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Publications
A brief listing of our publications in chronological order: 2009Variants in MTNR1B influence fasting glucose levels.
(2009). Nat Genet. Jan;41(1):77-81. doi:10.1038/ng.290
[CiteXplore]
[PDF] [Link]
Integrating sequence, evolution and functional genomics in regulatory genomics.
(2009). Genome Biology 10: 202. doi:10.1186/gb-2009-10-1-202
[CiteXplore]
[PDF] [Link]
MAGETabulator, a suite of tools to support the microarray data format
MAGE-TAB.
(2009). Bioinformatics 25: 279-280. DOI 10.1093/bioinformatics/btn617
[CiteXplore]
[PDF] [Link]
2008ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression.
(2008). Nucl. Acids Res. doi:10.1093/nar/gkn889
[CiteXplore]
[PDF] [Link]
Data Storage and Analysis in ArrayExpress and Expression Profiler.
(2008). Mutat. Res. Sep; Chapter 7:Unit 7.13.
[CiteXplore]
[PDF]
The carcinoGENOMICS project: critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays.
(2008). Mutat. Res. 659(3): 202-10.
[CiteXplore]
[PDF]
Guidelines for reporting the use of mass spectrometry in proteomics.
(2008). Nat Biotech 26: 860-861.
[CiteXplore]
[PDF]
Guidelines for reporting the use of mass spectrometry informatics in proteomics.
(2008). Nat Biotech 26: 862-862.
[CiteXplore]
[PDF]
Guidelines for reporting the use of gel electrophoresis in proteomics.
(2008). Nat Biotech 26: 863-864.
[CiteXplore]
[PDF]
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
(2008). Nat Biotech 26: 889-896.
[CiteXplore]
[PDF]
The minimum information about a genome sequence (MIGS) specification.
(2008). Nat Biotech 26: 541-547.
[CiteXplore]
[PDF]
4DXpress: a database for cross-species expression pattern comparisons.
(2008). Nucleic Acids Res. 36(suppl_1): D847-D853.
[CiteXplore]
[PDF]
2007Gene expression databases.
(2007). Encyclopedia of Life Sciences
[Link]
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
(2007). Nat Biotech 25, 1251 - 1255
[CiteXplore]
[PDF]
Current approaches to gene regulatory network modelling.
(2007). BMC Bioinformatics. 27;8 Suppl 6:S9
[CiteXplore]
[PDF]
The metabolomics standards initiative (MSI)
(2007). Metabolomics 3, 175-178.
[Link]
[PDF]
Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments
(2007). Metabolomics 3, 179-188.
[Link]
[PDF]
Standard reporting requirements for biological samples in metabolomics experiments: environmental context
(2007). Metabolomics 3, 203-210.
[Link]
[PDF]
A roadmap for the establishment of standard data exchange structures for metabolomics
(2007). Metabolomics 3, 243-248.
[Link]
[PDF]
Metabolomics standards initiative: ontology working group work in progress
(2007). Metabolomics 3, 249-256.
[Link]
[PDF]
The Functional Genomics Experiment model (FuGE): an extensible framework for
standards in functional genomics.
(2007). Nat Biotech 25, 1127-1133.
[CiteXplore]
[PDF]
The Metabolomics Standards Initiative.
(2007). Nat Biotech 25, 846 - 848.
[CiteXplore]
[PDF]
The minimum information about a proteomics experiment (MIAPE)
(2007). Nat Biotech 25, 887 - 893.
[CiteXplore]
[PDF]
Standards for reporting bioscience data: a forward look.
(2007). Drug Discov Today 12(13-14):527-33
[CiteXplore]
Progress in standards for reporting omics data.
(2007). Curr Opin Drug Discov Devel 10(3):254-63
[CiteXplore]
Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.
(2007). Proteomics 7(3):337-9
[CiteXplore]
Proteomic data exchange and storage: the need for common standards and public repositories.
(2007). Methods Mol Biol 367:261-70
[CiteXplore]
Lineage-specific partitions in archaeal transcription.
(2007). Archaea. 2(2):117-25.
[CiteXplore]
[PDF]
Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins.
(2007). BMC Evol Biol. 23;7:29.
[CiteXplore]
[PDF]
Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster.
(2007). PLoS Comput Biol. 20;3(7):e144
[CiteXplore]
[PDF]
Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.
(2007). Genome Biology, 8:R73.
[CiteXplore]
[PDF]
PASSIM – an open source software system for managing information in biomedical studies.
(2007). BMC Bioinformatics, 8:52.
[CiteXplore]
[PDF]
ArrayExpress—a public database of microarray experiments and gene expression profiles.
