Thomas Lengauer

Thomas Lengauer

UNVERIFIED PROFILE

Are you Thomas Lengauer?   Register this Author

Register author
Thomas Lengauer

Thomas Lengauer

Publications by authors named "Thomas Lengauer"

Are you Thomas Lengauer?   Register this Author

100Publications

2156Reads

38Profile Views

Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data.

Authors:
Karl J V Nordström Florian Schmidt Nina Gasparoni Abdulrahman Salhab Gilles Gasparoni Kathrin Kattler Fabian Müller Peter Ebert Ivan G Costa Nico Pfeifer Thomas Lengauer Marcel H Schulz Jörn Walter

Nucleic Acids Res 2019 Nov;47(20):10580-10596

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/nar/gkz799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6847574PMC
November 2019

Clinical use, efficacy, and durability of maraviroc for antiretroviral therapy in routine care: A European survey.

Authors:
Andrea De Luca Patrizio Pezzotti Charles Boucher Matthias Döring Francesca Incardona Rolf Kaiser Thomas Lengauer Nico Pfeifer Eugen Schülter Anne-Mieke Vandamme Maurizio Zazzi Anna Maria Geretti

PLoS One 2019 21;14(11):e0225381. Epub 2019 Nov 21.

Institute of Infection and Global Health, University of Liverpool, Liverpool, England, United Kingdom.

View Article

Download full-text PDF

 Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0225381PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874206PMC
November 2019

Soluble immune markers in the different phases of chronic hepatitis B virus infection.

Authors:
Steffen B Wiegand Bastian Beggel Anika Wranke Elmira Aliabadi Jerzy Jaroszewicz Cheng-Jian Xu Yang Li Michael P Manns Thomas Lengauer Heiner Wedemeyer Anke R M Kraft Christine S Falk Markus Cornberg

Sci Rep 2019 Oct 1;9(1):14118. Epub 2019 Oct 1.

Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41598-019-50729-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773856PMC
October 2019

Failure of Dolutegravir First-Line ART with Selection of Virus Carrying R263K and G118R.

Authors:
Nadine Lübke Björn Jensen Falk Hüttig Torsten Feldt Andreas Walker Alexander Thielen Martin Däumer Martin Obermeier Rolf Kaiser Elena Knops Eva Heger Saleta Sierra Mark Oette Thomas Lengauer Jörg Timm Dieter Häussinger

N Engl J Med 2019 08;381(9):887-889

Heinrich Heine University Hospital, Düsseldorf, Germany.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1056/NEJMc1806554DOI Listing
August 2019

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

Authors:
Nadezhda T Doncheva Francisco S Domingues David R McGivern Tetsuro Shimakami Stefan Zeuzem Thomas Lengauer Christian M Lange Mario Albrecht Christoph Welsch

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:

View Article

Download full-text PDF

 Source
https://linkinghub.elsevier.com/retrieve/pii/S00222836193024
Publisher Site
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.

Authors:
Mazen Ahmad Volkhard Helms Olga V Kalinina Thomas Lengauer

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Fabian Müller Michael Scherer Yassen Assenov Pavlo Lutsik Jörn Walter Thomas Lengauer Christoph Bock

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

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

View Article

Download full-text PDF

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

Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters.

Authors:
Fatemeh Behjati Ardakani Kathrin Kattler Karl Nordström Nina Gasparoni Gilles Gasparoni Sarah Fuchs Anupam Sinha Matthias Barann Peter Ebert Jonas Fischer Barbara Hutter Gideon Zipprich Charles D Imbusch Bärbel Felder Jürgen Eils Benedikt Brors Thomas Lengauer Thomas Manke Philip Rosenstiel Jörn Walter Marcel H Schulz

Epigenetics Chromatin 2018 11 10;11(1):66. Epub 2018 Nov 10.

Excellence Cluster for Multimodal Computing and Interaction, Saarland Informatics Campus, Saarland University, Campus E1 7, Saarbrücken, 66123, Germany.

View Article

Download full-text PDF

 Source
https://epigeneticsandchromatin.biomedcentral.com/articles/1
Publisher Site
http://dx.doi.org/10.1186/s13072-018-0236-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6230222PMC
November 2018

A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains.

Authors:
Abdulrahman Salhab Karl Nordström Gilles Gasparoni Kathrin Kattler Peter Ebert Fidel Ramirez Laura Arrigoni Fabian Müller Julia K Polansky Cristina Cadenas Jan G Hengstler Thomas Lengauer Thomas Manke Jörn Walter

Genome Biol 2018 09 28;19(1):150. Epub 2018 Sep 28.

Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany.

