Homepage

Prof. Dr. Dr. Thomas Lengauer

Max-Planck-Institut für Informatik
Computational Biology and Applied Algorithmics

Campus E1 4
66123 Saarbrücken, Germany
email:   lengauer@mpi-inf.mpg.de
phone:   +49 681 9325 3000
fax:   +49 681 9325 3099
room:   501 (Building E1 4)

Recent Publications

Journal Publications

F. Schmidt, N. Gasparoni, G. Gasparoni, K. Gianmoena, C. Cadenas, J.K. Polansky, P. Ebert, K. Nordström, M. Barann, A. Sinha, S. Fröhler, J. Xiong, A.D. Amirabad, F. B. Ardakani, B. Hutter, G. Zipprich, B. Felder, J. Eils, B. Brors, W. Chen, J. Hengstler, A, Hamann, T. Lengauer, P. Rosenstiel, J. Walter, M.H. Schulz
Combining transcription factor binding affinities with an open-chromatin data for accurate gene expression prediction
Nucleic Acids Research 45, 1 (2017) 54-66.

A. Pironti, H. Walter, N. Pfeifer, E. Knops, N. Lübke, J. Büch, S. Di Gamberetto, R. Kaiser, T. Lengauer
Determination of phenotypic resistance cutoffs from routine clinical data
Journal of the Acquired Immune Deficiency Syndrome 74, 5 (2017) e129-e137.

M. Ahmad, V. Helms, O.V. Kalinina, T. Lengauer
Elucidating the energetic contributions to the binding free energy
Journal of Chemical Physics 146 (2017) 014105.

A. Pironti, N. Pfeifer, H. Walter, B.-E. O. Jensen, M. Zazzi, P. Gomes, R. Kaiser, T. Lengauer
Using drug exposure for predicting drug resistance – a data-driven genotypic resistance tool
PLOSONE 12, 4 (2017) e0174992.

E. Heger, R. Kaiser, E. Knops, M. Neumann-Fraune, E. Schülter, A. Pironti, T. Lengauer, H. Walter, S. Sierra
Short Communication: Results of the first international HIV-1 coreceptor proficiency panel test
Journal of Clinical Virology 93 (2017) 53-56.

M. Ahmad, V. Helms, O.V. Kalinina, T. Lengauer
The role of conformational changes in molecular recognition
Journal of Physical Chemistry B 120, 8 (2016) 2138-2144.

P. Kalaghatgi; A. M. Sikorski; E. Knops; D. Rupp; S. Sierra; E. Heger; M. Neumann-Fraune; B. Beggel; A. Walker; J. Timm; H. Walter; M. Obermeier; R. Kaiser; R. Bartenschlager; T. Lengauer
Geno2pheno[HCV] – A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents
PLOS ONE 11, 5 (2016) e0155869.

C. Auffray, R. Balling, I. Barroso, L. Benczze, M. Benson, J. Bergeron, E. Bernal-Delgado, N. Blomberg, C. Bock, A. Conesa, S. Del Signore, C. Delogne, P. Devilee, A. Di Meglio, R. Eijkemans, P. Flicek, N. Graf, V. Grimm, H.-J. Guchelaar, Y. Guo, I.G. Gut, A. Hanbury, S. Hanif, R.-D. Hilgers, A. Honrado, D.R. Hose, J. Houwing-Duistemaat, T. Hubbard, S.H. Janacek, H. Karanikas, T. Kievits, M. Kohler, A. Kremer, T. Lengauer, E. Maes, T. Meert, W. Müller, D. Nickel, P. Oledzki, B. Pedersen, M. Pietkovic, K. Pliakos, M. Rattray, J. Redon I Mas, R. Schneider, T. Sengstag, X.S. Picamal, W. Spek, M. Tome, L.A.I. Vaas, O. van Batenburg, M. Vandelaer, P. Varnai, P. Villoslada, J. A. Vizcaino, J.P.M. Wubbe, G. Zanetti
Making sense of big data in health research: Towards a European Union action plan
Genome Medicine 8, 1 (2016) 71.

S. Wallner, C. Schröder, E. Leitao, T. Berulava, D. Beißer, S. Rahmann, A. S. Richter, T. Manke, U. Bönisch, L. Arrigoni, S. Fröhler, F. Klironomos, W. Chen, N. Rajewsky, F. Müller, P. Ebert, T. Lengauer, M. Barann, M. Rosenstiel, P. Gasparoni, K. Nordström, J. Walter, B. Brors, G. Zipprich, B. Felder, L. Klein-Hitpass, , C. Attenberger, G. Schmitz, B. Horsthemke
Epigenetic dynamics of monocyte-to-macrophage differentiation
Epigenetics and Chromatin 9 (2016) 33.

P. Durek, K. Nordström, G. Gasparoni, A. Salhab, C. Kressler, M. de Almeida, K. Bassler, T. Ulas, F. Schmidt, J. Xiong, P. Glazar, F. Klironomos, A. Sinha, S. Kinkley, X. Yang, L. Arragoni, A. D. Amirabad, F. B. Ardakani, L. Feuerbach, O. Gorka, P. Ebert, F. Müller, N. Li, S. Frischbutter, S. Schlickeiser, C. Cendon, S. Fröhler, B. Felder, N. Gasparoni, C. D. Imbusch, B. Hutter, G. Zipprich, Y. Tauchmann, S. Reinke, G. Wassilew, U. Hoffmann, A. S. Richter, L. Sieverling, H.-D. Chang, U. Syrbe, U. Kalus, J. Eils, B. Brors, T. Manke, J. Ruland, T. Lengauer, N. Rajewsky, W. Chen, J. Dong, B. Sawitzki, H.-R. Chung, P. Rosenstiel, M. H. Schulz, J. Schultze, A. Radbruch, J. Walter, A. Hamann, J. K. Polansky
Epigenetic reprogramming during differentiation of human CD4+ T cells
Immunity 45, 5 (2016) 1148-1161.

P. Kalaghatgi, N. Pfeifer, T. Lengauer
Family-joining: a fast distance-based method for constructing generally labeled trees
Molecular Biology and Evolution 33, 10 (2016) 2720-2734.

M. Farlik, F. Halbritter, F. Müller, F. A. Choudry, P. Ebert, J. Klughammer, S, Farrow, A, Mathur, R. Uppal, H. Stunnenberg, W.H. Ouwehand, E. laurenti, T. Lengauer, M. Frontini. C. Bock
The BLUEPRINT of human hematopoietic differentiation inscribed in DNA methylation
Cell Stem Cell 19, 6 (2016) 808-822.

M. Döring, P. Borrego, J. Büch, A. Martins, G. Friedrich, R.J. Camacho, J. Eberle, R. Kaiser, T. Lengauer, N. Taveria, N. Pfeifer
A data-driven approach for the determination of HIV-2 coreceptor usage enables epidemiological studies and clinical decision support
Retrovirology 13, 1 (2016) 85.

F. Schweitzer, S.M. Müller-Schmucker, V. Dlugav, M. Däumer, D. Hammerschmidt, B.E.O. Jensen, T. Harrer, T. Lengauer, R. Kaiser, S. Trapp
Transmitted drug resistance associated mutations (RAMs) in therapy naïve human immunodeficiency virus-1 (HIV-1) infected patients: persistence via immune selection? – A multicentre cohort study
Submitted at European Journal of Medical Research (2015).

P. Ebert, F. Müller, K. Nordström, T. Lengauer, M.H. Schulz
A general concept for consistent documentation of computational analyses
Database (2015)

S. Caprari, S. Metzler, T. Lengauer, O. Kalinina
Sequence and structure analysis of distantly related viruses reveals extensive gene transfer between viruses and hosts and among viruses
Viruses 7, 10 (2015) 5388-5409.

M. Ahmad, V. Helms T. Lengauer, O. Kalinina
How molecular conformational changes affect changes in free energy
Journal of Chemical Theory and Computation 11, 7 (2015) 2945-2957.

M. Ahmad, V. Helms, T. Lengauer, O. Kalinina
The enthalpy-entropy compensation upon molecular conformational changes
Journal of Chemical Theory and Computation 11, 4 (2015) 1410-1418.

M. Dietzen, O. Kalinina, K. Taškova, B. Kneissl, A. K. Hildebrandt, E. Jaenicke, H. Decker, T. Lengauer, A. Hildebrandt
Large oligomeric complex structures can be computationally assembled by combining docked interfaces
Proteins: Structure Function and Bioinformatics 83, 10 (2015) 1887-1899.

