Alvis Brazma

Alvis Brazma

Senior Team Leader, Functional Genomics

PhD in Computer Science, Moscow State University, 1987. Postdoctoral research at New Mexico State University, USA. At EMBL-EBI since 1997.

Tel:+44 (0)1223 494 658 / Fax:+44 (0)1223 494 468

http://www.ebi.ac.uk/~brazma (personal homepage)

Research

Find out about research activity in the Brazma research group

Brazma team

Led by Dr Alvis Brazma, the Functional Genomics Team focuses on providing bioinformatics services and conducting research in gene expression and high-throughput sequencing applications to functional genomics. The team participates in software development related to biomedical informatics and systems microscopy, and is responsible for the Gene Expression Atlas, which is being developed to encompass proteomics and metabolomics data. Together with the Sarkans and Parkinson teams, the Functional Genomics team works on the ArrayExpress Archive of Functional Genomics Data and the BioSamples Database. Students in the team focus on data analysis and developing new methods and algorithms, integration of data across multiple platforms and types of data. The team is a major contributor to EMBL-EBI's training in transcriptomics and the use of EMBL-EBI tools.

Publications

2013

ArrayExpress update—trends in database growth and links to data analysis tools
RUSTICI, G., KOLESNIKOV N., BRANDIZI M., BURDETT T., DYLAG M., EMAM I., FARNE A., HASTINGS E., ISON J., KEAYS M., et al.
Nucleic acids research. Volume 41, Number D1, (2013), p.D987–D990

2012

The BioSample Database (BioSD) at the European Bioinformatics Institute
GOSTEV, M., FAULCONBRIDGE A., BRANDIZI M., FERNANDEZ-BANET J., Sarkans U., BRAZMA A., and Parkinson H.
Nucleic acids research. Volume 40, Number D1, (2012), p.D64–D70
Fully scalable online-preprocessing algorithm for short oligonucleotide microarray atlases
Lahti, L., Torrente A., Elo L. L., BRAZMA A., and Rung J.
arXiv preprint arXiv:1212.5932. (2012),
HSM–a hybrid system based approach for modelling intracellular networks
BRAZMA, A., Cerans K., Ruklisa D., Schlitt T., and Viksna J.
Gene. (2012),
Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma
Caldas, J., GEHLENBORG N., Kettunen E., Faisal A., Rönty M., Nicholson A. G., Knuutila S., BRAZMA A., and Kaski S.
Bioinformatics. Volume 28, Number 2, (2012), p.246–253
Tools for mapping high-throughput sequencing data
FONSECA, N. A., Rung J., BRAZMA A., and MARIONI J. C.
Bioinformatics. Volume 28, Number 24, (2012), p.3169–3177
MageComet—web application for harmonizing existing large-scale experiment descriptions
Xue, V., BURDETT T., Lukk M., TAYLOR J., BRAZMA A., and Parkinson H.
Bioinformatics. Volume 28, Number 10, (2012), p.1402–1403
Reuse of public genome-wide gene expression data
Rung, J., and BRAZMA A.
Nature Reviews Genetics. Volume 14, Number 2, (2012), p.89–99
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
Hoehndorf, Robert, Harris Midori A., Herre Heinrich, Rustici Gabriella, and Gkoutos Georgios V.
Bioinformatics (Oxford, England). Volume 28, (2012), p.1783–1789 doi:

2011

Quality metrics
Beisv{\aa}g, V., KAUFFMANN A., MALONE J., Foy C., Salit M., Schimmel H., Bongcam-Rudloff E., Landegren U., Parkinson H., Huber W., et al.
BioTechniques. Volume 50, Number 1, (2011), p.27–31
SAIL—a software system for sample and phenotype availability across biobanks and cohorts
GOSTEV, M., FERNANDEZ-BANET J., Rung J., Dietrich J., Prokopenko I., Ripatti S., McCarthy M. I., BRAZMA A., and KRESTYANINOVA M.
Bioinformatics. Volume 27, Number 4, (2011), p.589–591

2010

Annotare—a tool for annotating high-throughput biomedical investigations and resulting data
Shankar, R., Parkinson H., BURDETT T., HASTINGS E., Liu J., Miller M., Srinivasa R., White J., BRAZMA A., Sherlock G., et al.
Bioinformatics. Volume 26, Number 19, (2010), p.2470–2471
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays
Vainshtein, Y., Sanchez M., BRAZMA A., Hentze M. W., Dandekar T., and Muckenthaler M. U.
BMC bioinformatics. Volume 11, Number 1, (2010), p.112
International network of cancer genome projects
Hudson, T. J., Anderson W., Aretz A., Barker A. D., Bell C., Bernabé R. R., Bhan MK, Calvo F., Eerola I., Gerhard D. S., et al.
Nature. Volume 464, Number 7291, (2010), p.993–998

2009

The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback
Aligianni, S., Lackner D. H., Klier S., RUSTICI G., Wilhelm B. T., Marguerat S., Codlin S., BRAZMA A., de Bruin R. A. M., and Bähler J.
PLoS genetics. Volume 5, Number 8, (2009), p.e1000626
Visualization of large microarray experiments with space maps
GEHLENBORG, N., and BRAZMA A.
BMC Bioinformatics. Volume 10, Number Suppl 13, (2009), p.O7

