Lorenz Wernisch

Lorenz Wernisch

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Lorenz Wernisch

Lorenz Wernisch

Publications by authors named "Lorenz Wernisch"

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GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution.

Bioinformatics 2020 Mar;36(5):1484-1491

MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SR, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz778DOI Listing
March 2020

GPseudoRank: a permutation sampler for single cell orderings.

Bioinformatics 2019 02;35(4):611-618

MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6230469PMC
February 2019

Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate.

EMBO J 2019 01 26;38(1). Epub 2018 Sep 26.

Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK

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http://dx.doi.org/10.15252/embj.201899518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315289PMC
January 2019

Joining and splitting models with Markov melding.

Bayesian Anal 2019 Jan;14(1):81-109

MRC Biostatistics Unit, University of Cambridge, United Kingdom.

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http://dx.doi.org/10.1214/18-BA1104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324725PMC
January 2019

Branch-recombinant Gaussian processes for analysis of perturbations in biological time series.

Bioinformatics 2018 09;34(17):i1005-i1013

Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, UK.

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https://academic.oup.com/bioinformatics/article/34/17/i1005/
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http://dx.doi.org/10.1093/bioinformatics/bty603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129282PMC
September 2018

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets.

PLoS Comput Biol 2017 Oct 16;13(10):e1005781. Epub 2017 Oct 16.

MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1005781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658176PMC
October 2017

A comparison of machine learning and Bayesian modelling for molecular serotyping.

BMC Genomics 2017 Aug 11;18(1):606. Epub 2017 Aug 11.

MRC Biostatistics Unit, Robinson Way, Cambridge, CB2 0SR, UK.

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http://dx.doi.org/10.1186/s12864-017-3998-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5553679PMC
August 2017

Pseudotime estimation: deconfounding single cell time series.

Bioinformatics 2016 10 17;32(19):2973-80. Epub 2016 Jun 17.

MRC Biostatistics Unit, Cambridge CB2 0SR, UK.

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http://dx.doi.org/10.1093/bioinformatics/btw372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039927PMC
October 2016

BTR: training asynchronous Boolean models using single-cell expression data.

BMC Bioinformatics 2016 Sep 6;17(1):355. Epub 2016 Sep 6.

Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK.

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http://dx.doi.org/10.1186/s12859-016-1235-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012073PMC
September 2016

An optimal stratified Simon two-stage design.

Pharm Stat 2016 07 2;15(4):333-40. Epub 2016 Mar 2.

MRC Biostatistics Unit Hub for Trials Methodology Research, Coventry, UK.

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http://dx.doi.org/10.1002/pst.1742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405342PMC
July 2016

The Discovery and Validation of Biomarkers for the Diagnosis of Esophageal Squamous Dysplasia and Squamous Cell Carcinoma.

Cancer Prev Res (Phila) 2016 Jul 12;9(7):558-66. Epub 2016 Apr 12.

MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1158/1940-6207.CAPR-15-0379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777151PMC
July 2016

STEME: a robust, accurate motif finder for large data sets.

PLoS One 2014 13;9(3):e90735. Epub 2014 Mar 13.

MRC Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090735PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953122PMC
January 2016

Analysis of dysplasia in patients with Barrett's esophagus based on expression pattern of 90 genes.

Gastroenterology 2015 Nov 3;149(6):1511-1518.e5. Epub 2015 Aug 3.

MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2015.07.053DOI Listing
November 2015

Investigating inter-chromosomal regulatory relationships through a comprehensive meta-analysis of matched copy number and transcriptomics data sets.

BMC Genomics 2015 Nov 18;16:967. Epub 2015 Nov 18.

Biostatistics Unit, Medical Research Council, Robinson Way, Cambridge, CB2 0SR, UK.

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http://dx.doi.org/10.1186/s12864-015-2100-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650296PMC
November 2015

Key regulators control distinct transcriptional programmes in blood progenitor and mast cells.

EMBO J 2014 Jun 23;33(11):1212-26. Epub 2014 Apr 23.

Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK

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http://emboj.embopress.org/cgi/doi/10.1002/embj.201386825
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http://dx.doi.org/10.1002/embj.201386825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168288PMC
June 2014

Two novel pathway analysis methods based on a hierarchical model.

Bioinformatics 2014 Mar 11;30(5):690-7. Epub 2013 Oct 11.

Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge, CB2 0SR, UK, JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK and Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.

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http://dx.doi.org/10.1093/bioinformatics/btt583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933872PMC
March 2014

Comparison of methods for competitive tests of pathway analysis.