N. Lübke, S. Sierra, V. Di Cristanziano, E. Schülter, B. O. Jensen, M. Oette, T. Lengauer, R. Kaiser
Proviral DNA as target for HIV-1 resistance analysis
Intervirology 58, 3 (2015), 184-189.

S. Sierra, J.N. Dybowski, A. Pironti, D. Heider, L. Güney, A. Thielen, S. Reuter, S. Esser, G. Fätkenheuer, T. Lengauer, D. Hoffmann, H. Pfister, B. Jensen, R. Kaiser
Parameters influencing baseline HIV-1 genotypic tropism testing related to clinical outcome in patients on Maraviroc
PLOSONE 10, 5 (2015) e0125502.

A. Pironti, N. Pfeifer, S. Sierra, R. Kaiser, T. Lengauer
Effects of sequence alterations on results from genotypic tropism testing
Journal of Clinical Virology 65 (2015) 68-73.

Y. Assenov, F. Müller, P. Lutsik, J. Walter, T. Lengauer, C. Bock
Comprehensive analysis of DNA methylation with RnBeads
Nature Methods 11, 11 (2014) 1138-1140.

N. Pfeifer, H. Walter, T. Lengauer
Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies
Journal of the Acquired Immune Deficiency Syndrome (2014)

D. Becker, P. Lutsik, P. Ebert, C. Bock, T. Lengauer, J. Walter
BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives
Nucleic Acids Research 42, Web Server Issue (2014) W501-W507.

A.K. Hildebrandt, M. Dietzen, T. Lengauer, H.P. Lenhof, E. Althaus, A. Hildebrandt
Efficient computation of root mean square deviations under rigid tranformations
Journal of Computational Chemistry 35, 10 (2013) 765-771.

B. Beggel, M. Neumann-Fraune, R. Kaiser, J. Verheyen, T. Lengauer
Inferring phase information from sequencing chromatograms
PLOSONE 8, 12 (2013) e81687.

O. V. Kalinina, N. Pfeifer, T. Lengauer
Modelling binding between CCR5 and CXCR4 receptors and their ligands suggests the surface electrostatic potential of the co-receptor to be a key player in the HIV-1 tropism
Retrovirology 10, 11 (2013) 130.

M. Oette, S. Reuter, R. Kaiser, B. Jensen, T. Lengauer, G. Fätkenheuer, H. Knechten, M. Hower, A, Sagir, H. Pfister, D. Häussinger
For the RESINA Study Group, Ambulatory care for HIV-infected patients: differences in outcomes between hospital-based units and private practices: analysis of the RESINA cohort
European Journal of Medical Research 18 (2013) 48.

J. Dietz, S,E. Schelhorn, D. Fitting, U. Mihm, S. Susser, M.-W. Welker, C. Fülller, M. Däumer, G. Teuber, H. Wedemeyer, T. Berg, T. Lengauer, Stefan Z., E. Herrmann, C. Sarrazin
Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of HCV genotype 1-infected patients
Journal of Virology 87, 11 (2013) 6172-6181

K. Bozek, T. Lengauer, S. Sierra, R. Kaiser, F.S. Domingues
Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage
PLoS Computational Biology 9, 3 (2013) e1002977

T. Bhadra, M. Battacharya, L. Feuerbach,. T. Lengauer, S. Bandyopadhyay
DNA Methylation Patterns Facilitate the Identification of Transcription Start Sites: A Brain-specofoc Study
PLOSONE 8, 6 (2013) e66722

B. Beggel, C. Münk, M. Däumer, K. Hauck, D Häussinger, T. Lengauer, A, Ehrhardt
Full genome ultra-deep pyrosequencing associates G-to-A hypermutation of the hepatitis B virus genome with the natural progression of hepatitis B
Journal of Viral Hepatitis (2013)

L. Tolosi, J. Theißen, K. Halachev, B. Hero, F. Berthold, T. Lengauer
A method for finding consensus breakpoints in the cancer genome from copy number data
Bioinformatics (2013) 1793-1800

S. E. Schelhorn, M. Fischer, L. Tolosi, J. Altmüller, P. Nürnberg, H. Pfister, T. Lengauer, F. Berthold
Sensitive detection of viral transcripts in human tumor transcriptomes
PLOS Computational Biology 9,10 (2013) e1003228

E. Heger, A. Thielen, R. Gilles, M. Obermeier, T. Lengauer, R. Kaiser, S. Trapp
APOBEC3G/F a one possible driving source for co-receptor switch of the human immunodeficiency virus-1
Medical Microbiology and Immunology 201, 1 (2012) 7-16

L. Feuerbach, K. Halachev, Y. Assenov, F. Müller, C. Bock, T. Lengauer
Analyzing epigenome data in context of genome evolution and human diseases
Methods of Molecular Biology 856, Chapter 18 (2012), 431-467

D. Adams, L. Altucci, S.E. Antonarakis, J. Ballesteros, S. Beck, A. Bird, C. Bock, B. Boehm, E. Campo, A. Caricasole, F. Dahl, E.T. Dermitzakis, T. Enver, M. Esteller, X. Estivill, A. Ferguson-Smith, J. Fitzgibbon, P. Flicek, C. Giehl, T. Graf, F. Grosveld, R. Guigo, I. Gut, K. Helin, J. Jarvius, R. Kuppers, H. Lehrach, T. Lengauer, A. Lernmark, D. Leslie, M. Loeffler, E. Macintyre, A. Mai, J.H. Martens, S. Minucci, W.H. Ouwehand, P.G. Pelicci, H. Pendeville, B. Porse, V. Rakyan, W. Reik, M. Schrappe, D. Schübeler, M. Seifert, R. Siebert, D. Simmons, N. Soranzo, S. Spicuglia, M. Stratton, H.G.  Stunnenberg, A.  Tanay, D. Torrents, A. Valencia, E. Vellenga, M. Vingron, J. Walter, S. Willcocks
BLUEPRINT to decode the epigenetic signature written in blood
Nature Biotechnology 30. 2 (2012)  224-226

J. Bogojeska, D. Stöckel, M. Zazzi, R. Kaiser, F. Incardona, M. Rosen-Zvi, T. Lengauer
History-alignment models for bias-aware prediction of virological response to HIV combination therapy
Journal of Machine Learning Research  22 (Proceedings of AISTATS 2012) (2012) 118-126

C. Welsch, T. Shimakami, C. Hartmann, Y. Yang, F.S. Domingues, T. Lengauer, S. Zeuzem, S.M. Lemon
Peptidomimetic escape mechanisms due to genetic diversity in the ligand-binding site of the HCV NS3/4A serine protease
Gastroenterology 142, 3 (2012) 654-663

M. Bhattacharyya, L. Feuerbach, T. Bhadra, T. Lengauer, S. Bandyopadhyay
MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection Statistical
Applications in Molecular Biology and Genetics 11, 1 (2012) 1-25

M. Dietzen, E. Zotenko, A. Hildebrandt, T. Lengauer
On the applicability of normal modes in small-molecule docking
Journal of Chemical Information and Modeling 52, 3 (2012) 844-856

G. Lawyer, E. Schülter, R.  Kaiser, S. Reuter, M. Oette, T. Lengauer on behalf of the Resina study group
Endogenous or exogenous spreading of HIV-1 in Northrhine-Westphalia, Germany, investigated by phylodynamic analysis of the Resina cohort
Medical Microbiology and Immunology 201, 3 (2012) 259-269

J. Bogojeska, T. Lengauer
Hierarchical Bayes Model for Predicting Effectiveness of HIV Combination Therapies
Statistical Applications in Genetics and Molecular Biology 11, 3 (2012) Article 11

C. Bock, T. Lengauer
Managing drug resistance in cancer: lessons from HIV therapy
Nature Reviews Cancer 12, 7 (2012) 494-501

K. Bozek, M. Eckhardt, S. Sierra, R. Kaiser, H.-G. Kräusslich, B. Müller, T. Lengauer
An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data
Retrovirology 9, 1 (2012) 60

N. Pfeifer, T. Lengauer
Improving HIV coreceptor usage prediction in the clinic using hints from next generation sequencing data
Bioinformatics 28, 18 (2012), i589-i595

B. Beggel, M. Neumann-Fraune, M. Döring, G. Lawyer, R. Kaiser, J. Verheyen, T. Lengauer
Genotyping hepatitis B virus dual infections using population-based sequencing data
Journal of General Virology 93, Pt 9 (2012) 1899-1907

K. Halachev, H. Bast, T. Lengauer, C. Bock
Interactive exploration of large genome and epigenome datasets in real time
Genome Biology 13, 10 (2012) r96

