Thomas Lengauer

Thomas Lengauer

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Thomas Lengauer

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Near-Neighbor Interactions in the NS3-4A Protease of HCV Impact Replicative Fitness of Drug-Resistant Viral Variants.

J Mol Biol 2019 May 30;431(12):2354-2368. Epub 2019 Apr 30.

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany; Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt a.M., Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00222836193024
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http://dx.doi.org/10.1016/j.jmb.2019.04.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6554042PMC
May 2019

Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes.

J Chem Theory Comput 2019 Apr 6;15(4):2166-2178. Epub 2019 Mar 6.

Computational Biology Research Group , Max Planck Institute for Informatics , Saarland Informatics Campus, Campus E1 4 , 66123 Saarbrücken , Germany.

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http://dx.doi.org/10.1021/acs.jctc.8b01074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728065PMC
April 2019

RnBeads 2.0: comprehensive analysis of DNA methylation data.

Genome Biol 2019 03 14;20(1):55. Epub 2019 Mar 14.

Max Planck Institute for Informatics, Saarland Informatics Campus, 66123, Saarbrücken, Germany.

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http://dx.doi.org/10.1186/s13059-019-1664-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419383PMC
March 2019

geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data.

Nucleic Acids Res 2018 07;46(W1):W271-W277

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/nar/gky349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031006PMC
July 2018

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.

Bioinformatics 2017 09;33(18):2968

International Society for Computational Biology, Inc. (ISCB), 9650 Rockville Pike Bethesda, Maryland 20814, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870847PMC
September 2017

Using drug exposure for predicting drug resistance - A data-driven genotypic interpretation tool.

PLoS One 2017 10;12(4):e0174992. Epub 2017 Apr 10.

Department of Computational Biology and Applied Algorithmics, Max-Planck-Institut für Informatik, Saarbrücken, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0174992PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386274PMC
August 2017

Results of the first international HIV-1 coreceptor proficiency panel test.

J Clin Virol 2017 08 10;93:53-56. Epub 2017 Jun 10.

Institute of Virology, University of Cologne, 50935 Cologne, Germany.

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http://dx.doi.org/10.1016/j.jcv.2017.06.002DOI Listing
August 2017

Geno2pheno[HCV] - A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents.

PLoS One 2016 19;11(5):e0155869. Epub 2016 May 19.

German Center for Infection Research (DZIF)-Saarbrücken Partner Site, Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155869PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873220PMC
July 2017

DeepBlueR: large-scale epigenomic analysis in R.

Bioinformatics 2017 Jul;33(13):2063-2064

Max Planck Institute for Informatics.

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http://dx.doi.org/10.1093/bioinformatics/btx099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870546PMC
July 2017

Determination of Phenotypic Resistance Cutoffs From Routine Clinical Data.

J Acquir Immune Defic Syndr 2017 04;74(5):e129-e137

*Department of Computational Biology and Applied Algorithmics, Max-Planck-Institut für Informatik, Saarbrücken, Germany; †Medizinisches Infektiologiezentrum Berlin, Berlin, Germany; ‡Medizinisches Labor Stendal, Stendal, Germany; §Institute for Virology, University Clinic of Cologne, Germany; ‖Institute of Virology, University of Düsseldorf, Germany; and ¶Clinic of Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy.

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http://dx.doi.org/10.1097/QAI.0000000000001198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351752PMC
April 2017

Elucidating the energetic contributions to the binding free energy.

J Chem Phys 2017 Jan;146(1):014105

Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus E1 4, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1063/1.4973349DOI Listing
January 2017

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation.

Cell Stem Cell 2016 12 17;19(6):808-822. Epub 2016 Nov 17.

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.10.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5145815PMC
December 2016

A genotypic method for determining HIV-2 coreceptor usage enables epidemiological studies and clinical decision support.

Retrovirology 2016 Dec 20;13(1):85. Epub 2016 Dec 20.

Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Campus E 1 4, 66123, Saarbrücken, Germany.

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http://dx.doi.org/10.1186/s12977-016-0320-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5168878PMC
December 2016

Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees.

