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Year

Author(s) [non member]

Title

Type

Röttger, Richard

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

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

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

Rougemont, J

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

Roweis, Sam (ed.)

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

Rozowsky, J

2013

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

Journal Article

Roz, Luca

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

Rueckert, Ulrich

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

Ruelle, Jean

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

Ruether, Andreas

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

Ruggieri, Alessia

2007

[Flockerzi, Aline]
Maydt, Jochen
[Frank, Oliver]
[Ruggieri, Alessia]
[Maldener, Esther]
[Seifarth, Wolfgang]
[Medstrand, Patrik]
Lengauer, Thomas
[Meyerhans, Andreas]
[Leib-Mosch, Christine]
[Meese, Eckart]
[Mayer, Jens]

Expression pattern analysis of transcribed HERV sequences is complicated by ex vitvo recombination
In: Retrovirology [4], 39

Journal Article

Ruiz, Jeronimo C.

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

Ruiz, Lidia

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

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

Rupp, Kathrin

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

Rüschendorf, Franz

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

Rushbrook, Simon M.

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

Russell, Robert B.

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

Rust, Christian

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

Rutgeers, Paul

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

Rutgeerts, Paul

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

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

Ruusuvuori, Pekka (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

Ryde, Ulf

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

Saarela, Janna

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

Sabatino, Lina

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

Sadowski, Michael I.

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

Saigo, Hiroto

2011

[Yamanishi, Yoshihiro]
[Pauwels, Edouard]
Saigo, Hiroto
[Stovent, Veronique]

Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions
In: Journal of Chemical Information and Modeling [51], 1183-1194

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

2010

Saigo, Hiroto
[Hattori, Masahiro]
[Kashima, Hisashi]
[Tsuda, Koji]

Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism
In: BMC Bioinformatics [11], S31,1-S31,7

Electronic Journal Article

2008

Saigo, Hiroto
[Tsuda, Koji]

Iterative Subgraph Mining for Principal Component Analysis.
In: Proceedings of the IEEE International Conference on Data Mining (ICDM2008), DM934

Proceedings Article

Sakai, Naohiko

2002

[Nishida, Yoshiharu]
[Hirano, Kenichi]
[Tsukamoto, Kosuke]
[Nagano, Makoto]
[Ikegami, Chiaki]
Roomp, Kirsten
[Ishihara, Mitsuaki]
[Sakane, Naoki]
[Zhang, Zhongyan]
[Tsujii, Ken-ichi]
[Matsuyama, Akifumi]
[Ohama, Tohru]
[Matsuura, Fumihiko]
[Ishigami, Masato]
[Sakai, Naohiko]
[Hiraoka, Hisatoyo]
[Hattori, Hiroaki]
[Wellington, Cheryl L.]
[Yoshida, Yoshihide]
[Misugi, Susumu]
[Hayden, Michael R.]
[Egashira, Toru]
[Yamashita, Shizuya]
[Matsuzawa, Yuji]

Expression and Functional Analyses of Novel Mutations ot ATP-Binding Cassette Transporter-1 in Japanese Patients with High-Density Lipoprotein Deficiency
In: Biochemical and Biophysical Research Communications [290], 713-721

Journal Article

Sakane, Naoki

2002

Journal Article

Salakoski, Tapio

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

Salamat-Miller, Nazila

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

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

Salgado, Heladia

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

Salif Sow, Papa (ed.)

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

2012

HIV2EU: supporting standardized HIV-2 drug resistance interpretation in Europe
In: Journal of the International AIDS Society, 135

Poster

2012

[Sierra, Saleta]
[Dzbowski, Jan Nikolaj]
Pironti, Alejandro
[Gueney, L]
Thielen, Alexander
[Reuter, Stefan]
[Esser, Stefan]
[Fätkenheuer, Gerd]
Lengauer, Thomas
[Hider, Dominik]
[Hoffmann, Daniel]
[Pfister, Holger]
[Jensen, Björn]
[Kaiser, Rolf]

Optimisation of baseline genotypic testing for safe and efficient maraviroc administration
In: Journal of the International AIDS Society, 101-102

Poster

Salomonis, Nathan

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

Salpinia, Romina

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

Salpini, Romina

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

Salwinski, Lukasz

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

Sammeth, M

2013

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

Journal Article

Sanchez-Carbayo, Marta

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

Sanchez-Cespedes, Montse

2013

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

Journal Article

2012

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

Journal Article

Sanchez-Mut, Jose V.

2012

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

Journal Article

Sanderson, Jeremy D.

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

Sander, Oliver

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

2010

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

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

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

[Sierra, Saleta]
[Kaiser, Rolf]
Thielen, Alexander
[Sander, Oliver]
Lengauer, Thomas

Genotypic Analysis of HIV Co-Receptor Usage
In: Entry Inhibitoren - Neue Formen der HIV-Therapie, 31-39

Part of a Book

2008

Weinhold, Nils
Sander, Oliver
Domingues, Francisco S.
Lengauer, Thomas
Sommer, Ingolf

Local function conservation in sequence and structure space
In: PLoS Computational Biology [4], e1000105

Journal Article

2008

Sander, Oliver

Structural Descriptors for the Analysis of Protein Structure, Function, and Evolution
Universität des Saarlandes

Thesis - PhD thesis

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

2007

Lengauer, Thomas
Sander, Oliver
[Sierra, Saleta]
Thielen, Alexander
[Kaiser, Rolf]

Bioinformatics prediction of HIV coreceptor usage
In: Nature Biotechnology [25], 1407-1410

Journal Article

2007

Sommer, Ingolf
Müller, Oliver
Domingues, Francisco S.
Sander, Oliver
[Weickert, Joachim]
Lengauer, Thomas

Moment invariants as shape recognition technique for comparing protein binding sites
In: Bioinformatics [23], 3139-3146

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

2006

Sommer, Ingolf
[Toppo, Stefano]
Sander, Oliver
Lengauer, Thomas
[Tosatto, Silvio C. E.]

Improving the quality of protein structure models by selecting from alignment alternatives
In: BMC Bioinformatics [7], 1-11

Electronic Journal Article

2006

Sander, Oliver
Sommer, Ingolf
Lengauer, Thomas

Local protein structure prediction using discriminative models
In: BMC Bioinformatics [7], 1-13

Electronic Journal Article

2006

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

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

Journal Article

2004

Sander, Oliver

Local sequence-structure relationships in proteins
Friedrich-Alexander-Universität Erlangen-Nürnberg

Thesis - other

Sandford, Richard N.

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

Sandoval, Juan

2013

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

Journal Article

Sankoff, D. (ed.)

