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Alvis Brazma
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Research Profile (preview)
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19
Parkinson, Helen
18
Sarkans, Ugis
14
Vilo, Jaak
12
Kapushesky, Misha
11
Sherlock, Gavin
11
Stoeckert, Christian
10
Spellman, Paul
10
Sansone, Susanna-Assunta
9
Quackenbush, John
8
Shojatalab, Mohammadreza
8
Ball, Catherine
8
Causton, Helen
7
Holloway, Ele
7
Rayner, Tim
7
Rocca-Serra, Philippe
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Geonetwork of Alvis Brazma (preview)
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All Publications
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2009: Krestyaninova Maria; Zarins Andris; Viksna Juris; Kurbatova Natalja; Rucevskis Peteris; Neogi Sudeshna Guha; Gostev Mike; Perheentupa Teemu; Knuuttila Juha; Barrett Amy; Lappalainen Ilkka; Rung Johan; Podnieks Karlis; Sarkans Ugis; McCarthy Mark I; Brazma Alvis
A System for Information Management in BioMedical Studies--SIMBioMS.
Bioinformatics (Oxford, England) 2009;25(20):2768-9.
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2009: Aligianni Sofia; Lackner Daniel H; Klier Steffi; Rustici Gabriella; Wilhelm Brian T; Marguerat Samuel; Codlin Sandra; Brazma Alvis; de Bruin Robertus A M; Bähler Jürg
The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.
PLoS genetics 2009;5(8):e1000626.
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2009: Kauffmann Audrey; Rayner Tim F; Parkinson Helen; Kapushesky Misha; Lukk Margus; Brazma Alvis; Huber Wolfgang
Importing ArrayExpress datasets into R/Bioconductor.
Bioinformatics (Oxford, England) 2009;25(16):2092-4.
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2009: Caldas José; Gehlenborg Nils; Faisal Ali; Brazma Alvis; Kaski Samuel
Probabilistic retrieval and visualization of biologically relevant microarray experiments.
Bioinformatics (Oxford, England) 2009;25(12):i145-53.
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2009: Brazma Alvis
Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.
TheScientificWorldJournal 2009;9():420-3.
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2009: Vingron Martin; Brazma Alvis; Coulson Richard; van Helden Jacques; Manke Thomas; Palin Kimmo; Sand Olivier; Ukkonen Esko
Integrating sequence, evolution and functional genomics in regulatory genomics.
Genome biology 2009;10(1):202.
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2008: Rustici Gabriella; Kapushesky Misha; Kolesnikov Nikolay; Parkinson Helen; Sarkans Ugis; Brazma Alvis
Data storage and analysis in ArrayExpress and Expression Profiler.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2008;Chapter 7():Unit 7.13.
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2008: Sansone Susanna-Assunta; Rocca-Serra Philippe; Brandizi Marco; Brazma Alvis; Field Dawn; Fostel Jennifer; Garrow Andrew G; Gilbert Jack; Goodsaid Federico; Hardy Nigel; Jones Phil; Lister Allyson; Miller Michael; Morrison Norman; Rayner Tim; Sklyar Nataliya; Taylor Chris; Tong Weida; Warner Guy; Wiemann Stefan;
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".
Omics : a journal of integrative biology 2008;12(2):143-9.
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2008: Giegerich Robert; Brazma Alvis; Jonassen Inge; Ukkonen Esko; Vingron Martin
The BREW workshop series: a stimulating experience in PhD education.
Briefings in bioinformatics 2008;9(3):250-3.
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2008: Haudry Yannick; Berube Hugo; Letunic Ivica; Weeber Paul-Daniel; Gagneur Julien; Girardot Charles; Kapushesky Misha; Arendt Detlev; Bork Peer; Brazma Alvis; Furlong Eileen E M; Wittbrodt Joachim; Henrich Thorsten
4DXpress: a database for cross-species expression pattern comparisons.
Nucleic acids research 2008;36(Database issue):D847-53.