(2007). Nucleic Acids Res., Vol:35 (Issue: Database issue), D747-50.
[CiteXplore]
[PDF]
2006Modelling in molecular biology: describing transcription regulatory networks.
(2006). Philosophical Transactions Royal Society B, 361 (1467), 483-494 [DOI: 10.1098/rstb.2005.1806].
[Abstract]
[PDF - 385kb]
ArrayExpress service for reviewers/editors of DNA microarray papers.
(2006). Nat Biotechnol., 24(11), 1321-2.
[CiteXplore]
[PDF]
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
(2006). BMC Bioinformatics, 7, 489.
[CiteXplore]
[PDF]
Dawn Field and Susanna-Assunta Sansone. A Special Issue on Data Standards
(2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 84-93. [PDF]
Catherine A. Ball and Alvis Brazma. MGED Standards: Work in Progress
(2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 138-144. [PDF]
Oliver Fiehn, Bruce Kristal, Ben Van Ommen, Lloyd W. Sumner, Susanna-Assunta Sansone, Chris Taylor, Nigel Hardy, Rima Kaddurah-Daouk. Establishing Reporting Standards for Metabolomic and Metabonomic Studies: A Call for Participation
(2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 158-163. [PDF]
Susanna-Assunta Sansone, Philippe Rocca-Serra, Weida Tong, Jennifer Fostel, Norman Morrison, Andrew R. Jones. A Strategy Capitalizing on Synergies: The Reporting Structure for Biological Investigation (RSBI) Working Group
(2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 164-171. [PDF]
Norman Morrison, A. Joseph Wood, David Hancock, Sonia Shah, Luke Hakes, Tanya Gray, Bela Tiwari, Peter Kille, Andrew Cossins, Matthew Hegarty, Michael J. Allen, William H. Wilson, Peter Olive, Kim Last, Cas Kramer, Thierry Bailhache, Jonathan Reeves, Denise Pallett, Justin Warne, Karim Nashar, Helen Parkinson, Susanna-Assunta Sansone, Philippe Rocca-Serra, Robert Stevens, Jason Snape, Andy Brass, Dawn Field. Standard Annotation of Environmental OMICS Data: Application to the Transcriptomics Domain
(2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 172-178. [PDF]
Patricia L. Whetzel, Ryan R. Brinkman, Helen C. Causton, Liju Fan, Dawn Field, Jennifer Fostel, Gilberto Fragoso, Tanya Gray, Mervi Heiskanen, Tina Hernandez-Boussard, Norman Morrison, Helen Parkinson, Philippe Rocca-Serra, Susanna-Assunta Sansone, Daniel Schober, Barry Smith, Robert Stevens, Christian J. Stoeckert Jr., Chris Taylor, Joe White, Andrew Wood. Development of FuGO: An Ontology for Functional Genomics Investigations
(2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 199-204. [PDF]
Eric W. Deutsch, Catherine A. Ball, G. Steven Bova, Alvis Brazma, Roger E. Bumgarner, David Campbell, Helen C. Causton, Jeff Christiansen, Duncan Davidson, Lillian J. Eichner, Young Ah Goo, Sean Grimmond, Thorsten Henrich, Michael H. Johnson, Martin Korb, Jason C. Mills, Asa Oudes, Helen E. Parkinson, Laura E. Pascal, John Quackenbush, Mirana Ramialison, Martin Ringwald, Susanna-A. Sansone, Gavin Sherlock, Christian J. Stoeckert Jr., Jason Swedlow, Ronald C. Taylor, et al. Development of the Minimum Information Specification forIn SituHybridization and Immunohistochemistry Experiments (MISFISHIE)
(2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 205-208. [PDF]
Patricia L. Whetzel, Helen Parkinson and Christian J. Stoeckert, Jr. (2006). [17] Using Ontologies to Annotate Microarray Experiments
Methods in Enzymology (DNA Microarrays, Part B: Databases and Statistics): Academic Press, 411, 325-339. [doi:10.1016/S0076-6879(06)11017-4]. [Abstract] [PDF]
Alvis Brazma, Misha Kapushesky, Helen Parkinson, Ugis Sarkans and Mohammad Shojatalab . (2006). [20] Data Storage and Analysis in
ArrayExpress.
Methods in Enzymology (DNA Microarrays, Part B: Databases and Statistics): Academic Press, 411, 370-86. [doi:10.1016/S0076-6879(06)11020-4]. [Abstract] [PDF]
Alvis Brazma, Maria Krestyaninova and Ugis Sarkans. (2006). Standards for systems biology.