2001

Proceedings of the 5th Annual Conference on Research in Computational Molecular Biology (RECOMB2001)

Book

Sans, Miquel

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

Santacruz, Diana

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

Santoro, Maria Mercedes

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

[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

[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

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

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

Santoro, Mario

2009

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

Journal Article

Santos, Anderson R

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

Santos, Anderson R.

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

Santos, Fabricio R.

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

Santos, José Ramon

2010

Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure
In: Antiviral Research [88], 281-286

Journal Article

Santos, Marcos A

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

Sarrazin, Christoph

2011

[Hofmann, Wolf Peter]
[Chung, Tje Lin]
[Osbahr, Carola]
[Susser, Simone]
[Karey, Ursel]
[Mihm, Ulrike]
Welsch, Christoph
[Lötsch, Jörn]
[Sarrazin, Christoph]
[Zeuzem, Stefan]
[Herrmann, Eva]

Impact of ribavirin on HCV replicon RNA decline during treatment with interferon-α and the protease inhibitors boceprevir or telaprevir
In: Antiviral Therapy [16], 695-704

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

[Mihm, Ulrike]
[Hofmann, W.P.]
Welsch, Christoph
[Polta, A.]
Lengauer, Thomas
[Zeuzem, Stefan]
[Sarrazin, Christoph]
[Herrmann, E.]

Effect of ribavirin on the frequency of RNAse L cleavage sites within the hepatitis C viral genome
In: Journal of Viral Hepatitis [17], 217-221

Journal Article

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

2009

[Susser, Simone]
Welsch, Christoph
[Wang, Yalan]
[Zettler, Markus]
Domingues, Francisco S.
[Karey, Ursula]
[Hughes, Eric]
[Ralston, Robert]
[Tong, Xiao]
[Herrmann, Eva]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Characterization of resistance to the protease inhibitor boceprevir in hepatitis C virus-infected patients.
In: Hepatology [50], 1709-1718

Journal Article

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

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

2007

[Welker, Martin W.]
[Hofmann, Wolf-Peter]
[Welsch, Christoph]
[von Wagner, Michael]
[Herrmann, Eva]
[Lengauer, Thomas]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Correlation nonstructural (NS)4B amino acid variations with initial viral kinetics during interferon-alpha-based therapy in HCV-1b-infected patients
In: Journal of Viral Hepatitis [14], 338-349

Journal Article

2007

[Hofmann, Wolf Peter]
Welsch, Christoph
[Takahashi, Yoshitomo]
[Miyajima, Hiroaki]
[Mihm, Ulrike]
[Krick, Christoph]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Identification and in silico characterization of a novel compound heterozygosty associated with hereditary aceruloplasminemia
In: Scandinavian Journal of Gastroenterology [42], 1088-1094

Journal Article

2007

[Hofmann, Wolf Peter]
[Fernandez, B.]
[Herrmann, E.]
Welsch, Christoph
[Mihm, Ulrike]
[Kronenberg, B.]
[Feldmann, G.]
[Spengler, U.]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Somatic hypermutation and mRNA expression levels of the BCL-6 gene in patients with hepatitis C virus-associated lymphoproliferative diseases
In: Journal of Viral Hepatitis [14], 484-491

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

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

Sarrazin, C.

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

2011

[Welker, M.-W.]
Welsch, Christoph
[Ochs, D.]
[Hofmann, W. P.]
[Herrmann, E.]
[Piiper, A.]
[Hartmann, R. W.]
[Zeuzem, S.]
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Comparison of Envelope 2 CD81 binding regions in PBMC-derived versus serum-derived hepatitis C virus isolates: higher conservation of CD81 region 2 in PBMC isolates
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2007

Welsch, Christoph
Albrecht, Mario
Maydt, Jochen
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[Scheidig, A.]
Lengauer, Thomas
Zeuzem, S.

Structural and functional comparison of the non-structural protein 4B of flaviviridae
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Journal Article

2005

Lengauer, Thomas
Albrecht, Mario
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Welsch, Christoph
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Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection.
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2004

[Hofmann, W.P.]
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[Kronenberger, B.]
Merkwirth, Christian
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Lengauer, Thomas
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Association of HCV-related mixed cryoglobulinemia with specific mutational patterns of the HCV E2 protein and CD81 expression on peripheral B lymphocytes
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Sarrazin, Ulrike

2005

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

Journal Article

Sarrazin, U.

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

Sauerbruch, T.

2007

[Ahlenstiel, G.]
Roomp, Kirsten
Däumer, Martin
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Beerenwinkel, Niko
Kaiser, R.
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[Sauerbruch, T.]
Lengauer, Thomas
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Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level
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Saunders, Arven H.

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[Zacharek, Sima J.]
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Bock, Christoph
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Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci
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Savenkov, Igor

2007

Altmann, Andre
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Sing, Tobias
Savenkov, Igor
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Lengauer, Thomas

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
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2005

[Beerenwinkel, Niko]
Sing, Tobias
Lengauer, Thomas
Rahnenführer, Jörg
Roomp, Kirsten
Savenkov, Igor
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Computational methods for the design of effective therapies against drug resistant HIV strains
In: Bioinformatics [21], 3943-3950

Journal Article

Sayols, Sergi

2013

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

Journal Article

Sboner, A

2013

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

Journal Article

Scagliotti, Giorgio V.

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
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Schachter, Vincent

2009

[Frishman, Dmitrij]
Albrecht, Mario
Blankenburg, Hagen
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[Jensen, Lars J.]
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Lengauer, Thomas
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Protein-protein interactions: analysis and prediction
In: Modern Genome Annotation - The Biosapiens Network, 353-410

Part of a Book

Schader, Martin (ed.)

2003

Rahnenführer, Jörg

Efficient Clustering Methods for Tumor Classification with Microarrays
In: Proceedings of the 26th Annual Conference of the Gesellschaft für Klassifikation, 670-679

Proceedings Article

Schaefer, Christian

2013

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

Journal Article

Schäfer, M.

2003

Lengauer, Thomas
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Combinatorial Optimization Techniques for Three-Dimensional Arrangement Problems
In: Mathematics - Key Technology for the Future, 63-73

Part of a Book

2001

[Schäfer, M.]
Lengauer, Thomas

Automated Layout Generation and Wiring Area Estimation for 3D Electronic Modules
In: ASME Journal of Machanical Design [123], 330-336

Journal Article

Schapiro, Jonathan (ed.)

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

Scheidig, A.