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2007: Jones Andrew R; Miller Michael; Aebersold Ruedi; Apweiler Rolf; Ball Catherine A; Brazma Alvis; Degreef James; Hardy Nigel; Hermjakob Henning; Hubbard Simon J; Hussey Peter; Igra Mark; Jenkins Helen; Julian Randall K; Laursen Kent; Oliver Stephen G; Paton Norman W; Sansone Susanna-Assunta; Sarkans Ugis; Stoeckert Christian J; Taylor Chris F; Whetzel Patricia L; White Joseph A; Spellman Paul; Pizarro Angel
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Nature biotechnology 2007;25(10):1127-33.
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2007: Samsonova Anastasia A; Niranjan Mahesan; Russell Steven; Brazma Alvis
Prediction of gene expression in embryonic structures of Drosophila melanogaster.
PLoS computational biology 2007;3(7):e144.
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2007: Parkinson H; Kapushesky M; Shojatalab M; Abeygunawardena N; Coulson R; Farne A; Holloway E; Kolesnykov N; Lilja P; Lukk M; Mani R; Rayner T; Sharma A; William E; Sarkans U; Brazma A
ArrayExpress--a public database of microarray experiments and gene expression profiles.
Nucleic acids research 2007;35(Database issue):D747-50.
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2007: Schlitt Thomas; Brazma Alvis
Current approaches to gene regulatory network modelling.
BMC bioinformatics 2007;8 Suppl 6():S9.
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2007: Rustici Gabriella; van Bakel Harm; Lackner Daniel H; Holstege Frank C; Wijmenga Cisca; Bähler Jürg; Brazma Alvis
Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.
Genome biology 2007;8(5):R73.
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2007: Viksna Juris; Celms Edgars; Opmanis Martins; Podnieks Karlis; Rucevskis Peteris; Zarins Andris; Barrett Amy; Neogi Sudeshna Guha; Krestyaninova Maria; McCarthy Mark I; Brazma Alvis; Sarkans Ugis
PASSIM--an open source software system for managing information in biomedical studies.
BMC bioinformatics 2007;8():52.
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2006: Brazma Alvis; Parkinson Helen;
ArrayExpress service for reviewers/editors of DNA microarray papers.
Nature biotechnology 2006;24(11):1321-2.
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2006: Brazma Alvis; Krestyaninova Maria; Sarkans Ugis
Standards for systems biology.
Nature reviews. Genetics 2006;7(8):593-605.
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2006: Schlitt Thomas; Brazma Alvis
Modelling in molecular biology: describing transcription regulatory networks at different scales.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006;361(1467):483-94.
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2006: Quackenbush John; Stoeckert Christian; Ball Catherine; Brazma Alvis; Gentleman Robert; Huber Wolfgang; Irizarry Rafael; Salit Marc; Sherlock Gavin; Spellman Paul; Winegarden Neil
Top-down standards will not serve systems biology.
Nature 2006;440(7080):24.
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2006: Blake Jonathon; Schwager Christian; Kapushesky Misha; Brazma Alvis
ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.
Bioinformatics (Oxford, England) 2006;22(6):765-7.
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2006: Stoeckert Christian; Ball Catherine; Brazma Alvis; Brinkman Ryan; Causton Helen; Fan Liju; Fostel Jennifer; Fragoso Gilberto; Heiskanen Mervi; Holstege Frank; Morrison Norman; Parkinson Helen; Quackenbush John; Rocca-Serra Philippe; Sansone Susanna-Assunta; Sarkans Ugis; Sherlock Gavin; Stevens Robert; Taylor Chris; Taylor Ronald; Whetzel Patricia; White Joseph
Wrestling with SUMO and bio-ontologies.
Nature biotechnology 2006;24(1):21-2; author reply 23.
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2006: Rayner Tim F; Rocca-Serra Philippe; Spellman Paul T; Causton Helen C; Farne Anna; Holloway Ele; Irizarry Rafael A; Liu Junmin; Maier Donald S; Miller Michael; Petersen Kjell; Quackenbush John; Sherlock Gavin; Stoeckert Christian J; White Joseph; Whetzel Patricia L; Wymore Farrell; Parkinson Helen; Sarkans Ugis; Ball Catherine A; Brazma Alvis
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
BMC bioinformatics 2006;7():489.
