Alvis Brazma

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    Helen Parkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D868-72. 2009
  2. pmc The BioSample Database (BioSD) at the European Bioinformatics Institute
    Mikhail Gostev
    EMBL EBI, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 40:D64-70. 2012
  3. pmc Submission of microarray data to public repositories
    Catherine A Ball
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E317. 2004
  4. pmc PASSIM--an open source software system for managing information in biomedical studies
    Juris Viksna
    Institute of Mathematics and Computer Science, Riga, University of Latvia, Latvia
    BMC Bioinformatics 8:52. 2007
  5. pmc The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays
    Yevhen Vainshtein
    MMPU, Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
    BMC Bioinformatics 11:112. 2010
  6. pmc ArrayExpress--a public repository for microarray gene expression data at the EBI
    Alvis Brazma
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 31:68-71. 2003
  7. ncbi request reprint Standards for systems biology
    Alvis Brazma
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nat Rev Genet 7:593-605. 2006
  8. ncbi request reprint Microarray data representation, annotation and storage
    Alvis Brazma
    EMBL Outstation Hinxton, European Bioinformatics Institute, Cambridge, UK
    Adv Biochem Eng Biotechnol 77:113-39. 2002
  9. ncbi request reprint Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
    A Brazma
    European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Genet 29:365-71. 2001
  10. ncbi request reprint Gene expression data analysis
    A Brazma
    European Molecular Biology Laboratory, Outstation Hinxton the European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
    Microbes Infect 3:823-9. 2001

Detail Information

Publications80

  1. pmc ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    Helen Parkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D868-72. 2009
    ..In this update, we describe the ArrayExpress developments over the last two years...
  2. pmc The BioSample Database (BioSD) at the European Bioinformatics Institute
    Mikhail Gostev
    EMBL EBI, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 40:D64-70. 2012
    ..A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples@ebi.ac.uk...
  3. pmc Submission of microarray data to public repositories
    Catherine A Ball
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E317. 2004
  4. pmc PASSIM--an open source software system for managing information in biomedical studies
    Juris Viksna
    Institute of Mathematics and Computer Science, Riga, University of Latvia, Latvia
    BMC Bioinformatics 8:52. 2007
    ..There is a clear need for lightweight open source systems for patient and sample information management...
  5. pmc The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays
    Yevhen Vainshtein
    MMPU, Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
    BMC Bioinformatics 11:112. 2010
    ..The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available...
  6. pmc ArrayExpress--a public repository for microarray gene expression data at the EBI
    Alvis Brazma
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 31:68-71. 2003
    ..With an increasing number of organisations adopting MAGE-ML standard, the volume of submissions to ArrayExpress is increasing rapidly. The database can be accessed at http://www.ebi.ac.uk/arrayexpress...
  7. ncbi request reprint Standards for systems biology
    Alvis Brazma
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nat Rev Genet 7:593-605. 2006
    ..Why are some standards more successful than others, what are the prerequisites for a standard to succeed and what are the possible pitfalls?..
  8. ncbi request reprint Microarray data representation, annotation and storage
    Alvis Brazma
    EMBL Outstation Hinxton, European Bioinformatics Institute, Cambridge, UK
    Adv Biochem Eng Biotechnol 77:113-39. 2002
    ..We describe two data models--a simpler one called ArrayExpressB and the complete model ArrayExpressC, and discuss some implementation issues. For latest developments see http: wwwebi.ac.uk/arrayexpress..
  9. ncbi request reprint Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
    A Brazma
    European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Genet 29:365-71. 2001
    ..With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it...
  10. ncbi request reprint Gene expression data analysis
    A Brazma
    European Molecular Biology Laboratory, Outstation Hinxton the European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
    Microbes Infect 3:823-9. 2001
    ..We briefly discuss supervised and unsupervised data analysis and its applications, such as predicting gene function classes and cancer classification as well as some possible future directions...
  11. doi request reprint Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges
    Alvis Brazma
    Microarray Informatics Group, European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    ScientificWorldJournal 9:420-3. 2009
    ..The MGED Society has already proposed draft guidelines for Minimum Information about a high-throughput SeQuencing Experiment (MINSEQE)...
  12. ncbi request reprint Gene expression data analysis
    A Brazma
    European Molecular Biology Laboratory, Outstation Hinxton the European Bioinformatics Institute, Cambridge, UK
    FEBS Lett 480:17-24. 2000
    ..Then we discuss how the gene expression matrix can be used to predict putative regulatory signals in the genome sequences. In conclusion we discuss some possible future directions...