View Article

Download full-text PDF

 Source
https://genomebiology.biomedcentral.com/articles/10.1186/s13
Publisher Site
http://dx.doi.org/10.1186/s13059-018-1510-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161375PMC
September 2018

From hype to reality: data science enabling personalized medicine.

Authors:
Holger Fröhlich Rudi Balling Niko Beerenwinkel Oliver Kohlbacher Santosh Kumar Thomas Lengauer Marloes H Maathuis Yves Moreau Susan A Murphy Teresa M Przytycka Michael Rebhan Hannes Röst Andreas Schuppert Matthias Schwab Rainer Spang Daniel Stekhoven Jimeng Sun Andreas Weber Daniel Ziemek Blaz Zupan

BMC Med 2018 08 27;16(1):150. Epub 2018 Aug 27.

Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, SI-1000, Ljubljana, Slovenia.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/s12916-018-1122-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6109989PMC
August 2018

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

Authors:
Matthias Döring Joachim Büch Georg Friedrich Alejandro Pironti Prabhav Kalaghatgi Elena Knops Eva Heger Martin Obermeier Martin Däumer Alexander Thielen Rolf Kaiser Thomas Lengauer Nico Pfeifer

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.

View Article

Download full-text PDF

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

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development.

Authors:
Wei-Hung Pan Felix Sommer Maren Falk-Paulsen Thomas Ulas Philipp Best Antonella Fazio Priyadarshini Kachroo Anne Luzius Marlene Jentzsch Ateequr Rehman Fabian Müller Thomas Lengauer Jörn Walter Sven Künzel John F Baines Stefan Schreiber Andre Franke Joachim L Schultze Fredrik Bäckhed Philip Rosenstiel

Genome Med 2018 04 13;10(1):27. Epub 2018 Apr 13.

Institute for Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/s13073-018-0534-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5899322PMC
April 2018

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

Authors:
Bonnie Berger Theresa Gaasterland Thomas Lengauer Christine A Orengo Bruno Gaeta Scott Markel Alfonso Valencia

Bioinformatics 2017 09;33(18):2968

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

View Article

Download full-text PDF

 Source
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.

Authors:
Alejandro Pironti Nico Pfeifer Hauke Walter Björn-Erik O Jensen Maurizio Zazzi Perpétua Gomes Rolf Kaiser Thomas Lengauer

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Eva Heger Rolf Kaiser Elena Knops Maria Neumann-Fraune Eugen Schuelter Alejandro Pironti Thomas Lengauer Hauke Walter Saleta Sierra

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

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

View Article

Download full-text PDF

 Source
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.

Authors:
Prabhav Kalaghatgi Anna Maria Sikorski Elena Knops Daniel Rupp Saleta Sierra Eva Heger Maria Neumann-Fraune Bastian Beggel Andreas Walker Jörg Timm Hauke Walter Martin Obermeier Rolf Kaiser Ralf Bartenschlager Thomas Lengauer

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Felipe Albrecht Markus List Christoph Bock Thomas Lengauer

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

Max Planck Institute for Informatics.

View Article

Download full-text PDF

 Source
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.

Authors:
Alejandro Pironti Hauke Walter Nico Pfeifer Elena Knops Nadine Lübke Joachim Büch Simona Di Giambenedetto Rolf Kaiser Thomas Lengauer

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.

View Article

Download full-text PDF

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

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

Authors:
Florian Schmidt Nina Gasparoni Gilles Gasparoni Kathrin Gianmoena Cristina Cadenas Julia K Polansky Peter Ebert Karl Nordström Matthias Barann Anupam Sinha Sebastian Fröhler Jieyi Xiong Azim Dehghani Amirabad Fatemeh Behjati Ardakani Barbara Hutter Gideon Zipprich Bärbel Felder Jürgen Eils Benedikt Brors Wei Chen Jan G Hengstler Alf Hamann Thomas Lengauer Philip Rosenstiel Jörn Walter Marcel H Schulz

Nucleic Acids Res 2017 01 29;45(1):54-66. Epub 2016 Nov 29.

Cluster of Excellence for Multimodal Computing and Interaction, Saarland Informatics Campus, Saarland University, Saarbrücken, 66123, Germany

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/nar/gkw1061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224477PMC
January 2017

Elucidating the energetic contributions to the binding free energy.

Authors:
Mazen Ahmad Volkhard Helms Olga V Kalinina Thomas Lengauer

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.

View Article

Download full-text PDF

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

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation.

Authors:
Matthias Farlik Florian Halbritter Fabian Müller Fizzah A Choudry Peter Ebert Johanna Klughammer Samantha Farrow Antonella Santoro Valerio Ciaurro Anthony Mathur Rakesh Uppal Hendrik G Stunnenberg Willem H Ouwehand Elisa Laurenti Thomas Lengauer Mattia Frontini Christoph Bock

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:

View Article

Download full-text PDF

 Source
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.