Nat Rev Genet, 7, 593-605. [doi:10.1038/nrg1922]. [PDF]
Helen Parkison, Susanna-Assunta Sansone, Ugis Sarkans, Philippe Rocca-Serra and Alvis Brazma. (2006). Cell Biology - A Laboratory Handbook. ArrayExpress: A Public Repository for Microarray Data.
Academic Press, Third Edition, Vol 4, 95-102 [ISBN:0121647307]. [Amazon]
Aedin Culhane and Alvis Brazma. (2006). In Silico Technologies in Drug Target Identification and Validation - Mining of Gene-Expression Data.
CRC Press, Drug Discovery Series/6, 123-149 [ISBN:1574444786]. [Amazon]
A. Garcia Castro, P. Rocca-Serra, R. Stevens, C. Taylor, K. Nashar, M.A. Ragan, and S.A. Sansone. (2006). The use of concept maps during knowledge elicitation in ontology development processes. The nutrigenomics use case.
BMC Bioinformatics, 7(1), 267. [doi:10.1186/1471-2105-7-267]. [Abstract] [PDF]
T. Freeman and Alvis Brazma. (2006). Editorial (Special issue - Comparative & functional genomics workshop).
Briefings in Functional Genomics and Proteomics, 5, 1-3. [doi:10.1093/bfgp/ell016]. [PDF]
J. Blake, C. Schwager, M. Kapushesky and Alvis Brazma. (2006). ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.
Bioinformatics, 22, 765-7 [doi:10.1093/bioinformatics/btk022]. [Abstract] [PDF]
Genomics of Aspergillus fumigatus.
(2006).Rev Iberoam Micol.22(4):223-8.
[CiteXplore]
2005William C. Nierman, Arnab Pain, Michael J. Anderson, Jennifer R. Wortman, H. Stanley Kim, Javier Arroyo, Matthew Berriman, Keietsu Abe, David B. Archer, Clara Bermejo, Joan Bennett, Paul Bowyer, Dan Chen, Matthew Collins, Richard Coulsen, Robert Davies, Paul S. Dyer, Mark Farman, Nadia Fedorova, Natalie Fedorova, Tamara V. Feldblyum, Reinhard Fischer, Nigel Fosker, Audrey Fraser, Jose L. Garca, Maria J. Garc a, Arlette Goble, Gustavo H. Goldman, Katsuya Gomi, Sam Griffith-Jones, Ryan Gwilliam, Brian Haas, Hubertus Haas, David Harris, H. Horiuchi, Jiaqi Huang, Sean Humphray, Javier Jimnez, Nancy Keller, Hoda Khouri, Katsuhiko Kitamoto, Tetsuo Kobayashi, Sven Konzack, Resham Kulkarni, Toshitaka Kumagai, Anne Lafton, Jean-Paul Latg , Weixi Li, Angela Lord, Charles Lu, William H. Majoros, Gregory S. May, Bruce L. Miller, Yasmin Mohamoud, Maria Molina, Michel Monod, Isabelle Mouyna, Stephanie Mulligan, Lee Murphy, Susan O'Neil, Ian Paulsen, Miguel A. Pealva, Mihaela Pertea, Claire Price, Bethan L. Pritchard, Michael A. Quail, Ester Rabbinowitsch, Neil Rawlins, Marie-Adele Rajandream, Utz Reichard, Hubert Renauld, Geoffrey D. Robson, Santiago Rodriguez de C rdoba, Jose M. Rodrguez-Pe a, Catherine M. Ronning, Simon Rutter, Steven L. Salzberg, Miguel Sanchez, Juan C. Snchez-Ferrero, David Saunders, Kathy Seeger, Rob Squares, Steven Squares, Michio Takeuchi, Fredj Tekaia, Geoffrey Turner, Carlos R. Vazquez de Aldana, Janice Weidman, Owen White, John Woodward, Jae-Hyuk Yu, Claire Fraser, James E. Galagan, Kiyoshi Asai, Masayuki Machida, Neil Hall,, Bart Barrell and David W. Denning. (2005). Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.
