Martin Vingron

Martin Vingron

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Martin Vingron

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SVIM: structural variant identification using mapped long reads.

Bioinformatics 2019 Sep;35(17):2907-2915

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btz041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735718PMC
September 2019

DNA Motif Match Statistics Without Poisson Approximation.

J Comput Biol 2019 Aug 17;26(8):846-865. Epub 2019 Apr 17.

Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1089/cmb.2018.0144DOI Listing
August 2019

The Translational Landscape of the Human Heart.

Cell 2019 Jun 30;178(1):242-260.e29. Epub 2019 May 30.

Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.05.010DOI Listing
June 2019

The Distance Precision Matrix: computing networks from non-linear relationships.

Bioinformatics 2019 Mar;35(6):1009-1017

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty724DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420154PMC
March 2019

Predicting enhancers in mammalian genomes using supervised hidden Markov models.

BMC Bioinformatics 2019 Mar 27;20(1):157. Epub 2019 Mar 27.

Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, Berlin, 14195, Germany.

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http://dx.doi.org/10.1186/s12859-019-2708-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437899PMC
March 2019

Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions.

BMC Biol 2018 11 15;16(1):138. Epub 2018 Nov 15.

Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Ihnestraße 63-73, Berlin, 14195, Germany.

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http://dx.doi.org/10.1186/s12915-018-0585-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6238301PMC
November 2018

Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency.

Cell Stem Cell 2018 Aug 14;23(2):266-275.e6. Epub 2018 Jun 14.

Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany; Medical Faculty, University of Münster, 48149 Münster, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.05.020DOI Listing
August 2018

coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers.

PLoS Comput Biol 2018 08 24;14(8):e1006372. Epub 2018 Aug 24.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1006372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126874PMC
August 2018

Polymer physics predicts the effects of structural variants on chromatin architecture.

Nat Genet 2018 05 16;50(5):662-667. Epub 2018 Apr 16.

Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso di Monte Sant'Angelo, Naples, Italy.

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http://dx.doi.org/10.1038/s41588-018-0098-8DOI Listing
May 2018

An improved compound Poisson model for the number of motif hits in DNA sequences.

Bioinformatics 2017 Dec;33(24):3929-3937

Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860096PMC
December 2017

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.

Nucleic Acids Res 2017 Nov;45(19):11004-11018

Max Planck Institute for Molecular Genetics, Ihnestr. 63-73 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkx756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737366PMC
November 2017

Time-Dependent Gene Network Modelling by Sequential Monte Carlo.

IEEE/ACM Trans Comput Biol Bioinform 2016 Nov-Dec;13(6):1183-1193. Epub 2015 Oct 30.

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http://dx.doi.org/10.1109/TCBB.2015.2496301DOI Listing
October 2017

Haplotype-resolved sweet potato genome traces back its hexaploidization history.

Nat Plants 2017 Sep 21;3(9):696-703. Epub 2017 Aug 21.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany.

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http://dx.doi.org/10.1038/s41477-017-0002-zDOI Listing
September 2017

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns.

PLoS Comput Biol 2016 12 16;12(12):e1005249. Epub 2016 Dec 16.

Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1005249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161304PMC
December 2016

Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.

Nat Commun 2016 09 1;7:12621. Epub 2016 Sep 1.

Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Ihnestrasse 63-73, Berlin 14195, Germany.

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http://dx.doi.org/10.1038/ncomms12621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025757PMC
September 2016

Genome-wide Chromatin Profiling of Legionella pneumophila-Infected Human Macrophages Reveals Activation of the Probacterial Host Factor TNFAIP2.

J Infect Dis 2016 08 29;214(3):454-63. Epub 2016 Apr 29.

Institute for Lung Research/iLung Department of Medicine, Pulmonary, and Critical Care Medicine, University Medical Center Marburg, Philipps-University Universities of Giessen and arburg Lung Centre, German Center for Lung Research.

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http://dx.doi.org/10.1093/infdis/jiw171DOI Listing
August 2016

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs.

Cell Rep 2016 Feb 28;14(5):1246-1257. Epub 2016 Jan 28.

Structural Biology and BioComputing Programme, Spanish National Cancer Research Center - CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.01.008DOI Listing
February 2016

Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor.

Mol Biol Evol 2016 Jan 1;33(1):185-200. Epub 2015 Oct 1.

Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany

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http://dx.doi.org/10.1093/molbev/msv210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4693976PMC
January 2016

Reconstruction of gene networks using prior knowledge.