Authors:
Matthias Döring Pedro Borrego Joachim Büch Andreia Martins Georg Friedrich Ricardo Jorge Camacho Josef Eberle Rolf Kaiser Thomas Lengauer Nuno Taveira Nico Pfeifer

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.

View Article

Download full-text PDF

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

Erratum to: Making sense of big data in health research: towards an EU action plan.

Authors:
Charles Auffray Rudi Balling Inês Barroso László Bencze Mikael Benson Jay Bergeron Enrique Bernal-Delgado Niklas Blomberg Christoph Bock Ana Conesa Susanna Del Signore Christophe Delogne Peter Devilee Alberto Di Meglio Marinus Eijkemans Paul Flicek Norbert Graf Vera Grimm Henk-Jan Guchelaar Yi-Ke Guo Ivo Glynne Gut Allan Hanbury Shahid Hanif Ralf-Dieter Hilgers Ángel Honrado D Rod Hose Jeanine Houwing-Duistermaat Tim Hubbard Sophie Helen Janacek Haralampos Karanikas Tim Kievits Manfred Kohler Andreas Kremer Jerry Lanfear Thomas Lengauer Edith Maes Theo Meert Werner Müller Dörthe Nickel Peter Oledzki Bertrand Pedersen Milan Petkovic Konstantinos Pliakos Magnus Rattray Josep Redón I Màs Reinhard Schneider Thierry Sengstag Xavier Serra-Picamal Wouter Spek Lea A I Vaas Okker van Batenburg Marc Vandelaer Peter Varnai Pablo Villoslada Juan Antonio Vizcaíno John Peter Mary Wubbe Gianluigi Zanetti

Genome Med 2016 11 7;8(1):118. Epub 2016 Nov 7.

CRS4, Ed.1 POLARIS, 09129, Pula, Italy.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/s13073-016-0376-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100330PMC
November 2016

Epigenomic Profiling of Human CD4 T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development.

Authors:
Pawel Durek Karl Nordström Gilles Gasparoni Abdulrahman Salhab Christopher Kressler Melanie de Almeida Kevin Bassler Thomas Ulas Florian Schmidt Jieyi Xiong Petar Glažar Filippos Klironomos Anupam Sinha Sarah Kinkley Xinyi Yang Laura Arrigoni Azim Dehghani Amirabad Fatemeh Behjati Ardakani Lars Feuerbach Oliver Gorka Peter Ebert Fabian Müller Na Li Stefan Frischbutter Stephan Schlickeiser Carla Cendon Sebastian Fröhler Bärbel Felder Nina Gasparoni Charles D Imbusch Barbara Hutter Gideon Zipprich Yvonne Tauchmann Simon Reinke Georgi Wassilew Ute Hoffmann Andreas S Richter Lina Sieverling Hyun-Dong Chang Uta Syrbe Ulrich Kalus Jürgen Eils Benedikt Brors Thomas Manke Jürgen Ruland Thomas Lengauer Nikolaus Rajewsky Wei Chen Jun Dong Birgit Sawitzki Ho-Ryun Chung Philip Rosenstiel Marcel H Schulz Joachim L Schultze Andreas Radbruch Jörn Walter Alf Hamann Julia K Polansky

Immunity 2016 11;45(5):1148-1161

Experimental Rheumatology, German Rheumatism Research Centre, 10117 Berlin, Germany. Electronic address:

View Article

Download full-text PDF

 Source
https://linkinghub.elsevier.com/retrieve/pii/S10747613163043
Publisher Site
http://dx.doi.org/10.1016/j.immuni.2016.10.022DOI Listing
November 2016

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

Authors:
Prabhav Kalaghatgi Nico Pfeifer Thomas Lengauer

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.

View Article

Download full-text PDF

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

Epigenetic dynamics of monocyte-to-macrophage differentiation.

Authors:
Stefan Wallner Christopher Schröder Elsa Leitão Tea Berulava Claudia Haak Daniela Beißer Sven Rahmann Andreas S Richter Thomas Manke Ulrike Bönisch Laura Arrigoni Sebastian Fröhler Filippos Klironomos Wei Chen Nikolaus Rajewsky Fabian Müller Peter Ebert Thomas Lengauer Matthias Barann Philip Rosenstiel Gilles Gasparoni Karl Nordström Jörn Walter Benedikt Brors Gideon Zipprich Bärbel Felder Ludger Klein-Hitpass Corinna Attenberger Gerd Schmitz Bernhard Horsthemke

Epigenetics Chromatin 2016 29;9:33. Epub 2016 Jul 29.

Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/s13072-016-0079-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4967341PMC
August 2016

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

Authors:
Felipe Albrecht Markus List Christoph Bock Thomas Lengauer

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

Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.

View Article

Download full-text PDF

 Source
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.

Authors:
Nadine Lübke Veronica Di Cristanziano Saleta Sierra Elena Knops Eugen Schülter Björn Jensen Mark Oette Thomas Lengauer Rolf Kaiser

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

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

View Article

Download full-text PDF

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

Making sense of big data in health research: Towards an EU action plan.

Authors:
Charles Auffray Rudi Balling Inês Barroso László Bencze Mikael Benson Jay Bergeron Enrique Bernal-Delgado Niklas Blomberg Christoph Bock Ana Conesa Susanna Del Signore Christophe Delogne Peter Devilee Alberto Di Meglio Marinus Eijkemans Paul Flicek Norbert Graf Vera Grimm Henk-Jan Guchelaar Yi-Ke Guo Ivo Glynne Gut Allan Hanbury Shahid Hanif Ralf-Dieter Hilgers Ángel Honrado D Rod Hose Jeanine Houwing-Duistermaat Tim Hubbard Sophie Helen Janacek Haralampos Karanikas Tim Kievits Manfred Kohler Andreas Kremer Jerry Lanfear Thomas Lengauer Edith Maes Theo Meert Werner Müller Dörthe Nickel Peter Oledzki Bertrand Pedersen Milan Petkovic Konstantinos Pliakos Magnus Rattray Josep Redón I Màs Reinhard Schneider Thierry Sengstag Xavier Serra-Picamal Wouter Spek Lea A I Vaas Okker van Batenburg Marc Vandelaer Peter Varnai Pablo Villoslada Juan Antonio Vizcaíno John Peter Mary Wubbe Gianluigi Zanetti

Genome Med 2016 06 23;8(1):71. Epub 2016 Jun 23.

CRS4, Ed.1 POLARIS, 09129, Pula, Italy.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/s13073-016-0323-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919856PMC
June 2016

A general concept for consistent documentation of computational analyses.

Authors:
Peter Ebert Fabian Müller Karl Nordström Thomas Lengauer Marcel H Schulz

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

View Article

Download full-text PDF

 Source
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.

Authors:
Mazen Ahmad Volkhard Helms Olga V Kalinina Thomas Lengauer

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.

View Article

Download full-text PDF

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

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

Authors:
Alfonso Valencia Scott Markel Bruno Gaeta Terry Gaasterland Thomas Lengauer Bonnie Berger Christine Orengo

F1000Res 2016 11;5. Epub 2016 Feb 11.

International Society for Computational Biology, Inc. (ISCB), Bethesda, MD, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.12688/f1000research.8051.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786891PMC
March 2016

ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing.

Authors:
Bonnie Berger Terry Gaasterland Thomas Lengauer Christine Orengo Bruno Gaeta Scott Markel Alfonso Valencia

PLoS Comput Biol 2016 Mar 24;12(3):e1004816. Epub 2016 Mar 24.

International Society for Computational Biology, Inc. (ISCB).

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1371/journal.pcbi.1004816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807037PMC
March 2016

Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc.

Authors:
Saleta Sierra J Nikolai Dybowski Alejandro Pironti Dominik Heider Lisa Güney Alex Thielen Stefan Reuter Stefan Esser Gerd Fätkenheuer Thomas Lengauer Daniel Hoffmann Herbert Pfister Björn Jensen Rolf Kaiser

PLoS One 2015 13;10(5):e0125502. Epub 2015 May 13.

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

View Article

Download full-text PDF

 Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125502PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430318PMC
February 2016

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

Authors:
Alejandro Pironti Nico Pfeifer Rolf Kaiser Hauke Walter Thomas Lengauer

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.

View Article

Download full-text PDF

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

Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces.

Authors:
Matthias Dietzen Olga V Kalinina Katerina Taškova Benny Kneissl Anna-Katharina Hildebrandt Elmar Jaenicke Heinz Decker Thomas Lengauer Andreas Hildebrandt

Proteins 2015 Oct 24;83(10):1887-99. Epub 2015 Aug 24.

Institute of Computer Science, Johannes Gutenberg University, Staudingerweg 9, Mainz, 55128, Germany.

View Article

Download full-text PDF

 Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049452PMC
http://dx.doi.org/10.1002/prot.24873DOI Listing
October 2015

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

Authors:
Silvia Caprari Saskia Metzler Thomas Lengauer Olga V Kalinina

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.

View Article

Download full-text PDF

 Source
http://www.mdpi.com/1999-4915/7/10/2882
Publisher Site
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.

