1355-1367

Journal Article

2010

Bock, Christoph
[Tomazou, Eleni M.]
[Brinkman, Arie B.]
Müller, Fabian
[Simmer, Femke]
[Gu, Hongcang]
[Jäger, Natalie]
[Gnirke, Andreas]
[Stunnenberg, Hendrik G.]
[Meissner, Alexander]

Quantitative comparison of genome-wide DNA methylation mapping technologies
In: Nature Biotechnology [28], 1106-1114

Journal Article

Brinkman, Fiona S.

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Bröcker, J.

2004

Merkwirth, Christian
[Bröcker, J.]
[Ogorzalek, Maciej]
Wichard, J.D.

Finite iteration DT-CNN - new design and operation principles
In: Proceedings (ISCAS-04) : 2004 IEEE International Symposium on Circuits and Systems. - Vol. 5, Blind signal processing, computer-aided network design, invited sessions, neural sytems and applications, power systems and power electronic circuits, 504-507

Proceedings Article

2004

[Wichard, J.D.]
[Ogorzalek, Maciej]
Merkwirth, Christian
[Bröcker, J.]

Finite iteration DT-CNN with stationary templates
In: Proceedings of the 8th IEEE International Workshop on Cellular Neural Networks and their Applications (CNNA 2004), 459-464

Proceedings Article

Bromberg, Yana

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

Brommonschenkel, Sergio

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Brooks-Wilson, A

2001

[Clee, Susanne M.]
[Zwinderman, A.H.]
[Engert, J.C.]
[Zwarts, K.Y.]
[Molhuizen, H.O.]
Roomp, Kirsten
[Jukema, J.W.]
[van Wijland, M]
[van Dam, M]
[Hudson, T.J.]
[Brooks-Wilson, A]
[Genest, Jacques Jr]
[Kastelein, J.J.P.]
[Hayden, Michael R.]

Common genetic variation in ABCA1 is associated with altered lipoprotein levels and a modified risk for coronary artery disease
In: Circulation [103], 1198-205

Journal Article

2000

Age and residual cholesterol efflux affect HDL cholesterol levels and coronary artery disease in ABCA1 heterozygotes
In: Journal of Clinical Investigation [106], 1263-70

Journal Article

1999

Mutations in ABC1 in Tangier disease and familial high-density lipoprotein
In: Nature Genetics [22], 336-45

Journal Article

Brooks-Wilson, A.

1999

Mutations in the ABC1 gene in familial HDL deficiency with defective cholesterol efflux
In: The Lancet [354], 1341-6

Journal Article

Brownlie, Alison

2002

[Wellington, Cheryl L.]
[Yang, Yu-Zhou]
[Zhou, Stephen]
[Clee, Susanne M.]
[Tan, Bing]
[Hirano, Kenichi]
[Zwarts, K.Y.]
[Kwok, Anita]
[Gelfer, Allison]
[Marcil, Michel]
[Newman, Scott]
Roomp, Kirsten
[Singaraja, Roshni]
[Collins, Jennifer A.]
[Zhang, Lin-Hua]
[Groen, Albert K.]
[Hovingh, Kees]
[Brownlie, Alison]
[Tafuri, Sherrie]
[Genest, Jacques Jr]
[Kastelein, J.J.P.]
[Hayden, Michael R.]

Truncation mutations in ABCA1 suppress normal upregulation of full-length ABCA1 by 9-cis-retinoic acid and 22-R-hydroxycholesterol
In: Journal of Lipid Research [43], 1939-1949

Journal Article

Brown, James R.

2011

[Kumar, Vinod]
Sun, Peng
[Vamathevan, Jessica]
[Li, Yong]
[Ingraham, Karen]
[Palmer, Leslie]
[Huang, Jianzhong]
[Brown, James R.]

Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles
In: Antimicrobial Agents and Chemotherapy [55], 4267-4276

Journal Article

Brun-Veziet, Francoise

2012

[Obermeier, Martin]
[Camacho, Ricardo]
[Charpentier, Charlotte]
[Deschamps, Diane]
[Eberle, Joseph]
[Gürtler, Lutz]
[Ruelle, Jean]
Pironti, Alejandro
[Brun-Veziet, Francoise]
[Stürmer, Martin]
[Kaiser, Rolf]

HIV2EU: supporting standardized HIV-2 drug resistance interpretation in Europe
In: Journal of the International AIDS Society, 135

Poster

Brun-Vezinet, Francoise

2010

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
In: HIV Medicine [Early View], 1-8

Electronic Journal Article

Brun-Vezinet, F.

