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MPI-INF D3 Publications

MPI-INF D3 Publications

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BibTeX cite keyAuthor/EditorYearTitleType
Talwar2003Talwar, Priti
Lengauer, Thomas
Wittmann, Christoph
Mangadu, Vidya
Heinzle, Elmar
2003Towards cellular function through metabolite screening
In: Proceedings of the 3rd Annual Conference on Metabolic Profiling: Pathways in Discovery, 7
Proceedings Article
Talwar2003aTalwar, Priti
Wittmann, Christoph
Lengauer, Thomas
Heinzle, Elmar
2003Software tool for automated processing of 13C labeling data from mass spectrometry data
In: BioTechniques [35], 1214-1215
Journal Article
Talwar2004aTalwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
Velagapudi, VR
Wittmann, Christoph
Heinzle, Elmar
2004Computational 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
Talwar2004bTalwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
Velagapudi, VR
Wittmann, Christoph
Heinzle, Elmar
2004Computational Methods For Metabolite Screening
In: Proceedings of the 5th International Conference on Systems Biology (ICSB 2004), 1
Poster
Talwar2005Talwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
Wittmann, Christoph
Velagapudi, VR
Heinzle, Elmar
2005Computational Methods for Protein Function Prediction using Metabolomics Data
In: Proceedings of International Workshop on Systems Biology 2005, 1
Poster
Talwar2006Talwar, Priti
Lengauer, Thomas
Wittmann, Christoph
Velagapudi, V. R.
Heinzle, Elmar
2006Development of Computational Methods for Analysis of Metabolic Profiling Data
In: Proceedings of International Conference on Systems Biology (ICSB 2006), Japan, 42-42
Proceedings Article
Talwar2006aTalwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
Heinzle, Elmar
Velagapudi, VR
Wittmann, Christoph
2005Towards 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
talwar2008Talwar, Priti2008Development of Computational Methods for Metabolic Network Analysis based on Metabolomics Data
Universität des Saarlandes
Thesis - PhD thesis
Thielen2006Thielen, Alexander2006Prediction of linear B-cell epitopes and MHC class II binding peptides
Eberhardt-Karls-Universität Tübingen
Thesis - Masters thesis
Thielen2008EDRWThielen, Alexander
Sichtig, Nadine
Braun, Patrick
Däumer, Martin
Walter, Hauke
Noah, Christian
Wolf, Eva
Müller, Harm
Stürmer, Martin
Lengauer, Thomas
Kaiser, Rolf
Obermeier, Martin
2009Performance 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
Thielen2008EntryThielen, Alexander
Kaiser, Rolf
Lengauer, Thomas
2008Improving HIV-1 coreceptor usage prediction from genotype with regions outside of V3
In: Reviews in Antiviral Therapy, 81-82
Poster
Thielen2008IDRWThielen, Alexander
Harrigan, P Richard
Low, Andrew J.
Moores, A
Altmann, Andre
Bozek, Kasia
Heger, Eva
Sichtig, Nadine
Kaiser, Rolf
Lengauer, Thomas
2008Improved genotypic prediction of HIV-1 coreceptor usage by incorporating V2 loop sequence variation
In: Antiviral Therapy, A100
Poster
Thielen2009IDRWThielen, Alexander
Altmann, André
Bogojeska, Jasmina
Kaiser, Rolf
Lengauer, Thomas
2009Estimating 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
Thielen2010Thielen, Alexander
Sichtig, Nadine
Kaiser, Rolf
Lam, Jeffrey
Harrigan, P. Richard
Lengauer, Thomas
2010Improved 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
Thielen2010EDRWThielen, Alexander
Lengauer, Thomas
Harrigan, P Richard
Swenson, Luke
Dong, Winnie WY
McGovern, Rachel A
Lewis, Marilyn
James, Ian
Heera, Jayvant
Valdez, Hernan
2010Mutations 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
Thielen2010gp41Thielen, Alexander
Lengauer, Thomas
Swenson, Luke C
Dong, Winnie W.Y.