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

Schelhorn, Sven-Eric

2013

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

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

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

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

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

2007

Schelhorn, Sven-Eric

Prediction of Domain and Motif Interactions from Protein Networks
Universität des Saarlandes

Thesis - Masters thesis

Scheller, Nicoletta

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

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Scherer, C

2005

[Voets, Marieke]
Antes, Iris
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[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

Scherer, Christiane

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

Scherer, S

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[Clee, Susanne M.]
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Roomp, Kirsten
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Scheubert, Kerstin (ed.)

2012

Röttger, Richard
Kreutzer, Christoph
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Baumbach, Jan

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

Electronic Proceedings Article

Schewe, Katarzyna E.

2008

[Lucas, Simon]
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Antes, Iris
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[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

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Schilling, Martin

2007

[Kamradt, Jörn]
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[Wahrheit, Kerstin]
Tolosi, Laura
Rahnenführer, Jörg
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[Walker, Robert]
[Davis, Sean]
[Stöckle, Michael]
[Meltzer, Paul]
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Detection of Novel Amplicons in Prostate Cancer by Comprehensive Genomic Profiling of Prostate Cancer Cell Lines Using Oligonucleotide-Based ArrayCGH
In: PLoS ONE [2], e769

Electronic Journal Article

Schirmacher, Peter

2011

[Reiss, Simon]
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[Backes, Perdita]
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[Kaderali, Lars]
[Poenisch, Marion]
Blankenburg, Hagen
[Hiet, Marie-Sophie]
[Longerich, Thomas]
Diehl, Sarah
Ramírez, Fidel
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Lengauer, Thomas
Albrecht, Mario
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Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
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Schleicher, Jana (ed.)

2012

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

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

Electronic Proceedings Article

Schlicker, Andreas

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

2010

Schlicker, Andreas
Albrecht, Mario

FunSimMat update: new features for exploring functional similarity
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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

Schlicker, Andreas

Ontology-based Similarity Measures and their Application in Bioinformatics
Universität des Saarlandes

Thesis - PhD thesis

2008

Schlicker, Andreas
Albrecht, Mario

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

Journal Article

2008

[Welsch, Christoph]
Domingues, Francisco S.
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Antes, Iris
Hartmann, Christoph
Mayr, Gabriele
Schlicker, Andreas
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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

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

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

Journal Article

2006

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

A new measure for functional similarity of gene products based on Gene Ontology
In: BMC Bioinformatics [7], 1-16

Electronic Journal Article

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

2005

Schlicker, Andreas

A Global Approach to Comparative Genomics: Comparison of Functional Annotation over the Taxonomic Tree
Universität des Saarlandes

Thesis - Masters thesis

2004

Schlicker, Andreas

Automated Differential Analysis of Proteomes
Universität des Saarlandes

Thesis - Bachelor thesis

Schmeisser, Norbert

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

Schmeisser, N.

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

Schmidt, Barbara

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

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.]
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[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

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

Schmidt, B.

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

Schmitt, Ina

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

Schmit, J

2012

Etravirine in protease inhibitor-free antiretroviral combination therapies
In: Journal of the International AIDS Society, 155-156

Poster

Schnaible, Volker

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

Schneider, Maria Paula Cruz

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

Schneider, Maria P. 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

Schneider, Maria P.C.

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

Schneider, Reinhard

2012

[Rost, Burkhard]
[Gaasterland, Terry]
Lengauer, Thomas
[Linial, Michal]
[Markel, Scott]
[McKay, B. J. Morrison]
[Schneider, Reinhard]
[Horton, Paul]
[Kelso, Janet]

Paving the future: finding suitable ISMB venues
In: Bioinformatics [28], 2556-2559

Journal Article

Schneider, R.

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.]
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[Thoppae, G.]
[Vingron, M.]
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[Werner, T.]
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The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Schneider, Till

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

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

Schneweis, Karl-Eduard

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

Schnierle, Barbara S

2010

[Kamp, Christel]
[Wolf, Timo]
[Bravo, Ignacio G]
[Kraus, Benjamin]
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[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

Schnoes, Alexandra M

2013

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

Journal Article

Schölkopf, B (ed.)

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

Schomburg, D.

2004

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

Journal Article

Schön, J.C.

2004

[Hannemann, A.]
[Schön, J.C.]
[Jansen, M.]
[Putz, H.]
Lengauer, Thomas

Modelling amorphous Si3B3N7: Structure and elastic properties
In: Physical Review [B 70], 144201-144201

Journal Article

Schork, Andrew J.

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

Schramm, Christoph

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

Schramm, Johannes

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

Schrappe, Martin

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

Schreiber, Falk

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

Schreiber, Stefan

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

2010

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

Journal Article

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

2008

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

Journal 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

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

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

[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

[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

2004

Hahn, Andreas
[Costello, Christine M.]
[Lu, Tim]
Lengauer, Thomas
[Schreiber, Stefan]

Expression analysis for inflammatory bowel disease
In: Workshop Poster Competition, ?

Poster

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

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
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

2002

Hahn, Andreas
[Costello, Christine M.]
[Lu, Tim]
Lengauer, Thomas
[Schreiber, Stefan]

Expression analysis for inflammatory bowel disease
In: Proceedings of the n?th Conference on, ?

Poster

Schrumpf, Erik

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

Schübeler, Dirk

2012

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

Journal Article

Schuelter, Eugen

2012

Etravirine in protease inhibitor-free antiretroviral combination therapies
In: Journal of the International AIDS Society, 155-156

Poster

2011

[Sierra, Saleta]
[Kaiser, Rolf]
[Lübke, Nadine]
Thielen, Alexander
[Schuelter, Eugen]
[Heger, Eva]
[Däumer, Martin]
[Reuter, Stefan]
[Esser, Stefan]
[Fätkenheuer, Gerd]
[Pfister, Herbert]
[Oette, Mark]
Lengauer, Thomas

Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach
In: Journal of Visualized Experiments [58], e3264,1-e3264,9

Electronic Journal Article

Schüffler, Peter

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

Schüffler, Peter

MethMarker – A toolkit for design, optimization and validation of DNA methylation biomarkers for cancer diagnosis and therapy optimization
Universität des Saarlandes

Thesis - Masters thesis

2007

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

Schugardt, Nancy

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

Schuldenzucker, Ulrike

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

Schülter, Eugen

2012

Pironti, Alejandro
Lengauer, Thomas
[Kaiser, Rolf]
[Schülter, Eugen]
[Verheyen, Jens]

Characterization of HIV-1 Gag Subtype C
In: Abstract Book. 9th Workshop on HIV \& Hepatitis Treatment Strategies \& Antiviral Drug Resistance, 40-41

Poster

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

Lawyer, Glenn
[Schülter, Eugen]
[Kaiser, Rolf]
[Reuter, Stefan]
[Oette, Mark]
Lengauer, Thomas

Endogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort
In: Medical Microbiology and Immunology [201], 259-269

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

[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

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

[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

[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

[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

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

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

[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

[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

[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

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

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

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

Schülter, E.