Mol Biol Evol 2016 10 19;33(10):2720-34. Epub 2016 Jul 19.

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/molbev/msw123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026249PMC
October 2016

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.

Nucleic Acids Res 2016 Jul 15;44(W1):W581-6. Epub 2016 Apr 15.

Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/nar/gkw211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987868PMC
July 2016

Proviral DNA as a Target for HIV-1 Resistance Analysis.

Intervirology 2015 27;58(3):184-9. Epub 2015 Jun 27.

Institute of Virology, University of Cologne, Cologne, Germany.

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http://dx.doi.org/10.1159/000431093DOI Listing
June 2016

A general concept for consistent documentation of computational analyses.

Database (Oxford) 2015 8;2015:bav050. Epub 2015 Jun 8.

Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany Graduate School of Computer Science, Saarland University, Saarbrücken, Germany Department of Genetics, Saarland University, Saarbrücken, Germany and Cluster of Excellence on Multimodal Computing and Interaction, Saarland University, Saarbrücken, Germany Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany Graduate School of Computer Science, Saarland University, Saarbrücken, Germany Department of Genetics, Saarland University, Saarbrücken, Germany and Cluster of Excellence on Multimodal Computing and Interaction, Saarland University, Saarbrücken, Germany

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http://dx.doi.org/10.1093/database/bav050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460408PMC
March 2016

The Role of Conformational Changes in Molecular Recognition.

J Phys Chem B 2016 Mar 1;120(9):2138-44. Epub 2016 Mar 1.

Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics , Campus E1 4, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1021/acs.jpcb.5b11593DOI Listing
March 2016

Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences.

J Int AIDS Soc 2014 2;17(4 Suppl 3):19743. Epub 2014 Nov 2.

Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4225326PMC
http://dx.doi.org/10.7448/IAS.17.4.19743DOI Listing
January 2016

Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses.

Viruses 2015 Oct 19;7(10):5388-409. Epub 2015 Oct 19.

Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany.

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http://www.mdpi.com/1999-4915/7/10/2882
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http://dx.doi.org/10.3390/v7102882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632390PMC
October 2015

How Molecular Conformational Changes Affect Changes in Free Energy.

J Chem Theory Comput 2015 Jul;11(7):2945-57

Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics , Campus E1 4, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1021/acs.jctc.5b00235DOI Listing
July 2015

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.

F1000Res 2015 15;4:12. Epub 2015 Jan 15.

International Society for Computational Biology, La Jolla, CA, USA ; Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA.

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http://dx.doi.org/10.12688/f1000research.6038.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457108PMC
June 2015

Effects of sequence alterations on results from genotypic tropism testing.

J Clin Virol 2015 Apr 10;65:68-73. Epub 2015 Feb 10.

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E 14, 66123 Saarbrücken,Germany.

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http://dx.doi.org/10.1016/j.jcv.2015.02.006DOI Listing
April 2015

Enthalpy-Entropy Compensation upon Molecular Conformational Changes.

J Chem Theory Comput 2015 Apr 11;11(4):1410-8. Epub 2015 Mar 11.

Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics , Campus E1 4, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1021/ct501161tDOI Listing
April 2015

Inferring short-range linkage information from sequencing chromatograms.

PLoS One 2013 20;8(12):e81687. Epub 2013 Dec 20.

Department of Computational Biology and Applied Algorithms, Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081687PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869653PMC
March 2015

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.

Bioinformatics 2015 Feb 2;31(4):616-7. Epub 2015 Feb 2.