F. Simmer, A.B. Brinkmann, Y. Assenov, F. Matarese, A. Kaan, T. Lengauer, C. Bock, V. Colantuoni, L. Altucci, H.G. Stunnenberg
Comparative genome-wide DNA methylation analysis of colorectal tumor and matched human tissue
Epigenetics 7, 12 (2012) 1355-1367

S. Reiss, I.Rebhan, P.Backes, I. Romero-Brey, H. Erfle, P. Matula, L. Kaderali, M. Poenisch, H.Blankenburg, M.S. Hiet, T.Longerich, S. Diehl, F. Ramirez, T. Balla, K.Rohr, A. Kaul, S. Bühler, R. Pepperkok, T. Lengauer, M. Albrecht, R. Eils, P. Schirmacher, V. Lohmann, R. Bartenschlager
Recruitment  and Activation of a Lipid Kinase by Hepatitis C Virus NS5A Is Essential for Integrity of the Membranous Replication Compartment
Cell Host Microbe, 9, 1 (2011) 32-45

H. Saigo, A. Altmann, F. Müller, J. Bogojeska, S. Nowozin, T. Lengauer
Learning from treatment history to predict anti HIV-1 therapy
Statistical Applications in Genetics and Molecular Biology 10, 1 (2011) Article 6

S. Reuter, M.  Oette, F.C. Wilhelm, B. Beggel, R. Kaiser, M. Balduin, F. Schweitzer, J. Verheyen, O. Adams, T.  Lengauer, G. Fätkenheuer, H.  Pfister, D. Häussinger
Prevalence and characteristics of hepatitis B and C virus infections in treatment-naive HIV-infected patients
Med Micobiol Immunol 200, 1 (2011) 39-49

A. Thielen, T. Lengauer, P.R. Harrigan, L. Swenson, W.W.Y. Dong, R. McGovern, M. Lewis, I. James, J.  Heera, H. Valdez
Mutations in the gp41-protein are correlated with coreceptor tropism but do not improve prediction methods substantially
Antiviral Therapy 16, 3 (2011) 319-328

M. Zazzi, R. Kaiser, A. Sönnerborg, D. Struck, A. Altmann, M. Prosperi, M. Rosen-Zvi, A. Petroczi, Y. Peres, E. Schülter, C.A. Boucher, F. Brun-Vezinet, R. Harrigan, L. Morris, M. Obermeier, C.-F. Perno, P. Phanuphak, D. Pillay, R.W. Shafer, A.-M. Vandamme, K. Van Laethem, A. Wensing, T. Lengauer, F. Incardona
Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
HIV Medicine 12, 4 (2011) 211-218

M. Däumer, R. Kaiser, R. Klein, T. Lengauer, B. Thiele, A. Thielen
Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis
BMC Medical Informatics and Decision Making 11, 1(2011) 30

L. Feuerbach, R.B. Lyngsø, T. Lengauer, J. Hein
Reconstructing the ancestral germline methylation state of young repeats
Molecular Biology and Evolution 28, 6 (2011) 1777-1784

P. Lutsik, L. Feuerbach, J. Arand, T. Lengauer, J. Walter, C. Bock
BiQ Analyzer HT: Locus-specific analysis of DNA methylation by high-throughput bisulfate sequencing
Nucleic Acids Research 39 (2011) W551-W556

E. Schülter, M. Oette, M. Balduin, S. Reuter, J. Rockstroh, G. Fätkenheuer, S. Esser, T. Lengauer, A. Agacfidan, H. Pfister, R. Kaiser. B. Akqül
HIV prevalence and route of transmission in Turkish immigrants living in North-Rhine Westfalia, Germany
Medical Microbiology and Immunology 200, 4 (2011) 219-223

L. Tolosi, T. Lengauer
Classification with correlated features: unreliability of feature ranking and solutions
Bioinformatics 27, 14 (2011) 1986-1994

A.F. Fernandez, Y. Assenov, J.I. Martin-Subero, B. Balint, R. Siebert, H. Taniguchi, H. Yamamoto, M. Hidalgo, A.-C. Tan, O. Galm, I. Ferrer, M. Sanchez-Cespedes, A. Villanueva, J. Carmona, J.V. Sanchez-Mut, M. Berdasco, V. Moreno, G. Capella, D. Monk, E. Ballestar, S. Ropero, R. Martinez, M. Sanchez-Carbayo, F. Prosper, X. Agirre, M.F. Fraga, O. Graña, L. Perez-Jurado, J. Mora, S. Puig, J. Prat, L. Badimon, A.A. Puca, S.J. Meltzer, T. Lengauer, J. Bridgewater, C. Bock, Manel Esteller
A DNA methylation fingerprint of 1,628 human samples
Genome Res 22, 2 (2011) 407-419

G. Lawyer, A. Altmann, A. Thielen, M. Zazzi, A. Sönnerborg, T. Lengauer
HIV-1 mutational pathways under multidrug therapy
AIDS Research and Therapy 8, 1 (2011) 26

S. Sierra, R. Kaiser, N. Lübke, A. Thielen, E, Schülter, E. Heger, M. Däumer, S. reuter, S. Esser, G. Fätkenheuer, H. Pfister, M. Oette, T. Lengauer
Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach
Journal of Visualized Experiments 85 (2011)

Ziller, M.J., Müller, F., Liao, J., Zhang, Y., Gu, H., Bock, C., Poyle, P., Epstein, C.B., Bernsetin, B.,  Lengauer, T., Gnirke, A., Meissner, A.
Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types
PLoS Genetics, 7, 12 (2011) e1002389

J.  Bogojeska, S. Bickel, A. Altmann, T. Lengauer
Dealing with sparse data in predicting outcomes of HIV combination therapies
Bioinformatics 26, 17 (2010) 2085-2092

A. Schlicker, T. Lengauer, M. Albrecht
Improving disease gene prioritization using the semantic similarity of gene ontology terms
Bioinformatics 26, 18 (2010) i561-i567

K. Bozek, T. Lengauer
Positive selection of HIV host factors and the evolution of lentivirus genes
BMC Evolutionary Biology 10, 1 (2010) 186

D. Emig, N. Salomonis, J. Baumbach, T. Lengauer, B.R. Conklin, M. Albrecht
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
Nucleic Acids Research 38 Suppl (2010) W755-62

A. Thielen, N. Sichtig, R. Kaiser, J. Lam, P.R. Harrigan, T. Lengauer
Improved prediction of Human Immunodeficiency Virus-1 coreceptor usage with sequence information from the second hypervariable loop of gp120
Journal of Infectious Diseases 202, 9 (2010) 1435-1443

C.M. Lange, K. Roomp, A. Dragan, J. Nattermann, M. Michalk, U. Spengler, V. Weich, T. Berg, T. Lengauer, S. Zeuzem, C. Sarrazin
HLA class I allele associations with novel HCV polymorphisms and outcome of antiviral therapy in patients with chronic hepatitis C
Journal of Hepatology 53, 6 (2010) 1022-1028

U. Mihm, W.P. Hofmann, C. Welsch, A. Polta, T. Lengauer, S. Zeuzem, C. Sarrazin, E. Herrmann
Effect of ribavirin on teh frequency of RNAse L cleavage sites within the hepatitis C viral genome
J. Viral Hepatitis 17, 3 (2010) 217-221

H. Weisser, A. Altmann, S. Sierra, F. Incardona, D. Struck, A. Sönnerborg, R. Kaiser, M. Zazzi, M. Tschochner, H. Walter, T. Lengauer
Only Slight Impact of Predicted Replicative Capacity for Therapy Response Prediction
PLoSOne 5, 2 (2010) e9044

K. Roomp, I. Antes, T. Lengauer
Predicting MHC class I epitopes in large datasets
BMC Bioinformatics 11,1 (2010) 90

C. Bock, G. von Kuster, K. Halachev, J. Taylor, A. Nekrutenko, T. Lengauer
Web-based analysis of (epi-) genome data using EpiGRAPH and Galaxy
Methods in Molecular Biology, Vol. 628 (2010) 275-296

Däumer, M., Awerkiew, S., Aragon, S.S., Kartashev, V., Poplavskaja, T. Klein, R., Sichtig, N., Thielen, B., Lengauer, T., Roomp,K., Pfister, H., Kaiser, R.
Short Communication: Selection of Thymidine Analogue Resistance Mutational Patterns in Children from a Common HIV Type 1 Subtype G Source
AIDS Research and Human Retroviruses, 26, 3 (2010): 275-278

A. Altmann, L. Tolosi, O. Sander, T. Lengauer
Permutation importance: an unbiased feature importance measure
Bioinformatics 26, 10 (2010)  1340-1347