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

Schulz-Gasch, T.

2004

Merkwirth, Christian
[Mauser, H.]
[Schulz-Gasch, T.]
[Roche, O.]
[Stahl, M.]
Lengauer, Thomas

Ensemble methods for classification in cheminformatics
In: Journal of Chemical Information and Modeling [44], 1971-1978

Journal Article

Schulze-Kremer, S.

2004

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

Journal Article

Schulz, Herbert

2007

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

Journal Article

Schulz, Marcel Holger

2013

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

Journal Article

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

Schulz, Wolfgang A.

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

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

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

Schürmann, Manfred

2005

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

Journal Article

Schuster, P. (ed.)

2007

Proceedings ISMB2007

Proceedings

Schuster, Stefan (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

Schwarzer, K.

2004

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

Journal Article

Schweitzer, Finja

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

Schweizer, Sabine

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

Schwienbacher, Christine

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

Schwinger, Eberhard

2005

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

Journal Article

Searle, SM

2013

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

Journal Article

Seclen, Eduardo

2011

[Seclen, Eduardo]
[Soriano, Vincente]
[González, Maria M]
[Gómez, Sagrario]
Thielen, Alexander
[Poveda, Eva]

High Concordance between the Position-Specific Scoring Matrix and Geno2pheno Algorithms for Genotypic Interpretation of HIV-1 Tropism: V3 Length as the Major Cause of Disagreement
In: Journal of Clinical Microbiology [49], 3380-3382

Journal Article

Seegert, Dirk

2005

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

Journal Article

2004

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

Journal Article

Seemayer, Stefan

2013

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

Journal Article

Seidel, Christopher W.

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

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

Seifarth, Wolfgang

2007

Expression pattern analysis of transcribed HERV sequences is complicated by ex vitvo recombination
In: Retrovirology [4], 39

Journal Article

Seifert, Martin

2012

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

Journal Article

Selbig, Joachim

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

2005

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

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

[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

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

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

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
[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

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

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

Selbig, J.

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

Selbig, J. (ed.)

2007

European Journal of Medical Research

Journal

Sensen, C. W.

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

Sensen, C.W.

1999

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

Journal Article

Serafin, Alice

2013

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

Journal Article

Setty, Yaki

2012

Setty, Yaki

Multi-scale computational modeling of developmental biology
In: Bioinformatics [28], 2022-2028

Journal Article

Seyffert, Nubia

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

Shafer, Robert

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

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

Shafer, Robert W

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

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

Poster

Shafer, Robert W.

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

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

Shafer, R.W.

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

Shah, Kinjal

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

Shah, Tejas

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

Shapiro, Geoffrey I.

2009

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

Journal Article

Shatkay, Hagit

2013

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

Journal Article

Shawe-Taylor, John (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

Sheffer, Tobias

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

Shimakami, Testsuro

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

Shimakami, Tetsuro

2012

[Welsch, Christoph]
[Shimakami, Tetsuro]
[Hartmann, Christoph]
[Yang, Yan]
[Domingues, Francisco S.]
Lengauer, Thomas
[Zeuzem, Stefan]
[Lemon, Stanley M.]

Peptidomimetic Escape Mechanisms Arise via Genetic Diversity in the Ligand-Binding Site of the Hepatitis C Virus NS3/4A Serine Protease
In: Gastroenterology [142], 654-663

Journal Article

2011

[Shimakami, Tetsuro]
Welsch, Christoph
[Yamane, Daisuke]
[McGivern, David R.]
[Yi, MinKyung]
[Zeuzem, Stefan]
[Lemon, Stanley M.]

Protease Inhibitor-Resistant Hepatitis C Virus Mutants With Reduced Fitness From Impaired Production of Infectious Virus
In: Gastroenterology [140], 667-675

Journal Article

Shimamura, Takeshi

2009

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

Journal Article

Shioda, Tatsuo

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

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

Sichtig, Nadine

2010

Thielen, Alexander
[Sichtig, Nadine]
[Kaiser, Rolf]
[Lam, Jeffrey]
[Harrigan, P. Richard]
Lengauer, Thomas

Improved prediction of HIV-1 coreceptor usage with sequence information from the second hypervariable loop of gp120
In: Journal of Infectious Diseases [202], 1435-1443

Journal Article

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

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

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

[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

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

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

Siebert, Reiner

2012

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

Journal Article

2012

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

Journal Article

Sierra-Aragon, Saleta

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

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

Sierra Aragon, Saleto

2010

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

Sierra, Saleta

2014

Pironti, Alejandro
Sierra, Saleta
Kaiser, Rolf
Lengauer, Thomas
Pfeifer, Nico

Simulation of Sanger-sequencing errors in the context of genotypic tropism determination
In: Antiviral Therapy, A81

Poster

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

2012

Optimisation of baseline genotypic testing for safe and efficient maraviroc administration
In: Journal of the International AIDS Society, 101-102

Poster

2011

Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach
In: Journal of Visualized Experiments [58], e3264,1-e3264,9

Electronic Journal Article

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

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

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

[Sierra, Saleta]
[Kaiser, Rolf]
Thielen, Alexander
[Sander, Oliver]
Lengauer, Thomas

Genotypic Analysis of HIV Co-Receptor Usage
In: Entry Inhibitoren - Neue Formen der HIV-Therapie, 31-39

Part of a Book

2007

Lengauer, Thomas
Sander, Oliver
[Sierra, Saleta]
Thielen, Alexander
[Kaiser, Rolf]

Bioinformatics prediction of HIV coreceptor usage
In: Nature Biotechnology [25], 1407-1410

Journal Article

2007

[Sierra, Saleta]
[Kaiser, Rolf]
Thielen, Alexander
Lengauer, Thomas

Genotypic coreceptor analysis.
In: European Journal of Medical Research [12], 453-462

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

Sierra, S.

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

2009

Lengauer, Thomas
[Sierra, S.]
[Kaiser, Rolf]

Resistenzbestimmung
In: MMW Fortschritte in der Medizin [151], 74-75

Journal Article

2002

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

Silva Rojas, Hilda Victoria (ed.)

2010

Ramirez, Fidel

Tutorial Cytoscape
In: Bioinformática: Aplicaciones a la genómica y proteómica, 73-98

Part of a Book

Silva, Aartur

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

Silva, Artur

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

[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

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

Electronic Journal Article

Silverberg, Mark S.

