Alvis Brazma

Alvis Brazma

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Alvis Brazma

Publications by authors named "Alvis Brazma"

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A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.

Cell 2019 Sep;178(6):1465-1477.e17

Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.08.018DOI Listing
September 2019

Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ.

BMC Bioinformatics 2019 May 31;20(1):296. Epub 2019 May 31.

Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV 1459, Latvia.

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http://dx.doi.org/10.1186/s12859-019-2909-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544977PMC
May 2019

ArrayExpress update - from bulk to single-cell expression data.

Nucleic Acids Res 2019 Jan;47(D1):D711-D715

European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323929PMC
January 2019

A call for public archives for biological image data.

Nat Methods 2018 11;15(11):849-854

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1038/s41592-018-0195-8DOI Listing
November 2018

The BioStudies database-one stop shop for all data supporting a life sciences study.

Nucleic Acids Res 2018 01;46(D1):D1266-D1270

European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkx965DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753238PMC
January 2018

clustComp, a bioconductor package for the comparison of clustering results.

Bioinformatics 2017 Dec;33(24):4001-4003

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860092PMC
December 2017

Impact of Alternative Splicing on the Human Proteome.

Cell Rep 2017 08;20(5):1229-1241

The Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.07.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5554779PMC
August 2017

The Image Data Resource: A Bioimage Data Integration and Publication Platform.

Nat Methods 2017 Aug 19;14(8):775-781. Epub 2017 Jun 19.

Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK.

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http://dx.doi.org/10.1038/nmeth.4326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536224PMC
August 2017

Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.

PLoS One 2016 20;11(6):e0157484. Epub 2016 Jun 20.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157484PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913919PMC
July 2017

The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.

Bioinformatics 2017 Jul;33(14):2218-2220

Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870697PMC
July 2017

Orchestrating differential data access for translational research: a pilot implementation.

BMC Med Inform Decis Mak 2017 03 23;17(1):30. Epub 2017 Mar 23.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s12911-017-0424-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363029PMC
March 2017

Subtype-specific micro-RNA expression signatures in breast cancer progression.

Int J Cancer 2016 09 9;139(5):1117-28. Epub 2016 May 9.

Department of Cancer Genetics, Institute for Cancer Research, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital Radiumhospitalet, Oslo, Norway.

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http://dx.doi.org/10.1002/ijc.30142DOI Listing
September 2016

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.

Nat Commun 2016 06 2;7:11778. Epub 2016 Jun 2.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/ncomms11778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895710PMC
June 2016

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

PLoS One 2015 4;10(9):e0137367. Epub 2015 Sep 4.

University of Cambridge, Cancer Research UK - Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137367PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560434PMC
May 2016

Modelling-based experiment retrieval: a case study with gene expression clustering.

Bioinformatics 2016 05 6;32(9):1388-94. Epub 2016 Jan 6.

Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland and.

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http://dx.doi.org/10.1093/bioinformatics/btv762DOI Listing
May 2016

The BioStudies database.

Mol Syst Biol 2015 Dec 23;11(12):847. Epub 2015 Dec 23.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704487PMC
http://dx.doi.org/10.15252/msb.20156658DOI Listing
December 2015

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.

Skelet Muscle 2015 9;5:35. Epub 2015 Oct 9.

Lund University Diabetes Center, Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital Malmö, Lund University, Malmö, 20502 Sweden.

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http://www.skeletalmusclejournal.com/content/5/1/35
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http://dx.doi.org/10.1186/s13395-015-0059-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600214PMC
October 2015

Cellular phenotype database: a repository for systems microscopy data.

Bioinformatics 2015 Aug 9;31(16):2736-40. Epub 2015 Apr 9.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btv199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528631PMC
August 2015

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress.

RNA Biol 2014 9;11(6):702-14. Epub 2014 Jul 9.

Department of Genetics, Evolution & Environment and UCL Cancer Institute; University College London; London, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156502PMC
http://dx.doi.org/10.4161/rna.29196DOI Listing
July 2015

RNA-Seq gene profiling--a systematic empirical comparison.

PLoS One 2014 30;9(9):e107026. Epub 2014 Sep 30.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107026PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4182317PMC
June 2015

ArrayExpress update--simplifying data submissions.

Nucleic Acids Res 2015 Jan 31;43(Database issue):D1113-6. Epub 2014 Oct 31.

