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List of works by Alvis Brazma

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Submission of microarray data to public repositories

scientific article
A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection

scientific article
Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing

scientific article
Expression Profiler: next generation--an online platform for analysis of microarray data

scientific article (publication date: July 2004)
RNA-Seq Gene Profiling - A Systematic Empirical Comparison

scientific article published on September 30, 2014
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article
Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes.

scientific article
Importing ArrayExpress datasets into R/Bioconductor

scientific article published on 08 June 2009
Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes

scientific article
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".

scientific article
ArrayExpress: a public database of gene expression data at EBI.

scientific article
Approaches to the automatic discovery of patterns in biosequences.

scientific article
A pipeline for RNA-seq data processing and quality assessment

scientific article
ArrayExpress update - from bulk to single-cell expression data

scientific article published on 01 January 2019
The Image Data Resource: A Bioimage Data Integration and Publication Platform

scientific article
Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.

scientific article
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

scientific article published on 18 June 2015
The BioSample Database (BioSD) at the European Bioinformatics Institute

scientific article
On the Importance of Standardisation in Life Sciences

scientific article published on 01 February 2001
Impact of Alternative Splicing on the Human Proteome

scientific article
Towards reconstruction of gene networks from expression data by supervised learning

scientific article
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

scientific article
Building and analysing genome-wide gene disruption networks.

scientific article published in January 2002
Mining for putative regulatory elements in the yeast genome using gene expression data

scientific article
Probabilistic retrieval and visualization of biologically relevant microarray experiments

scientific article published on June 2009
The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback

scientific article
Updates to BioSamples database at European Bioinformatics Institute

scientific article
Funding high-throughput data sharing

scientific article
A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging

scientific article published on 9 October 2015
The European Bioinformatics Institute's data resources.

scientific article
4DXpress: a database for cross-species expression pattern comparisons

scientific article published on 04 October 2007
A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.

scientific article
A System for Information Management in BioMedical Studies--SIMBioMS.

scientific article
Modelling gene networks at different organisational levels

scientific article
Subtype-specific micro-RNA expression signatures in breast cancer progression

scientific article
The underlying principles of scientific publication.

scientific article published in November 2002
Data storage and analysis in ArrayExpress

scientific article
ArrayExpress service for reviewers/editors of DNA microarray papers

scientific article published in November 2006
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

scientific article published on 21 March 2018
PASSIM--an open source software system for managing information in biomedical studies

scientific article published on 9 February 2007
Genomic basis for RNA alterations in cancer

scientific article published on 05 February 2020
MGED standards: work in progress

scientific article published on January 2006
Gene expression data analysis#1Abridged version of article in FEBS Lett. 480 (2000) 17–24; with permission from Elsevier Science. PII of original article: S0014-5793(00)01772-5

scientific article published on 01 August 2001
The ArrayExpress gene expression database: a software engineering and implementation perspective

scientific article published on 25 November 2004
The BioStudies database-one stop shop for all data supporting a life sciences study.

scientific article published on 23 October 2017
Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants

scientific article published on August 18, 2014
Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress

scientific article
Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma

scientific article published on 23 March 2017
Modelling in molecular biology: describing transcription regulatory networks at different scales

scientific article (publication date: 29 March 2006)
A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings

scientific article

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