M.-W.Welker, C.  Welsch, A. Meyer, I. Antes,  M. Albrecht, N.  Forstier, B. Kronenberger, T. Lengauer, A. Piiper, S. Zeuzem, C. Sarrazin
Homodimerization oft he hepatitis C virus nonstructural protein 4B depdends on the integrity of an aminoterminal basic leucine zipper
Protein Science 19,7 (2010) 1327-1336

U. Mihm, O. Ackermann, C. Welsch, E. Herrmann, W.-P. Hofmann, N. Grigorian, M.W. Welker, T. Lengauer, S. Zeuzem, C. Sarrazin
Clinical relevance of the IFN-activated 2´-5´-oligoadenylate synthetase (OAS)/RNase L system for treatment response in chronic hepatitis C
Journal of Hepatology  50, 1 (2009) 49-58

C. Hartmann, I. Antes, T. Lengauer
Virtual screening with modeled or flexible side-chain conformations
Proteins: Structure, Function and Bioinformatics 74, 3 (2009) 712-726

M. Trignetti, T. Sing, V. Svicher, M.M. Santoro, F. Forbici, R. D’Arrigo, M.C. Bellocchi, M. Santoro, P. Marconi, M. Zaccarelli, M.P. Tortta, R. Bellagamba, P. Narciso, A. Antinori, T. Lengauer, C.F. Perno, F. Ceccherini-Silberstein
Dynamics of NRTI resistance mutations during therapy interruption
AIDS Research and Human Retroviruses 25, 1 (2009) 57-64

C. Bock, K. Halachev, J. Büch, T. Lengauer
EpiGRAPH: A user-friendly software for advanced (epi-) genome analysis and prediction
Genome Biology 10, 2 (2009) R14

A. Altmann, M. Däumer, N. Beerenwinkel, Y. Peres, E. Schülter, J. Büch, S.-Y. Rhee, A. Sönnerborg, W.J. Fessel, R.W. Shafer, M. Zazzi, R. Kaiser, T. Lengauer
Predicting response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database
Journal of Infectious Diseases 199, 7 (2009) 999-1006

A. Altmann, T. Sing, H. Vermeiren, B. Winters, E. van Craenenbroeck, K. van der Borght, S.-Y. Ree, R.W. Shafer, E. Schülter, R. Kaiser, Y. Peres, A. Sönnerborg, W.J. Fessel, F. Incardona, M. Zazzi, L. Bacheler, H. van Vlijmen, T. Lengauer
Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype
Antiviral Therapy 14, 2 (2009) 273-283

H. Blankenburg, R.D. Finn, A. Prlić, A. Jenkinson, F. Ramírez, D. Emig, S.-E. Schelhorn, J. Büch, T. Lengauer, M. Albrecht
DASMI: exchanging, annotating, and assessing molecular interaction data
Bioinformatics 25, 10 (2009) 1321-1328

K. Bozek, A. Thielen, S. Sierra, R. Kaiser, T. Lengauer
V3-loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV
PLoSOne 4, 10 (2009) e7387

P. Schüffler, T. Mikeska, T. Lengauer, C. Bock
MethMarker: optimized assay design for epigenetic biomarker development and high-throughput epigenotyping
Genome Biology 10, 10 (2009) R105

C. Welsch, F.S. Domingues, I. Antes, C. Hartmann, G. Mayr, A. Schlicker, C. Sarrazin, M. Albrecht, S. Zeuzem, T. Lengauer
Molecular basis of Telaprevir (VX-950) Resistance at positions V36 and T54 in chronic hepatitis C
Genome Biology 9, 1 (2008) R16

H. Zhu, I. Sommer, T. Lengauer, F.S. Domingues
Alignment of non-covalent interactions at protein-protein interfaces
PLoSOne 3, 4 (2008) e1926

J. Bogojeska, T. Lengauer, J. Rahnenführer
Stability analysis of mixtures of mutagenetic trees
BMC Bioinformatics 9, 1 (2008) 165

C. Bock, J. Walter, M. Paulsen, T. Lengauer
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping
Nucleic Acids Research 36, 10 (2008) e55

N. Weinhold, O. Sander, F.S. Domingues, T. Lengauer, I. Sommer
Local function conservation in sequence and structure space
PLoS Computational Biology 4, 7 (2008) e1000105

N. Weinhold, O. Sander, F.S. Domingues, T. Lengauer, I. Sommer
Local function conservation in sequence and structure space
PLoS Computational Biology 4, 7 (2008) e1000105

Y. Assenov, F. Ramirez, S.E. Schelhorn, T. Lengauer, M. Albrecht
Computing topological parameters of biological networks
Bioinformatics 24, 2 (2008) 282-284.

C. Bock, T. Lengauer
Computational Epigenetics
Bioinformatics 24, 1 (2008) 1-10

D. Emig, M. Cline, K. Klein, A. Kunert, P. Mutzel, T. Lengauer, M. Albrecht
Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks
Journal of Integrative Bioinformatics 5, 2 (2008) 101

A. Altmann, M. Rosen-Zvi, M. Prosperi, E. Aharoni, H. Neuvirth, E. Schülter, J. Büch, D. Struck, Y. Peres, F. Incardona, A. Sönnerborg, R. Kaiser, M. Zazzi, T. Lengauer
Comparison of classifier fusion methods for predicting response to anti-HIV therapy
PLoSOne 3, 10 (2008) e3470

J. Bogojeska, A. Alexa, A. Altmann, T. Lengauer, J. Rahnenführer
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
Bioinformatics 24, 20 (2008) 2391-2392

D. Emig, M.S. Cline, T. Lengauer, M. Albrecht
Integrating expression data with domain interaction networks
Bioinformatics 24, 21 (2008) 2546-2548

S.E. Schelhorn, T. Lengauer, M. Albrecht
An integrative approach for predicting interactions of protein regions
Bioinformatics 24, 16 (2008) i35-41

M.L. Tress, P.L. Martelli, A. Frankish, G. Reeves, J. J. Wesselink, C. Yeats, P.Ísólfur Ólason, M. Albrecht, H. Hegyi, A. Giorgetti, D. Raimondo, J. Lagarde, R. Laskowski, G. Lopez, M.I. Sadowski, J. Watson, P. Fariselli, I.Rossi, A. Nagy, W. Kai, Z. Størling, M. Orsini, Y. Assenov, H. Blankenburg, C. Huthmacher, F. Ramirez, A. Schlicker, F. Denoued, P. Jones, S. Kerrien, S.E. Orchard, E. Birney, S. Brunak, R. Casadio, R. Guigo, J. Harrow, H. Hermjakob, D.T. Jones, T. Lengauer, C.A. Orengo, L. Patthy, J.M. Thornton, A. Tramontano, A. Valencia
Implications of alternative splicing in the ENCODE protein complement
PNAS 104, 13 (2007) 5495-5500

A. Schlicker, J. Rahnenführer, M. Albrecht, T. Lengauer, F.S. Domingues
GOTax: Investigating biological processes and biochemical activities along the taxonomic tree
Genome Biology 8, 3 (2007) R33

C. Hartmann, I. Antes, T. Lengauer
IRECS: Selection of side-chain conformations in protein models
Protein Science 16, 7 (2007) 1294-1307

C. Bock, J. Walter, M. Paulsen, T. Lengauer
CpG island mapping by epigenome prediction
PLoS Computational Biology 3, 6 (2007) e110

F. Ramirez, A. Schlicker, Y. Assenov, T. Lengauer, M. Albrecht
Computational analysis of human protein interaction networks
Proteomics 7, 15 (2007) 2541-2552

A. Flockerzi, J. Maydt, O. Frank, A. Ruggieri, E. Maldener, W. Seifarth, P. Medstrand, T. Lengauer, A. Meyerhans, C.Leib-Mosch, E. Meese, J. Mayer
Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination
Retrovirology 4, 1 (2007) 39

R. Ketter, S. Urbschat,  W. Henn, Y.-J. Kim, W. Feiden, N. Beerenwinkel, T. Lengauer, W.-I. Steudel, K.D. Zang, J. Rahnenführer
Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas
International Journal of Cancer 121, 7 (2007) 1473-1480

Steffen, C. Thiele, S. Tietze, C. Strassnig, A. Kämper, T. Lengauer, G. Wenz, J. Apostolakis
Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening
Chemistry – A European Journal  13, 24(2007) 6801-6809

C. Welsch, M. Albrecht, J. Maydt, E. Herrmann, M.-W. Welker, C. Sarrazin, A. Scheidig, T. Lengauer, S. Zeuzem
Structural and functional comparison of the non-structural protein 4B of Flaviviridae
Journal of Molecular Graphics and Modeling 26, 2 (2007) 546-557