Nature, 438, 1151-1156 [doi:10.1038/nature04332]. [Abstract] [PDF]
Alasdair C. Ivens, Christopher S. Peacock, Elizabeth A. Worthey, Lee Murphy, Gautam Aggarwal, Matthew Berriman, Ellen Sisk, Marie-Adele Rajandream, Ellen Adlem, Rita Aert, Atashi Anupama, Zina Apostolou, Philip Attipoe, Nathalie Bason, Christopher Bauser, Alfred Beck, Stephen M. Beverley, Gabriella Bianchettin, Katja Borzym, Gordana Bothe, Carlo V. Bruschi, Matt Collins, Eithon Cadag, Laura Ciarloni, Christine Clayton, Richard M. R. Coulson, Ann Cronin, Angela K. Cruz, Robert M. Davies, Javier De Gaudenzi, Deborah E. Dobson, Andreas Duesterhoeft, Gholam Fazelina, Nigel Fosker, Alberto Carlos Frasch, Audrey Fraser, Monika Fuchs, Claudia Gabel, Arlette Goble, André Goffeau, David Harris, Christiane Hertz-Fowler, Helmut Hilbert, David Horn, Yiting Huang, Sven Klages, Andrew Knights, Michael Kube, Natasha Larke, Lyudmila Litvin, Angela Lord, Tin Louie, Marco Marra, David Masuy, Keith Matthews, Shulamit Michaeli, Jeremy C. Mottram, Silke Müller-Auer, Heather Munden, Siri Nelson, Halina Norbertczak, Karen Oliver, Susan O'Neil, Martin Pentony, Thomas M. Pohl, Claire Price, Bénédicte Purnelle, Michael A. Quail, Ester Rabbinowitsch, Richard Reinhardt, Michael Rieger, Joel Rinta, Johan Robben, Laura Robertson, Jeronimo C. Ruiz, Simon Rutter, David Saunders, Melanie Schäfer, Jacquie Schein, David C. Schwartz, Kathy Seeger, Amber Seyler, Sarah Sharp, Heesun Shin, Dhileep Sivam, Rob Squares, Steve Squares, Valentina Tosato, Christy Vogt, Guido Volckaert, Rolf Wambutt, Tim Warren, Holger Wedler, John Woodward, Shiguo Zhou, Wolfgang Zimmermann, Deborah F. Smith, Jenefer M. Blackwell, Kenneth D. Stuart, Bart Barrell, and Peter J. Myler. (2005). The Genome of the Kinetoplastid Parasite, Leishmania major.
Science, 309, 436-442 [DOI: 10.1126/science.1112680]. [Abstract] [PDF]
Arnab Pain, Hubert Renauld, Matthew Berriman, Lee Murphy, Corin A. Yeats, William Weir, Arnaud Kerhornou, Martin Aslett, Richard Bishop, Christiane Bouchier, Madeleine Cochet, Richard M. R. Coulson, Ann Cronin, Etienne P. de Villiers, Audrey Fraser, Nigel Fosker, Malcolm Gardner, Arlette Goble, Sam Griffiths-Jones, David E. Harris, Frank Katzer, Natasha Larke, Angela Lord, Pascal Maser, Sue McKellar, Paul Mooney, Fraser Morton, Vishvanath Nene, Susan O'Neil, Claire Price, Michael A. Quail, Ester Rabbinowitsch, Neil D. Rawlings, Simon Rutter, David Saunders, Kathy Seeger, Trushar Shah, Robert Squares, Steven Squares, Adrian Tivey, Alan R. Walker, John Woodward, Dirk A. E. Dobbelaere, Gordon Langsley, Marie-Adele Rajandream, Declan McKeever, Brian Shiels, Andrew Tait, Bart Barrell, and Neil Hall. (2005). Genome of the host-cell transforming parasite Theileria annulata compared with T. parva.
Science, 309, 131-133 [DOI: 10.1126/science.1110418]. [Abstract] [PDF]
Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress.
G. Mukherjee, N. Abeygunawardena, H. Parkinson, S. Contrino, S. Durinck, A. Farne, E. Holloway, P. Lilja, Y. Moreau, A. Oezcimen, T. Rayner, A. Sharma, A. Brazma, U. Sarkans, and M. Shojatalab. Plant Physiol., 2005, 139: 632-636. [Abstract] [PDF]
Fusing microarray experiments with multivariate regression.
W.R. Gilks, B.D.M. Tom and A. Brazma. Bioinformatics, 2005, vol 21, suppl. 2: ii137-ii143.doi:10.1093/bioinformatics/bti1123. [Abstract] [PDF]
A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.
A. Torrente, M. Kapushesky and A. Brazma. Bioinformatics, 2005, doi:10.1093/bioinformatics/bti644. [Abstract] [PDF] [Suppl. Info]. OPEN ACCESS ARTICLE.