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

Simgen, Birgit

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

Simmer, Femke

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

Simmer, F.

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

Simmons, David

2012

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

Journal Article

Simonovic, Milan

2011

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

Journal Article

Simos, Theodore (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

Sina, Christian

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

Singaraja, Roshni

2002

[Zwarts, K.Y.]
[Clee, Susanne M.]
[Zwinderman, A.H.]
[Engert, J.C.]
[Singaraja, Roshni]
[Loubser, O]
[James, E]
Roomp, Kirsten
[Hudson, T.J.]
[Jukema, J.W.]
[Kastelein, J.J.P.]
[Hayden, Michael R.]

ABCA1 regulatory variants influence coronary artery disease independent of effects on plasma lipid levels
In: Clinical Genetics [61], 115-125

Journal Article

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

Sing, Tobias

2011

Journal Article

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

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]

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

2008

Sing, Tobias

Model-Based Anti HIV Therapy
Universität des Saarlandes

Thesis - PhD thesis

2007

Journal Article

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

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

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

Poster

2007

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

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

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

Poster

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

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

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

Lengauer, Thomas
Sing, Tobias

Bioinformatics-assisted anti-HIV therapy
In: Nature Reviews Microbiology [4], 790-797

Journal Article

2006

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

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

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

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

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

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

[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

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

Sing, Tobias

Learning localized rule mixtures by maximizing the area under the ROC curve, with an application to the prediction of HIV-1 coreceptor usage
Universität Freiburg

Thesis - Masters thesis

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

Sipos, Bence

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

Sippl, Manfred J.

2004

[Prlic, Andreas]
Domingues, Francisco S.
[Lackner, Peter]
[Sippl, Manfred J.]

WILMA-automated annotation of protein sequences
In: Bioinformatics [20], 127-128

Journal Article

Siu, Shirley Weng-In

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

2005

Siu, Shirley Weng-In

Computational prediction of MHC-peptide interactions
Universität des Saarlandes

Thesis - Masters thesis

Skieceviciene, Jurgita

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

Skrabal, Katharina

2007

[Skrabal, Katharina]
[Low, Andrew J.]
[Dong, Winnie]
Sing, Tobias
[Cheung, Peter K.]
[Mammano, Fabrizio]
[Harrigan, P. Richard]

Journal Article

Skunca, Nives

2013

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

Journal Article

Sloot, Peter

2010

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

Smalter, Aaron M.

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

Smith, Zachary D.

2011

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

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

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

Smolinska, Agnieszka

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

Smuc, Tomislav

2013

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

Journal Article

Soares, Siomar C.

2012

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

Electronic 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

Söderhäll, Cilla

2007

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

Journal Article

Sokolov, Artem

2013

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

Journal Article

Solorzano, ND

2013

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

Journal Article

Solovyev, V

2013

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

Journal Article

Sommer, Ingolf

2013

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

Journal Article

2009

Sommer, Ingolf

From Protein Structure to Function
Universität des Saarlandes

Thesis - Habilitation thesis

2008

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

Alignment of Non-Covalent Interactions at Protein-Protein Interfaces
In: PLoS ONE [3], e1926

Journal Article

2008

Weinhold, Nils
Sander, Oliver
Domingues, Francisco S.
Lengauer, Thomas
Sommer, Ingolf

Local function conservation in sequence and structure space
In: PLoS Computational Biology [4], e1000105

Journal Article

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

2008

[Watson, James D.]
[Thornton, Janet M.]
[Tress, Michael L.]
[Lopez, Gonzalo]
[Valencia, Alfonso]
[Redfern, Oliver]
[Orengo, Christine A.]
Sommer, Ingolf
Domingues, Francisco S.

Structure to function
In: Modern Genome Annotation, 239-262

Part of a Book

2007

Sommer, Ingolf
Müller, Oliver
Domingues, Francisco S.
Sander, Oliver
[Weickert, Joachim]
Lengauer, Thomas

Moment invariants as shape recognition technique for comparing protein binding sites
In: Bioinformatics [23], 3139-3146

Journal Article

2007

Sommer, Ingolf

Protein Fold Recognition Based on Distant Homologs
In: Bioinformatics - From Genomes to Therapies 1. The Building Blocks: Molecular Sequences and Structures, 351-388

Part of a Book

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

2006

Lengauer, Thomas
Domingues, F.S.
Sommer, Ingolf
Zhu, Hongbo

Analysis and prediction of protein-protein-interaction types
In: BMC Bioinformatics [7], -

Journal Article

2006

Sommer, Ingolf
[Toppo, Stefano]
Sander, Oliver
Lengauer, Thomas
[Tosatto, Silvio C. E.]

Improving the quality of protein structure models by selecting from alignment alternatives
In: BMC Bioinformatics [7], 1-11

Electronic Journal Article

2006

Sander, Oliver
Sommer, Ingolf
Lengauer, Thomas

Local protein structure prediction using discriminative models
In: BMC Bioinformatics [7], 1-13

Electronic Journal Article

2006

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

NOXclass: prediction of protein-protein interaction types
In: BMC Bioinformatics [7], 1-15

Electronic Journal Article

2005

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

Analysis and prediction of protein-protein interaction types
In: 4th European Conference on Computational Biology (ECCB05), 1

Poster

2004

[Öhsen von, Niklas]
Sommer, Ingolf
[Zimmer, Ralf]
Lengauer, Thomas

Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures
In: Bioinformatics [20], 2228-2235

Journal Article

2004

Sommer, Ingolf
Rahnenführer, Jörg
Domingues, Francisco S.
[de Lichtenberg, Ulrik]
Lengauer, Thomas

Predicting Protein Structure Classes from Function Predictions
In: Bioinformatics [20], 770-776

Journal Article

2004

Domingues, Francisco S.
Lengauer, Thomas
Sommer, Ingolf

Protein Structure Prediction and Databases
In: Nature Encyclopedia of the Human Genome, 864-867

Part of a Book

2004

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

Journal Article

2003

[von Öhsen, Niklas]
Sommer, Ingolf
[Zimmer, Ralf]

Profile-Profile Alignment: A Powerful Tool For Protein Structure Prediction
In: Pacific Symposium on Biocomputing, PSB 2003, 252-263

Proceedings Article

2002

Sommer, Ingolf
[Zien, Alexander]
[Öhsen von, Niklas]
[Zimmer, Ralf]
Lengauer, Thomas

Confidence measures for protein fold recognition
In: Bioinformatics [18], 802-812

Journal Article

Sonnerborg, Anders

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

Etravirine in protease inhibitor-free antiretroviral combination therapies
In: Journal of the International AIDS Society, 155-156

Poster

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

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

2010

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

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

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

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

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

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

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

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

Poster

Sonnerborg, Andras

2007

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

Poster

Sönnerborg, 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

Soranzo, Nicole

2012

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

Journal Article

Soriano, Vincente

2011

[Seclen, Eduardo]
[Soriano, Vincente]
[González, Maria M]
[Gómez, Sagrario]
Thielen, Alexander
[Poveda, Eva]

Journal Article

Sos, Martin L.