B. Kupfer, T. Sing, P. Schüffler, R. Hall, R. Kurz, A. McKeown, K.-E. Schneweis, W. Eberl, J. Oldenburg, H.H. Brackmann, J.K. Rockstroh, U. Spengler, M.P. Däumer, R. Kaiser, T. Lengauer, B. Matz
Fifteen years of env V3 evolution in six individuals clonally infected with human immunodeficiency virus type 1
 Journal of Medical Virology 79, 11 (2007) 1629-1639

A. Steffen, C. Thiele, S. Tietze, C. Strassnig, A. Kämper, T. Lengauer, G. Wenz, J. Apostolakis
Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening
Chemistry 13, 24 (2007) 6801-6809

F. Ceccherini-Silberstein, V. Svicher, T. Sing, A. Artese, M.M. Santoro, C. Gori, A. Bertoli, S. Alcaro, G. Palamara, A. d’Arminio Monforte, A. Antinori, T. Lengauer, C.F. Perno, ICoNA Study Group, INMI-Collaborative Group for Clinical Use of HIV Genotype Resistance Test
Additional mutations in HIV-1 reverse transcriptase involved in the regulation of resistance to non-nucleoside inhibitors
Journal of Virology 81, 20 (2007) 11507-11519

G. Ahlenstiel, K. Roomp, M. Schulz, M. Däumer, M. Vogel, E. Voigt, J. Nattermann, N. Beerenwinkel, H.-D. Nischalke, J.K. Rockstroh, T. Sauerbruch, T. Lengauer, U. Spengler
Influence of HLA system and antiviral therapy on the evolution of HIV-1 escape mutations
Clinical and Vaccine Immunology 14, 10 (2007) 1266-1273

T. Sing, A.J. Low, N. Beerenwinkel, O. Sander, P.K. Cheung, F.S. Domingues, J. Büch, M. Däumer, R. Kaiser, T. Lengauer, R. Harrigan
Predicting HIV Co-receptor usage based on genetic and clinical covariates
Antivrial Therapy 12, 7 (2007) 1097-1106

Steffen, M. Karasz, C. Thiele, T. Lengauer, A. Kämper, G. Wenz, J. Apostolakis
Combined similarity and QSPR virtual screening for guest molecules of b-cyclodextrin
New Journal of Chemistry 31, 11 (2007) 1941-1949

N. Scheller, P. Resa-Infante, S. de la Luna, R.P. Galao, M. Albrecht, L. Kaestner, P. Lipp, T. Lengauer, A. Meyerhans, J. Diez
Identification of PatL1: a human homolog to yeast P body component Pat1
Biochimica et Biophysica Acta – Molecular Cell Research 1773, 12 (2007) 1786-1792

F. S. Domingues, J. Rahnenführer, T. Lengauer
Conformational analysis of alternative protein structures
Bioinformatics 23, 23 (2007) 3131-3138

I. Sommer, O. Müller, F. S. Domingues, O. Sander, J. Weickert, T. Lengauer
Moment invariants as shape recognition technique for comparing protein binding sites
Bioinformatics 23, 23 (2007) 3139-3146

O. Sander, T. Sing, I. Sommer, A.J. Low, P.K. Cheung, P. Harrigan, T. Lengauer, F.S. Domingues
Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage
PLoS Computational Biology 3, 3 (2007) e58

A. Schlicker, C. Huthmacher, F. Ramirez, T. Lengauer, M. Albrecht
Functional evaluation of domain-domain interactions and human protein interaction networks
Bioinformatics 23, 7 (2007) 859-865

A. Altmann, N. Beerenwinkel, T. Sing, I. Savenkov, M. Däumer, R. Kaiser, S.-Y. Rhee, J. Fessel, R. Shafer, T. Lengauer
Improved prediction of response to anti-HIV combination therapy using probabilistic genetic barriers
Antiviral Therapy 12, 2 (2006) 169-178 (Abstract)

V. R. Velagapudi, C. Wittmann, T. Lengauer, P. Talwar, E. Heinzle
Metabolic high-content screening of Saccharomyces cerevisiae reveals superior performance of single gene deletion strains
Process Biochemistry 41, 10 (2006) 2170-2179

W.A. Schulz, A. Alexa, V. Jung, C. Hader, M.J. Hoffmann, M. Yamanaka, S. Fritzsche, A. Wlazinski, M. Müller, T. Lengauer, R. Engers, A.R. Florl, B. Wullich, J. Rahnenführer
Factor integration analysis from chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer
Molecular Cancer 6 (2007) 14

J. Hampe, A. Franke, P. Rosenstiel, A. Till, M. Teuber, K. Huse, M. Albrecht, R. Häsler, B. Sipos, G. Mayr, F.M. de la Vega, J. Briggs, S. Günther, N.J. Prescott, C.M. Onnie, U.R. Fölsch, T. Lengauer, M. Platzer, C.G. Mathew, M. Krawczak, S. Schreiber
A genome-wide association scan of non-synonymous SNPs identifies a susceptibility variant for Crohn disease in the autophagy-related 16-like (ATG16L1) gene
Nature Genetics 39,2 (2007) 207-211

M.-W. Welker, W.-P. Hofmann, C. Welsch, M. von Wagner, E. Hermann, T. Lengauer, S. Zeuzem, C. Sarrazin
Correlation of nonstructural (NS)4B amino acid variations with initial viral kinetics during interferon alpha-based therapy in HCV 1b-infected patients
Journal of Viral Hepatitis 14, 5 (2007) 338-349

G. Plotz, C. Welsch, L. Giron-Monzon, P. Friedhoff, M. Albrecht, A. Pilper, R. Biondi, T. Lengauer, S. Zeuzem, J. Raedle
Mutations in the MutSα interaction interface of MLH1 can abolish DNA mismatch repair
Nucleic Acids Research 34, 22 (2006) 574-6586

J. Yin, N. Beerenwinkel, J. Rahnenführer, T. Lengauer
Model selection for mixtures of mutagenetic trees
Statistical Applications in Genetics and Molecular Biology 5, 1 (2006) Article 17

Lehmann, C. Däumer, M., Boussaad, I., Sing, T., Beerenwinkel, N., Lengauer, T., Schmeisser, N., Wyen, C., Fätkenheuer, G., Kaiser, R.
Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART
Journal of Clinical Virology 37, 4 (2006) 300-304

I. Antes, S. Siu, T. Lengauer
DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations
Bioinformatics 22, 14 (2006) e16-e24

I. Sommer, S. Toppo, O. Sander, T. Lengauer, S.C.E. Tosatto
Improving the quality of protein structure models by selecting from alignment alternatives
BMC Bioinformatics 7 (2006), Article 346

A. Schlicker, F. Domingues, J. Rahnenführer, T. Lengauer
A new measure for functional similarity of gene products based on gene ontology
BMC Bioinformatics 7, 1 (2006) Article 302

A. Steffen, A. Kämper, T. Lengauer
Flexible docking of ligands into synthetic receptors using a two-sided incremental construction algorithm
Journal of Chemical Information and Modeling 46, 4 (2006) 1695-1703

U. Mihm, N. Grigorian, C. Welsch, E. Herrmann, B. Kronenberger, G. Teuber, M. von Wagner, W.-P. Hofmann, M. Albrecht, T. Lengauer, S. Zeuzem, C. Sarrazin
Amino acid variations in HCV p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C
Antiviral Therapy 11, 4 (2006) 507-519

A. Alexa, J. Rahnenführer, T. Lengauer
Improved significance scoring of functional groups from gene expression data by decorrelating GO graph structure
Bioinformatics 22, 13 (2006) 1600-1607

B. Heil, J. Ludwig. H. Lichtenberg, T. Lengauer
Computational recognition of potassium channel sequences
Bioinformatics 22, 13 (2006) 1562-1568

V. Svicher, T. Sing, M.M. Santoro, F. Forbici, F. Rodgriguez-Barrios, A, Bertoli, N. Beerenwinkel, M.C. Bellocchi, F. Gago, A. d'Arminio Monforte, A. Antinori, T. Lengauer, F. Ceccherini-Silberstein, C.F. Perno
Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
Journal of Virology 80, 14 (2006) 7186-7198

J. Maydt, T. Lengauer
Recco: Recombination analysis using cost optimization
Bioinformatics 22, 9 (2006) 1064-1071

W.I.M.Tameling, J.H.Vossen, M. Albrecht, T. Lengauer, J.A. Berden, M.A. Haring, B.J.C. Cornelissen, F.L.W. Takken
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation
Plant Physiol 140, 4 (2006) 1233-1245.