  13. ncbi request reprint The ArrayExpress gene expression database: a software engineering and implementation perspective
    Ugis Sarkans
    EMBL Outstation Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:1495-501. 2005
    ..Our experience will be both relevant and useful for most bioinformaticians involved in developing information systems for a wide range of high-throughput technologies...
  14. pmc Gene expression atlas at the European bioinformatics institute
    Misha Kapushesky
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 38:D690-8. 2010
    ..Currently, the database contains information about more than 200,000 genes from nine species and almost 4500 biological conditions studied in over 30,000 assays from over 1000 independent studies...
  15. pmc Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress
    Gaurab Mukherjee
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Plant Physiol 139:632-6. 2005
    ..The AtMIAMExpress submission tool is available at http://www.ebi.ac.uk/at-miamexpress/. The software is open source and is available from http://sourceforge.net/projects/miamexpress/. For information, contact miamexpress@ebi.ac.uk...
  16. doi request reprint Data storage and analysis in ArrayExpress and Expression Profiler
    Gabriella Rustici
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Curr Protoc Bioinformatics . 2008
    ....
  17. pmc ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
    Helen Parkinson
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 39:D1002-4. 2011
    ..Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy...
  18. pmc Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
    Robert Petryszak
    European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL EBI, Hinxton, CB10 1SD, UK
    Nucleic Acids Res 42:D926-32. 2014
    ....
  19. ncbi request reprint ArrayExpress: a public database of gene expression data at EBI
    Philippe Rocca-Serra
    EMBL Outstation Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
    C R Biol 326:1075-8. 2003
    ..Data retrieval is performed through a dedicated web interface. Relevant results may be exported to ExpressionProfiler, the EBI based expression analysis tool available online (http://www.ebi.ac.uk/arrayexpress)...
  20. pmc ArrayExpress update--trends in database growth and links to data analysis tools
    Gabriella Rustici
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 41:D987-90. 2013
    ..Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data...
  21. ncbi request reprint Fusing microarray experiments with multivariate regression
    Walter R Gilks
    MRC Biostatistics Unit, Cambridge, UK
    Bioinformatics 21:ii137-43. 2005
    ..Also, the variability in the quality of experimentation should be taken into account...
  22. pmc SAIL--a software system for sample and phenotype availability across biobanks and cohorts
    Mikhail Gostev
    Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Bioinformatics 27:589-91. 2011
    ..Users can query for the available samples by various parameters combining them via logical expressions. The system can be scaled to hold data from millions of samples with thousands of variables...
  23. pmc Updates to BioSamples database at European Bioinformatics Institute
    Adam Faulconbridge
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 42:D50-2. 2014
    ....
  24. pmc Modeling sample variables with an Experimental Factor Ontology
    James Malone
    Microarray Informatics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Bioinformatics 26:1112-8. 2010
    ..These are subject to rapid change, are often not interoperable and present complexities that are a barrier to biological resource users...
  25. pmc Importing ArrayExpress datasets into R/Bioconductor
    Audrey Kauffmann
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 25:2092-4. 2009
    ..However, easy ways for importing datasets from ArrayExpress into R/Bioconductor have been lacking. Here, we present such a tool that is suitable for both interactive and automated use...
  26. pmc The European Bioinformatics Institute's data resources
    Catherine Brooksbank
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 31:43-50. 2003
    ..The EBI's databases and tools are all available on our website at www.ebi.ac.uk...
  27. pmc Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments
    Misha Kapushesky
    European Bioinformatics Institute, EMBL, Hinxton, UK and Dana Farber Cancer Institute, Boston, MA, USA
    Nucleic Acids Res 40:D1077-81. 2012
    ..08 (August 2011), the database supports 19 species, which contains expression data measured for 19,014 biological conditions in 136,551 assays from 5598 independent studies...
  28. pmc Annotare--a tool for annotating high-throughput biomedical investigations and resulting data
    Ravi Shankar
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5307, USA
    Bioinformatics 26:2470-1. 2010
    ..Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis...
  29. ncbi request reprint The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?"
    Susanna Assunta Sansone
    EMBL EBI The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    OMICS 12:143-9. 2008
    ..This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC)...