2009

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

Journal Article

Souza, Michael L

2013

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

Journal Article

Sowdhamini, R. (ed.)

2004

Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computional Biology 2004 (ISMB/ECCB 2004)

Proceedings

Sow, Papa Salif (ed.)

2014

Pironti, Alejandro
Pfeifer, Nico
[Kaiser, Rolf]
[Walter, Hauke]
Lengauer, Thomas

Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences
In: Abstract Supplement of the HIV Drug Therapy Glasgow Congress 2014, 155

Poster

Speicher, Nora

2012

Speicher, Nora

Towards the identification of cancer subtypes by integrative clustering of molecular data
Universität des Saarlandes

Thesis - Masters thesis

Speicher, Nora K.

2010

Speicher, Nora K.

Network analysis of viral host factors
Universität des Saarlandes

Thesis - Bachelor thesis

Spengler, Ulrich

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

2007

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

Spengler, U.

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

[Hofmann, Wolf Peter]
[Fernandez, B.]
[Herrmann, E.]
Welsch, Christoph
[Mihm, Ulrike]
[Kronenberg, B.]
[Feldmann, G.]
[Spengler, U.]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Somatic hypermutation and mRNA expression levels of the BCL-6 gene in patients with hepatitis C virus-associated lymphoproliferative diseases
In: Journal of Viral Hepatitis [14], 484-491

Journal Article

Spicuglia, Salvatore

2012

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

Journal Article

Spiegelstein, Ofer

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

Springstubbe, S.

2004

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

Journal Article

Srivastava, Brijesh

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

Stade, Björn

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

Stahl, M.

2004

Merkwirth, Christian
[Mauser, H.]
[Schulz-Gasch, T.]
[Roche, O.]
[Stahl, M.]
Lengauer, Thomas

Ensemble methods for classification in cheminformatics
In: Journal of Chemical Information and Modeling [44], 1971-1978

Journal Article

Stanke, M

2013

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

Journal Article

Steffen, Andreas

2008

Steffen, Andreas

Computational Approaches in Supramolecular Chemistry with a special Focus on Virtual Screening
Universität des Saarlandes

Thesis - PhD thesis

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

Steffen, Andreas
Kämper, Andreas
Lengauer, Thomas

Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm
In: Journal of Chemical Information and Modeling [46], 1695-1703

Journal Article

2006

Steffen, Andreas
Kämper, Andreas
Lengauer, Thomas

Virtual screening for guest molecules of a biosensor
In: Biosensors 2006: The ninth world congress on biosensors, O66

Proceedings Article

2005

Steffen, Andreas
Kämper, Andreas
Lengauer, Thomas

FlexR - A new tool for predicting the structure of synthetic host-guest complexes
In: Synthetic Receptors 2005: Second World Congress on Synthetic Receptors, O7

Proceedings Article

2004

Steffen, Andreas
Kämper, Andreas
Lengauer, Thomas

Development of a new tool for predicting the structure of host-guest complexes
In: Proceedings of the 2nd Summer School Medicinal Chemistry Regensburg 2004, 83

Poster

2004

Steffen, Andreas
Kämper, Andreas
Lengauer, Thomas

FlexR - Predicting the structure of host-guest complexes
In: Proceedings of the Annual Meeting of the German Pharmaceutical Society - Joint Meeting 2004 (DPhG 2004), 130

Poster

Steijger, T

2013

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

Journal Article

Stenzel, Annette

2005

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

Journal Article

Sternberg, Michael J E

2013

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

Journal Article

Sterneck, Martina

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

Steudel, Wolf-Ingo

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

[Ketter, Ralf]
[Kim, Yoo-Jin]
[Storck, Simone]
Rahnenführer, Jörg
[Romeike, Bernd F.M.]
[Steudel, Wolf-Ingo]
[Zang, Klaus D.]
[Henn, Wolfram]

Hyperdiploidy defines a distinct cytogenetic entity of meningiomas
In: Journal of Neuro-Oncology [83], 213-221

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

Stevenson, BJ

2013

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

Journal Article

Stöckel, Daniel

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

2010

Stöckel, Daniel

History Based HIV Therapy Outcome Prediction
Universität des Saarlandes

Thesis - Masters thesis

2008

Stöckel, Daniel

Protein Surface Remeshing and Characterisation Using Morse-Smale Complexes
Universität des Saarlandes

Thesis - Bachelor thesis

Stockhammer, Florian

2005

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

Journal Article

Stockinger, H

2013

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

Journal Article

Stöckle, Michael

2007

[Kamradt, Jörn]
[Jung, Volker]
[Wahrheit, Kerstin]
Tolosi, Laura
Rahnenführer, Jörg
[Schilling, Martin]
[Walker, Robert]
[Davis, Sean]
[Stöckle, Michael]
[Meltzer, Paul]
[Wullich, Bernd]

Detection of Novel Amplicons in Prostate Cancer by Comprehensive Genomic Profiling of Prostate Cancer Cell Lines Using Oligonucleotide-Based ArrayCGH
In: PLoS ONE [2], e769

Electronic Journal Article

Stohr, H.

1995

[Stohr, H.]
Roomp, Kirsten
[Felbor, U.]
[Weber, B. H.]

Genomic organization of the human tissue inhibitor of metalloproteinases-3 (TIMP3)
In: Genome Research [5], 483-7

Journal Article

Stokkers, Pieter C. F.

2008

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

Journal Article

Stoll, Monika

2007

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

Journal Article

2004

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

Journal Article

Stoll, Stefan W.

2010

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

Journal Article

Storck, Simone

2007

[Ketter, Ralf]
[Kim, Yoo-Jin]
[Storck, Simone]
Rahnenführer, Jörg
[Romeike, Bernd F.M.]
[Steudel, Wolf-Ingo]
[Zang, Klaus D.]
[Henn, Wolfram]

Hyperdiploidy defines a distinct cytogenetic entity of meningiomas
In: Journal of Neuro-Oncology [83], 213-221

Journal Article

Størling, Zenia

2007

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

Journal Article

Stovent, Veronique

2011

[Yamanishi, Yoshihiro]
[Pauwels, Edouard]
Saigo, Hiroto
[Stovent, Veronique]

Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions
In: Journal of Chemical Information and Modeling [51], 1183-1194

Journal Article

Stoye, Jens

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

Strachan, David

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

Strachan, David P.