2011

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

Brunak, Søren

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Brunner, Susanne

2010

[Brunner, Susanne]
[Hurni, Severine]
[Streckeisen, Philipp]
Mayr, Gabriele
Albrecht, Mario
[Yahiaoui, Nabila]
[Keller, Beat]

Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles
In: The Plant Journal [64], 433-445

Journal Article

Bryson, Kevin

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Buchan, Daniel W A

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Buchert, Eva

2010

Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL)
In: Nature Genetics [42], 292-294

Journal Article

Bucher, P

2013

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Büch, Joachim

2011

Pironti, Alejandro
Altmann, André
Büch, Joachim
Lengauer, Thomas

A Computational Method for Predicting First-Line Antiretroviral Therapy Success
In: Abstract Book. 9th Workshop on HIV & Hepatitis Treatment Strategies & Antiviral Drug Resistance, 94

Poster

2010

Altmann, Andre
Pironti, Alejandro
Perner, Juliane
Büch, Joachim
Lengauer, Thomas

Poster

2009

Blankenburg, Hagen
Ramírez, Fidel
Büch, Joachim
Albrecht, Mario

DASMIweb: online integration, analysis and assessment of distributed protein interaction data
In: Nucleic Acids Research [37], W122-W128

Electronic Journal Article

2009

Blankenburg, Hagen
[Finn, Robert D.]
[Prlić, Andreas]
[Jenkinson, Andrew M.]
Ramírez, Fidel
Emig, Dorothea
Schelhorn, Sven-Eric
Büch, Joachim
Lengauer, Thomas
Albrecht, Mario

DASMI: exchanging, annotating and assessing molecular interaction data
In: Bioinformatics [25], 1321-1328

Journal Article

2009

Bock, Christoph
Halachev, Konstantin
Büch, Joachim
Lengauer, Thomas

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data
In: Genome Biology [10], R14.1-R14.14

Journal Article

2009

Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation of
geno2pheno-THEO on a Large Clinical Database
In: The Journal of Infectious Diseases [199], 999-1006

Journal Article

2008

Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy
In: PLoS ONE [3], e3470

Journal Article

2008

The EuResist approach for predicting response to anti HIV-1 therapy
In: Reviews in Antiviral Therapy, 107

Poster

2008

Feuerbach, Lars
Christopher, Bock
Halachev, Konstantin
Büch, Joachim
Lengauer, Thomas

Towards Comparative Epigenomics: A Software Toolkit For Cross-Species Epigenome Data Analysis
In: Abstracts of the 2nd MC-GARD Meeting, 230

Electronic Proceedings Article

2007

Sing, Tobias
Low, Andrew J.
Beerenwinkel, Niko
Sander, Oliver
[Cheung, Peter K.]
Domingues, Francisco S.
Büch, Joachim
[Däumer, Martin]
[Kaiser, Rolf]
Lengauer, Thomas
[Harrigan, P. Richard]

Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
In: Antiviral Therapy [12], 1097-1106

Journal Article

2006

Roomp, Kirsten
Beerenwinkel, Niko
Sing, Tobias
[Schülter, Eugen]
Büch, Joachim
[Sierra-Aragon, Saleta]
[Däumer, Martin]
[Hoffmann, Daniel]
[Kaiser, Rolf]
Lengauer, Thomas
[Selbig, Joachim]

Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV
In: Lecture Notes in Computer Science [4075], 185-194

Journal Article

Bueno, Clara

2012

A promoter DNA demethylation landscape of human hematopoietic differentiation
In: Nucleic Acids Research [40], 116-131

Journal Article

Bühler, Sandra

2011

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
In: Cell Host & Microbe [9], 32-45

Journal Article

Bullinger, H.J. (ed.)

