Alvis Brazma

Alvis Brazma received the Ph.D. degree in computer science, Moscow State University, Moscow, in 1988. He also received the M.S. degree in mathematics and physics from University of Latvia, Riga, in 1982. In 1988–1990, he was a Research Scientist, University of Latvia; in 1990-1991, a Postdoctor in New Mexico State University; in 1995–1997, a Visiting Scientist, Helsinki University; in 1992–1997, an Associate Professor in University of Latvia; in 1997–2000, a Scientist in EMBL-EBI; and in 2000–2003, a Team Leader in EMBL-EBI. His professional activities till 2007 are varoius. He is in MGED Board of Directors; an Associate Editor of Bioinformatics, 2002–2006 and in the Board of Editors since 2007; in the Board of Editors of Environmental Health Perspectives, 2003–2006, SAB of Edinburgh Mouse Gene Expression Database; SAB of the Biological Atlas of Insulin Receptors (BAIR), Wellcome Trust BBSRC Data Sharing Working Group; Steering Committee of the European Computational Biology Conference, 2001–2005, Bioinformatics Task Force of National Cancer Research Institute (NCRI), UK; EMBL Graduation Committee alternate member Programme committees of ISMB, WABI, Wellcome Trust conferences on Comparative and Functional Genomics (Hinxton, October 2003, October 2005, Asia Pacific Bioinformatics Conference, Grant application reviewing for FP6 (EC), Norwegian Functional Genomics Programme (FUGE), German Strategic Genome Initiative (DFG, GABI future), Genome Canada, Wellcome Trust, European Science Foundation, MRC, BBSRC, Dutch Genome initiative; Reviewing for Nature, Nature Biotechnology, Nature Medicine, Nature Cell Biology, Nature Reviews Genetics, Science, Journal of Molecular Biology, EMBO journal, Genome Research, Cell, FEBS letters, Nucleic Acids Research, Genome Biology, Bioinformatics, BMC Bioinformatics Organising committee of the Wellcome Trust/CSH conference on Functional Genomics and Systems Biology, Organiser/coorganiser of seven EMBO courses at EBI and EMBL HD; Bioinformatics Research and Education Workshop (BREW) (23-25 April, 2006, Hinxton).

Biography Updated on 23 January 2008

Personal Home Page

http://www.ebi.ac.uk/~brazma/

Articles in Scholarly Journals [Incomplete List]