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

Strassnig, Christian

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

Stratton, Michael

2012

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

Journal Article

Streckeisen, Philipp

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

Strowitzki, Martin

2005

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

Journal Article

Struck, D

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

Struck, Daniel

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

2010

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

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

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

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

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

Journal Article

2008

Proceedings Article

Stuart, Philip E.

2010

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

Journal Article

Stückrath, Isabel

2009

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

Journal Article

Stulc, T

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

Stunnenberg, Hendrik G

2012

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

Journal Article

Stunnenberg, Hendrik G.

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

Stunnenberg, Henk G.

2012

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

Journal Article

Stunnenberg, H.G.

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

Stürmer, Martin

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

2012

HIV2EU: supporting standardized HIV-2 drug resistance interpretation in Europe
In: Journal of the International AIDS Society, 135

Poster

2009

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

Suarez-Álvarez, Beatriz

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

Subramani, Suresh

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

Suda, T

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

Suhai, S.

2004

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

Journal Article

Sundet, Jostein K.

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

Sun, Deqiang

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

[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

Sun, Peng

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

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

Suopanki, Jaana

2006

An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis
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Journal Article

Supek, Fran

2013

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

Journal Article

Susser, Simone

2011

[Hofmann, Wolf Peter]
[Chung, Tje Lin]
[Osbahr, Carola]
[Susser, Simone]
[Karey, Ursel]
[Mihm, Ulrike]
Welsch, Christoph
[Lötsch, Jörn]
[Sarrazin, Christoph]
[Zeuzem, Stefan]
[Herrmann, Eva]

Impact of ribavirin on HCV replicon RNA decline during treatment with interferon-α and the protease inhibitors boceprevir or telaprevir
In: Antiviral Therapy [16], 695-704

Journal Article

2009

Characterization of resistance to the protease inhibitor boceprevir in hepatitis C virus-infected patients.
In: Hepatology [50], 1709-1718

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

Susser, S.

2013

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

Journal Article

Su, Gang

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

Sventoraityte, Jurgita

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

Svichera, Valentina

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

Svicher, Valentina

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

Swanstrom, Ronald

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

Swenson, Luke

2010

Thielen, Alexander
Lengauer, Thomas
[Harrigan, P Richard]
[Swenson, Luke]
[Dong, Winnie WY]
[McGovern, Rachel A]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]

Mutations within GP41 are correlated with coreceptor tropism but do not substantially improve coreceptor usage prediction
In: Reviews in Antiviral Therapy & Infectious Diseases, 47-47

Poster

Swenson, Luke C

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

2011

Thielen, Alexander
Lengauer, Thomas
[Swenson, Luke C]
[Dong, Winnie W.Y.]
[McGovern, Rachel A]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]
[Harrigan, P Richard]

Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially
In: Antiviral Therapy [16], 319-328

Journal Article

Swenson, Luke C.

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

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

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

"{o}r

"{o}nen, Petri

2013

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

Journal Article

Tafuri, Sherrie

2002

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

Takahashi, Yoshitomo

2007

[Hofmann, Wolf Peter]
Welsch, Christoph
[Takahashi, Yoshitomo]
[Miyajima, Hiroaki]
[Mihm, Ulrike]
[Krick, Christoph]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Identification and in silico characterization of a novel compound heterozygosty associated with hereditary aceruloplasminemia
In: Scandinavian Journal of Gastroenterology [42], 1088-1094

Journal Article

Takken, Frank L. W.

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

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

Talwalkar, Ameet S

2013

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

Journal Article

Talwar, Priti

2008

Talwar, Priti

Development of Computational Methods for Metabolic Network Analysis based on Metabolomics Data
Universität des Saarlandes

Thesis - PhD thesis

2006

Talwar, Priti
Lengauer, Thomas
[Wittmann, Christoph]
[Velagapudi, V. R.]
[Heinzle, Elmar]

Development of Computational Methods for Analysis of Metabolic Profiling Data
In: Proceedings of International Conference on Systems Biology (ICSB 2006), Japan, 42-42

Proceedings Article

2006

[Velagapudi, Vidya R.]
[Wittmann, Christoph]
Lengauer, Thomas
Talwar, Priti
[Heinzle, Elmar]

Metabolic high- content screening of Saccharomyces cerevisiae reveals superior performance of single gene deletion strains
In: Process Biochemistry [41], 2170-2179

Journal Article

2005

Talwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
[Wittmann, Christoph]
[Velagapudi, VR]
[Heinzle, Elmar]

Computational Methods for Protein Function Prediction using Metabolomics Data
In: Proceedings of International Workshop on Systems Biology 2005, 1

Poster

2005

Hahn, Andreas
Rahnenführer, Jörg
Talwar, Priti
Lengauer, Thomas

Confirmation of human protein interaction data by human expression data
In: BMC Bioinformatics [6], 1-11

Journal Article

2005

Talwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
[Heinzle, Elmar]
[Velagapudi, VR]
[Wittmann, Christoph]

Towards computational analysis of metabolic profiling data for protein function prediction.
In: Proceedings of the Yeast Systems Biology, 6th International Conference on Systems Biology (ICSB 2005), 1

Poster

2004

Talwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
[Velagapudi, VR]
[Wittmann, Christoph]
[Heinzle, Elmar]

Computational Methods For Metabolite Screening
In: Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology + 3rd European Conference on Computational Biology (ISMB/ECCB 2004), 1

Poster

2004

Talwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
[Velagapudi, VR]
[Wittmann, Christoph]
[Heinzle, Elmar]

Computational Methods For Metabolite Screening
In: Proceedings of the 5th International Conference on Systems Biology (ICSB 2004), 1

Poster

2003

Talwar, Priti
[Wittmann, Christoph]
Lengauer, Thomas
[Heinzle, Elmar]

Software tool for automated processing of 13C labeling data from mass spectrometry data
In: BioTechniques [35], 1214-1215

Journal Article

2003

Talwar, Priti
Lengauer, Thomas
[Wittmann, Christoph]
[Mangadu, Vidya]
[Heinzle, Elmar]

Towards cellular function through metabolite screening
In: Proceedings of the 3rd Annual Conference on Metabolic Profiling: Pathways in Discovery, 7

Proceedings Article

Tamasawa, N

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

Tameling, Wladimir I.