Authors:
Mazen Ahmad Volkhard Helms Thomas Lengauer Olga V Kalinina

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Peter D Karp Bonnie Berger Diane Kovats Thomas Lengauer Michal Linial Pardis Sabeti Winston Hide Burkhard Rost

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Alejandro Pironti Saleta Sierra Rolf Kaiser Thomas Lengauer Nico Pfeifer

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.

View Article

Download full-text PDF

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

Enthalpy-Entropy Compensation upon Molecular Conformational Changes.

Authors:
Mazen Ahmad Volkhard Helms Thomas Lengauer Olga V Kalinina

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.

View Article

Download full-text PDF

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

Inferring short-range linkage information from sequencing chromatograms.

Authors:
Bastian Beggel Maria Neumann-Fraune Rolf Kaiser Jens Verheyen Thomas Lengauer

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Peter D Karp Bonnie Berger Diane Kovats Thomas Lengauer Michal Linial Pardis Sabeti Winston Hide Burkhard Rost

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

View Article

Download full-text PDF

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

How to write a presubmission inquiry.

Authors:
Thomas Lengauer Ruth Nussinov

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Yassen Assenov Fabian Müller Pavlo Lutsik Jörn Walter Thomas Lengauer Christoph Bock

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

Max Planck Institute for Informatics, Saarbrücken, Germany.

View Article

Download full-text PDF

 Source
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.

Authors:
Nico Pfeifer Hauke Walter Thomas Lengauer

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Daniel Becker Pavlo Lutsik Peter Ebert Christoph Bock Thomas Lengauer Jörn Walter

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

Department of Genetics, Saarland University, Saarbrücken 66123, Germany

View Article

Download full-text PDF

 Source
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.

Authors:
Sven-Eric Schelhorn Matthias Fischer Laura Tolosi Janine Altmüller Peter Nürnberg Herbert Pfister Thomas Lengauer Frank Berthold

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

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

View Article

Download full-text PDF

 Source
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.

Authors:
Anna K Hildebrandt Matthias Dietzen Thomas Lengauer Hans-Peter Lenhof Ernst Althaus Andreas Hildebrandt

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

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

View Article

Download full-text PDF

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

DNA methylation patterns facilitate the identification of microRNA transcription start sites: a brain-specific study.

Authors:
Tapas Bhadra Malay Bhattacharyya Lars Feuerbach Thomas Lengauer Sanghamitra Bandyopadhyay

PLoS One 2013 24;8(6):e66722. Epub 2013 Jun 24.

Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India.

View Article

Download full-text PDF

 Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066722PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691241PMC
March 2014

Personalized HIV therapy to control drug resistance.

Authors:
Thomas Lengauer Nico Pfeifer Rolf Kaiser

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

View Article

Download full-text PDF

 Source
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.

Authors:
Katarzyna Bozek Thomas Lengauer Saleta Sierra Rolf Kaiser Francisco S Domingues

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

Max Planck Institute for Computer Science, Saarbrucken, Germany.

View Article

Download full-text PDF

 Source
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.

Authors:
Olga V Kalinina Nico Pfeifer Thomas Lengauer

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.

View Article

Download full-text PDF

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

Ambulatory care for HIV-infected patients: differences in outcomes between hospital-based units and private practices: analysis of the RESINA cohort.

Authors:
Mark Oette Stefan Reuter Rolf Kaiser Björn Jensen Thomas Lengauer Gerd Fätkenheuer Heribert Knechten Martin Hower Abdurrahman Sagir Herbert Pfister Dieter Häussinger

Eur J Med Res 2013 Nov 21;18:48. Epub 2013 Nov 21.

Clinic for General Medicine, Gastroenterology, and Infectious Diseases Augustinerinnen Hospital, Jakobstrasse 27-31, Koln 50678, Germany.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/2047-783X-18-48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177128PMC
November 2013

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

Authors:
Laura Toloşi Jessica Theißen Konstantin Halachev Barbara Hero Frank Berthold Thomas Lengauer

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.

View Article

Download full-text PDF

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

Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of hepatitis C virus genotype 1-infected patients.

Authors:
Julia Dietz Sven-Eric Schelhorn Daniel Fitting Ulrike Mihm Simone Susser Martin-Walter Welker Caterina Füller Martin Däumer Gerlinde Teuber Heiner Wedemeyer Thomas Berg Thomas Lengauer Stefan Zeuzem Eva Herrmann Christoph Sarrazin

J Virol 2013 Jun 27;87(11):6172-81. Epub 2013 Mar 27.