  30. ncbi request reprint Data storage and analysis in ArrayExpress
    Alvis Brazma
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Methods Enzymol 411:370-86. 2006
    ..This chapter describes all major ArrayExpress components from the user perspective: how to submit to, retrieve from, and analyze data in ArrayExpress...
  31. pmc Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008
  32. pmc Prediction of gene expression in embryonic structures of Drosophila melanogaster
    Anastasia A Samsonova
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
    PLoS Comput Biol 3:e144. 2007
    ..Our novel organism-independent method will be of considerable utility in enriching the annotation of gene function and expression in complex multicellular organisms...
  33. pmc Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study
    Gabriella Rustici
    EMBL Outstation Hinxton, European Bioinformatics Institute, Cambridge CB10 1SD, UK
    Genome Biol 8:R73. 2007
    ..All cells must adjust to environmental fluctuations in metal levels, because levels that are too low or too high can be detrimental. Here we explore the conservation of metal homoeostasis in two distantly related yeasts...
  34. pmc Large scale comparison of global gene expression patterns in human and mouse
    Xiangqun Zheng-Bradley
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Genome Biol 11:R124. 2010
    ....
  35. pmc A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
    Tim F Rayner
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Bioinformatics 7:489. 2006
    ..However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support...
  36. pmc A pipeline for RNA-seq data processing and quality assessment
    Angela Goncalves
    EMBL Outstation Hinxton, European Bioinformatics Institute, Cambridge, UK
    Bioinformatics 27:867-9. 2011
    ..It may be run locally on a user's own computer or remotely on a distributed R-cloud farm at the European Bioinformatics Institute. It can be used to analyse user's own datasets or public RNA-seq datasets from the ArrayExpress Archive...
  37. ncbi request reprint The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
    Henning Hermjakob
    European Bioinformatics Institute, EBI Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Biotechnol 22:177-83. 2004
    ....
  38. doi request reprint Tools for mapping high-throughput sequencing data
    Nuno A Fonseca
    EMBL Outstation, European Bioinformatics Institute EBI, Hinxton, Cambridge CB10 ISD, UK
    Bioinformatics 28:3169-77. 2012
    ..To accomplish this task, numerous software tools have been proposed. Determining the mappers that are most suitable for a specific application is not trivial...
  39. ncbi request reprint A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings
    Aurora Torrente
    EMBL Outstation Hinxton, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:3993-9. 2005
    ..Biological interpretation of multiple clustering results requires understanding how different clusters relate to each other. It is particularly non-trivial to compare the results of a hierarchical and a flat, e.g. k-means, clustering...
  40. ncbi request reprint Periodic gene expression program of the fission yeast cell cycle
    Gabriella Rustici
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nat Genet 36:809-17. 2004
    ....
  41. pmc A System for Information Management in BioMedical Studies--SIMBioMS
    Maria Krestyaninova
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SD, UK
    Bioinformatics 25:2768-9. 2009
    ..Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented...
  42. pmc Extensive compensatory cis-trans regulation in the evolution of mouse gene expression
    Angela Goncalves
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 22:2376-84. 2012
    ..We propose that expression levels of genes regulated by this mechanism are fine-tuned by cis variants that arise following regulatory changes in trans, suggesting that many cis variants are not the primary targets of natural selection...
  43. doi request reprint Reuse of public genome-wide gene expression data
    Johan Rung
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Rev Genet 14:89-99. 2013
    ..We will discuss these challenges and provide recommendations that we believe can improve the utility of such data...
  44. ncbi request reprint MGED standards: work in progress
    Catherine A Ball
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94301, USA
    OMICS 10:138-44. 2006
    ..We discuss here how these standards have been established, how they have evolved, and how they are used...
  45. ncbi request reprint Funding high-throughput data sharing
    Catherine A Ball
    Department of Biochemistry, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305 5307, USA
    Nat Biotechnol 22:1179-83. 2004
  46. pmc From gene networks to gene function
    Thomas Schlitt
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Genome Res 13:2568-76. 2003
    ....
  47. pmc Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes
    Claudia Kutter
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
    Nat Genet 43:948-55. 2011
    ..Thus, synthesis of functional tRNA isotypes has been highly constrained, although the usage of individual tRNA genes has evolved rapidly...
  48. pmc Modelling in molecular biology: describing transcription regulatory networks at different scales
    Thomas Schlitt
    European Bioinformatics Institute Wellcome Trust Genome Campus EMBL EBI, Cambridge CB10 1SD, UK
    Philos Trans R Soc Lond B Biol Sci 361:483-94. 2006
    ..The first two classes of models have reached a genome-wide scale, while for the other model classes high-throughput technologies are yet to make a major impact...