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

Tanay, Amos

2012

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

Journal Article

Taniguchi, Hiroaki

2012

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

Journal Article

Tan, Aik-Choon

2012

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

Journal Article

Tan, Bing

2002

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

Taron, Miquel

2013

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

Journal Article

Taubert, Jan

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

Tauch, Andreas

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

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

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

Taylor, James

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

Teixeira, Santuza M. R.

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

Tejasvi, Trilokraj

2010

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

Journal Article

Teuber, Gerlinde

2006

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

Teuber, G.

2013

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

Journal Article

Teuber, Markus

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

Teufel, Andreas

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

The International IBD Genetics Consortium,

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

The International PSC Study Group,

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

The UK-PSCSC Consortium,

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

Theißen, J.

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

Thielen, Alex

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

Thielen, Alexander

2012

[Heger, Eva]
[Thielen, Alexander]
[Gilles, Ramona]
[Obermeier, Martin]
Lengauer, Thomas
[Kaiser, Rolf]
[Trapp, Susanna]

APOBEC3G/F a one possible driving source for co-receptor switch of the human immunodeficiency virus-1
In: Medical Microbiology and Immunology [201], 7-16

Journal Article

2012

Thielen, Alexander
Lengauer, Thomas

Geno2pheno[454]: A Web Server for the Prediction of HIV-1 Coreceptor Usage from Next-Generation Sequencing Data
In: Intervirology [55], 113-117

Journal Article

2012

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

Journal Article

2012

Optimisation of baseline genotypic testing for safe and efficient maraviroc administration
In: Journal of the International AIDS Society, 101-102

Poster

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

2011

[Heger, Eva]
Thielen, Alexander
[Gilles, Ramona]
[Obermeier, Martin]
Lengauer, Thomas
[Kaiser, Rolf]
[Trapp, Susanna]

APOBEC3G/F as one possible driving force for co-receptor switch of the human immunodeficiency virus-1
In: Medical Microbiology and Immunology [201], 7-16

Journal Article

2011

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

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

2011

Thielen, Alexander

Genotypic Analysis of HIV-1 Coreceptor Usage
Universität des Saarlandes

Thesis - PhD thesis

2011

[Däumer, Martin]
[Kaiser, Rolf]
[Klein, Rolf]
Lengauer, Thomas
[Thiele, Bernhard]
Thielen, Alexander

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis
In: BMC Medical Informatics and Decision Making [11], 30,1-30,8

Electronic Journal Article

2011

[Seclen, Eduardo]
[Soriano, Vincente]
[González, Maria M]
[Gómez, Sagrario]
Thielen, Alexander
[Poveda, Eva]

Journal Article

2011

[Knoepfel, Stefanie]
[Di Giallonardoc, Francesca]
[Däumer, Martin]
Thielen, Alexander
[Metzner, Karin J]

In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing
In: Journal of Virological Methods [71], 329-338

Journal Article

2011

Thielen, Alexander
Lengauer, Thomas
[Swenson, Luke C]
[Dong, Winnie W.Y.]
[McGovern, Rachel A]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]
[Harrigan, P Richard]

Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially
In: Antiviral Therapy [16], 319-328

Journal Article

2011

Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach
In: Journal of Visualized Experiments [58], e3264,1-e3264,9

Electronic Journal Article

2010

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

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

Journal Article

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

2010

Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure
In: Antiviral Research [88], 281-286

Journal Article

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

2010

Journal Article

2010

Thielen, Alexander
[Sichtig, Nadine]
[Kaiser, Rolf]
[Lam, Jeffrey]
[Harrigan, P. Richard]
Lengauer, Thomas

Improved prediction of HIV-1 coreceptor usage with sequence information from the second hypervariable loop of gp120
In: Journal of Infectious Diseases [202], 1435-1443

Journal Article

2010

Thielen, Alexander
Lengauer, Thomas
[Harrigan, P Richard]
[Swenson, Luke]
[Dong, Winnie WY]
[McGovern, Rachel A]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]

Mutations within GP41 are correlated with coreceptor tropism but do not substantially improve coreceptor usage prediction
In: Reviews in Antiviral Therapy & Infectious Diseases, 47-47

Poster

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

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

Poster

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

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

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

2008

[Sierra, Saleta]
[Kaiser, Rolf]
Thielen, Alexander
[Sander, Oliver]
Lengauer, Thomas

Genotypic Analysis of HIV Co-Receptor Usage
In: Entry Inhibitoren - Neue Formen der HIV-Therapie, 31-39

Part of a Book

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

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

Thielen, Alexander
[Kaiser, Rolf]
Lengauer, Thomas

Improving HIV-1 coreceptor usage prediction from genotype with regions outside of V3
In: Reviews in Antiviral Therapy, 81-82

Poster

2008

Däumer, Martin
[Kaiser, Rolf]
[Klein, Rolf]
Lengauer, Thomas
[Thiele, Bernhard]
Thielen, Alexander

Inferring viral tropism from genotype with massively parallel sequencing; qualitative and quantitative analysis
In: Antiviral Therapy, A101

Poster

2007

Lengauer, Thomas
Sander, Oliver
[Sierra, Saleta]
Thielen, Alexander
[Kaiser, Rolf]

Bioinformatics prediction of HIV coreceptor usage
In: Nature Biotechnology [25], 1407-1410

Journal Article

2007

[Sierra, Saleta]
[Kaiser, Rolf]
Thielen, Alexander
Lengauer, Thomas

Genotypic coreceptor analysis.
In: European Journal of Medical Research [12], 453-462

Journal Article

2006

Thielen, Alexander

Prediction of linear B-cell epitopes and MHC class II binding peptides
Eberhardt-Karls-Universität Tübingen

Thesis - Masters thesis

Thielen, Bernhard

2010

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

Thiele, Bernhard

2011

[Däumer, Martin]
[Kaiser, Rolf]
[Klein, Rolf]
Lengauer, Thomas
[Thiele, Bernhard]
Thielen, Alexander

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis
In: BMC Medical Informatics and Decision Making [11], 30,1-30,8

Electronic Journal Article

2008

Däumer, Martin
[Kaiser, Rolf]
[Klein, Rolf]
Lengauer, Thomas
[Thiele, Bernhard]
Thielen, Alexander

Inferring viral tropism from genotype with massively parallel sequencing; qualitative and quantitative analysis
In: Antiviral Therapy, A101

Poster

Thiele, Carolin

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]
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Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
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Finding Regions of Aberrant DNA Copy Number Associated With Tumor Phenotype
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