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MPI-INF D3 Publications

MPI-INF D3 Publications

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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
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
Bleif, Sabrina
Hannemann, Frank
Lisurek, Michael
von Kries, Jens Peter
Zapp, Josef
Dietzen, Matthias
Antes, Iris
Bernhardt, Rita
Identification of CYP106A2 as a Regioselective Allylic Bacterial Diterpene Hydroxylase
In: ChemBioChem [12], 576-582
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
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
Doncheva, Nadezhda T.
Klein, Karsten
Domingues, Francisco S.
Albrecht, Mario
Analyzing and visualizing residue networks of protein structures
In: Trends in Biochemical Sciences [36], 179-182
Emig, Dorothea
Albrecht, Mario
Tissue-specific proteins and functional implications
In: Journal of Proteome Research [10], 1893-1903
Emig, Dorothea
Kacprowski, Tim
Albrecht, Mario
Measuring and analyzing tissue specificity of human genes and protein complexes
In: EURASIP Journal on Bioinformatics and Systems Biology [2011], 5,1-5,6
Feuerbach, Lars
Lyngso, Rune B.
Lengauer, Thomas
Hein, Jotun
Reconstructing the ancestral germline methylation state of young repeats
In: Molecular Biology and Evolution [28], 1777-1784
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
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
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
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
Krol, Elizaveta
Blom, Jochen
Winnebald, Jörn
Berhörster, Alexander
Barnett, Melanie J.
Goesmann, Alexander
Baumbach, Jan
Becker, Anke
RhizoRegNet - A database of rhizobial transcription factors and regulatory networks.
In: Journal of Biotechnology [155], 127-134
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
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
Lutsik, Pavlo
Feuerbach, Lars
Arand, Julia
Lengauer, Thomas
Walter, Jörn
Bock, Christoph
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
In: Nucleic Acids Research [39], W551-W556
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
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
Reiss, Simon
Rebhan, Ilka
Backes, Perdita
Romero-Brey, Ines
Erfle, Holger
Matula, Petr
Kaderali, Lars
Poenisch, Marion
Blankenburg, Hagen
Hiet, Marie-Sophie
Longerich, Thomas
Diehl, Sarah
Ramírez, Fidel
Balla, Tamas
Rohr, Karl
Kaul, Artur
Bühler, Sandra
Pepperkok, Rainer
Lengauer, Thomas
Albrecht, Mario
Eils, Roland
Schirmacher, Peter
Lohmann, Volker
Bartenschlager, Ralf
Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
In: Cell Host & Microbe [9], 32-45
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
Attachment IconErratum 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
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
Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients
In: Medical Microbiology and Immunology [200], 39-49
Roomp, Kirsten
Domingues, Francisco S.
Predicting interactions between T cell receptors and MHC-peptide complexes
In: Molecular Immunology [48], 553-562
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
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
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
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
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
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
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
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
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
Tolosi, Laura
Lengauer, Thomas
Classification with correlated features: unreliability of feature ranking and solutions
In: Bioinformatics [27], 1986-1994
Welker, M.-W.
Welsch, Christoph
Ochs, D.
Hofmann, W. P.
Herrmann, E.
Piiper, A.
Hartmann, R. W.
Zeuzem, S.
Sarrazin, C.
Kronenberger, Bernd
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
In: Journal of Viral Hepatitis [18], 181-192
Wittkop, Tobias
Emig, Dorothea
Truss, Anke
Albrecht, Mario
Böcker, Sebastian
Baumbach, Jan
Comprehensive cluster analysis with Transitivity Clustering
In: Nature Protocols [6], 285-295
Wittkop, Tobias
Rahmann, Sven
Roettger, Richard
Boecker, Sebastian
Baumbach, Jan
Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis
In: Internet Mathematics [7], 255-273
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
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
Zacharek, Sima J.
Fillmore, Christine M.
Lau, Allison N.
Gludish, David W.
Chou, alan
Ho, Joshua W. K.
Zamponi, Raffaella
Gazit, Roi
Bock, Christoph
Jäger, Natalie
Smith, Zachary D.
Kim, Tae-min
Saunders, Arven H.
Wong, Janice
Lee, Joo-Hyeon
Roach, Rebecca R.
Rossi, Derrick J.
Meissner, Alex
Gimelbrant, Alexander A.
Park, Peter J.
Kim, Carla F.
Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci
In: Cell Stem Cell [9], 272-280
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
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