  49. ncbi request reprint ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression
    Jonathon Blake
    EMBL Meyerhofstr 1 D 69117 Heidelberg, Germany
    Bioinformatics 22:765-7. 2006
    ..Chromosome Co-Localization probability calculator (ChroCoLoc) is a publicly available web-based tool for the analysis of co-localization of co-expressed genes identified by microarray experiments...
  50. ncbi request reprint Mining for putative regulatory elements in the yeast genome using gene expression data
    J Vilo
    European Bioinformatics Institute, EMBL Outstation, Hinxton, Cambridge, United Kingdom
    Proc Int Conf Intell Syst Mol Biol 8:384-94. 2000
    ..We clustered the 1,500 patterns to 62 groups for which we derived automatically alignments and consensus patterns. Of these 62 groups 48 had patterns that have matching sites in SCPD database...
  51. pmc ArrayExpress--a public repository for microarray gene expression data at the EBI
    H Parkinson
    European Bioinformatics Institute, EMBL EBI Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 33:D553-5. 2005
    ..Data can be visualized and analysed using Expression Profiler, the integrated data analysis tool. ArrayExpress is available at http://www.ebi.ac.uk/arrayexpress...
  52. doi request reprint HSM - a hybrid system based approach for modelling intracellular networks
    Alvis Brazma
    European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Gene 518:70-7. 2013
    ..The algorithm also generates (in principle biologically verifiable) hypotheses about the mutations of λ-phage that should change its observable behaviour...
  53. pmc MageComet--web application for harmonizing existing large-scale experiment descriptions
    Vincent Xue
    Department of Computer Science, Hunter College, City University of New York, NY 10065, USA
    Bioinformatics 28:1402-3. 2012
    ..Curation of such experiments, however, is an expert activity which involves repetitive manipulation of text. Existing tools for automated curation are few, which bottleneck the analysis pipeline...
  54. pmc ArrayExpress--a public database of microarray experiments and gene expression profiles
    H Parkinson
    European Bioinformatics Institute, EMBL EBI Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 35:D747-50. 2007
    ..ArrayExpress supports community standards, including MIAME, MAGE-ML and more recently the proposal for a spreadsheet based data exchange format: MAGE-TAB. Availability: www.ebi.ac.uk/arrayexpress...
  55. ncbi request reprint Report on the thirteenth international workshop on the identification and functional, evolutionary and expression analysis of transcribed sequences: comparative and functional genomics workshop
    A Brazma
    European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, UK
    Cytogenet Genome Res 105:11-7. 2004
  56. ncbi request reprint Building and analysing genome-wide gene disruption networks
    J Rung
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 18:S202-10. 2002
    ..We can investigate questions such as network modularity, connectivity, and look for genes with particular roles in the network structure...
  57. pmc Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum
    Katherine Lawler
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    BMC Syst Biol 7:52. 2013
    ..The topological structure of transcriptional networks was also examined to investigate control mechanisms for mycotoxin biosynthesis and other processes...
  58. pmc Towards reconstruction of gene networks from expression data by supervised learning
    Lev A Soinov
    Microarray Informatics Group, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Genome Biol 4:R6. 2003
    ..We use a supervised learning approach to address this question by building decision-tree-related classifiers, which predict gene expression from the expression data of other genes...
  59. pmc A CD8+ T cell transcription signature predicts prognosis in autoimmune disease
    Eoin F McKinney
    Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Institute for Medical Research, Addenbrooke s Hospital, Cambridge, UK
    Nat Med 16:586-91, 1p following 591. 2010
    ..These subgroups, which are also found in the normal population and can be identified by measuring expression of only three genes, raise the prospect of individualized therapy and suggest new potential therapeutic targets in autoimmunity...
  60. ncbi request reprint The underlying principles of scientific publication
    Catherine A Ball
    Bioinformatics 18:1409. 2002
  61. doi request reprint Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
    Eric W Deutsch
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Biotechnol 26:305-12. 2008
    ..This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal...