Department of Internal Medicine 1, J. W. Goethe University Hospital, Frankfurt, Germany.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1128/JVI.02778-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648094PMC
June 2013

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

Authors:
Femke Simmer Arie B Brinkman Yassen Assenov Filomena Matarese Anita Kaan Lina Sabatino Alberto Villanueva Dori Huertas Manel Esteller Thomas Lengauer Christoph Bock Vittorio Colantuoni Lucia Altucci Hendrik G Stunnenberg

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.

View Article

Download full-text PDF

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

Paving the future: finding suitable ISMB venues.

Authors:
Burkhard Rost Terry Gaasterland Thomas Lengauer Michal Linial Scott Markel B J Morrison McKay Reinhard Schneider Paul Horton Janet Kelso

Bioinformatics 2012 Oct 13;28(19):2556-9. Epub 2012 Jul 13.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/bioinformatics/bts420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463122PMC
October 2012

EpiExplorer: live exploration and global analysis of large epigenomic datasets.

Authors:
Konstantin Halachev Hannah Bast Felipe Albrecht Thomas Lengauer Christoph Bock

Genome Biol 2012 Oct 3;13(10):R96. Epub 2012 Oct 3.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/gb-2012-13-10-r96DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491424PMC
October 2012

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

Authors:
Bastian Beggel Maria Neumann-Fraune Matthias Döring Glenn Lawyer Rolf Kaiser Jens Verheyen Thomas Lengauer

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Nico Pfeifer Thomas Lengauer

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Glenn Lawyer Eugen Schülter Rolf Kaiser Stefan Reuter Mark Oette Thomas Lengauer

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.

View Article

Download full-text PDF

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

Hierarchical Bayes model for predicting effectiveness of HIV combination therapies.

Authors:
Jasmina Bogojeska Thomas Lengauer

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

Max-Planck Institute for Informatics, Saarbrücken, Germany.

View Article

Download full-text PDF

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

Analyzing epigenome data in context of genome evolution and human diseases.

Authors:
Lars Feuerbach Konstantin Halachev Yassen Assenov Fabian Müller Christoph Bock Thomas Lengauer

Methods Mol Biol 2012 ;856:431-67

Max Planck Institute, Saarbrücken, Germany.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1007/978-1-61779-585-5_18DOI Listing
July 2012

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

Authors:
Katarzyna Bozek Manon Eckhardt Saleta Sierra Maria Anders Rolf Kaiser Hans-Georg Kräusslich Barbara Müller Thomas Lengauer

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Christoph Bock Thomas Lengauer

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.

View Article

Download full-text PDF

 Source
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.

View Article

Download full-text PDF

 Source
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.

Authors:
Alexander Thielen Thomas Lengauer

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

Max Planck Institute for Informatics, Saarbrücken, Germany.

View Article

Download full-text PDF

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

Predicting response to antiretroviral treatment by machine learning: the EuResist project.

Authors:
Maurizio Zazzi Francesca Incardona Michal Rosen-Zvi Mattia Prosperi Thomas Lengauer Andre Altmann Anders Sonnerborg Tamar Lavee Eugen Schülter Rolf Kaiser

Intervirology 2012 24;55(2):123-7. Epub 2012 Jan 24.

Department of Biotechnology, University of Siena, Siena, Italy.

View Article

Download full-text PDF

 Source
https://www.karger.com/Article/FullText/332008
Publisher Site
http://dx.doi.org/10.1159/000332008DOI Listing
May 2012

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

Authors:
Stefan Reuter Mark Oette Rolf Kaiser Thomas Lengauer Gerd Fätkenheuer Jürgen K Rockstroh Heribert Knechten Dieter Häussinger

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

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

View Article

Download full-text PDF

 Source
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.

Authors:
Mark Oette Stefan Reuter Rolf Kaiser Thomas Lengauer Gerd Fätkenheuer Heribert Knechten Martin Hower Herbert Pfister Dieter Häussinger

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

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

View Article

Download full-text PDF

 Source
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.

Authors:
Christoph Welsch Tetsuro Shimakami Christoph Hartmann Yan Yang Francisco S Domingues Thomas Lengauer Stefan Zeuzem Stanley M Lemon

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Matthias Dietzen Elena Zotenko Andreas Hildebrandt Thomas Lengauer

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

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

View Article

Download full-text PDF

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

BLUEPRINT to decode the epigenetic signature written in blood.