2007

Gene Expression Databases
BRAZMA, A., and Sarkans U.
eLS. (2007),

2006

Wrestling with SUMO and bio-ontologies
Stoeckert, C., Ball C., BRAZMA A., Brinkman R., Causton H., Fan L., Fostel J., Fragoso G., Heiskanen M., Holstege F., et al.
Nature biotechnology. Volume 24, Number 1, (2006), p.21–22
By MARK REIMERS and VINCENT J. CAREY
Lyng, H., Badiee A., Svendsrud DH, Hovig E., Myklebost O., Stokke T., Parkinson H., Sarkans U., Shojatalab M., ABEYGUNAWARDENA N., et al.
Nucleic Acids Res. Volume 33, (2006), p.D553–D555

2005

Algorithms for gene expression analysis
BRAZMA, A., and Culhane A. C.
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. (2005),
Reconstruction of gene regulatory networks under the Finite State Linear Model
Ruklisa, D., BRAZMA A., and Viksna J.
GENOME INFORMATICS SERIES. Volume 16, Number 2, (2005), p.225

2004

Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies
Stoeckert, C. J., QUACKENBUSH J., BRAZMA A., Ball C. A., and others
Drug Discovery Today: TARGETS. Volume 3, Number 4, (2004), p.159–164
Report on the thirteenth international workshop on the identification and functional, evolutionary and expression analysis of transcribed sequences: comparative and functional genomics workshop
BRAZMA, A., Freeman T., Gardiner K., Weissman S., Werner T., Korn B., and others
Cytogenetic and genome research. Volume 105, Number 1, (2004), p.11–17

2003

[Standardization of microarray experiment data]
BRAZMA, A., Ikeo K., Tateno Y., and others
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. Volume 48, Number 3, (2003), p.280
[Standardization of microarray experiment data]
BRAZMA, A., Ikeo K., Tateno Y., and others
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. Volume 48, Number 3, (2003), p.280
Microarray gene expression data analysis: a beginner's guide
Causton, H. C., QUACKENBUSH J., and Br{\=a}zma A.
(2003),

2002

Building and Analysing Genome-wide Disruption Networks
Rung, J., Schlitt T., BRAZMA A., Frievalds K., and Vito J.
Bioinformatics. Volume 1, (2002), p.1–9
Chip technology
Hoheisel, J. D., and BRAZMA A.
Volume 77, (2002),

2001

Gene expression data mining and analysis
BRAZMA, A., Robinson A., and Vilo J.
DNA Microarrays: Gene Expression Applications. (2001), p.105–129

2000

Morphological evolution of second-phase particles during thermomechanical processing of W-La2O3 alloy
Chen, Z., Zhou M., and Zuo T.
Scripta materialia. Volume 43, (2000), p.291–297
Morphological evolution of second-phase particles during thermomechanical processing of W-La2O3 alloy
Chen, Z., Zhou M., and Zuo T.
Scripta materialia. Volume 43, (2000), p.291–297

1999

Discovery of putative transcription factor binding sites from microarray-based gene expression profiles
Vilo, J., BRAZMA A., Jonassen I., and Ukkonen E.
Nature Genetics. Volume 23, (1999), p.79–80

1998

Mining the yeast genome expression and sequence data
BRAZMA, A.
The BioInformer. Volume 4, (1998),
Predicting gene regulatory elements in silico on a genomic scale
Br{\=a}zma, A., Jonassen I., Vilo J., and Ukkonen E.
Genome research. Volume 8, Number 11, (1998), p.1202–1215
Predicting gene regulatory elements from their expression data in the complete yeast genome
BRAZMA, A., Jonassen I., Vilo J., and Ukkonen E.
German Conference on Bioinformatics. (1998),
Mining the yeast genome expression and sequence data
BRAZMA, A.
The BioInformer. Volume 4, (1998),
Pattern discovery in biosequences
Br{\=a}zma, A., Jonassen I., Vilo J., and Ukkonen E.
Grammatical Inference. (1998), p.257–270

1996

Discovering unbounded unions of regular pattern languages from positive examples
Br{\=a}zma, A., Ukkonen E., and Vilo J.
Algorithms and Computation. (1996), p.95–104

1995

A pattern language for molecular biology
BRAZMA, A., and Gilbert D.
(1995),
Learning of regular expressions by pattern matching
Br{\=a}zma, A.
Computational Learning Theory. (1995), p.392–403

1994

Efficient learning of regular expressions from good examples
Br{\=a}zma, A., and Čer{\=a}ns K.
Algorithmic Learning Theory. (1994), p.76–90
Efficient algorithm for learning simple regular expressions from noisy examples
Br{\=a}zma, A.
Algorithmic Learning Theory. (1994), p.260–271

1993

Learning a subclass of regular expressions by recognizing periodic repetitions
Br{\=a}zma, A.
Proceedings of the Fourth Scandinavian Conference on Artificial intelligence–-93. (1993), p.137–146
Efficient identification of regular expressions from representative examples
Br{\=a}zma, A.
Proceedings of the sixth annual conference on Computational learning theory. (1993), p.236–242

1991

Inductive synthesis of dot expressions
Br{\=a}zma, A.
Baltic Computer Science. (1991), p.156–212

Services

ArrayExpress
BioMedBridges
BioSamples
Expression Atlas

Team members

Benedetto Fiorelli
Lynn French
Catherine Kirsanova
Nataliya Kryvych
Karyn Megy
Robert Petryszak
Gabriella Rustici
Shyamasree Saha