Validation of Toxicogenomics-Based Test Systems: ECVAM-ICCVAM/NICEATM Considerations for Regulatory Use
R. Corvi, H. Ahr, S. Albertini, D.H. Blakey, L. Clerici, S. Coecke, G.R. Douglas, L. Gribaldo, J.P. Groten, B. Haase, K. Hamernik, T. Hartung, T. Inoue, I. Indans, D. Maurici, G. Orphanides, D. Rembges, S. Sansone, J.R. Snape, E. Toda, W. Tong, J.H. Delft, B. Weis, and L.M. Schechtman. Environ Health Perspect., 2005, doi:10.1289/ehp.8247. [PDF - 518kb].
Summary recommendations for standardization and reporting of metabolic analyses.
J.C. Lindon, J.K. Nicholson, H. Holmes, H.C. Keun, A. Craig, J.T.M. Pearce, S.J. Bruce, N. Hardy, S.A. Sansone et al. (The Standard Metabolic Reporting Structures working group). Nat Biotechnol., 2005, 23: 833-838. [Abstract] [PDF].
BioMart and Bioconductor: a powerful link between
biological databases and microarray data analysis.
S. Durinck, Y. Moreau, A. Kasprzyk, S. Davis, B. De Moor, A. Brazma and W. Huber. Bioinformatics, 2005, Vol 21: 3439-40. [Abstract] [PDF].
Defining best practice for microarray analyses in nutrigenomic studies
P Garosi, C De Filippo, M van Erk, P Rocca-Serra, SA Sansone and R Elliott. British Journal of Nutrition, 2005, Vol 93, No 4: 425–432;DOI: 10.1079/BJN20041385. [Abstract].
Minireview: Modelling gene networks at different organisational levels
T. Schlitt and A. Brazma. FEBS Letters, 2005, 579: 1859-1866 [Abstract]
[PDF].
Standardization initiatives in the (eco)toxicogenomics domain: a review.
S.A. Sansone, N. Morrison, P. Rocca-Serra and J. Fostel. Comp Funct Genom 2004; 5: 633-641 [Abstract]
[PDF].
ArrayExpress-a public repository for microarray gene expression data at the EBI.
H. Parkinson, U. Sarkans, M. Shojatalab, N. Abeygunawardena, S. Contrino, R. Coulson, A. Farne, G. Garcia Lara, E. Holloway, M. Kapushesky, P. Lilja, G.
Mukherjee, A. Oezcimen, T. Rayner, P. Rocca-Serra, A. Sharma, S. Sansone,
and A. Brazma. Nucl. Acids Res., 2005, 33: D553-D555; doi:10.1093/nar/gki056 [Abstract]
[PDF] OPEN ACCESS ARTICLE.
The ArrayExpress gene expression database: a software engineering and implementation perspective.
U. Sarkans, H. Parkinson, G. Garcia Lara, A. Oezcimen, A. Sharma, N. Abeygunawardena, S. Contrino, E. Holloway, P. Rocca-Serra, G. Mukherjee, M. Shojatalab, M. Kapushesky, S. Sansone, A. Farne, T. Rayner, and A. Brazma. Bioinformatics, 2005, Vol. 21 No. 8: 1495-1501; doi:10.1093/bioinformatics/bti157 [Abstract] [PDF].
2004
Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum.
Coulson, R.M.R., Hall, N. & Ouzounis, C.A., 2004, Genome Res., 14: 1548-1554. [Abstract] [PDF]
Expression profiling of the Leishmania life cycle: cDNA arrays identify developmentally regulated genes present but not annotated in the genome.
Almeida, R., Gilmartin, B.J., McCann, S.H., Norrish, A., Ivens, A.C., Lawson, D., Levick, M.P., Smith, D.F., Dyall, S.D., Vetrie, D., Freeman, T.C., Coulson, R.M.R., Sampaio, I., Schneider, H., & Blackwell, J.M., 2004, Mol Biochem Parasitol., 136: 87-100. [Abstract] [PDF]
Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies.
C.J. Stoeckert, J. Quackenbush, A. Brazma and C.A. Ball. Drug Discovery Today: Targets, 2004, Vol.3, No.4: 159-164.
Supervised learning-aided optimization of expert-driven functional protein sequence annotation.
L. Soinov, A. Kanapin and M. Kapushesky. Algorithms in Bioinformatics, WABI 2004, Lecture Notes in Computer Science,
Lecture Notes in Bioinformatics, V.3240, ISBN: 3-540-23018-1. [PDF].
Submission of Microarray Data to Public Repositories.
C.A. Ball, A. Brazma, H. Causton, S. Chervitz, R. Edgar, P. Hingamp, J.C. Matese, H. Parkinson, J. Quackenbush, M. Ringwald, S. Sansone, G. Sherlock, P. Spellman, C. Stoeckert, Y. Tateno, R. Taylor, J. White and N. Winegarden. PLoS Biology, 2, e317: 1276-1277. [PDF].