BMC Syst Biol 2015 Nov 20;9:84. Epub 2015 Nov 20.

Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, Berlin, D-14195, Germany.

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http://dx.doi.org/10.1186/s12918-015-0233-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654848PMC
November 2015

Comprehensive genomic profiles of small cell lung cancer.

Nature 2015 Aug 13;524(7563):47-53. Epub 2015 Jul 13.

1] Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany. [2] Department of Pathology, University Hospital Cologne, 50937 Cologne, Germany.

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http://dx.doi.org/10.1038/nature14664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861069PMC
August 2015

Somatic neurofibromatosis type 1 (NF1) inactivation events in cutaneous neurofibromas of a single NF1 patient.

Eur J Hum Genet 2015 Jun 8;23(6):870-3. Epub 2014 Oct 8.

1] FG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany [2] Institute for Medical Genetics and Human Genetics, Universitätsmedizin Berlin, Charité Berlin - Campus Virchow, Berlin, Germany.

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http://dx.doi.org/10.1038/ejhg.2014.210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795057PMC
June 2015

Translational regulation shapes the molecular landscape of complex disease phenotypes.

Nat Commun 2015 May 26;6:7200. Epub 2015 May 26.

Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rossle-Strasse 10, 13125 Berlin, Germany.

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http://www.nature.com/articles/ncomms8200
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http://dx.doi.org/10.1038/ncomms8200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455061PMC
May 2015

histoneHMM: Differential analysis of histone modifications with broad genomic footprints.

BMC Bioinformatics 2015 Feb 22;16:60. Epub 2015 Feb 22.

Groningen Bioinformatics Center, University of Groningen, Nijenborgh 7, AG, Groningen, 9747, The Netherlands.

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http://dx.doi.org/10.1186/s12859-015-0491-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4347972PMC
February 2015

Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling.

Nucleic Acids Res 2014 Dec 20;42(22):13689-95. Epub 2014 Nov 20.

Otto-Warburg-Laboratories Epigenomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany

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http://dx.doi.org/10.1093/nar/gku1234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267652PMC
December 2014

Inferring the paths of somatic evolution in cancer.

Bioinformatics 2014 Sep 7;30(17):2456-63. Epub 2014 May 7.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany and Department of Biosystems Science and Engineering, ETH Zurich and Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu319DOI Listing
September 2014

Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana.

Front Plant Sci 2014 13;5:273. Epub 2014 Jun 13.

Group of Plant System Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China ; Group of Plant System Biology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences Shanghai, China.

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http://dx.doi.org/10.3389/fpls.2014.00273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055858PMC
July 2014

Condition-specific target prediction from motifs and expression.

Bioinformatics 2014 Jun 14;30(12):1643-50. Epub 2014 Feb 14.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btu066DOI Listing
June 2014

Natural variation of histone modification and its impact on gene expression in the rat genome.

Genome Res 2014 Jun 2;24(6):942-53. Epub 2014 May 2.

Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner site Berlin, 13125 Berlin, Germany.

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http://dx.doi.org/10.1101/gr.169029.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032858PMC
June 2014

Finding associations among histone modifications using sparse partial correlation networks.

PLoS Comput Biol 2013 5;9(9):e1003168. Epub 2013 Sep 5.

Computational Molecular Biology, MPI for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1003168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764007PMC
April 2014

CD74-NRG1 fusions in lung adenocarcinoma.

Cancer Discov 2014 Apr 27;4(4):415-22. Epub 2014 Jan 27.

1Department of Translational Genomics; 2Department I of Internal Medicine; 3Laboratory of Translational Cancer Genomics; 4Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne-Bonn; 5Center for Molecular Medicine Cologne (CMMC); 6Cologne Center for Genomics (CCG); 7Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); 8Department of Pathology, University Hospital Medical Center, University of Cologne; 9Blackfield AG; 10Max Planck Institute for Neurological Research; 11Thoracic Surgery, Lungenklinik Merheim, Kliniken der Stadt Köln gGmbH; 12Institute of Human Genetics, Cologne; 13Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin; 14Department of Prostate Cancer Research, Institute of Pathology; 15Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn; 16Institute of Pathology; 17Department of Internal Medicine II, Jena University Hospital, Friedrich-Schiller-University, Jena; 18Institute for Pathology Bad Berka, Bad Berka, Germany;19Division of Molecular Oncology, Aichi Cancer Center Research Institute; 20Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan; Departments of 21Surgery and22Pathology, St. Vincent's Hospital; 23Department of Haematology and Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia;24Department of Pathology, 25CHU Grenoble Institut National de la Santé et de la Recherche Medicale (INSERM) U823, Institute Albert Bonniot, Grenoble-Alpes University, Grenoble, France; 26Laboratory of Oncology IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo; 27Laboratory for Molecular Medicine and Biotechnology, University Campus Bio-Medico, Rome, Italy; 28Center for the Biology of Disease, VIB, Leuven; and 29Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium.