McGovern, Rachel A
Lewis, Marilyn
James, Ian
Heera, Jayvant
Valdez, Hernan
Harrigan, P Richard
2011Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially
In: Antiviral Therapy [16], 319-328
Journal Article
Thielen2011Thielen, Alexander
Lengauer, Thomas
2012Geno2pheno[454]: A Web Server for the Prediction of HIV-1 Coreceptor Usage from Next-Generation Sequencing Data
In: Intervirology [55], 113-117
Journal Article
Thielen2011dissThielen, Alexander2011Genotypic Analysis of HIV-1 Coreceptor Usage
Universität des Saarlandes
Thesis - PhD thesis
Tolosi2006Tolosi, Laura2006Analysis of Array CGH Data for the Estimation of Genetic Tumor Progression
Universität des Saarlandes
Thesis - Masters thesis
tolosi2009Sos, 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.
2009Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740
Journal Article
Tolosi2011Tolosi, Laura
Lengauer, Thomas
2011Classification with correlated features: unreliability of feature ranking and solutions
In: Bioinformatics [27], 1986-1994
Journal Article
Tolosi2012thTolosi, Laura2012Finding Regions of Aberrant DNA Copy Number Associated With Tumor Phenotype
Universität des Saarlandes
Thesis - PhD thesis
Trajkovski2004Trajkovski, Igor2004Analysis of protein binding pocket flexibility
Universität des Saarlandes
Thesis - Masters thesis
Verheyen2006Verheyen, Jens
Litau, Elena
Sing, Tobias
Däumer, Martin
Balduin, Melanie
Oette, Mark
Fätkenheuer, Gerd
Rockstroh, Jürgen K.
Schuldenzucker, Ulrike
Hoffmann, Daniel
Pfister, Herbert
Kaiser, Rolf
2006Compensatory 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
Verheyen2008aVerheyen, Jens
Altmann, Andre
Knops, Elena
Schülter, Eugen
Sichtig, Nadine
Reuter, Stefan
Fätkenheuer, Gerd
Pfister, Herbert
Kaiser, Rolf
2008Relevance of HIV gag cleavage site mutations in failures of protease inhibitor therapies
In: Antiviral Therapy, A53
Poster
Volkamer2006aVolkamer, Andrea2005Attachment IconImplementation of a method to filter
out compounds with toxic, reactive
and unsuitable functional groups
Universität des Saarlandes
Thesis - Bachelor thesis
Volkamer2007Volkamer, Andrea2007Automated generation of pharmacophore type constraints to improve FlexX docking
Universität des Saarlandes
Thesis - Masters thesis
vonOehsen2003von Öhsen, Niklas
Sommer, Ingolf
Zimmer, Ralf
2003Profile-Profile Alignment: A Powerful Tool For Protein Structure Prediction
In: Pacific Symposium on Biocomputing, PSB 2003, 252-263
Proceedings Article
Weimann2009aWeimann, Aaron2009Using multidimensional Scaling for visualizing similarities of proteins
Universität des Saarlandes
Thesis - Bachelor thesis
Weimann2011aWeimann, Aaron2011Functional Profiling in Metagenomics
Universität des Saarlandes
Thesis - Masters thesis
Weinhold2006Weinhold, Nils2006Inference of Protein Function based on Functionally Conserved Regions in Sequence and Structure Space
Universität des Saarlandes
Thesis - Masters thesis
Weinhold2008Weinhold, Nils
Sander, Oliver
Domingues, Francisco S.