European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK

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http://dx.doi.org/10.1093/nar/gku1057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383899PMC
January 2015

Variation in genomic landscape of clear cell renal cell carcinoma across Europe.

Nat Commun 2014 Oct 29;5:5135. Epub 2014 Oct 29.

1] Department of Human Genetics, McGill University, 1205 Dr Penfield Avenue, Montreal, Quebec, Canada H3A 1B1 [2] Fondation Jean Dausset - Centre d'Etude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France [3] Centre National de Génotypage, CEA - Institute de Génomique, 2 rue Gaston Crémieux, 91000 Evry, France.

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http://dx.doi.org/10.1038/ncomms6135DOI Listing
October 2014

Updates to BioSamples database at European Bioinformatics Institute.

Nucleic Acids Res 2014 Jan 21;42(Database issue):D50-2. Epub 2013 Nov 21.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkt1081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965081PMC
January 2014

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.

BMC Syst Biol 2013 Jun 27;7:52. Epub 2013 Jun 27.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/1752-0509-7-52DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703260PMC
June 2013

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.

Nucleic Acids Res 2013 May 5;41(10):e110. Epub 2013 Apr 5.

Department of Veterinary Bioscience, University of Helsinki, Agnes Sjöbergin katu 2, PO Box 66, FI-00014 University of Helsinki, Finland.

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http://dx.doi.org/10.1093/nar/gkt229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664815PMC
May 2013

HSM - a hybrid system based approach for modelling intracellular networks.

Gene 2013 Apr 21;518(1):70-7. Epub 2012 Dec 21.

European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.gene.2012.11.084DOI Listing
April 2013

Reuse of public genome-wide gene expression data.

Nat Rev Genet 2013 Feb 27;14(2):89-99. Epub 2012 Dec 27.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1038/nrg3394DOI Listing
February 2013

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

Genome Res 2012 Dec 23;22(12):2376-84. Epub 2012 Aug 23.

European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1101/gr.142281.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514667PMC
December 2012

Tools for mapping high-throughput sequencing data.

Bioinformatics 2012 Dec 11;28(24):3169-77. Epub 2012 Oct 11.

EMBL Outstation, European Bioinformatics Institute (EBI), Hinxton, Cambridge CB10 ISD, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts605DOI Listing
December 2012

MageComet--web application for harmonizing existing large-scale experiment descriptions.

Bioinformatics 2012 May 2;28(10):1402-3. Epub 2012 Apr 2.

Department of Computer Science, Hunter College, City University of New York, NY 10065, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348561PMC
May 2012

The BioSample Database (BioSD) at the European Bioinformatics Institute.

Nucleic Acids Res 2012 Jan 16;40(Database issue):D64-70. Epub 2011 Nov 16.

EMBL-EBI, the European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkr937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245134PMC
January 2012

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.

Bioinformatics 2012 Jan 20;28(2):246-53. Epub 2011 Nov 20.

Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btr634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3259436PMC
January 2012

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes.

Nat Genet 2011 Aug 28;43(10):948-55. Epub 2011 Aug 28.

Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK.

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http://dx.doi.org/10.1038/ng.906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184141PMC
August 2011

Large scale comparison of global gene expression patterns in human and mouse.

Genome Biol 2010 23;11(12):R124. Epub 2010 Dec 23.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/gb-2010-11-12-r124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046484PMC
June 2011

A pipeline for RNA-seq data processing and quality assessment.

Bioinformatics 2011 Mar 13;27(6):867-9. Epub 2011 Jan 13.

EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051320PMC
March 2011

Contributions of the EMERALD project to assessing and improving microarray data quality.

Biotechniques 2011 Jan;50(1):27-31

Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.

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https://www.future-science.com/doi/10.2144/000113591
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http://dx.doi.org/10.2144/000113591DOI Listing
January 2011

Learning about gene regulatory networks from gene deletion experiments.

Comp Funct Genomics 2002 ;3(6):499-503

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1002/cfg.220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2448417PMC
June 2010

A CD8+ T cell transcription signature predicts prognosis in autoimmune disease.

Nat Med 2010 May 18;16(5):586-91, 1p following 591. Epub 2010 Apr 18.

Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, UK.

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http://dx.doi.org/10.1038/nm.2130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504359PMC
May 2010

Modeling sample variables with an Experimental Factor Ontology.

Bioinformatics 2010 Apr 3;26(8):1112-8. Epub 2010 Mar 3.

Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853691PMC
April 2010

International network of cancer genome projects.

Authors:
Thomas J Hudson Warwick Anderson Axel Artez Anna D Barker Cindy Bell Rosa R Bernabé M K Bhan Fabien Calvo Iiro Eerola Daniela S Gerhard Alan Guttmacher Mark Guyer Fiona M Hemsley Jennifer L Jennings David Kerr Peter Klatt Patrik Kolar Jun Kusada David P Lane Frank Laplace Lu Youyong Gerd Nettekoven Brad Ozenberger Jane Peterson T S Rao Jacques Remacle Alan J Schafer Tatsuhiro Shibata Michael R Stratton Joseph G Vockley Koichi Watanabe Huanming Yang Matthew M F Yuen Bartha M Knoppers Martin Bobrow Anne Cambon-Thomsen Lynn G Dressler Stephanie O M Dyke Yann Joly Kazuto Kato Karen L Kennedy Pilar Nicolás Michael J Parker Emmanuelle Rial-Sebbag Carlos M Romeo-Casabona Kenna M Shaw Susan Wallace Georgia L Wiesner Nikolajs Zeps Peter Lichter Andrew V Biankin Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Martin L Ferguson Peter Geary D Neil Hayes Thomas J Hudson Amber L Johns Arek Kasprzyk Hidewaki Nakagawa Robert Penny Miguel A Piris Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver P Andrew Futreal Hiroyuki Aburatani Mónica Bayés David D L Botwell Peter J Campbell Xavier Estivill Daniela S Gerhard Sean M Grimmond Ivo Gut Martin Hirst Carlos López-Otín Partha Majumder Marco Marra John D McPherson Hidewaki Nakagawa Zemin Ning Xose S Puente Yijun Ruan Tatsuhiro Shibata Michael R Stratton Hendrik G Stunnenberg Harold Swerdlow Victor E Velculescu Richard K Wilson Hong H Xue Liu Yang Paul T Spellman Gary D Bader Paul C Boutros Peter J Campbell Paul Flicek Gad Getz Roderic Guigó Guangwu Guo David Haussler Simon Heath Tim J Hubbard Tao Jiang Steven M Jones Qibin Li Nuria López-Bigas Ruibang Luo Lakshmi Muthuswamy B F Francis Ouellette John V Pearson Xose S Puente Victor Quesada Benjamin J Raphael Chris Sander Tatsuhiro Shibata Terence P Speed Lincoln D Stein Joshua M Stuart Jon W Teague Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia David A Wheeler Honglong Wu Shancen Zhao Guangyu Zhou Lincoln D Stein Roderic Guigó Tim J Hubbard Yann Joly Steven M Jones Arek Kasprzyk Mark Lathrop Nuria López-Bigas B F Francis Ouellette Paul T Spellman Jon W Teague Gilles Thomas Alfonso Valencia Teruhiko Yoshida Karen L Kennedy Myles Axton Stephanie O M Dyke P Andrew Futreal Daniela S Gerhard Chris Gunter Mark Guyer Thomas J Hudson John D McPherson Linda J Miller Brad Ozenberger Kenna M Shaw Arek Kasprzyk Lincoln D Stein Junjun Zhang Syed A Haider Jianxin Wang Christina K Yung Anthony Cros Anthony Cross Yong Liang Saravanamuttu Gnaneshan Jonathan Guberman Jack Hsu Martin Bobrow Don R C Chalmers Karl W Hasel Yann Joly Terry S H Kaan Karen L Kennedy Bartha M Knoppers William W Lowrance Tohru Masui Pilar Nicolás Emmanuelle Rial-Sebbag Laura Lyman Rodriguez Catherine Vergely Teruhiko Yoshida Sean M Grimmond Andrew V Biankin David D L Bowtell Nicole Cloonan Anna deFazio James R Eshleman Dariush Etemadmoghadam Brooke B Gardiner Brooke A Gardiner James G Kench Aldo Scarpa Robert L Sutherland Margaret A Tempero Nicola J Waddell Peter J Wilson John D McPherson Steve Gallinger Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Debabrata Mukhopadhyay Lynda