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http://dx.doi.org/10.1158/2159-8290.CD-13-0633DOI Listing
April 2014

Synthetic sickness or lethality points at candidate combination therapy targets in glioblastoma.

Int J Cancer 2013 Nov 4;133(9):2123-32. Epub 2013 Jun 4.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.

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http://doi.wiley.com/10.1002/ijc.28235
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http://dx.doi.org/10.1002/ijc.28235DOI Listing
November 2013

Inferring nucleosome positions with their histone mark annotation from ChIP data.

Bioinformatics 2013 Oct 26;29(20):2547-54. Epub 2013 Aug 26.

Otto-Warburg-Laboratories, Epigenomics and Computational Molecular Biology, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btt449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789549PMC
October 2013

Genome-wide kinase-chromatin interactions reveal the regulatory network of ERK signaling in human embryonic stem cells.

Mol Cell 2013 Jun 30;50(6):844-55. Epub 2013 May 30.

Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672, Singapore.

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http://dx.doi.org/10.1016/j.molcel.2013.04.030DOI Listing
June 2013

P53 binding sites in transposons.

Front Genet 2012 20;3:40. Epub 2012 Mar 20.

Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics Berlin, Germany.

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http://dx.doi.org/10.3389/fgene.2012.00040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308033PMC
October 2012

T cells become licensed in the lung to enter the central nervous system.

Nature 2012 Aug;488(7413):675-9

Institute for Multiple Sclerosis Research, Department of Neuroimmunology, Gemeinnützige Hertie-Stiftung and University Medical Centre Göttingen, 37073 Göttingen, Germany.

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http://dx.doi.org/10.1038/nature11337DOI Listing
August 2012

Detection of interacting transcription factors in human tissues using predicted DNA binding affinity.

BMC Genomics 2012 17;13 Suppl 1:S2. Epub 2012 Jan 17.

Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1186/1471-2164-13-S1-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583127PMC
June 2012

R2KS: a novel measure for comparing gene expression based on ranked gene lists.

J Comput Biol 2012 Jun;19(6):766-75

CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Shanghai, China.

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http://dx.doi.org/10.1089/cmb.2012.0026DOI Listing
June 2012

Predicting the outcome of renal transplantation.

J Am Med Inform Assoc 2012 Mar-Apr;19(2):255-62. Epub 2011 Aug 28.

Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1136/amiajnl-2010-000004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277611PMC
May 2012

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.

Bioinformatics 2012 Apr 1;28(7):1024-5. Epub 2012 Feb 1.

Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts064DOI Listing
April 2012

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.

Bioinformatics 2012 Apr 24;28(8):1086-92. Epub 2012 Feb 24.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324515PMC
April 2012

CpG deamination creates transcription factor-binding sites with high efficiency.

Genome Biol Evol 2011 19;3:1304-11. Epub 2011 Oct 19.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/gbe/evr107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228489PMC
March 2012

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.

Bioinformatics 2012 Mar 11;28(5):619-27. Epub 2012 Jan 11.

Department of Computer Science, Freie Universität Berlin, Takustrasse 9, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts019DOI Listing
March 2012

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.

Bioinformatics 2012 Mar 12;28(5):656-63. Epub 2012 Jan 12.

Department for Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289921PMC
March 2012

Modeling read counts for CNV detection in exome sequencing data.

Stat Appl Genet Mol Biol 2011 Nov 8;10(1). Epub 2011 Nov 8.

Max Planck Institute for Molecular Genetics.

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http://dx.doi.org/10.2202/1544-6115.1732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517018PMC
November 2011

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.

Nat Protoc 2011 Nov 3;6(12):1860-9. Epub 2011 Nov 3.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1038/nprot.2011.409DOI Listing
November 2011

Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series.

BMC Bioinformatics 2011 Aug 18;12:347. Epub 2011 Aug 18.

Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.