C. Bock, M. Paulsen, S. Tierling, T. Mikeska, T. Lengauer, J. Walter
CpG island methylation in human lymphocytes is highly correlated with DNA sequence patterns, repeat frequencies and predicted DNA structure
PLoS Genetics 2, 3 (2006) e26.

A. Kämper, J. Apostolakis, M. Rarey, C. M. Marian, T. Lengauer
Fully automated flexible docking of ligands into synthetic receptors using forward and inverse docking strategies
Journal of Chemical Information and Modeling 46, 2 (2006) 903-911

D. Neumann, O. Kohlbacher, C. Merkwirth, T. Lengauer
Prediction of percutaneous drug absorption
Journal of Chemical Information and Modeling 46, 1 (2006) 424-429

H. Zhu, F. S. Domingues, I. Sommer. T. Lengauer
Analysis and prediction of protein-protein-interaction types
BMC Bioinformatics 7, 1 (2006) Article 27

O. Sander, I. Sommer, T. Lengauer
Local protein structure prediction using discriminative models
BMC Bioinformatics 7, 1 (2006) Article 14

M. Ralser, M. Albrecht, U. Nonhoff, T. Lengauer, H. Lehrach, S. Krobitsch
Ataxin-2 interacts with the cytoplasmatic poly(A)-binding protein 1 and is implicated in RNA-processing pathways
Journal of Molecular Biology 346, 1 (2005) 203-214

M. Albrecht, D. Choubey, T. Lengauer
The HIN domain of IFI-200 proteins consists of two OB folds
Biochemical and Biophysical Research Communications 327, 3 (2005) 679-687

S. Ulmschneider, U. Müller-Vieira, C. Klein, I. Antes, T. Lengauer, R.W. Hartmann
Synthesis and evaluation of imidalzolymethylene-tetrahydronaphtalenes and -indanes: Potent inhibitors of Aldosterone Synthase
Journal of Medicinal Chemistry 48, 6 (2005) 1796-1805

N. Beerenwinkel, J. Rahnenführer, R. Kaiser, D. Hoffmann, J. Selbig, T. Lengauer
Mtreemix: a software package for learning and using mixture models of mutagenetic trees
Bioinformatics 21, 9 (2005) 2106-2107

N. Beerenwinkel, M. Däumer, T. Sing, J. Rahnenführer, T. Lengauer, J. Selbig, D. Hoffmann, R. Kaiser
Estimating HIV evolutionary pathways and the genetic barrier to drug resistance
Journal of Infectious Diseases 191, 11 (2005) 1953-1960

J. Rahnenführer, N. Beerenwinkel, B. Wullich, W.A. Schulz, C. Hartmann, A. von Deimling, T. Lengauer
Estimating cancer survival and clinical outcome based on genetic tumor progression scores
Bioinformatics 21, 10 (2005) 2438-2446

R. Valentonyte, J. Hampe, K. Huse, P. Rosenstiel, M. Albrecht, A. Stenzel, M. Nagy, K.I. Gaede, A. Franke, R, Haeseler, A. Koch, T. Lengauer, D. Seegert, N. Reiling, S. Ehlers, E. Schweinger, M. Platzer, M. Krawczak, J. Müller-Querheim, M. Schürmann, S. Schreiber
Sarcoidosis is associated with a truncating splice site mutation in BTNL2
Nature Genetics 37, 4 (2005) 357-364

M. J. van Duist, M. Albrecht, D. Gaichino, T. Lengauer, M. De Marchi. M. Podswiadek, L. Punzi
A new CARD15 variant in Blau syndrome
European Journal of Human Genetics 13, 6 (2005) 742-747

A. Hahn, J. Rahnenführer, P. Talwar, T. Lengauer
Confirmation of human protein interaction data by human expression data
BMC Bioinformatics 6, 1 (2005) 12

N. Beerenwinkel, J. Rahnenführer, M. Däumer, D. Hoffmann, R. Kaiser, J. Selbig, T. Lengauer
Learning multiple evolutionary pathways from cross-sectional data
Journal of Computational Biology 12, 6 (2005) 584-598

C.M. Costello, N. Mah, R. Häsler, P. Rosenstiel, G.H. Waetzig, A. Hahn, T. Lu, Y. Gurbuz, S. Nikolaus, M. Albrecht, J. Hampe, R. Lucius, G. Klöppel, H. Eickhoff, H. Lehrach, T. Lengauer, S, Schreiber
Dissection of inflammatory bowel disease transcriptome using genome-wide cDNA microarrays identifies novel candidate disease genes
PLoS Medicine 2, 8 (2005) e199

T. Sing, O. Sander, N. Beerenwinkel, T. Lengauer
ROCR - Visualizing classifier performance in R
erscheint in Bioinformatics 21, 20 (2005) 3940-3941

C. Sarrazin, U. Mihm, E. Herrmann, C. Welsch, M. Albrecht, U. Sarrazin, S. Traver, T. Lengauer, S. Zeuzem
Replication enhancing mutations of the Hepatitis C virus replicon: Prevalence and clinical significance in patients with chronic Hepatitis C
Journal of Infectious Diseases 192, 10 (2005) 1710-1719

M. Albrecht, C. Huthmacher, S.C.E. Tosatto, T. Lengauer
Decomposing protein networks into domain-domain interactions, Proceedings of the Fourth European Conference on Computational Biology (ECCB 2005)
Bioinformatics 21, Suppl. 2 (2005) ii220-ii221

I. Antes, C. Merkwirth, T. Lengauer
POEM: Parameter optimization using ensemble methods: application to target specific scoring functions
Journal of Chemical Information and Modeling 45, 5 (2005) 1291-1302

N. Beerenwinkel, T. Sing, T. Lengauer, J. Rahnenführer, K. Roomp, I. Savenkov, R. Fischer, D. Hoffmann, J. Selbig, K. Korn, H. Walter, T. Berg, P. Braun, G. Fätkenheuer, M. Oette, J. Rockstroh, B. Kupfer, R. Kaiser, M. Däumer
Computational methods for the design of effective therapies against drug resistant HIV strains
Bioinformatics 21, 21 (2005)3943-3950

C. Merkwirth, T. Lengauer
Automatic Generation of complementary descriptors with molecular graph networks
Journal of Chemical Information and Modeling 45, 5 (2005) 1159-1168

S. Wemmert, R. Ketter, J. Rahnenführer, N. Beerenwinkel, M. Strowitzki, W. Feiden, C. Hartmann, T. Lengauer, F. Stockhammer, K. D. Zang, E. Meese, W.-I. Steudel, A. von Deimling, S. Urbschat
Patients with high grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment
Neoplasia 7, 10 (2005) 883-893

G. Hessler, M. Zimmermann, H. Matter, A. Evers, T. Naumann, T. Lengauer, M. Rarey
Multiple-Ligand-Based Virtual Screening: Methods and Applications of the MTree Approach
Journal of Medicinal Chemistry 48, 21 (2005) 6575-6584

C. Bock, S. Reither, T. Mikeska, M. Paulsen, J. Walter, T. Lengauer
BiQ Analyzer: Visulaization and quality control for DNA methylation data from bisulphite sequencing
Bioinformatics 21, 21 (2005) 4067-4068

J. Bojunga, C. Welsch, I. Antes, M. Albrecht, T. Lengauer, S. Zeuzem
Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency
Human Genetics 117, 6 (2005) 558-564

M. Ralser, U. Nonhoff, M. Albrecht, T. Lengauer, E.E. Wanker, H. Lehrach, S. Krobitsch
Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways
Human Molecular Genetics 14, 19 (2005) 2893-2909

S. Castellano, A.V. Lobanov, C. Chapple, S.V. Novolesov, M. Albrecht, D. Hua, A. Lescure, T. Lengauer, A. Krol, V.N. Gladyshev, R. Guigo
Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the novel SelJ family
Proceedings of the National Academy of Sciences 102, 45 (2005) 16188-16193

M. Albrecht, T. Lengauer
Survey on PABC recognition motif PAM2
Biochem. Biophys .Res. Comm. 316, 1 (2004) 129-138

M. Stoll, B. Corneliussen, C.M. Costello, G.H. Waetzig, B. Mellgard, W.A. Koch, P. Rosenstiel, M. Albrecht, P.J.P. Croucher, d. Seegert, s. Nikolaus, J. Hampe, T. Lengaur, S. Pierrou, U.R. Foelsch, C.G. Mathew, M. Lagerstrom-Fermer, S. Schreiber
Generic variation in DLF5 confers susceptibility to inflammatory bowel disease
Nature Genetics 36, 5 (2004) 476-480