International Society for Computational Biology, La Jolla, CA, USA, SRI International, Menlo Park, CA, USA, Department of Mathematics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA, Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbruecken, Germany, Hebrew University & Institute of Advanced Studies, Jerusalem, Israel, Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA, Department of Immunology and Infectious Disease, Harvard School of Public Health, Cambridge, MA, USA, Broad Institute of Harvard and MIT, Cambridge, MA, USA, Sheffield Institute for Translational Neuroscience, Harvard School of Public Health, Boston, MA, USA, Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany and Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA International Society for Computational Biology, La Jolla, CA, USA, SRI International, Menlo Park, CA, USA, Department of Mathematics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA, Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbruecken, Germany, Hebrew University & Institute of Advanced Studies, Jerusalem, Israel, Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA, Department of Immunology and Infectious Disease, Harvard School of Public Health, Cambridge, MA, USA, Broad Institute of Harvard and MIT, Cambridge, MA, USA, Sheffield Institute for Translational Neuroscience, Harvard School of Public Health, Boston, MA, USA, Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany and Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA International Society for Computational Biology, La Jolla, CA, USA, SRI International, Menlo Park, CA, USA, Department o

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http://dx.doi.org/10.1093/bioinformatics/btv019DOI Listing
February 2015

How to write a presubmission inquiry.

PLoS Comput Biol 2015 Feb 26;11(2):e1004098. Epub 2015 Feb 26.

Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.

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http://dx.doi.org/10.1371/journal.pcbi.1004098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342337PMC
February 2015

Comprehensive analysis of DNA methylation data with RnBeads.

Nat Methods 2014 Nov 28;11(11):1138-1140. Epub 2014 Sep 28.

Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1038/nmeth.3115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216143PMC
November 2014

Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies.

J Acquir Immune Defic Syndr 2014 Oct;67(2):107-12

*Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany; and †MVZ Medizinisches Infektiologiezentrum Berlin, Berlin, Germany.

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http://dx.doi.org/10.1097/QAI.0000000000000283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175123PMC
October 2014

BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.

Nucleic Acids Res 2014 Jul 29;42(Web Server issue):W501-7. Epub 2014 May 29.

Department of Genetics, Saarland University, Saarbrücken 66123, Germany

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http://dx.doi.org/10.1093/nar/gku457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086109PMC
July 2014

Sensitive detection of viral transcripts in human tumor transcriptomes.

PLoS Comput Biol 2013 3;9(10):e1003228. Epub 2013 Oct 3.

Max-Planck-Institute for Informatics, Campus E1.4, Saarbrücken, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1003228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789765PMC
May 2014

Efficient computation of root mean square deviations under rigid transformations.

J Comput Chem 2014 Apr 19;35(10):765-71. Epub 2013 Dec 19.

Institute for Informatics, Johannes-Gutenberg-University Mainz, Mainz, 55128, Germany.

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http://dx.doi.org/10.1002/jcc.23513DOI Listing
April 2014

Personalized HIV therapy to control drug resistance.

Drug Discov Today Technol 2014 Mar;11:57-64

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http://dx.doi.org/10.1016/j.ddtec.2014.02.004DOI Listing
March 2014

Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage.

PLoS Comput Biol 2013 21;9(3):e1002977. Epub 2013 Mar 21.

Max Planck Institute for Computer Science, Saarbrucken, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1002977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605109PMC
November 2013

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 2013 Nov 11;10:130. Epub 2013 Nov 11.

Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, Saarbrücken 66123, Germany.

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http://dx.doi.org/10.1186/1742-4690-10-130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833284PMC
November 2013

A method for finding consensus breakpoints in the cancer genome from copy number data.

Bioinformatics 2013 Jul 28;29(14):1793-800. Epub 2013 May 28.

Department of Computational Biology and Applied Algorithmics, Max-Planck-Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btt300DOI Listing
July 2013

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues.

Epigenetics 2012 Dec 18;7(12):1355-67. Epub 2012 Oct 18.

Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.

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http://dx.doi.org/10.4161/epi.22562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528691PMC
December 2012

Genotyping hepatitis B virus dual infections using population-based sequence data.

J Gen Virol 2012 Sep 13;93(Pt 9):1899-907. Epub 2012 Jun 13.

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1099/vir.0.043042-0DOI Listing
September 2012

Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data.

Bioinformatics 2012 Sep;28(18):i589-i595

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436800PMC
September 2012

Endogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort.

Med Microbiol Immunol 2012 Aug 20;201(3):259-69. Epub 2012 Jan 20.

Department of Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1007/s00430-011-0228-8DOI Listing
August 2012

Hierarchical Bayes model for predicting effectiveness of HIV combination therapies.