  62. ncbi request reprint An open letter on microarray data from the MGED Society
    Catherine Ball
    Stanford University, USA
    Microbiology 150:3522-4. 2004
  63. pmc Standards for microarray data: an open letter
    Catherine Ball
    Environ Health Perspect 112:A666-7. 2004
  64. pmc Expression Profiler: next generation--an online platform for analysis of microarray data
    Misha Kapushesky
    European Bioinformatics Institute, United Kingdom
    Nucleic Acids Res 32:W465-70. 2004
    ..EP:NG is an open-source project, encouraging broad distribution and further extensions from the scientific community...
  65. ncbi request reprint [Standardization of microarray experiment data]
    Alvis Brazma
    Tanpakushitsu Kakusan Koso 48:280-5. 2003
  66. pmc Global transcriptional responses of fission yeast to environmental stress
    Dongrong Chen
    The Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
    Mol Biol Cell 14:214-29. 2003
    ..Promoter motifs associated with some of the groups of coregulated genes were identified. We compare and contrast global regulation of stress genes in fission and budding yeasts and discuss evolutionary implications...
  67. ncbi request reprint Standards for microarray data
    Catherine A Ball
    Science 298:539. 2002
  68. ncbi request reprint Correlating gene promoters and expression in gene disruption experiments
    Kimmo Palin
    Department of Computer Science, University of Helsinki, Finland
    Bioinformatics 18:S172-80. 2002
    ..g. knockouts)...
  69. pmc Design and implementation of microarray gene expression markup language (MAGE-ML)
    Paul T Spellman
    Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, CA 94720 3206, USA
    Genome Biol 3:RESEARCH0046. 2002
    ..Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies...
  70. ncbi request reprint Modelling gene networks at different organisational levels
    Thomas Schlitt
    British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
    FEBS Lett 579:1859-66. 2005
    ..The first two classes of models have reached a genome-wide scale, while for the other model classes high throughput technologies are yet to make a major impact...
  71. ncbi request reprint BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
    Steffen Durinck
    Department of Electronical Engineering, ESAT SCD, K U Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Bioinformatics 21:3439-40. 2005
    ..g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining...
  72. ncbi request reprint The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
    Andrew R Jones
    School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    Nat Biotechnol 25:1127-33. 2007
    ..Such advances are important for transparent data management and mining in functional genomics and systems biology...
  73. pmc 4DXpress: a database for cross-species expression pattern comparisons
    Yannick Haudry
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D847-53. 2008
    ..4DXpress will be an invaluable tool for developmental as well as for computational biologists interested in gene regulation and evolution. 4DXpress is available at http://ani.embl.de/4DXpress...
  74. ncbi request reprint ArrayExpress service for reviewers/editors of DNA microarray papers
    Alvis Brazma
    Nat Biotechnol 24:1321-2. 2006
  75. doi request reprint The BREW workshop series: a stimulating experience in PhD education
    Robert Giegerich
    Center of Biotechnology, Bielefeld University, Postfach 10 01 31, D 33501 Bielefeld, Germany
    Brief Bioinform 9:250-3. 2008
    ..We describe the BREW experience and argue that this type of event constitutes an attractive component of PhD education in computational biology and beyond...
  76. ncbi request reprint Reconstruction of gene regulatory networks under the finite state linear model
    Dace Ruklisa
    Institute of Mathematics and Computer Science, University of Latvia, Rainis boulevard 29, Riga LV 1459, Latvia
    Genome Inform 16:225-36. 2005
    ..Experiments on reconstruction of random networks are performed to estimate the running time of the algorithm in practice, as well as the number of measurements needed for successful network reconstruction...
  77. ncbi request reprint Wrestling with SUMO and bio-ontologies
    Christian Stoeckert
    Nat Biotechnol 24:21-2; author reply 23. 2006
  78. ncbi request reprint Protein interaction verification and functional annotation by integrated analysis of genome-scale data
    Patrick Kemmeren
    Genomics Laboratory, Department of Biomedical Genetics, University Medical Center Utrecht, P O Box 85060, 3508 AB Utrecht, The Netherlands
    Mol Cell 9:1133-43. 2002
    ..This study shows how integration improves the utility of different types of functional genomic data and how well this contributes to functional annotation...
  79. ncbi request reprint Top-down standards will not serve systems biology
    John Quackenbush
    Nature 440:24. 2006
  80. ncbi request reprint Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)
    Eric W Deutsch
    Institute for Systems Biology, Seattle, Washington 98103, USA
    OMICS 10:205-8. 2006
    ..The full specification will soon be published as a version 1.0 proposal to the community, upon which a more full discussion must take place so that the final specification may be achieved with the involvement of the whole community...