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2006: Brazma Alvis; Kapushesky Misha; Parkinson Helen; Sarkans Ugis; Shojatalab Mohammad
Data storage and analysis in ArrayExpress.
Methods in enzymology 2006;411():370-86.
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2006: Ball Catherine A; Brazma Alvis
MGED standards: work in progress.
Omics : a journal of integrative biology 2006;10(2):138-44.
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2005: Torrente Aurora; Kapushesky Misha; Brazma Alvis
A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.
Bioinformatics (Oxford, England) 2005;21(21):3993-9.
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2005: Mukherjee Gaurab; Abeygunawardena Niran; Parkinson Helen; Contrino Sergio; Durinck Steffen; Farne Anna; Holloway Ele; Lilja Per; Moreau Yves; Oezcimen Ahmet; Rayner Tim; Sharma Anjan; Brazma Alvis; Sarkans Ugis; Shojatalab Mohammadreza
Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.
Plant physiology 2005;139(2):632-6.
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2005: Gilks Walter R; Tom Brian D M; Brazma Alvis
Fusing microarray experiments with multivariate regression.
Bioinformatics (Oxford, England) 2005;21 Suppl 2():ii137-43.
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2005: Durinck Steffen; Moreau Yves; Kasprzyk Arek; Davis Sean; De Moor Bart; Brazma Alvis; Huber Wolfgang
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
Bioinformatics (Oxford, England) 2005;21(16):3439-40.
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2005: Sarkans Ugis; Parkinson Helen; Lara Gonzalo Garcia; Oezcimen Ahmet; Sharma Anjan; Abeygunawardena Niran; Contrino Sergio; Holloway Ele; Rocca-Serra Philippe; Mukherjee Gaurab; Shojatalab Mohammadreza; Kapushesky Misha; Sansone Susanna-Assunta; Farne Anna; Rayner Tim; Brazma Alvis
The ArrayExpress gene expression database: a software engineering and implementation perspective.
Bioinformatics (Oxford, England) 2005;21(8):1495-501.
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2005: Schlitt Thomas; Brazma Alvis
Modelling gene networks at different organisational levels.
FEBS letters 2005;579(8):1859-66.
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2005: Parkinson H; Sarkans U; Shojatalab M; Abeygunawardena N; Contrino S; Coulson R; Farne A; Lara G Garcia; Holloway E; Kapushesky M; Lilja P; Mukherjee G; Oezcimen A; Rayner T; Rocca-Serra P; Sharma A; Sansone S; Brazma A
ArrayExpress--a public repository for microarray gene expression data at the EBI.
Nucleic acids research 2005;33(Database issue):D553-5.
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2005: Ruklisa Dace; Brazma Alvis; Viksna Juris
Reconstruction of gene regulatory networks under the finite state linear model.
Genome informatics. International Conference on Genome Informatics 2005;16(2):225-36.
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2004: Ball Catherine; Brazma Alvis; Causton Helen; Chervitz Steve; Edgar Ron; Hingamp Pascal; Matese John C; Icahn Carl; Parkinson Helen; Quackenbush John; Ringwald Martin; Sansone Susanna-Assunta; Sherlock Gavin; Spellman Paul; Stoeckert Christian; Tateno Yoshio; Taylor Ronald; White Joseph; Winegarden Neil;
An open letter on microarray data from the MGED Society.
Microbiology (Reading, England) 2004;150(Pt 11):3522-4.
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2004: Ball Catherine A; Brazma Alvis; Causton Helen; Chervitz Steve; Edgar Ron; Hingamp Pascal; Matese John C; Parkinson Helen; Quackenbush John; Ringwald Martin; Sansone Susanna-Assunta; Sherlock Gavin; Spellman Paul; Stoeckert Chris; Tateno Yoshio; Taylor Ronald; White Joseph; Winegarden Neil
Submission of microarray data to public repositories.
PLoS biology 2004;2(9):E317.
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2004: Ball Catherine A; Sherlock Gavin; Brazma Alvis
Funding high-throughput data sharing.
Nature biotechnology 2004;22(9):1179-83.