Lengauer, Thomas
Sommer, Ingolf
2008Attachment IconLocal function conservation in sequence and structure space
In: PLoS Computational Biology [4], e1000105
Journal Article
Weiss2005aWeiss, Julia2005Attachment IconGenerating Frequency Profiles from Multiple
Structure Alignments
Universität des Saarlandes
Thesis - Bachelor thesis
Weisser2007Weisser, Hendrik2007Estimating the local variance of protein structure models
Universität des Saarlandes
Thesis - Masters thesis
Weisser2010aWeisser, Hendrik
Altmann, André
Sierra, Saleta
Incardona, Francesca
Struck, Daniel
Sönnerborg, Anders
Kaiser, Rolf
Zazzi, Maurizio
Tschochner, Monika
Walter, Hauke
Lengauer, Thomas
2010Only Slight Impact of Predicted Replicative Capacity for Therapy Response Prediction
In: PLoSOne [5], e9044,1-e9044,10
Electronic Journal Article
Welker2011Welker, M.-W.
Welsch, Christoph
Ochs, D.
Hofmann, W. P.
Herrmann, E.
Piiper, A.
Hartmann, R. W.
Zeuzem, S.
Sarrazin, C.
Kronenberger, Bernd
2011Comparison 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
Journal Article
Welsch2011Hofmann, Wolf Peter
Chung, Tje Lin
Osbahr, Carola
Susser, Simone
Karey, Ursel
Mihm, Ulrike
Welsch, Christoph
Lötsch, Jörn
Sarrazin, Christoph
Zeuzem, Stefan
Herrmann, Eva
2011Impact 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
Welsch2012zWelsch, Christoph
Schweizer, Sabine
Shimakami, Testsuro
Domingues, Francisco S.
Kim, Seungtaek
Lemon, Stanley, M.
Antes, Iris
2012Ketoamide Resistance and Hepatitis C Virus Fitness in Val55 Variants
of the NS3 Serine Protease
In: Antimicrobial Agents and Chemotherapy [56], 1907-1915
Journal Article
Wemmert05Wemmert, 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
2005Attachment IconPatients with high grade gliomas harboring delections of chromosomes 9p and 10q benefit from temozolomide treatment
In: Neoplasia [7], 883-893
Journal Article
Wittkop2010Wittkop, Tobias
Emig, Dorothea
Lange, Sita
Rahmann, Sven
Albrecht, Mario
Morris, John H.
Böcker, Sebastian
Stoye, Jens
Baumbach, Jan
2010Partitioning biological data with transitivity clustering
In: Nature Methods [7], 419-420
Journal Article
Wittkop2011Wittkop, Tobias
Emig, Dorothea
Truss, Anke
Albrecht, Mario
Böcker, Sebastian
Baumbach, Jan
2011Comprehensive cluster analysis with Transitivity Clustering
In: Nature Protocols [6], 285-295
Journal Article
Wohlers2010Wohlers, Inken
Domingues, Francisco S.
Klau, Gunnar W.
2010Towards optimal alignment of protein structure distance matrices
In: Bioinformatics [26], 2273-2280
Journal Article
Xi2011Xi, Yuanxin
Bock, Christoph
Müller, Fabian
Sun, Deqiang
Meissner, Alexander
Li, Wei
2011RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing
In: Bioinformatics [28], 430-432
Journal Article
Xi2012Xi, Yuanxin
Bock, Christoph
Müller, Fabian
Sun, Deqiang
Meissner, Alexander
Li, Wei
2012RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
In: Bioinformatics [28], 430-432
Journal Article
Yalak2004aYalak, Garif2005Attachment IconAnalysis of Mutations in the Death Domains, Death Effector Domains, Caspase
Recruitment Domains, and Pyrin Domains
Universität des Saarlandes
Thesis - Bachelor thesis
Yamanishir2011Yamanishi, Yoshihiro
Pauwels, Edouard
Saigo, Hiroto
Stovent, Veronique
2011Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions
In: Journal of Chemical Information and Modeling [51], 1183-1194
Journal Article
Yin05Yin, Junming
Beerenwinkel, Niko
Rahnenführer, Jörg
Lengauer, Thomas
2006Attachment IconModel Selection for Mixtures of Mutagenetic Trees
In: Statistical Applications in Genetics and Molecular Biology [5], Article 17
Journal Article
Yin2005aYin, Junming2005Model Selection for Mixtures of Mutagenetic Trees
Universität des Saarlandes
Thesis - Masters thesis
Zacharek2011Zacharek, 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.