PLoS One 2012 31;7(7):e41018. Epub 2012 Jul 31.

Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0041018PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409204PMC
April 2013

Transcription factor and chromatin features predict genes associated with eQTLs.

Nucleic Acids Res 2013 Feb 28;41(3):1450-63. Epub 2012 Dec 28.

MRC Biostatistics Unit, Institute of Public Health, Robinson Way, Cambridge CB2 0SR, UK.

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http://dx.doi.org/10.1093/nar/gks1339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561974PMC
February 2013

Cell signalling regulates dynamics of Nanog distribution in embryonic stem cell populations.

J R Soc Interface 2013 Jan 8;10(78):20120525. Epub 2012 Nov 8.

Biostatistics Unit, Medical Research Council, Cambridge, UK.

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http://dx.doi.org/10.1098/rsif.2012.0525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565777PMC
January 2013

Displaying R spatial statistics on Google dynamic maps with web applications created by Rwui.

Int J Health Geogr 2012 Sep 24;11:41. Epub 2012 Sep 24.

MRC Biostatistics Unit, Robinson Way, Cambridge, UK.

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http://dx.doi.org/10.1186/1476-072X-11-41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548681PMC
September 2012

Transcription factor co-localization patterns affect human cell type-specific gene expression.

BMC Genomics 2012 Jun 21;13:263. Epub 2012 Jun 21.

MRC Biostatistics Unit, Institute of Public Health, Robinson Way, Cambridge, UK.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-13-263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3441573PMC
June 2012

New gene functions in megakaryopoiesis and platelet formation.

Authors:
Christian Gieger Aparna Radhakrishnan Ana Cvejic Weihong Tang Eleonora Porcu Giorgio Pistis Jovana Serbanovic-Canic Ulrich Elling Alison H Goodall Yann Labrune Lorna M Lopez Reedik Mägi Stuart Meacham Yukinori Okada Nicola Pirastu Rossella Sorice Alexander Teumer Katrin Voss Weihua Zhang Ramiro Ramirez-Solis Joshua C Bis David Ellinghaus Martin Gögele Jouke-Jan Hottenga Claudia Langenberg Peter Kovacs Paul F O'Reilly So-Youn Shin Tõnu Esko Jaana Hartiala Stavroula Kanoni Federico Murgia Afshin Parsa Jonathan Stephens Pim van der Harst C Ellen van der Schoot Hooman Allayee Antony Attwood Beverley Balkau François Bastardot Saonli Basu Sebastian E Baumeister Ginevra Biino Lorenzo Bomba Amélie Bonnefond François Cambien John C Chambers Francesco Cucca Pio D'Adamo Gail Davies Rudolf A de Boer Eco J C de Geus Angela Döring Paul Elliott Jeanette Erdmann David M Evans Mario Falchi Wei Feng Aaron R Folsom Ian H Frazer Quince D Gibson Nicole L Glazer Chris Hammond Anna-Liisa Hartikainen Susan R Heckbert Christian Hengstenberg Micha Hersch Thomas Illig Ruth J F Loos Jennifer Jolley Kay Tee Khaw Brigitte Kühnel Marie-Christine Kyrtsonis Vasiliki Lagou Heather Lloyd-Jones Thomas Lumley Massimo Mangino Andrea Maschio Irene Mateo Leach Barbara McKnight Yasin Memari Braxton D Mitchell Grant W Montgomery Yusuke Nakamura Matthias Nauck Gerjan Navis Ute Nöthlings Ilja M Nolte David J Porteous Anneli Pouta Peter P Pramstaller Janne Pullat Susan M Ring Jerome I Rotter Daniela Ruggiero Aimo Ruokonen Cinzia Sala Nilesh J Samani Jennifer Sambrook David Schlessinger Stefan Schreiber Heribert Schunkert James Scott Nicholas L Smith Harold Snieder John M Starr Michael Stumvoll Atsushi Takahashi W H Wilson Tang Kent Taylor Albert Tenesa Swee Lay Thein Anke Tönjes Manuela Uda Sheila Ulivi Dirk J van Veldhuisen Peter M Visscher Uwe Völker H-Erich Wichmann Kerri L Wiggins Gonneke Willemsen Tsun-Po Yang Jing Hua Zhao Paavo Zitting John R Bradley George V Dedoussis Paolo Gasparini Stanley L Hazen Andres Metspalu Mario Pirastu Alan R Shuldiner L Joost van Pelt Jaap-Jan Zwaginga Dorret I Boomsma Ian J Deary Andre Franke Philippe Froguel Santhi K Ganesh Marjo-Riitta Jarvelin Nicholas G Martin Christa Meisinger Bruce M Psaty Timothy D Spector Nicholas J Wareham Jan-Willem N Akkerman Marina Ciullo Panos Deloukas Andreas Greinacher Steve Jupe Naoyuki Kamatani Jyoti Khadake Jaspal S Kooner Josef Penninger Inga Prokopenko Derek Stemple Daniela Toniolo Lorenz Wernisch Serena Sanna Andrew A Hicks Augusto Rendon Manuel A Ferreira Willem H Ouwehand Nicole Soranzo

Nature 2011 Nov 30;480(7376):201-8. Epub 2011 Nov 30.

Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr 1, 85764 Neuherberg, Germany.

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http://dx.doi.org/10.1038/nature10659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335296PMC
November 2011

STEME: efficient EM to find motifs in large data sets.

Nucleic Acids Res 2011 Oct 23;39(18):e126. Epub 2011 Jul 23.

MRC Biostatistics Unit, Institute of Public Health, Forvie Site, Robinson Way, Cambridge CB2 0SR, UK.

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http://dx.doi.org/10.1093/nar/gkr574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185442PMC
October 2011

Creating web applications for spatial epidemiological analysis and mapping in R using Rwui.

Source Code Biol Med 2011 Apr 1;6(1). Epub 2011 Apr 1.

MRC Biostatistics Unit, Robinson Way, Cambridge, CB2 0SR, UK.

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http://dx.doi.org/10.1186/1751-0473-6-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077334PMC
April 2011

Empirical Bayesian models for analysing molecular serotyping microarrays.

BMC Bioinformatics 2011 Mar 31;12:88. Epub 2011 Mar 31.

MRC Biostatistics Unit, Robinson Way, Cambridge, CB2 0SR, UK.

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http://dx.doi.org/10.1186/1471-2105-12-88DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076268PMC
March 2011

Using temporal correlation in factor analysis for reconstructing transcription factor activities.

EURASIP J Bioinform Syst Biol 2008 :172840

School of Crystallography, Birkbeck College, University of London, Malet Street, London, UK.

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http://dx.doi.org/10.1155/2008/172840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171388PMC
June 2010

The heat shock response of Mycobacterium tuberculosis: linking gene expression, immunology and pathogenesis.

Comp Funct Genomics 2002 ;3(4):348-51

Department of Infectious Diseases and Microbiology, Faculty of Medicine, Centre for Molecular Microbiology and Infection, Imperial College of Science Technology and Medicine, London SW7 2AZ, UK.

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http://dx.doi.org/10.1002/cfg.183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2448437PMC
June 2010

Can replication save noisy microarray data?

Authors:
Lorenz Wernisch

Comp Funct Genomics 2002 ;3(4):372-4

School of Crystallography, Birkbeck College, London WC1E 7HX, UK.

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http://dx.doi.org/10.1002/cfg.196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2448442PMC
June 2010

Statistical model comparison applied to common network motifs.

BMC Syst Biol 2010 Mar 3;4:18. Epub 2010 Mar 3.

Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Edifici GAIA, Rambla de Sant Nebridi s/n 08222, Terrassa, Barcelona, Spain.

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http://dx.doi.org/10.1186/1752-0509-4-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855527PMC
March 2010

An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis.

BMC Syst Biol 2010 Mar 31;4:37. Epub 2010 Mar 31.

School of Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK.

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http://dx.doi.org/10.1186/1752-0509-4-37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867773PMC
March 2010

Variable structure motifs for transcription factor binding sites.

BMC Genomics 2010 Jan 14;11:30. Epub 2010 Jan 14.

MRC Biostatistics Unit, Institute of Public Health, Forvie Site, Cambridge, CB2 0SR, UK.

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http://dx.doi.org/10.1186/1471-2164-11-30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824720PMC
January 2010

Transcriptional programs: modelling higher order structure in transcriptional control.

BMC Bioinformatics 2009 Jul 16;10:218. Epub 2009 Jul 16.

MRC Biostatistics Unit, Institute of Public Health, University Forvie Site, Cambridge CB2 0SR, UK.

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http://dx.doi.org/10.1186/1471-2105-10-218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725141PMC
July 2009

Estimating translational selection in eukaryotic genomes.

Mol Biol Evol 2009 Feb 25;26(2):451-61. Epub 2008 Nov 25.

School of Crystallography, Birkbeck College, London, UK.

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http://dx.doi.org/10.1093/molbev/msn272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639113PMC
February 2009

A Bayesian Change point model for differential gene expression patterns of the DosR regulon of Mycobacterium tuberculosis.