Funding high-throughput data sharing.
C.A. Ball, G. Sherlock and A. Brazma. Nature Biotechnology, 22: 1179-83. [PDF].
Periodic gene expression program of the fission yeast cell cycle.
G. Rustici, J. Mata, K. Kivinen, P. Li , C.J. Penkett, G. Burns, J. Hayles, A. Brazma, P. Nurse and J. Bhler. Nature Genetics, 2004, 36, 809-817 (doi:10.1038/ng1377). [Abstract] [PDF].
Expression Profiler: next generation-an online platform for analysis of microarray data.
M. Kapushesky, P. Kemmeren, A.C. Culhane, S. Durinck, J. Ihmels, C. K rner, M. Kull, A. Torrente, U. Sarkans, J. Vilo and A. Brazma. Nucleic Acids Research, 2004, 32(Web Server issue):W465-W470. [Abstract] [PDF].
Meeting Report: EU-US Workshop on Molecular Signatures of
DNA damage-induced Stress Responses.
M. Sander, C. Desaintes, R. Pelroyc, W. Ferro,
B. Van Houten, S. Amundsonf, A. Lehmanng, L. Mullenders,
S. Sansone, P. Stambrook, B. van Zeeland,
H. Vrieling and A. Wennborg. Mutation Research, 2004, 550:145-181. [PDF].
COMe: the ontology of bioinorganic proteins.
K. Degtyarenko and S. Contrino. BMC Structural Biology, 2004, 4:3. [Abstract] [PDF].
Database development in toxicogenomics: issues and efforts.
W. B. Mattes, S. D. Pettit, S. Sansone, P. R. Bushel, and
M. D. Waters. (2004). Environ Health Perspect Toxicogenomics:doi:10.1289/txg.6697. [Abstract] [PDF].
The HUPO PSI's molecular interaction
format- a community standard for the representation of protein interaction
data.
H. Hermjacob, L. Montecchi-Palazzi...S. Orchard, U.
Sarkans...H. Mersch, P. Kersey, M. Lappe..W. Zhu..A.
Brazma...and R. Apweiler. Nature Biotechnology, 2004, 22 (2): 177-183. [Abstract] [PDF].
EnsMart: a generic system for fast and flexible access to biological data.
A. Kasprzyk, D. Keefe, D. Smedley, D. London, W. Spooner, T. Cox, C. Melsopp, M. Hammond, P. Rocca-Serra and E. Birney. Genome Research, 2004, 14 (1): 160-169. [Abstract] [PDF].
2003
Gene Expression Databases
A. Brazma and U. Sarkans. 2003, Nature Encyclopedia Of The Human Genome, Nature Publishing Group, 628-632. [Publisher].
ArrayExpress: a public database of gene expression data at EBI.
P. Rocca-Serra, A. Brazma, H. Parkinson, U. Sarkans, M. Shojatalab, S. Contrino, J. Vilo, N. Abeygunawardena, G. Mukherjee, E. Holloway, M. Kapushesky, P. Kemmeren, G. Garcia Lara, A. Oezcimen and S. Sansone. Comptes Rendus Biologies, October-November 2003,
Vol. 326 (Issues 10-11): 1075-1078 . [Abstract] [PDF].
Standardization of microarray experiment data.
A. Brazma, K. Ikeo, Y. Tateno. Tanpakushitsu Kakusan Koso. Review. Japanese., 2003, 48(3): 280-5. [PubMed].
Supervised classification for gene network reconstruction.
L.A. Soinov. Biochemical Society Transactions, 2003, 31, 6: 1497-1502. [PDF] Mounted on the
Internet with the permission of The Biochemical Society (2003).
From Gene Networks to Gene Function.
T. Schlitt, K. Palin, J. Rung, S. Dietmann, M. Lappe, E. Ukkonen, and A. Brazma. Genome Research, 2003, 13: 2577-2587. [Abstract] [Full Text] [PDF]
Meeting report: Unraveling nature's networks.
L. Soinov and M. Kapushesky. Genome Biology, 2003, 4(10): 341.1 - 341.3. [Full Text] [PDF]
Expression Profiler.
J.
Vilo, M. Kapushesky, P. Kemmeren, U. Sarkans and A.
Brazma. In Parmigiani, G., Garrett, E.S., Irizarry,
R. and Zeger, S.L. (eds), The Analysis of Gene Expression
Data: Methods and Software, Springer Verlag, 2003, New
York, NY. [Accompanying
web page] [Amazon
UK] [Amazon.com]
Microarray Gene Expression Data
Analysis: A Beginner's Guide.