2011Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci
In: Cell Stem Cell [9], 272-280
Journal Article
Zazzi2010aZazzi, 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
2010Prediction 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
Zazzi2012Zazzi, Maurizio
Incardona, Francesca
Rosen-Zvi, Michal
Prosperi, Mattia
Lengauer, Thomas
Altmann, Andre
Sonnerborg, Anders
Lavee, Tamar
Schülter, Eugen
Kaiser, Rolf
2012Predicting Response to Antiretroviral Treatment by Machine Learning:
The EuResist Project
In: Intervirology [55], 123-127
Journal Article
ZazziEU2006Zazzi, 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
2007EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -
Poster
ZeidlerBachelor2012Zeidler, Michael2012Cloudbasierte Analyse von viralen Sequenzdaten der neuesten Generation
Universität des Saarlandes
Thesis - Bachelor thesis
Zhang2009Zhang, Yingying
Rohde, Christian
Tierling, Sascha
Jurkowski, Tomasz P.
Bock, Christoph
Santacruz, Diana
Ragozin, Sergey
Reinhardt, Richard
Groth, Marco
Walter, Jörn
Jeltsch, Albert
2009Attachment IconDNA 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
Zhu2005Zhu, Hongbo
Domingues, Francisco S.
Sommer, Ingolf
Lengauer, Thomas
2005Analysis and prediction of protein-protein interaction types
In: 4th European Conference on Computational Biology (ECCB05), 1
Poster
Zhu2006Zhu, Hongbo
Domingues, Francisco S.
Sommer, Ingolf
Lengauer, Thomas
2006NOXclass: prediction of protein-protein interaction types
In: BMC Bioinformatics [7], 1-15
Electronic Journal Article
Zhu2008Zhu, Hongbo
Sommer, Ingolf
Lengauer, Thomas
Domingues, Francisco S.
2008Attachment IconAlignment of Non-Covalent Interactions at Protein-Protein Interfaces
In: PLoS ONE [3], e1926
Journal Article
Zhu2010aZhu, Hongbo2010Characterization, classification and alignment of protein-protein interfaces
Universität des Saarlandes
Thesis - PhD thesis
Ziller2011Ziller, Michael J.
Müller, Fabian
Liao, Jing
Zhang, Yingying
Gu, Hongcang
Bock, Christoph
Boyle, Patrick
Epstein, Charles B.
Bernstein, Bradley E.
Lengauer, Thomas
Gnirke, Andreas
Meissner, Alexander
2011Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
In: PLoS Genetics [17], e1002389,1-e1002389,15
Electronic Journal Article
Ziller2013Ziller, Michael J.
Gu, Hongcang
Müller, Fabian
Donaghey, Julie
Tsai, Linus T.-Y.
Kohlbacher, Oliver
De Jager, Philip L.
Rosen, Evan D.
Bennett, David A.
Bernstein, Bradley E.
Gnirke, Andreas
Meissner, Alexander
2013Charting a dynamic DNA methylation landscape of the human genome
In: Nature [500], 477–481
Journal Article
Zimmer2006aZimmer, Tobias2006Functional Site Scaffolds
Universität des Saarlandes
Thesis - Bachelor thesis
Zotenko2008Zotenko, Elena
Mestre, Julian
O'Leary, Dianne
Przytycka, Teresa
2008Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality
In: PLoS Computational Biology [4], e1000140
Journal Article
?Ifrim, Georgiana2005A Bayesian Learning Approach to Concept-Based Document Classification
Universität des Saarlandes
Thesis - Masters thesis
?Johannsen, Daniel2010Random Combinatorial Structures and Randomized Search Heuristics
Universität des Saarlandes
Thesis - PhD thesis

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