Chin Ronald A DePinho Sarah Thayer Lakshmi Muthuswamy Kamran Shazand Timothy Beck Michelle Sam Lee Timms Vanessa Ballin Youyong Lu Jiafu Ji Xiuqing Zhang Feng Chen Xueda Hu Guangyu Zhou Qi Yang Geng Tian Lianhai Zhang Xiaofang Xing Xianghong Li Zhenggang Zhu Yingyan Yu Jun Yu Huanming Yang Mark Lathrop Jörg Tost Paul Brennan Ivana Holcatova David Zaridze Alvis Brazma Lars Egevard Egor Prokhortchouk Rosamonde Elizabeth Banks Mathias Uhlén Anne Cambon-Thomsen Juris Viksna Fredrik Ponten Konstantin Skryabin Michael R Stratton P Andrew Futreal Ewan Birney Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Sancha Martin Jorge S Reis-Filho Andrea L Richardson Christos Sotiriou Hendrik G Stunnenberg Giles Thoms Marc van de Vijver Laura van't Veer Fabien Calvo Daniel Birnbaum Hélène Blanche Pascal Boucher Sandrine Boyault Christian Chabannon Ivo Gut Jocelyne D Masson-Jacquemier Mark Lathrop Iris Pauporté Xavier Pivot Anne Vincent-Salomon Eric Tabone Charles Theillet Gilles Thomas Jörg Tost Isabelle Treilleux Fabien Calvo Paulette Bioulac-Sage Bruno Clément Thomas Decaens Françoise Degos Dominique Franco Ivo Gut Marta Gut Simon Heath Mark Lathrop Didier Samuel Gilles Thomas Jessica Zucman-Rossi Peter Lichter Roland Eils Benedikt Brors Jan O Korbel Andrey Korshunov Pablo Landgraf Hans Lehrach Stefan Pfister Bernhard Radlwimmer Guido Reifenberger Michael D Taylor Christof von Kalle Partha P Majumder Rajiv Sarin T S Rao M K Bhan Aldo Scarpa Paolo Pederzoli Rita A Lawlor Massimo Delledonne Alberto Bardelli Andrew V Biankin Sean M Grimmond Thomas Gress David Klimstra Giuseppe Zamboni Tatsuhiro Shibata Yusuke Nakamura Hidewaki Nakagawa Jun Kusada Tatsuhiko Tsunoda Satoru Miyano Hiroyuki Aburatani Kazuto Kato Akihiro Fujimoto Teruhiko Yoshida Elias Campo Carlos López-Otín Xavier Estivill Roderic Guigó Silvia de Sanjosé Miguel A Piris Emili Montserrat Marcos González-Díaz Xose S Puente Pedro Jares Alfonso Valencia Heinz Himmelbauer Heinz Himmelbaue Victor Quesada Silvia Bea Michael R Stratton P Andrew Futreal Peter J Campbell Anne Vincent-Salomon Andrea L Richardson Jorge S Reis-Filho Marc van de Vijver Gilles Thomas Jocelyne D Masson-Jacquemier Samuel Aparicio Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Hendrik G Stunnenberg Laura van't Veer Douglas F Easton Paul T Spellman Sancha Martin Anna D Barker Lynda Chin Francis S Collins Carolyn C Compton Martin L Ferguson Daniela S Gerhard Gad Getz Chris Gunter Alan Guttmacher Mark Guyer D Neil Hayes Eric S Lander Brad Ozenberger Robert Penny Jane Peterson Chris Sander Kenna M Shaw Terence P Speed Paul T Spellman Joseph G Vockley David A Wheeler Richard K Wilson Thomas J Hudson Lynda Chin Bartha M Knoppers Eric S Lander Peter Lichter Lincoln D Stein Michael R Stratton Warwick Anderson Anna D Barker Cindy Bell Martin Bobrow Wylie Burke Francis S Collins Carolyn C Compton Ronald A DePinho Douglas F Easton P Andrew Futreal Daniela S Gerhard Anthony R Green Mark Guyer Stanley R Hamilton Tim J Hubbard Olli P Kallioniemi Karen L Kennedy Timothy J Ley Edison T Liu Youyong Lu Partha Majumder Marco Marra Brad Ozenberger Jane Peterson Alan J Schafer Paul T Spellman Hendrik G Stunnenberg Brandon J Wainwright Richard K Wilson Huanming Yang