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2004: Ball Catherine; Brazma Alvis; Causton Helen; Chervitz Steve; Edgar Ron; Hingamp Pascal; Matese John C; Parkinson Helen; Quackenbush John; Ringwald Martin; Sansone Susanna-Assunta; Sherlock Gavin; Spellman Paul; Stoeckert Christian; Tateno Yoshio; Taylor Ronald; White Joseph; Winegarden Neil;
Standards for microarray data: an open letter.
Environmental health perspectives 2004;112(12):A666-7.
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2004: Rustici Gabriella; Mata Juan; Kivinen Katja; Lió Pietro; Penkett Christopher J; Burns Gavin; Hayles Jacqueline; Brazma Alvis; Nurse Paul; Bähler Jürg
Periodic gene expression program of the fission yeast cell cycle.
Nature genetics 2004;36(8):809-17.
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2004: Kapushesky Misha; Kemmeren Patrick; Culhane Aedín C; Durinck Steffen; Ihmels Jan; Körner Christine; Kull Meelis; Torrente Aurora; Sarkans Ugis; Vilo Jaak; Brazma Alvis
Expression Profiler: next generation--an online platform for analysis of microarray data.
Nucleic acids research 2004;32(Web Server issue):W465-70.
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2003: Schlitt Thomas; Palin Kimmo; Rung Johan; Dietmann Sabine; Lappe Michael; Ukkonen Esko; Brazma Alvis
From gene networks to gene function.
Genome research 2003;13(12):2568-76.
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2003: Rocca-Serra Philippe; Brazma Alvis; Parkinson Helen; Sarkans Ugis; Shojatalab Mohammadreza; Contrino Sergio; Vilo Jaak; Abeygunawardena Niran; Mukherjee Gaurab; Holloway Ele; Kapushesky Misha; Kemmeren Patrick; Lara Gonzalo Garcia; Oezcimen Ahmet; Sansone Susanna-Assunta
ArrayExpress: a public database of gene expression data at EBI.
Comptes rendus biologies 2003;326(10-11):1075-8.
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2003: Brazma Alvis; Ikeo Kazuho; Tateno Yoshio
[Standardization of microarray experiment data]
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 2003;48(3):280-5.
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2003: Chen Dongrong; Toone W Mark; Mata Juan; Lyne Rachel; Burns Gavin; Kivinen Katja; Brazma Alvis; Jones Nic; Bähler Jürg
Global transcriptional responses of fission yeast to environmental stress.
Molecular biology of the cell 2003;14(1):214-29.
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2003: Brazma Alvis; Parkinson Helen; Sarkans Ugis; Shojatalab Mohammadreza; Vilo Jaak; Abeygunawardena Niran; Holloway Ele; Kapushesky Misha; Kemmeren Patrick; Lara Gonzalo Garcia; Oezcimen Ahmet; Rocca-Serra Philippe; Sansone Susanna-Assunta
ArrayExpress--a public repository for microarray gene expression data at the EBI.
Nucleic acids research 2003;31(1):68-71.
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2003: Brooksbank Catherine; Camon Evelyn; Harris Midori A; Magrane Michele; Martin Maria Jesus; Mulder Nicola; O'Donovan Claire; Parkinson Helen; Tuli Mary Ann; Apweiler Rolf; Birney Ewan; Brazma Alvis; Henrick Kim; Lopez Rodrigo; Stoesser Guenter; Stoehr Peter; Cameron Graham
The European Bioinformatics Institute's data resources.
Nucleic acids research 2003;31(1):43-50.
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2003: Soinov Lev A; Krestyaninova Maria A; Brazma Alvis
Towards reconstruction of gene networks from expression data by supervised learning.
Genome biology 2003;4(1):R6.
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2002: Ball Catherine A; Sherlock Gavin; Parkinson Helen; Rocca-Sera Philippe; Brooksbank Catherine; Causton Helen C; Cavalieri Duccio; Gaasterland Terry; Hingamp Pascal; Holstege Frank; Ringwald Martin; Spellman Paul; Stoeckert Christian J; Stewart Jason E; Taylor Ronald; Brazma Alvis; Quackenbush John;
The underlying principles of scientific publication.
Bioinformatics (Oxford, England) 2002;18(11):1409.