Stat Appl Genet Mol Biol 2012 ;11(3):Article 11

Max-Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1515/1544-6115.1769DOI Listing
August 2012

An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data.

Retrovirology 2012 Jul 25;9:60. Epub 2012 Jul 25.

Department of Computational Biology and Applied Algorithmics, Max Planck for Computer Sciences, Campus E1 4 66123, Saarbrücken, Germany.

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http://dx.doi.org/10.1186/1742-4690-9-60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464718PMC
July 2012

Managing drug resistance in cancer: lessons from HIV therapy.

Nat Rev Cancer 2012 06 7;12(7):494-501. Epub 2012 Jun 7.

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

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http://dx.doi.org/10.1038/nrc3297DOI Listing
June 2012

Bioinformatical assistance of selecting anti-HIV therapies: where do we stand?

Authors:
Thomas Lengauer

Intervirology 2012 24;55(2):108-12. Epub 2012 Jan 24.

Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1159/000332000DOI Listing
May 2012

Geno2pheno[454]: a Web server for the prediction of HIV-1 coreceptor usage from next-generation sequencing data.

Intervirology 2012 24;55(2):113-7. Epub 2012 Jan 24.

Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1159/000332002DOI Listing
May 2012

Risk factors associated with older age in treatment-naive HIV-positive patients.

Intervirology 2012 24;55(2):147-53. Epub 2012 Jan 24.

Clinic for Gastroenterology, Hepatology and Infectious Diseases, University Hospital, Düsseldorf, Germany.

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http://dx.doi.org/10.1159/000332014DOI Listing
May 2012

Epidemiology of transmitted drug resistance in chronically HIV-infected patients in Germany: the RESINA study 2001-2009.

Intervirology 2012 24;55(2):154-9. Epub 2012 Jan 24.

Clinic for General Medicine, Gastroenterology and Infectious Diseases, Augustinerinnen Hospital, Cologne, Germany.

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http://dx.doi.org/10.1159/000332015DOI Listing
May 2012

Peptidomimetic escape mechanisms arise via genetic diversity in the ligand-binding site of the hepatitis C virus NS3/4A serine protease.

Gastroenterology 2012 Mar 7;142(3):654-63. Epub 2011 Dec 7.

Division of Infectious Diseases, Department of Medicine, Inflammatory Diseases Institute, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599--7292, USA.

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http://dx.doi.org/10.1053/j.gastro.2011.11.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288278PMC
March 2012

On the applicability of elastic network normal modes in small-molecule docking.

J Chem Inf Model 2012 Mar 23;52(3):844-56. Epub 2012 Feb 23.

Max-Planck-Institut für Informatik, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1021/ci2004847DOI Listing
March 2012

APOBEC3G/F as one possible driving force for co-receptor switch of the human immunodeficiency virus-1.

Med Microbiol Immunol 2012 Feb 15;201(1):7-16. Epub 2011 May 15.

University of Cologne, Cologne, Germany.

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http://dx.doi.org/10.1007/s00430-011-0199-9DOI Listing
February 2012

MicroRNA transcription start site prediction with multi-objective feature selection.

Stat Appl Genet Mol Biol 2012 Jan 6;11(1):Article 6. Epub 2012 Jan 6.

Indian Statistical Institute, Kolkata.

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http://dx.doi.org/10.2202/1544-6115.1743DOI Listing
January 2012

HIV prevalence and route of transmission in Turkish immigrants living in North-Rhine Westphalia, Germany.

Med Microbiol Immunol 2011 Nov 2;200(4):219-23. Epub 2011 Apr 2.

Institute of Virology, University of Cologne, Fürst-Pückler-Strasse 56, 50935 Cologne, Germany.

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http://link.springer.com/10.1007/s00430-011-0193-2
Publisher Site
http://dx.doi.org/10.1007/s00430-011-0193-2DOI Listing
November 2011

Preserving charge and oxidation state of Au(III) ions in an agent-functionalized nanocrystal model system.