Nature 2010 Apr;464(7291):993-8

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http://dx.doi.org/10.1038/nature08987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.

BMC Bioinformatics 2010 Mar 1;11:112. Epub 2010 Mar 1.

MMPU, Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.

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http://dx.doi.org/10.1186/1471-2105-11-112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838865PMC
March 2010

Gene expression atlas at the European bioinformatics institute.

Nucleic Acids Res 2010 Jan 11;38(Database issue):D690-8. Epub 2009 Nov 11.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkp936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808905PMC
January 2010

Integrating sequence, evolution and functional genomics in regulatory genomics.

Genome Biol 2009 30;10(1):202. Epub 2009 Jan 30.

Computational Molecular Biology, Max-Planck-Institut für molekulare Genetik, Berlin, Germany.

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http://dx.doi.org/10.1186/gb-2009-10-1-202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687781PMC
September 2009

Importing ArrayExpress datasets into R/Bioconductor.

Bioinformatics 2009 Aug 8;25(16):2092-4. Epub 2009 Jun 8.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723004PMC
August 2009

Probabilistic retrieval and visualization of biologically relevant microarray experiments.

Bioinformatics 2009 Jun;25(12):i145-53

Department of Information and Computer Science, Helsinki Institute for Information Technology, Helsinki University of Technology, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btp215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687969PMC
June 2009

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.

Authors:
Alvis Brazma

ScientificWorldJournal 2009 May 29;9:420-3. Epub 2009 May 29.

Microarray Informatics Group, European Bioinformatics Institute, EMBl-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1100/tsw.2009.57DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5823224PMC
May 2009

Data storage and analysis in ArrayExpress and Expression Profiler.

Curr Protoc Bioinformatics 2008 Sep;Chapter 7:Unit 7.13

European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1002/0471250953.bi0713s23DOI Listing
September 2008

The BREW workshop series: a stimulating experience in PhD education.

Brief Bioinform 2008 May 23;9(3):250-3. Epub 2008 Jan 23.

Center of Biotechnology, Bielefeld University, Postfach 10 01 31, D-33501 Bielefeld, Germany.

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http://dx.doi.org/10.1093/bib/bbn002DOI Listing
May 2008

4DXpress: a database for cross-species expression pattern comparisons.

Nucleic Acids Res 2008 Jan 4;36(Database issue):D847-53. Epub 2007 Oct 4.

European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkm797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238840PMC
January 2008

MGED standards: work in progress.

OMICS 2006 ;10(2):138-44

Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94301, USA.

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November 2007

Current approaches to gene regulatory network modelling.

BMC Bioinformatics 2007 Sep 27;8 Suppl 6:S9. Epub 2007 Sep 27.

Department of Medical and Molecular Genetics, King's College London School of Medicine, 8th floor Guy's Tower, London SE1 9RT, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1995542PMC
September 2007

Prediction of gene expression in embryonic structures of Drosophila melanogaster.

PLoS Comput Biol 2007 Jul;3(7):e144

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.0030144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1924873PMC
July 2007

Data storage and analysis in ArrayExpress.

Methods Enzymol 2006 ;411:370-86

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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December 2006

ArrayExpress service for reviewers/editors of DNA microarray papers.

Nat Biotechnol 2006 Nov;24(11):1321-2

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November 2006

Reconstruction of gene regulatory networks under the finite state linear model.

Genome Inform 2005 ;16(2):225-36

Institute of Mathematics and Computer Science, University of Latvia, Rainis boulevard 29, Riga LV-1459, Latvia.

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September 2006

Standards for systems biology.

Nat Rev Genet 2006 Aug;7(8):593-605

European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1038/nrg1922DOI Listing
August 2006

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.

Bioinformatics 2006 Mar 23;22(6):765-7. Epub 2005 Dec 23.

EMBL Meyerhofstr 1 D-69117 Heidelberg, Germany.

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March 2006

Modelling in molecular biology: describing transcription regulatory networks at different scales.

Philos Trans R Soc Lond B Biol Sci 2006 Mar;361(1467):483-94

European Bioinformatics Institute Wellcome Trust Genome Campus EMBL-EBI, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1098/rstb.2005.1806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609346PMC
March 2006

A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.

Bioinformatics 2005 Nov 1;21(21):3993-9. Epub 2005 Sep 1.

EMBL Outstation-Hinxton, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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November 2005

Fusing microarray experiments with multivariate regression.

Bioinformatics 2005 Sep;21 Suppl 2:ii137-43

MRC Biostatistics Unit, Cambridge, UK.

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September 2005