2007

Lengauer, Thomas

Bioinformatik
In: Technologiefüher - Grundlagen, Anwendungen, Trends, 4

Part of a Book

Büning, Carsten

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

Buning, Christian

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

2002

[Hindle, Sally A.]
[Rarey, Matthias]
[Buning, Christian]
Lengauer, Thomas

Flexible docking under pharmacophore type constraints
In: Journal of Computer-Aided Molecular Design [16], 129-149

Journal Article

2001

Claussen, C.
Buning, Christian
[Rarey, Matthias]
Lengauer, Thomas

FlexE: Efficient Molecular Docking Considering Protein Structure Variations
In: Journal of Molecular Biology [308], 377-395

Journal Article

Bureik, M.

2005

[Ulmschneider, Sarah]
[Mueller-Vieira, Ursula]
[Mitrenga, Markus]
[Hartmann, Rolf W.]
[Oberwinkler-Marchais, S]
[Klein, Christian D.]
[Bureik, M.]
[Bernhardt, R.]
Antes, Iris
Lengauer, Thomas

Synthesis and Evaluation of Imidazolylmethylenetetrahydronaphthalenes and Imidazolylmethyleneindanes: Potent Inhibitors of Aldosterone Synthase
In: Journal of Medicinal Chemistry [48], 1796-1805

Journal Article

Burson, Cathy

2002

[Bozinov, Daniel]
Rahnenführer, Jörg
[Burson, Cathy]
[Spiegelstein, Ofer]

Automated Grid Alignment for High-Throughput Analysis of Microarray Images (CIIST-02)
In: Proceedings of the 2002 International Conference on Imaging Science, Systems, and Technology, 161-167

Proceedings Article

Büttner, Reinhard

2007

[Mikeska, Thomas]
Bock, Christoph
[El-Maarri, Osman]
[Hübner, Anika]
[Ehrentraut, Denise]
[Schramm, Johannes]
[Felsberg, Jörg]
[Kahl, Philip]
[Büttner, Reinhard]
[Pietsch, Torsten]
[Waha, Andreas]

Optimization of Quantitative MGMT Promoter Methylation Analysis Using Pyrosequencing and Combined Bisulfite Restriction Analysis
In: Journal of Molecular Diagnostics [9], 368-381

Journal Article

Buzón, Maria José

2010

[Codoñer, Francisco M]
[Pou, Christian]
Thielen, Alexander
[García, Federico]
[Delgado, Rafael]
[Dalmau, David]
[Santos, José Ramon]
[Buzón, Maria José]
[Martínez-Picado, Javier Alvarez-Tejado, Miguel]
[Clotet, Bonaventura]
[Ruiz, Lidia]
[Paredes, Roger]

Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure
In: Antiviral Research [88], 281-286

Journal Article

Calvanese, Vincenzo

2012

A promoter DNA demethylation landscape of human hematopoietic differentiation
In: Nucleic Acids Research [40], 116-131

Journal Article

Calvez, Vincent

2011

Journal Article

Camacho, R (ed.)

2005

Characterization of novel HIV Drug Resistance Mutations using clustering, multidimensional scaling and SVM-based feature ranking
In: Knowledge Discovery in Databases: PKDD 2005., 285-296

Proceedings Article

Camacho, Ricardo

2012

HIV2EU: supporting standardized HIV-2 drug resistance interpretation in Europe
In: Journal of the International AIDS Society, 135

Poster

Camacho, Richardo

2012

[Schuelter, Eugen]
[Lübcke, Nadine]
[Jensen, Björn]
[Zazzi, Maurizio]
[Sönnerborg, Anders]
Lengauer, Thomas
[Incardona, Francesca]
[Camacho, Richardo]
[Schmit, J]
[Clotet, Bonaventura]
[Kaiser, Rolf]
Pironti, Alejandro

Etravirine in protease inhibitor-free antiretroviral combination therapies
In: Journal of the International AIDS Society, 155-156

Poster

Campo, Elias

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Capella, Gabriel

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Cappielloh, Giuseppina

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975–983

Journal Article

Cappiello, Giuseppina

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975-983

Journal Article

Caricasole, Andrea

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Carlberg, Carsten (ed.)

2010

Emig, Dorothea
Kacprowski, Tim
Albrecht, Mario

Measuring and analyzing tissue specificity of human genes and protein complexes
In: Seventh International Workshop on Computational Systems
Biology, WCSB 2010, 27-30

Proceedings Article

Carmona, F. Javier

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Carmona, Javier

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Carneiro, Adriana R.