I. Sommer, J. Rahnenführer, F.S. Domingues, U. de Lichtenberg, T. Lengauer
Predicting protein structure classes from function predictions
Bioinformatics 20, 5 (2004) 770-776

N. von Öhsen, I. Sommer, R. Zimmer, T. Lengauer
Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures
Bioinformatics 20, 14 (2004) 2228-2235

M. Albrecht, M. Golatta, U. Wüllner, T. Lengauer
Structural and functional analysis of Ataxin-2 and Ataxin-3
European Journal of Biochemistry 271, 15 (2004) 3155-3170

A. Hannemann, J. C. Schön, M. Jansen, H. Putz, T. Lengauer
Modelling amorphous Si3B3N7,: Structure and elastic properties
Physical Review B 70, 14 144201 (2004)

F. Domingues, J. Rahnenführer, T. Lengauer
Automated clustering of ensembles of alternative models in protein structure databases
Protein Engineering, Design and Selection 17, 6 (2004) 537-543

C. Merkwirth, H. Mauser, T. Schulz-Gasch, O. Roche, M. Stahl, T. Lengauer
Ensemble methods for classification in cheminformatics
Journal Chemical Information and Computer Science 44,6 (2004) 1971-1978

J. Rahnenführer, F.S. Domingues, J. Maydt, T. Lengauer
Calculating the statistical significance of changes in pathway activity from gene expression data
Statistical Applications in Genetics and Molecular Biology 3, 1 (2004) Article 16.

M. Albrecht, T. Lengauer
Novel Sm-like proteins with long C-terminal tails and associated methyl tranferases
FEBS Letters 569, 1-3 (2004 18-26

W.P. Hofmann, E. Herrmann, B. Kronenberger, c. Merkwirth, C. Welsch, T. Lengauer, S. Zeuzem, C. Sarrazin
Association of HCV-related mixed cryoglobulinemia with specific mutational patterns of the HCV E2 protein and CD81 expression on peripheral B lymphocytes
Blood 104, 4 (2004) 1228-1229.

M. Albrecht, F.S. Domingues, S. Schreiber, T. Lengauer,
Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2
FEBS Letters 554 3 (2003) 520-528.

M. Albrecht, F.S. Domingues, S. Schreiber, T. Lengauer,
Identification of mammalian orthologs associates PYPAF5 with distinct functional roles
FEBS Letters 538 1-3 (2003) 173-177.

P. Talwar, C. Wittmann, E. Heinzle, T. Lengauer
Software tool for automated processing of 13C labeling data from mass spectrometric data
BioTechniques 35, 6 (2003)

M. Albrecht, T. Lengauer, S. Schreiber,
Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence
FEBS Letters 538 (2003) 173-177.

N. Beerenwinkel, M. Däumer, M. Oette, K. Korn, D. Hoffmann, R. Kaiser, T. Lengauer, J. Selbig, H. Walter,
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes
Nucleic Acids Res. 31, 13 (2003) 3850-3855.

A. Zien, J. Fluck, R. Zimmer. T. Lengauer,
Microrarrays: How many do you need?
Journal of Computational Biology 10, 3-4 (2003) 653-667.

M. Albrecht, D. Hoffmann, B. O. Evert, I. Schmitt, U. Wüllner, T. Lengauer,
Structural Modeling of Ataxin-3 reveals distant homology to adaptins
Proteins: Structure, Function and Genetics 50, 2 (2002) 355-370.

I. Sommer, A. Zien, N. von Öhsen, R. Zimmer, T. Lengauer,
Confidence Measures for Protein Fold Recognition
Bioinformatics 18, 6, (2002) 802-12.

S. Hindle, M. Rarey, C. Buning, T. Lengauer,
Flexible Docking Under Pharmacophore Constraint
Journal of Computer-Aided Molecular Design 16, 2, (2002), 129-149.

N. Beerenwinkel, B. Schmidt, H. Walter, R. Kaiser, T. Lengauer, D. Hoffmann, K. Korn, J. Selbig,
Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype
Proceedings of the National Academy of Sciences 99, 12 (2002) 8271-8276.

D. Hanisch, R. Zimmer, T. Lengauer,
ProML - the Protein Markup Language for specification of protein sequences, structures and families,
In Silico Biology 2, 0029 (2002).

M. Albrecht, D. Hanisch, R. Zimmer, T. Lengauer,
Improving fold recognition of protein threading by experimental distance constraints,
In Silico Biology 2, 0030 (2002).

J. Freudenberg, R. Zimmer, T. Lengauer,
A hypergraph-based method for unification of existing protein structure- and sequence-families
In Silico Biology 2, 0031 (2002).

N. Beerenwinkel, B. Schmidt, H. Walter, R. Kaiser, T. Lengauer, D. Hoffmann, K. Korn, J. Selbig,
Geno2pheno: a new machine learning approach to predicting phenotypic drug resistance from genotype
Antiviral Therapy 6 (Supplement 1) (2001) 104.

N. Beerenwinkel, B. Schmidt, H. Walter, R. Kaiser, T. Lengauer, D. Hoffmann, K. Korn, J. Selbig,
Geno2pheno: A system for the interpretation of genotypic HIV drug resistance tests
IEEE Intelligent Systems 16, 6 (2001) 35-41.

M. Schäfer, T. Lengauer,
Automated Layout Generation and Wiring Area Estimation for 3D Electronic Modules
ASME Journal of Mechanical Design 123, 3 (2001) 330-336.

T. Lengauer, M. Lügering,
Provably Good Global Routing of Integrated Circuits
SIAM Journal on Optimization 11, 1 (2001), 1-30.

H. Claußen, C. Buning, M. Rarey, T. Lengauer,
FlexE: efficient molecular docking considering protein structure variations
Journal of Molecular Biology 308, 2 (2001) 377-395.

C. Lemmen, M. Zimmermann, T. Lengauer,
Molecular Superpositioning as an Effective Tool for Virtual Database Screening
Perspectives in Drug Discovery and Design 20, 1 (2000) 43-62.

A. Zien, R. Zimmer, T. Lengauer,
A Simple Iterative Approach to Parameter Optimization
Journal of Computational Biology (2000) 7, 3/4 (2000) 483-501.

R. Küffner, A. Zien, R. Zimmer, T. Lengauer,
Pathway analysis in metabolic databases via Differential Metabolic Display (DMD)
Bioinformatics 16, 9 (2000) 825-836.

A. Zien, G. Rätsch, S. Mika, T. Lengauer, K. Müller,
Engineering Support Vector Machines Kernels That Recognize Translation Initiation Sites
Bioinformatics 16, 9 (2000) 799-807.

M. Rarey, T. Lengauer,
A Recursive Algorithm for Efficient Combinatorial Library Docking
Perspectives of Drug Discovery and Design 20, 1 (2000) 63-81.

C. Lemmen, T. Lengauer,
Computational Methods for the Structural Alignment of Molecules
Journal of Computer-Aided Molecular Design 14, 3 (2000) 215-232.

J. Selbig, T. Mevissen, T. Lengauer,
Decision Tree-based Formation of Consensus Protein Secondary Structure Prediction
Bioinformatics 15, 12 (1999) 1039-1046.

B. Kramer, G. Metz, M. Rarey, T. Lengauer,
Ligand Docking and Screening With FlexX
Medical Chemistry Research 9, 7/8 (1999) 463-478.

D. Hoffmann, B. Kramer, T. Washio, T. Steinmetzer, M. Rarey, T. Lengauer,
Two-stage Method for Protein Ligand Docking
Journal of Medicinal Chemistry 42 (1999) 4422-4433.

R. Thiele, R. Zimmer, T. Lengauer,
Protein Threading by Recursive Dynamic Programming
Journal of Molecular Biology 290 (1999) 757-779.

D. Hofmann, T. Lengauer,
Prediction of Crystal Structures of Organic Molecules
Journal of Molecular Structure 474 (1999) 13-23.

B. Kramer, M. Rarey, T. Lengauer,
Evaluation of the FlexX Incremental Construction Algorithm for Protein-Ligand Docking
PROTEINS: Structure, Function and Genetics 37 (1999) 228-241.

M. Rarey, B. Kramer, T. Lengauer,
Docking of Hydrophobic Ligands With Interaction-based Matching Algorithms
Bioinformatics 15, 3 (1999) 243-250.

M. Rarey, B. Kramer, T. Lengauer,
The Particle Concept: Placing Discrete Water Molecules During Protein-Ligand Docking Predictions
PROTEINS: Structure, Functions and Genetics 34 (1999) 17-28.