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2002: Ball Catherine A; Sherlock Gavin; Parkinson Helen; Rocca-Sera Philippe; Brooksbank Catherine; Causton Helen C; Cavalieri Duccio; Gaasterland Terry; Hingamp Pascal; Holstege Frank; Ringwald Martin; Spellman Paul; Stoeckert Christian J; Stewart Jason E; Taylor Ronald; Brazma Alvis; Quackenbush John;
Standards for microarray data.
Science (New York, N.Y.) 2002;298(5593):539.
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2002: Spellman Paul T; Miller Michael; Stewart Jason; Troup Charles; Sarkans Ugis; Chervitz Steve; Bernhart Derek; Sherlock Gavin; Ball Catherine; Lepage Marc; Swiatek Marcin; Marks W L; Goncalves Jason; Markel Scott; Iordan Daniel; Shojatalab Mohammadreza; Pizarro Angel; White Joe; Hubley Robert; Deutsch Eric; Senger Martin; Aronow Bruce J; Robinson Alan; Bassett Doug; Stoeckert Christian J; Brazma Alvis
Design and implementation of microarray gene expression markup language (MAGE-ML).
Genome biology 2002;3(9):RESEARCH0046.
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2002: Kemmeren Patrick; van Berkum Nynke L; Vilo Jaak; Bijma Theo; Donders Rogier; Brazma Alvis; Holstege Frank C P
Protein interaction verification and functional annotation by integrated analysis of genome-scale data.
Molecular cell 2002;9(5):1133-43.
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2002: Schlitt Thomas; Brazma Alvis
Learning about gene regulatory networks from gene deletion experiments.
Comparative and functional genomics 2002;3(6):499-503.
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2002: Rung J; Schlitt T; Brazma A; Freivalds K; Vilo J
Building and analysing genome-wide gene disruption networks.
Bioinformatics (Oxford, England) 2002;18 Suppl 2():S202-10.
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2002: Palin Kimmo; Ukkonen Esko; Brazma Alvis; Vilo Jaak
Correlating gene promoters and expression in gene disruption experiments.
Bioinformatics (Oxford, England) 2002;18 Suppl 2():S172-80.
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2002: Brazma Alvis; Sarkans Ugis; Robinson Alan; Vilo Jaak; Vingron Martin; Hoheisel Jörg; Fellenberg Kurt
Microarray data representation, annotation and storage.
Advances in biochemical engineering/biotechnology 2002;77():113-39.
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2001: Brazma A; Hingamp P; Quackenbush J; Sherlock G; Spellman P; Stoeckert C; Aach J; Ansorge W; Ball C A; Causton H C; Gaasterland T; Glenisson P; Holstege F C; Kim I F; Markowitz V; Matese J C; Parkinson H; Robinson A; Sarkans U; Schulze-Kremer S; Stewart J; Taylor R; Vilo J; Vingron M
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Nature genetics 2001;29(4):365-71.
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2001: Brazma A; Vilo J
Gene expression data analysis.
Microbes and infection / Institut Pasteur 2001;3(10):823-9.
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2000: Brazma A; Vilo J
Gene expression data analysis.
FEBS letters 2000;480(1):17-24.
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2000: Brazma A; Robinson A; Cameron G; Ashburner M
One-stop shop for microarray data.
Nature 2000;403(6771):699-700.
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2000: Vilo J; Brazma A; Jonassen I; Robinson A; Ukkonen E
Mining for putative regulatory elements in the yeast genome using gene expression data.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 2000;8():384-94.
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1998: Brazma A; Jonassen I; Vilo J; Ukkonen E
Predicting gene regulatory elements in silico on a genomic scale.
Genome research 1998;8(11):1202-15.
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1998: Brazma A; Jonassen I; Eidhammer I; Gilbert D
Approaches to the automatic discovery of patterns in biosequences.
Journal of computational biology : a journal of computational molecular cell biology 1998;5(2):279-305.
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1997: Brazma A; Vilo J; Ukkonen E; Valtonen K
Data mining for regulatory elements in yeast genome.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1997;5():65-74.
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1996: Brazma A; Jonassen I; Ukkonen E; Vilo J
Discovering patterns and subfamilies in biosequences.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1996;4():34-43.
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