2011

[Ramos, Rommel T.J.]
[Carneiro, Adriana R.]
Baumbach, Jan
[Azevedo, Vasco]
[Schneider, Maria P.C.]
[Silva, Artur]

Analysis of quality raw data of second generation sequencers with Quality Assessment Software
In: BMC Research Notes [4], 130,1-130,6

Journal Article

Carneiro, Newton P.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Carneir, Aadriana Ribeiro

2011

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study
In: Journal of Microbiological Methods [86], 218-223

Journal Article

Carrera, Ana Clara

2012

A promoter DNA demethylation landscape of human hematopoietic differentiation
In: Nucleic Acids Research [40], 116-131

Journal Article

Casadio, Rita

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Castellano, Sergi

2005

[Castellano, Sergi]
[Lobanov, Alexey V.]
[Chapple, Charles]
[Novoselov, Sergey V.]
Albrecht, Mario
[Hua, Deame]
[Lescure, Alain]
Lengauer, Thomas
[Krol, Alain]
[Gladyshev, Vadim N.]
[Guigó, Roderic]

Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family
In: Proceedings of the National Academy of Sciences [102], 16188-16193

Journal Article

Castro, Ieso M.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Castro, Thiago L. P.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Ceccherini-Silbersteina, Francesca

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975–983

Journal Article

Ceccherini-Silberstein, Francesca

2011

Journal Article

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975-983

Journal Article

2009

Dynamics of NRTI resistance mutations during therapy interruption
In: AIDS Research and Human Retroviruses [25], 57-64

Journal Article

2009

[Alcaro, Stefano]
[Artese, Anna]
[Ceccherini-Silberstein, Francesca]
[Ortuso, Francesca]
[Perno, Carlo Federico]
Sing, Tobias
[Svicher, Valentina]

Journal Article

2007

Journal Article

2006

Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
In: Journal of Virology [80], 7186-7198

Journal Article

2005

A highly ordered network of HIV-1 RT mutations regulates the continuous escape from antiviral drugs
In: International Workshop in HIV Dynamics and Evolution, -

Proceedings Article

2005

Additional Mutations in HIV-1 Reverse Transcriptase are Involved in the Highly Ordered Regulation of NRTI Resistance
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -

Proceedings Article

2005

Characterization of novel HIV Drug Resistance Mutations using clustering, multidimensional scaling and SVM-based feature ranking
In: Knowledge Discovery in Databases: PKDD 2005., 285-296

Proceedings Article

Centoa, Valeria

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975–983

Journal Article

Cento, Valeria

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975-983

Journal Article

Ceol, Arnaud

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Cerdeira, Louise

2012

PIPS: Pathogenicity Island Prediction Software
In: PLoS One [7], e30848,1-e30848,10

Electronic Journal Article

Cerdeira, Louise Teixeira

2011

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study
In: Journal of Microbiological Methods [86], 218-223

Journal Article

Cerdeira, Louise T.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Cesareni, Gianni

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Ceska, R

2000

Age and residual cholesterol efflux affect HDL cholesterol levels and coronary artery disease in ABCA1 heterozygotes
In: Journal of Clinical Investigation [106], 1263-70

Journal Article

Chandler, David

2003

Antes, Iris
[Wang, Hongyun]
[Chandler, David]
[Oster, George]

The unbinding of ATP from F1-ATPase
In: Biophysical Journal [85], 695-706

Journal Article

2002

Antes, Iris
[Chandler, David]
[Oster, George]

A classical dynamics study of the unbinding of ATP from the F0F1-ATPase
In: Poster book of the European Conference on Computational Biology, Saarbrücken, Germany 2002, -

Poster

Chan, Dennison

2010

[Swenson, Luke C.]
[Moores, Andrew]
[Low, Andrew J.]
Thielen, Alexander
[Dong, Winnie]
[Woods, Conan]
[Jensen, Mark A.]
[Wynhoven, Brian]
[Chan, Dennison]
[Glascock, Christopher]
[Harrigan, P. Richard]

Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA
In: Journal of Acquired Immune Deficiency Syndromes [54], 506-510

Journal Article

2008

[Moores, Andrew]
Thielen, Alexander
[Dong, Winnie]
Low, Andrew J.
[Woods, Conan]
[Jensen, Mark]
[Wynhoven, Brian]
[Chan, Dennison]
[Glascock, Christopher]
[Harrigan, P Richard]