Authors:
David Adams Lucia Altucci Stylianos E Antonarakis Juan Ballesteros Stephan Beck Adrian Bird Christoph Bock Bernhard Boehm Elias Campo Andrea Caricasole Fredrik Dahl Emmanouil T Dermitzakis Tariq Enver Manel Esteller Xavier Estivill Anne Ferguson-Smith Jude Fitzgibbon Paul Flicek Claudia Giehl Thomas Graf Frank Grosveld Roderic Guigo Ivo Gut Kristian Helin Jonas Jarvius Ralf Küppers Hans Lehrach Thomas Lengauer Åke Lernmark David Leslie Markus Loeffler Elizabeth Macintyre Antonello Mai Joost H A Martens Saverio Minucci Willem H Ouwehand Pier Giuseppe Pelicci Hèléne Pendeville Bo Porse Vardhman Rakyan Wolf Reik Martin Schrappe Dirk Schübeler Martin Seifert Reiner Siebert David Simmons Nicole Soranzo Salvatore Spicuglia Michael Stratton Hendrik G Stunnenberg Amos Tanay David Torrents Alfonso Valencia Edo Vellenga Martin Vingron Jörn Walter Spike Willcocks

Nat Biotechnol 2012 Mar 7;30(3):224-6. Epub 2012 Mar 7.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nbt.2153DOI Listing
March 2012

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

Authors:
Eva Heger Alexander Thielen Ramona Gilles Martin Obermeier Thomas Lengauer Rolf Kaiser Susanna Trapp

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

University of Cologne, Cologne, Germany.

View Article

Download full-text PDF

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

A DNA methylation fingerprint of 1628 human samples.

Authors:
Agustin F Fernandez Yassen Assenov Jose Ignacio Martin-Subero Balazs Balint Reiner Siebert Hiroaki Taniguchi Hiroyuki Yamamoto Manuel Hidalgo Aik-Choon Tan Oliver Galm Isidre Ferrer Montse Sanchez-Cespedes Alberto Villanueva Javier Carmona Jose V Sanchez-Mut Maria Berdasco Victor Moreno Gabriel Capella David Monk Esteban Ballestar Santiago Ropero Ramon Martinez Marta Sanchez-Carbayo Felipe Prosper Xabier Agirre Mario F Fraga Osvaldo Graña Luis Perez-Jurado Jaume Mora Susana Puig Jaime Prat Lina Badimon Annibale A Puca Stephen J Meltzer Thomas Lengauer John Bridgewater Christoph Bock Manel Esteller

Genome Res 2012 Feb 25;22(2):407-19. Epub 2011 May 25.

Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

 Source
http://genome.cshlp.org/cgi/doi/10.1101/gr.119867.110
Publisher Site
http://dx.doi.org/10.1101/gr.119867.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266047PMC
February 2012

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

Authors:
Malay Bhattacharyya Lars Feuerbach Tapas Bhadra Thomas Lengauer Sanghamitra Bandyopadhyay

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

Indian Statistical Institute, Kolkata.

View Article

Download full-text PDF

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

Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach.

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

J Vis Exp 2011 Dec 1(58). Epub 2011 Dec 1.

Institute of Virology, University of Cologne.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.3791/3264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369655PMC
December 2011

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.

Authors:
Michael J Ziller Fabian Müller Jing Liao Yingying Zhang Hongcang Gu Christoph Bock Patrick Boyle Charles B Epstein Bradley E Bernstein Thomas Lengauer Andreas Gnirke Alexander Meissner

PLoS Genet 2011 Dec 8;7(12):e1002389. Epub 2011 Dec 8.

Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.

View Article

Download full-text PDF

 Source
http://dx.plos.org/10.1371/journal.pgen.1002389
Publisher Site
http://dx.doi.org/10.1371/journal.pgen.1002389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234221PMC
December 2011

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

Authors:
Eugen Schülter Mark Oette Melanie Balduin Stefan Reuter Jürgen Rockstroh Gerd Fätkenheuer Stefan Esser Thomas Lengauer Ali Agacfidan Herbert Pfister Rolf Kaiser Baki Akgül

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.

View Article

Download full-text PDF

 Source
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

Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially.

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

Antivir Ther 2011 ;16(3):319-28

Max Planck Institute for Informatics, Saarbrücken, Germany.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.3851/IMP1769DOI Listing
September 2011

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

Authors:
Stefan Müllegger Wolfgang Schöfberger Mohammad Rashidi Thomas Lengauer Florian Klappenberger Katharina Diller Kamuran Kara Johannes V Barth Eva Rauls Wolf Gero Schmidt Reinhold Koch

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Pavlo Lutsik Lars Feuerbach Julia Arand Thomas Lengauer Jörn Walter Christoph Bock

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.

View Article

Download full-text PDF

 Source
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.

Authors:
Laura Tolosi Thomas Lengauer

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.

View Article

Download full-text PDF

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

HIV-1 mutational pathways under multidrug therapy.

Authors:
Glenn Lawyer André Altmann Alexander Thielen Maurizio Zazzi Anders Sönnerborg Thomas Lengauer

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

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

View Article

Download full-text PDF

 Source
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.