ACS Nano 2011 Aug 18;5(8):6480-6. Epub 2011 Jul 18.

Institute of Semiconductor and Solid State Physics, Centre for Nanobionics and Photochemical Sciences (CNPS), Johannes Kepler University, 4040 Linz, Austria.

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http://dx.doi.org/10.1021/nn201708cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160148PMC
August 2011

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.

Nucleic Acids Res 2011 Jul 11;39(Web Server issue):W551-6. Epub 2011 May 11.

Department of Genetics/Epigenetics, Saarland University, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/nar/gkr312DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125748PMC
July 2011

Classification with correlated features: unreliability of feature ranking and solutions.

Bioinformatics 2011 Jul 16;27(14):1986-94. Epub 2011 May 16.

Department of Computational Biology and Applied Algorithmics, Max-Planck-Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr300DOI Listing
July 2011

HIV-1 mutational pathways under multidrug therapy.

AIDS Res Ther 2011 Jul 27;8:26. Epub 2011 Jul 27.

Department of Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1186/1742-6405-8-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3162516PMC
July 2011

Reconstructing the ancestral germ line methylation state of young repeats.

Mol Biol Evol 2011 Jun 6;28(6):1777-84. Epub 2011 Jan 6.

Computational Biology and Applied Algorithmics, Max Planck Institute für Informatik, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/molbev/msr001DOI Listing
June 2011

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.

BMC Med Inform Decis Mak 2011 May 13;11:30. Epub 2011 May 13.

Institute of Immunology and Genetics, Pfaffplatz 10, 67655 Kaiserslautern, Germany.

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http://dx.doi.org/10.1186/1472-6947-11-30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112379PMC
May 2011

Learning from past treatments and their outcome improves prediction of in vivo response to anti-HIV therapy.

Stat Appl Genet Mol Biol 2011 14;10:Article 6. Epub 2011 Jan 14.

Max Planck Institute for Informatics, Munich, Germany.

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http://dx.doi.org/10.2202/1544-6115.1604DOI Listing
April 2011

Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.

Med Microbiol Immunol 2011 Feb 19;200(1):39-49. Epub 2010 Sep 19.

Clinic of Gastroenterology, Hepatology and Infectious Diseases, University Hospital, Moorenstr. 5, 40225 Duesseldorf, Germany.

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http://dx.doi.org/10.1007/s00430-010-0172-zDOI Listing
February 2011

HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection.

J Hepatol 2010 Dec 3;53(6):1022-8. Epub 2010 Aug 3.

Klinikum der J.W. Goethe-Universität Frankfurt am Main, Medizinische Klinik 1, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.

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http://dx.doi.org/10.1016/j.jhep.2010.06.011DOI Listing
December 2010

Dealing with sparse data in predicting outcomes of HIV combination therapies.

Bioinformatics 2010 Sep 12;26(17):2085-92. Epub 2010 Jul 12.

Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken and Nokia Gate 5, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btq361DOI Listing
September 2010

Improving disease gene prioritization using the semantic similarity of Gene Ontology terms.

Bioinformatics 2010 Sep;26(18):i561-7

Max Planck Institute for Informatics, Department of Computational Biology and Applied Algorithmics, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btq384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935448PMC
September 2010

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.

Nucleic Acids Res 2010 Jul 31;38(Web Server issue):W755-62. Epub 2010 May 31.

Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/nar/gkq405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896198PMC
July 2010

Positive selection of HIV host factors and the evolution of lentivirus genes.

BMC Evol Biol 2010 Jun 18;10:186. Epub 2010 Jun 18.

Max Planck Institute for Informatics Computational Biology and Applied Algorithmics, Campus E1 4, 66123 SaarbrA(1/4)cken, Germany.

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http://link.springer.com/content/pdf/10.1186%2F1471-2148-10-
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http://dx.doi.org/10.1186/1471-2148-10-186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906474PMC
June 2010

Permutation importance: a corrected feature importance measure.

Bioinformatics 2010 May 12;26(10):1340-7. Epub 2010 Apr 12.

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btq134DOI Listing
May 2010