Improved detection of X4 virus by V3 genotyping: application to plasma RNA and proviral DNA
In: Antiviral Therapy, A99

Poster

2007

[Low, Andrew J.]
[Dong, Winnie]
[Chan, Dennison]
Sing, Tobias
[Swanstrom, Ronald]
[Jensen, Mark]
[Pillai, Satish]
[Good, Benjamin]
[Harrigan, P. Richard]

Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates
In: AIDS [21], F19-F26

Journal Article

Chapman, Douglas

2009

[Harrigan, P Richard]
[McGovern, Rachel]
[Dong, Winnie]
Thielen, Alexander
[Jensen, Mark]
[Mo, Theresa]
[Chapman, Douglas]
[Lewis, Marilyn]
[James, Ian]
[Valdez, Hernan]

Screening for HIV tropism using population-based V3 genotypic analysis: a retrospective outcome analysis using stored plasma screening samples from MOTIVATE-1
In: Abstracts presented at the XVIII International HIV Drug Resistance Workshop : Basic Principles & Clinical Implications, A17-A17

Poster

Chapman, Douglass

2011

[Swenson, Luke C.]
[Mo, Theresa]
[Dong, Winnie W. Y.]
[Zhong, Xiaoyin]
[Woods, Conan K.]
[Jensen, Mark A.]
Thielen, Alexander
[Chapman, Douglass]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]
[Harrigan, P. Richard]

Deep Sequencing to Infer HIV-1 Co-Receptor Usage: Application to Three Clinical Trials of Maraviroc in Treatment-Experienced Patients
In: The Journal of Infectious Diseases [203], 237-245

Journal Article

2011

[Swenson, Luke C]
[Mo, Theresa]
[Dong, Winnie WY]
[Zhong, Xiaoyin]
[Woods, Conan K]
Thielen, Alexander
[Jensen, Mark A]
[Knapp, David JHF]
[Chapman, Douglass]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]
[Harrigan, P Richard]

Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc.
In: Clinical Infectious Diseases [53], 732-742

Journal Article

2010

[McGovern, Rachel A]
Thielen, Alexander
[Mo, Theresa]
[Dong, Winnie]
[Woods, Conan K]
[Chapman, Douglass]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]
[Harrigan, P Richard]

Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies
In: AIDS [24], 2517-2525

Journal Article

Chapman, Roger W.

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Chapple, Charles

2005

[Castellano, Sergi]
[Lobanov, Alexey V.]
[Chapple, Charles]
[Novoselov, Sergey V.]
Albrecht, Mario
[Hua, Deame]
[Lescure, Alain]
Lengauer, Thomas
[Krol, Alain]
[Gladyshev, Vadim N.]
[Guigó, Roderic]

Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family
In: Proceedings of the National Academy of Sciences [102], 16188-16193

Journal Article

Charpentier, Charlotte

2012

HIV2EU: supporting standardized HIV-2 drug resistance interpretation in Europe
In: Journal of the International AIDS Society, 135

Poster

Chautard, Emilie

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Chazouilleres, Olivier

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Cheng, Jianlin

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Chen, Guoan

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Chen, Tzu-Hsiu

2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Cheung, Peter K.

2007

[Skrabal, Katharina]
[Low, Andrew J.]
[Dong, Winnie]
Sing, Tobias
[Cheung, Peter K.]
[Mammano, Fabrizio]
[Harrigan, P. Richard]

Determining human immunodeficiency virus coreceptor use in a clinical setting: Degree of correlation between two phenotypic assays and a bioinformatic model
In: Journal of Clinical Microbiology [45], 279-284

Journal Article

2007

Sing, Tobias
Low, Andrew J.
Beerenwinkel, Niko
Sander, Oliver
[Cheung, Peter K.]
Domingues, Francisco S.
Büch, Joachim
[Däumer, Martin]
[Kaiser, Rolf]
Lengauer, Thomas
[Harrigan, P. Richard]

Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
In: Antiviral Therapy [12], 1097-1106

Journal Article

2007

Sander, Oliver
Sing, Tobias
Sommer, Ingolf
[Low, Andrew J.]
[Cheung, Peter K.]
[Harrigan, P. Richard]
Lengauer, Thomas
Domingues, Francisco S.

Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
In: PLoS Computational Biology [3], 555-564

Journal Article

Chiang, Derek

2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Chitale, Meghana

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