  1. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
    Nature Biotechnology, vol. 25, no. 10, Article ID nbt1347, 6 pages, 2007
  2. ArrayExpress--a public database of microarray experiments and gene expression profiles
    Nucleic Acids Research, vol. 35, no. Database, pp. D747–D750, 2007
  3. BMC Bioinformatics, vol. 8, no. 1, p. 52, 2007
  4. Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster
    PLoS Computational Biology, vol. 3, no. 7, p. e144, 2007
  5. BMC Bioinformatics, vol. 7, no. 1, p. 489, 2006
  6. Modelling in molecular biology: describing transcription regulatory networks at different scales
    Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 361, no. 1467, pp. 483–494, 2006
  7. ArrayExpress service for reviewers/editors of DNA microarray papers
    Nature Biotechnology, vol. 24, no. 11, Article ID nbt1106-1321, 1 pages, 2006
  8. Standards for systems biology
    Nature Reviews Genetics, vol. 7, no. 8, Article ID nrg1922, 12 pages, 2006
  9. MGED Standards: Work in Progress
    OMICS: A Journal of Integrative Biology, vol. 10, no. 2, pp. 138–144, 2006
  10. Development of the Minimum Information Specification forIn SituHybridization and Immunohistochemistry Experiments (MISFISHIE)
    OMICS: A Journal of Integrative Biology, vol. 10, no. 2, pp. 205–208, 2006
  11. Editorial
    Briefings in Functional Genomics and Proteomics, vol. 5, no. 1, pp. 1–3, 2006
  12. ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression
    Bioinformatics, vol. 22, no. 6, pp. 765–767, 2006
  13. [20] Data Storage and Analysis in ArrayExpress
    Methods in Enzymology, vol. 411, pp. 370–386, 2006
  14. Top-down standards will not serve systems biology
    Nature, vol. 440, no. 7080, Article ID 440024a, 1 pages, 2006
  15. Wrestling with SUMO and bio-ontologies
    Nature Biotechnology, vol. 24, no. 1, Article ID nbt0106-21b, 1 pages, 2006
  16. Modelling gene networks at different organisational levels
    FEBS Letters, vol. 579, no. 8, pp. 1859–1866, 2005
  17. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
    Bioinformatics, vol. 21, no. 16, pp. 3439–3440, 2005
  18. A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings
    Bioinformatics, vol. 21, no. 21, pp. 3993–3999, 2005
  19. Fusing microarray experiments with multivariate regression
    Bioinformatics, vol. 21, no. suppl_2, pp. ii137–ii143, 2005
  20. Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress
    PLANT PHYSIOLOGY, vol. 139, no. 2, pp. 632–636, 2005
  21. Expression Profiler: next generation--an online platform for analysis of microarray data
    Nucleic Acids Research, vol. 32, no. Web Server, pp. W465–W470, 2004
  22. ArrayExpress--a public repository for microarray gene expression data at the EBI
    Nucleic Acids Research, vol. 33, no. Database issue, pp. D553–D555, 2004
  23. An open letter on microarray data from the MGED Society
    Microbiology, vol. 150, no. 11, pp. 3522–3524, 2004
  24. Submission of Microarray Data to Public Repositories
    PLoS Biology, vol. 2, no. 9, p. e317, 2004
  25. Report on the thirteenth international workshop on the identification and functional, evolutionary and expression analysis of transcribed sequences: comparative and functional genomics workshop
    Cytogenetic and Genome Research, vol. 105, no. 1, pp. 11–17, 2004
  26. The ArrayExpress gene expression database: a software engineering and implementation perspective
    Bioinformatics, vol. 21, no. 8, pp. 1495–1501, 2004
  27. Periodic gene expression program of the fission yeast cell cycle
    Nature Genetics, vol. 36, no. 8, Article ID ng1377, 8 pages, 2004
  28. The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data
    Nature Biotechnology, vol. 22, no. 2, Article ID nbt926, 6 pages, 2004
  29. Funding high-throughput data sharing
    Nature Biotechnology, vol. 22, no. 9, Article ID nbt0904-1179, 4 pages, 2004
  30. Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies
    Drug Discovery Today: TARGETS, vol. 3, no. 4, pp. 159–164, 2004
  31. ArrayExpress: a public database of gene expression data at EBI
    Comptes Rendus Biologies, vol. 326, no. 10-11, pp. 1075–1078, 2003
  32. Global Transcriptional Responses of Fission Yeast to Environmental Stress
    Molecular Biology of the Cell, vol. 14, no. 1, pp. 214–229, 2003
  33. The European Bioinformatics Institute's data resources
    Nucleic Acids Research, vol. 31, no. 1, pp. 43–50, 2003
  34. ArrayExpress--a public repository for microarray gene expression data at the EBI
    Nucleic Acids Research, vol. 31, no. 1, pp. 68–71, 2003
  35. From Gene Networks to Gene Function
    Genome Research, vol. 13, no. 12, pp. 2568–2576, 2003
  36. An open letter to the scientific journals
    Bioinformatics, vol. 18, no. 11, pp. 1409–1409, 2002
  37. Learning about gene regulatory networks from gene deletion experiments
    Comparative and Functional Genomics, vol. 3, no. 6, pp. 499–503, 2002
  38. A guide to microarray experiments-an open letter to the scientific journals
    The Lancet, vol. 360, no. 9338, pp. 1019–1019, 2002
  39. Protein Interaction Verification and Functional Annotation by Integrated Analysis of Genome-Scale Data
    Molecular Cell, vol. 9, no. 5, pp. 1133–1143, 2002
  40. Gene expression data analysis
    Microbes and Infection, vol. 3, no. 10, pp. 823–829, 2001
  41. On the Importance of Standardisation in Life Sciences
    Bioinformatics, vol. 17, no. 2, pp. 113–114, 2001
  42. Nature Genetics, vol. 29, no. 4, pp. 365–371, 2001
  43. Nature, vol. 403, no. 6771, pp. 699–700, 2000
  44. Gene expression data analysis
    FEBS Letters, vol. 480, no. 1, pp. 17–24, 2000
  45. Models of inductive synthesis
    The Journal of Logic Programming, vol. 9, no. 2-3, pp. 221–233, 1990
  46. Inductive synthesis of programs: State of the art, problems, prospects
    Cybernetics, vol. 23, no. 6, pp. 818–826, 1988
  47. Generalized regular expressions—A language for synthesis of programs with branching in loops
    Theoretical Computer Science, vol. 46, pp. 175–195, 1986