BMC Genomics 2008 Feb 22;9:87. Epub 2008 Feb 22.

School of Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK.

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http://dx.doi.org/10.1186/1471-2164-9-87DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275270PMC
February 2008

A comparative study of S/MAR prediction tools.

BMC Bioinformatics 2007 Mar 2;8:71. Epub 2007 Mar 2.

School of Crystallography, Birkbeck College, Malet Street, London, UK.

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http://dx.doi.org/10.1186/1471-2105-8-71DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1847452PMC
March 2007

A Hidden Markov model web application for analysing bacterial genomotyping DNA microarray experiments.

Appl Bioinformatics 2006 ;5(4):211-8

School of Crystallography, Birkbeck College, University of London, London, UK.

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http://dx.doi.org/10.2165/00822942-200605040-00003DOI Listing
February 2007

Factor analysis for gene regulatory networks and transcription factor activity profiles.

BMC Bioinformatics 2007 Feb 23;8:61. Epub 2007 Feb 23.

School of Crystallography, Birkbeck College, University of London, London, UK.

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http://dx.doi.org/10.1186/1471-2105-8-61DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821042PMC
February 2007

Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma.

BMC Genomics 2006 Oct 9;7:252. Epub 2006 Oct 9.

Bioinformatics Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.

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http://dx.doi.org/10.1186/1471-2164-7-252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618401PMC
October 2006

Archaeology and evolution of transfer RNA genes in the Escherichia coli genome.

RNA 2006 Jun 17;12(6):933-42. Epub 2006 Apr 17.

School of Crystallography, Birkbeck College, University of London, UK.

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http://dx.doi.org/10.1261/rna.2272306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1464854PMC
June 2006

Applying GIFT, a Gene Interactions Finder in Text, to fly literature.

Bioinformatics 2005 Sep 12;21(17):3582-3. Epub 2005 Jul 12.

School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK.

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http://dx.doi.org/10.1093/bioinformatics/bti578DOI Listing
September 2005

A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context.

Nucleic Acids Res 2005 7;33(10):3253-62. Epub 2005 Jun 7.

School of Crystallography, Birkbeck College London WC1E 7HX, UK.

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http://dx.doi.org/10.1093/nar/gki634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1143694PMC
June 2005

Reconstruction of gene networks using Bayesian learning and manipulation experiments.

Bioinformatics 2004 Nov 4;20(17):2934-42. Epub 2004 Jun 4.

Department of Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK.

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http://dx.doi.org/10.1093/bioinformatics/bth337DOI Listing
November 2004

The influence of reduced oxygen availability on pathogenicity and gene expression in Mycobacterium tuberculosis.

Tuberculosis (Edinb) 2004 ;84(3-4):205-17

TB Research Group, Health Protection Agency, Porton Down, CAMR, Salisbury, Wiltshire SP4 0JG, UK.

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http://dx.doi.org/10.1016/j.tube.2003.12.011DOI Listing
November 2004

Solving the riddle of codon usage preferences: a test for translational selection.

Nucleic Acids Res 2004 24;32(17):5036-44. Epub 2004 Sep 24.

School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK.

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http://dx.doi.org/10.1093/nar/gkh834DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC521650PMC
October 2004

Predicting metal-binding site residues in low-resolution structural models.

J Mol Biol 2004 Sep;342(1):307-20

Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, WC1E 6BT, UK.

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http://dx.doi.org/10.1016/j.jmb.2004.07.019DOI Listing
September 2004

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome.

Nucleic Acids Res 2003 Dec;31(23):6976-85

School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC290265PMC
http://dx.doi.org/10.1093/nar/gkg897DOI Listing
December 2003

Identifying structural domains in proteins.

Methods Biochem Anal 2003 ;44:365-85

European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.

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April 2003

Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays.

Microbiology 2002 Oct;148(Pt 10):3129-3138

Department of Medical Microbiology, St George's Hospital Medical School, Cranmer Terrace, London SW17 0RE, UK3.

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http://dx.doi.org/10.1099/00221287-148-10-3129DOI Listing
October 2002

Folding free energy function selects native-like protein sequences in the core but not on the surface.

Proc Natl Acad Sci U S A 2002 Oct 4;99(21):13554-9. Epub 2002 Oct 4.

Unité de Conformation de Macromolécules Biologiques, CP160/16, Université Libre de Bruxelles, 50 Avenue F. D. Roosevelt, 1050 Brussels, Belgium.

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http://dx.doi.org/10.1073/pnas.212068599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129712PMC
October 2002