C. Lemmen, T. Lengauer, G. Klebe,
FlexS: A Method for Fast Flexible Ligand Superposition
Journal of Medicinal Chemistry 41,23 (1998) 4502-4520.

C. Lemmen, C. Hiller, T. Lengauer,
RigFit: A New Approach to Superimposing Ligand Molecules
Journal of Computer-Aided Molecular Design 12,5 (1998) 491-502.

R. Heckmann, T. Lengauer,
Computing Upper and Lower Bounds on Textile Nesting Problems
European Journal of Operational Research 108,3 (1998) 473-489.

D. Hofmann, T. Lengauer,
Crystal Structure Prediction based on Statistical Potentials
Journal of Molecular Modeling 4 (1998) 132-144.

D. Hofmann, T. Lengauer,
A Discrete Algorithm for Crystal Structure Prediction of Organic Molecules
Acta Crystallographica A53 (1997) 225-235.

C. Lemmen, T. Lengauer,
Time-Efficient Flexible Superposition of Medium-Sized Molecules
Journal of Computer-Aided Molecular Design 11,4 (1997) 357-368.

M. Rarey, B. Kramer, T. Lengauer,
Multiple Automatic Base Selection: Protein-Ligand Docking Based on Incremental Construction without Manual Intervention
Journal of Computer-Aided Molecular Design 11,4 (1997) 369-384.

B. Kramer, M. Rarey, T. Lengauer,
CASP-2 Experiences With Docking Flexible Ligands Using FlexX
PROTEINS: Structure, Function, and Genetics, Suppl. 1 (1997) 221-225.


Invited papers

F. S. Domingues, T. Lengauer,
Finding Protein Function from Sequence and Structure Data
Applied Bioinformatics 2,1 (2003) 3-12.

T. Lengauer, M. Schäfer,
Combinatorial Optimization Techniques for Three-Dimensional Arrangement Problems, in Mathematics - Key Technology for the Future
(W. Jäger, H.-J. Krebs, eds.), Springer Verlag, Heidelberg (2003) 63-73.

T. Lengauer,
Computational Biology at the Beginning of the Postgenomic Era
Symposium "Dagstuhl, 10 Years", R. Wilhelm, ed., Springer Lecture Notes in Computer Science No.2000 (2000)

T. Lengauer, R. Zimmer,
Structure Prediction Methods for Drug Design
Briefings in Bioinformatics 1,3 (2000) 275-288.

T. Lengauer,
Computational Biology - Algorithms and More
Proceedings of the Eighth European Symposium on Algorithms (ESA 2000), M. Paterson, ed., Springer Lecture Notes in Computer Science No.1879 (2000) 9-19.

T. Lengauer,
The Flex Approach - An Alternative for Receptor-Ligand Docking and Computing Crystal Conformations
Chapter 25 of Computer-Assisted Lead Finding and Optimization - Current Tools for Medicinal Chemistry (H. van de Waterbeemd, B. Testa, G. Folkers, Hrsg.), Verlag Helvetica Acta, Basel, Switzerland(1997) 399-420.

T. Lengauer,
Molekulare Bioinformatik: Eine interdisziplinäre Herausforderung
In: Highlights der Informatik (I. Wegener Hrsg.), Springer Verlag, Heidelberg (1996).

T. Lengauer, M. Rarey,
Methods for Predicting Molecular Complexes Involving Proteins
Current Opinion in Structural Biology 5 (1996).


Articles in refereed conference proceedings that have not appeared in journals

N. Beerenwinkel, J. Rahnenführer, M. Däumer, D. Hoffmann, R. Kaiser, J. Selbig, T. Lengauer
Learning multiple evolutionary pathways from cross-sectional data
Proceeding of the Eighth Annual Conference on Computational Biology (RECOMB 2004) (2004) 36-44.

N. Beerenwinkel, T. Lengauer, M. Däumer, R. Kaiser, H. Walter, K. Korn, D. Hoffmann, J. Selbig,
Methods for optimizing antiviral combination therapies
to appear in Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology (ISMB2003) (2003), in Bioinformatics 19, Suppl. 1 (2003) i16-i25.

D. Hanisch, A. Zien, R. Zimmer, T. Lengauer,
Co-clustering of biological networks and gene expression data
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB2002) (2002).

N. Beerenwinkel, B. Schmidt, H. Walter, R. Kaiser, T. Lengauer, D. HOffmann, K. Korn, J. Selbig
Identifying drug resistance-associated patterns in HIV genotypes
Proceedings of the German Conference on Bioinformatics (2001) 126-130.

H. Claußen, C. Buning, M. Rarey, T. Lengauer,
Molecular Docking into the Flexible Active Site of Aldose Reductase Using FlexE
Rational Approaches to Drug Design: Proceedings of 13th European Symposium on Quantitative Structure-Activity Relationships, Prous Science, Barcelona (2001) 324-333.

J. Apostolakis, D. Hofmann, T. Lengauer,
Using simple learning machines to derive a new potential for modeling
Rational Approaches to Drug Design: Proceedings of 13th European Symposium on Quantitative Structure-Activity Relationships, Prous Science, Barcelona (2001) 125-134.

A. Zien, T. Aigner, R. Zimmer, T. Lengauer,
Centralization: A biologically sensible method for the normalization of gene expression data
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB2001), Bioinformatics, Vol. 17 Suppl. 1 (2001) 323-331.

A. Zien, R. Küffner, R. Zimmer., T. Lengauer,
Analysis of Gene Expression Data With Pathway Scores
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (ISMB2000), AAAI Press (2000) 407-417.

C. Lemmen, A. Zien, R. Zimmer, T. Lengauer,
Application of Parameter Optimization to Molecular Comparison Problems
Pacific Symposium on Biocomputing (PSB'99), World Scientific, New Jersey (1999) 482-493.

C. Lemmen, T. Lengauer,
Fragment-based Screening of Ligand Databases
Proceedings of EURO-QSAR'98 (1998).

M. Peinado, T. Lengauer,
Random generation of Embedded Graphs and an Extension to Dobrushin Uniqueness
Proceedings of the Thirtieth Annual ACM Symposium on Theory of Computing, ACM Press (1998) 176-185.

M. Peinado, T. Lengauer,
'Go with the Winners': Generators with Applications to Molecular Modeling
Proceedings of the 1st International Workshop on Randomization and Approximation Techniques in Computer Science (Random'97) (J. Rolim, ed.), Springer Lecture Notes in Computer Science No. 1269 (1997) 135-149.

M. Peinado, T. Lengauer,
'Go with the Winners': Generators with Applications to Molecular Modeling
Proceedings of Random'97, Springer Lecture Notes in Computer Science (1997).

M. Peinado T. Lengauer,
Parallel 'Go With the Winners' Algorithms in the LogP Model
Proceedings of the 11th International ParallelProcessing Symposium, IEEE Computer Society Press, Los Alamitos, California (1997), 656-664.

I. Koch, T. Lengauer,
Detection of Distant Structural Similarities in a Set of Proteins Using an Efficient Graph-Based Algorithm
Fifth International Symposium on Intelligent Systems for Molecular Biology, AAAI Press (1997).

R. Zimmer, T. Lengauer,
Fast and Numerically Stable Parametric Alignment of Biosequences
Proceedings of the First Annual Conference on Research in Computational Molecular Biology (RECOMB'97) (1997), 344-353.

M. Rarey, B. Kramer, C. Bernd, T. Lengauer
Time-efficient docking of similar flexible ligands
Biocomputing: Proceedings of the 1996 Pacific Symposium (L. Hunter, T. Klein, eds.), World-Scientific Puclishing Co. Singapore (1996).

E. Frank, T. Lengauer
APPlaUSE: Area and Performance Optimization in a unified Placement and systhesis environment
Proceedings of the International Conference on Computer-Aided Design (ICCAD) (1995) 662-667

H. Schmidt, D. Theune, R. Thiele, T. Lengauer
EMC-driven midway routing on PCBs.
Proceedings of the European Design and Test Conference (EDAC-ETC'95) (1995) 486-491.

M. Rarey, B. Kramer, T. Lengauer
Time-efficient docking of flexible ligands into active sites of proteins
Third International Symposium on Intelligent Systems for Molecular Biology (c. Rawlings et al., eds.), AAAI Press, Menlo Park, CA (1995) 300-308.

R. Thiele, R. Zimmer, T. Lengauer
Recursive dynamic programming for adaptive sequence and structure alignment
Third International Symposium on Intelligent Systems for Moledular Biology (C. Rawlings et al., eds.), AAAI Press, Menlo Park, CA (1995) 384-392.