Authors:
Lars Feuerbach Rune B Lyngsø Thomas Lengauer Jotun Hein

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.

View Article

Download full-text PDF

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

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

Authors:
Martin Däumer Rolf Kaiser Rolf Klein Thomas Lengauer Bernhard Thiele Alexander Thielen

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

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

View Article

Download full-text PDF

 Source
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.

Authors:
Hiroto Saigo Andre Altmann Jasmina Bogojeska Fabian Müller Sebastian Nowozin Thomas Lengauer

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

Max Planck Institute for Informatics, Munich, Germany.

View Article

Download full-text PDF

 Source
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.

Authors:
Stefan Reuter Mark Oette Frank Clemens Wilhelm Bastian Beggel Rolf Kaiser Melanie Balduin Finja Schweitzer Jens Verheyen Ortwin Adams Thomas Lengauer Gerd Fätkenheuer Herbert Pfister Dieter Häussinger

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.

View Article

Download full-text PDF

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

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment.

Authors:
Simon Reiss Ilka Rebhan Perdita Backes Ines Romero-Brey Holger Erfle Petr Matula Lars Kaderali Marion Poenisch Hagen Blankenburg Marie-Sophie Hiet Thomas Longerich Sarah Diehl Fidel Ramirez Tamas Balla Karl Rohr Artur Kaul Sandra Bühler Rainer Pepperkok Thomas Lengauer Mario Albrecht Roland Eils Peter Schirmacher Volker Lohmann Ralf Bartenschlager

Cell Host Microbe 2011 Jan;9(1):32-45

The Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.chom.2010.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433060PMC
January 2011

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

Authors:
Christian Markus Lange Kirsten Roomp Anette Dragan Jacob Nattermann Monika Michalk Ulrich Spengler Viola Weich Thomas Lengauer Stefan Zeuzem Thomas Berg Christoph Sarrazin

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.

View Article

Download full-text PDF

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

Improved prediction of HIV‐1 coreceptor usage with sequence information from the second hypervariable loop of gp120.

Authors:
Alexander Thielen Nadine Sichtig Rolf Kaiser Jeffrey Lam P Richard Harrigan Thomas Lengauer

J Infect Dis 2010 Nov;202(9):1435-43

Max Planck Institute for Informatics, Saarbrücken, Canada.

View Article

Download full-text PDF

 Source
https://academic.oup.com/jid/article-lookup/doi/10.1086/6566
Publisher Site
http://dx.doi.org/10.1086/656600DOI Listing
November 2010

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

Authors:
Jasmina Bogojeska Steffen Bickel André Altmann Thomas Lengauer

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.

View Article

Download full-text PDF

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

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

Authors:
Andreas Schlicker Thomas Lengauer Mario Albrecht

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

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

View Article

Download full-text PDF

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

Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper.

Authors:
Martin-Walter Welker Christoph Welsch Aline Meyer Iris Antes Mario Albrecht Nicole Forestier Bernd Kronenberger Thomas Lengauer Albrecht Piiper Stefan Zeuzem Christoph Sarrazin

Protein Sci 2010 Jul;19(7):1327-36

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1002/pro.409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2974824PMC
July 2010

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.

Authors:
Dorothea Emig Nathan Salomonis Jan Baumbach Thomas Lengauer Bruce R Conklin Mario Albrecht

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

Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.

View Article

Download full-text PDF

 Source
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.

Authors:
Katarzyna Bozek Thomas Lengauer

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.

View Article

Download full-text PDF

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

Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy.

Authors:
Christoph Bock Greg Von Kuster Konstantin Halachev James Taylor Anton Nekrutenko Thomas Lengauer

Methods Mol Biol 2010 ;628:275-96

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

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1007/978-1-60327-367-1_15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6529944PMC
May 2010

Permutation importance: a corrected feature importance measure.

Authors:
André Altmann Laura Toloşi Oliver Sander Thomas Lengauer

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.

View Article

Download full-text PDF

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

Short communication: selection of thymidine analogue resistance mutational patterns in children infected from a common HIV type 1 subtype G source.

Authors:
Martin Däumer Sabine Awerkiew Saleta Sierra Aragón Vladimir Kartashev Tatjana Poplavskaja Rolf Klein Nadine Sichtig Bernhard Thiele Thomas Lengauer Kirsten Roomp Herbert Pfister Rolf Kaiser

AIDS Res Hum Retroviruses 2010 Mar;26(3):275-8

Institut of Virology, University of Cologne, Cologne, Germany.

View Article

Download full-text PDF

 Source
http://www.liebertpub.com/doi/10.1089/aid.2009.0233
Publisher Site
http://dx.doi.org/10.1089/aid.2009.0233DOI Listing
March 2010