H.C. Causton, J.
Quackenbush and A. Brazma. Blackwell Publishing, April
2003, ISBN 1-40510-682-4. [Amazon]
The MGED ontology: a framework
for describing functional genomics experiments.
C. J. Stoeckert Jr and H. Parkinson. Comparative and
Functional Genomics, 2003, 4: 127–132. [PDF]
Conference Report: Standards and
ontologies for functional genomics: towards unified
ontologies for biology and biomedicine.
M.A.
Harris and H. Parkinson. Comparative and Functional
Genomics, 2003, 4: 116–120. [PDF]
Global Transcriptional Responses
of Fission Yeast to Environmental Stress.
D.
Chen, W.M. Toone, J. Mata, R. Lyne, G. Burns, K. Kivinen,
A. Brazma, N. Jones and J. Bahler. Molecular Biology
of the Cell, 2003, 14: 214-229. [PDF]
ArrayExpress—a public repository
for microarray gene expression data at the EBI.
A. Brazma, H. Parkinson, U. Sarkans, M. Shojatalab,
J. Vilo, N. Abeygunawardena, E. Holloway, M. Kapushesky,
P. Kemmeren, G.G. Lara, A. Oezcimen, P. Rocca-Serra
and S. Sansone Nucleic Acids Research, 2003, 31: 68-71.
[PDF]
The European Bioinformatics Institute's
data resources.
R. Apweiler, E. Birney, A. Brazma,
C. Brooksbank, G. Cameron, E. Camon, M. Harris, K. Henrick,
R. Lopez, M. Magrane, M. Martin, N. Mulder, C. O'Donovan,
H. Parkinson, P. Stoehr, G. Stoesser and M. Tuli. Nucleic
Acids Research, 2003, 31: 43-50. [PDF]
Towards reconstruction of gene
networks from expression data by supervised learning.
L.A. Soinov, M.A. Krestyaninova and A. Brazma. Genome
Biology, 2003, 4(1): R6. [HTML]
[PDF]2002
Learning about gene regulatory
networks from gene deletion experiments.
T. Schlitt
and A. Brazma. Comparative and Functional Genomics,
2002, Vol 3 (Issue 6): 499-503. [PDF]
Building and analysing genome-wide
gene disruption networks.
J. Rung, T. Schlitt,
A. Brazma, K. Freivalds and J. Vilo. Bioinformatics,
2002, 18 (Suppl. 2): S202-S210. [PubMed]
[PDF]
Correlating gene promoters and
expression in gene disruption experiments.
Kimmo
Palin, Esko Ukkonen, Alvis Brazma and Jaak Vilo. Bioinformatics,
2002, 18 (Suppl. 2): S172-S180. [PubMed]
[PDF]
A guide to microarray experiments
- an open letter to the scientific journals.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank
C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P,
Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr,
Stewart JE, Taylor R, Brazma A, Quackenbush J; MGED.
THE LANCET, 2002 Sep 28; 360(9338):1019. [PubMed]
[PDF]
The underlying principles of scientific
publication - An Open Letter to the scientific journals.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank
C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P,
Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr,
Stewart JE, Taylor R, Brazma A, Quackenbush J; MGED.
Bioinformatics, 2002 Nov,18(11):1409. [PubMed]
[PDF]
Standards for microarray data.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank
C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P,
Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr,
Stewart JE, Taylor R, Brazma A, Quackenbush J; Microarray
Gene Expression Data (MGED) Society. Science, 2002 Oct
18, 298(5593):539. [PubMed]
[PDF]
From genotype to phenotype: linking
bioinformatics and medical informatics ontologies. Manchester,
UK, 23-24 March 2002.
Holloway E., Comparative
and Functional Genomics, 2002, 3(5): 447-450. [PDF]
Design and implementation of microarray
gene expression markup language (MAGE-ML).
Paul
T Spellman, Michael Miller, Jason Stewart, Charles Troup,
Ugis Sarkans, Steve Chervitz, Derek Bernhart, Gavin
Sherlock, Catherine Ball, Marc Lepage, Marcin Swiatek,
WL Marks, Jason Goncalves, Scott Markel, Daniel Iordan,
Mohammadreza Shojatalab, Angel Pizarro, Joe White, Robert
Hubley, Eric Deutsch, Martin Senger, Bruce J Aronow,
Alan Robinson, Doug Bassett, Christian J Stoeckert Jr,
Alvis Brazma, Genome Biology, 2002, 3(9): research0046.1-0046.9.