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http://dx.doi.org/10.1186/1471-2105-12-347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180390PMC
August 2011

Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.

BMC Bioinformatics 2011 Jun 21;12:249. Epub 2011 Jun 21.

Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1186/1471-2105-12-249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3236061PMC
June 2011

DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach.

Algorithms Mol Biol 2011 Jun 23;6(1):18. Epub 2011 Jun 23.

Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1186/1748-7188-6-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152888PMC
June 2011

Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators.

Gene 2011 Mar 13;473(2):139-49. Epub 2010 Dec 13.

Key Laboratory of Aquatic Biodiversity and Conservation Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.

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https://linkinghub.elsevier.com/retrieve/pii/S03781119100045
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http://dx.doi.org/10.1016/j.gene.2010.11.011DOI Listing
March 2011

Studying the evolution of promoter sequences: a waiting time problem.

J Comput Biol 2010 Dec;17(12):1591-606

Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1089/cmb.2010.0084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119604PMC
December 2010

Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters.

Nucleic Acids Res 2010 Oct 21;38(18):6112-23. Epub 2010 May 21.

Department for Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkq402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952857PMC
October 2010

Introducing knowledge into differential expression analysis.

J Comput Biol 2010 Aug;17(8):953-67

Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://www.liebertpub.com/doi/10.1089/cmb.2010.0034
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http://dx.doi.org/10.1089/cmb.2010.0034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122906PMC
August 2010

TransFind--predicting transcriptional regulators for gene sets.

Nucleic Acids Res 2010 Jul 28;38(Web Server issue):W275-80. Epub 2010 May 28.

Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkq438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896106PMC
July 2010

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.

Nucleic Acids Res 2010 Jun 11;38(10):e112. Epub 2010 Feb 11.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkq041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879520PMC
June 2010

A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes.

BMC Bioinformatics 2010 May 20;11:267. Epub 2010 May 20.

CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, 320 Yue Yang Road, 200031, Shanghai, China.

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http://dx.doi.org/10.1186/1471-2105-11-267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098066PMC
May 2010

Quantifying the effect of sequence variation on regulatory interactions.

Hum Mutat 2010 Apr;31(4):477-83

Max Planck Institute for Molecular Genetics, Computational Biology, Ihnestrasse 73, Berlin, Germany.

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http://dx.doi.org/10.1002/humu.21209DOI Listing
April 2010

Histone modification levels are predictive for gene expression.

Proc Natl Acad Sci U S A 2010 Feb 1;107(7):2926-31. Epub 2010 Feb 1.

Max-Planck-Institut für Molekulare Genetik, Department of Computational Molecular Biology, Ihnestrasse 73, 14195 Berlin, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814872PMC
February 2010

CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses.

Nucleic Acids Res 2009 Oct 6;37(19):6305-15. Epub 2009 Sep 6.

Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin.

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http://dx.doi.org/10.1093/nar/gkp682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770660PMC
October 2009

Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments.

Mol Syst Biol 2009 7;5:287. Epub 2009 Jul 7.

Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.

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http://dx.doi.org/10.1038/msb.2009.45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2724975PMC
September 2009

Statistical detection of cooperative transcription factors with similarity adjustment.

Bioinformatics 2009 Aug 13;25(16):2103-9. Epub 2009 Mar 13.

Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73 and Mathematics and Computer Science, Free University of Berlin, Takustr. 9, 14195 Berlin, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722994PMC
August 2009

Special RECOMB 2008 Issue. Preface.

Authors:
Martin Vingron

J Comput Biol 2009 Aug;16(8):969

RECOMB 2008 Program Chair Max, Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Ihnestrasse 63-37, 14195 Berlin, Germany.

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August 2009

Maximum similarity: a new formulation of phylogenetic reconstruction.

J Comput Biol 2009 Jul;16(7):887-96

Department of Computer Science, Iowa State University, Ames, Iowa 50011-1040, USA.

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July 2009

Comparison of sequence-dependent tiling array normalization approaches.

BMC Bioinformatics 2009 Jun 30;10:204. Epub 2009 Jun 30.

Max-Planck-Institut für Molekulare Genetik, Department of Computational Molecular Biology, Berlin, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753852PMC
June 2009

Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse.

BMC Genomics 2009 Mar 31;10:144. Epub 2009 Mar 31.

Department of Computational Biology, Max Planck Institute for Molecular Genetics, Ihnestr 63-73, 14195 Berlin, Germany.

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March 2009