[PubMed]
[PDF]
Microarray Data Representation,
Annotation and Storage.
Alvis Brazma, Ugis Sarkans,
Alan Robinson, Jaak Vilo, Martin Vingron, Jorg Hoheisel,
and Kurt Fellenberg. Advances in Biochemical Engineering/Biotechnology,
2002, Vol.77(Chip Technology): pp. 113-139. [PubMed]
[Abstract]
Protein Interaction
Verification and Functional Annotation by Integrated
Patrick Kemmeren,
Nynke L. van Berkum, Jaak Vilo, Theo Bijma, Rogier Donders,
Alvis Brazma, and Frank C.P. Holstege. Molecular Cell
2002, May 24; 9(5) pp. 1133-1143. [Abstract] Analysis of Genome-Scale Data.
From genomes to
vaccines: Leishmania as a model.
Almeida R, Norrish
A, Levick M, Vetrie D, Freeman T, Vilo J, Ivens A, Lange
U, Stober C, McCann S, Blackwell JM. Philos Trans R Soc
Lond B Biol Sci 2002 Jan 29;357(1417):5-11. [PubMed] 2001Minimum information
about a microarray experiment (MIAME)—toward standards
for microarray data.
A Brazma, P Hingamp, J Quackenbush,
G Sherlock, P Spellman, C Stoeckert, J Aach, W Ansorge,
C A Ball, H C Causton, T Gaasterland, P Glenisson, F C
P Holstege, I F Kim, V Markowitz, J C Matese, H Parkinson,
A Robinson, U Sarkans, S Schulze-Kremer, J Stewart, R
Taylor, J Vilo & M Vingron, Nature Genetics, vol 29
(December 2001), pp 365 - 371. [PDF]
[PubMed]
Gene Expression Data Mining and
Analysis.
Alvis Brazma, Alan Robinson and Jaak
Vilo pp. 106-129. Book chapter: B. Jordan (editor):
DNA Microarrays: Gene Expression Applications, [Springer-Verlag]
[Amazon]
Regulatory sequence analysis: application
to interpretation of gene expression.
Jaak Vilo
and Katja Kivinen, European Neuropsychopharmacology,
Volume 11, Issue 6, December 2001, Pages 399-411. [PubMed]
Prediction of the coupling specificity
of G protein coupled receptors to their G proteins.
Steffen Möller, Jaak Vilo, Michael D.R. Croning,
ISMB-2001 July 2001. Bioinformatics 2001 17: S174-S181.
[PubMed]
On the importance of standardisation
in life sciences.
A. Brazma, Editorial, Bioinformatics,
Vol 17 (2001), 113-114. [PubMed]
2000
Gene Expression
Data Analysis.
Brazma, A., and Vilo, J., FEBS Letters
480 (2000) 17-24. [PubMed]
Mining for Putative Regulatory
Elements in the Yeast Genome Using Gene Expression Data.
Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan Robinson,
and Esko Ukkonen, ISMB'2000 August 2000. AAAI press.
pp. 384-394. [PubMed]
One-stop shop for microarray data.
Brazma, A., A. Robinson, G. Cameron, and M. Ashburner.
Commentary. Nature 403:699-700 (2000). [Nature]
[PubMed]
1998
Predicting Gene
Regulatory Elements in Silico on a Genomic Scale.
Brazma, A., I. Jonassen, J. Vilo, and E. Ukkonen. Genome
Research Vol 8, 11:1202-1215 (1998). [Genome
Research] [Pub
Med]
Pattern Discovery in Biosequences.
Brazma, A., I. Jonassen, J. Vilo, and E. Ukkonen. Lecture
Notes in Artificial Intelligence, Vol. 1433, Springer,
pp. 255-270 (1998).
Approaches to Automatic Discovery
of Patterns in Biosequences.
Brazma, A., I. Jonassen,
I. Eidhammer, and D. Gilbert. Journal of Computational
Biology 5:277-303 (1998) [Pub
Med].
1997
Data Mining for
Regulatory Elements in Yeast Genome.
Brazma, A.,
J. Vilo, E. Ukkonen, and K. Valtonen. In 'Proceedings
of the Fifth International Conference Intelligent Systems
for Molecular Biology' ISMB'97 , AAAI Press, pp. 65-74
(1997). [Pub
Med]
1996
Discovering patterns
and subfamilies in biosequences.
A. Brazma, I.
Jonassen, E. Ukkonen, J. Vilo. In Proc. of 4th International
Conference Intelligent Systems for Molecular Biology ISMB'96
, AAAI Press, 1996, p.34-43. [Pub
Med]
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