List of works - Alvis Brazma

An integrated encyclopedia of DNA elements in the human genome

scientific article

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

scientific article (publication date: December 2001)

International network of cancer genome projects

scientific article

Transcriptome and genome sequencing uncovers functional variation in humans

scientific article

A user's guide to the encyclopedia of DNA elements (ENCODE)

scientific article published in April 2011

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

scientific article

The PRIDE database and related tools and resources in 2019: improving support for quantification data

scientific article

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing

scientific article published on 12 September 2016

Global transcriptional responses of fission yeast to environmental stress

scientific article

ArrayExpress--a public repository for microarray gene expression data at the EBI

scientific article (publication date: 2003)

ArrayExpress update--simplifying data submissions

scientific article

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

scientific article (publication date: February 2004)

ArrayExpress--a public database of microarray experiments and gene expression profiles

scientific article published on 28 November 2006

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

scientific article

Periodic gene expression program of the fission yeast cell cycle.

scientific article published on 13 June 2004

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression

scientific article

ArrayExpress update--trends in database growth and links to data analysis tools

scientific article (publication date: 2013)

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

scientific article

A global map of human gene expression

scientific article

ArrayExpress--a public repository for microarray gene expression data at the EBI

scientific article

Modeling sample variables with an Experimental Factor Ontology

scientific article

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

scientific article

Design and implementation of microarray gene expression markup language (MAGE-ML)

scientific article

A CD8+ T cell transcription signature predicts prognosis in autoimmune disease

scientific article

Reuse of public genome-wide gene expression data

scientific article (publication date: 27 December 2012)

Gene expression data analysis

scientific article

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

scientific article published on 15 September 2013

Gene expression atlas at the European bioinformatics institute

scientific article

Predicting gene regulatory elements in silico on a genomic scale

scientific article

Protein interaction verification and functional annotation by integrated analysis of genome-scale data.

scientific article

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

scientific article

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

scientific article

Tools for mapping high-throughput sequencing data

scientific article

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

scientific article

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome

scientific article

From gene networks to gene function

scientific article

Expression Atlas: gene and protein expression across multiple studies and organisms.

scientific article

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals

scientific article

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges

scientific article (publication date: 29 May 2009)

Standards for microarray data

scientific article

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

scientific article published on August 2017

Current approaches to gene regulatory network modelling

scientific article (publication date: 27 September 2007)

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

scientific article

Variation in genomic landscape of clear cell renal cell carcinoma across Europe

scientific article published on 29 October 2014

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

scientific article

One-stop shop for microarray data

scientific article published in February 2000

Standards for systems biology

scientific article published on August 2006

Large scale comparison of global gene expression patterns in human and mouse.

scientific article published on 23 December 2010

Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications

scientific article published on 19 June 2014

List of works by Alvis Brazma

An integrated encyclopedia of DNA elements in the human genome

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

International network of cancer genome projects

Transcriptome and genome sequencing uncovers functional variation in humans

A user's guide to the encyclopedia of DNA elements (ENCODE)

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

The PRIDE database and related tools and resources in 2019: improving support for quantification data

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing

Global transcriptional responses of fission yeast to environmental stress

ArrayExpress--a public repository for microarray gene expression data at the EBI

ArrayExpress update--simplifying data submissions

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

ArrayExpress--a public database of microarray experiments and gene expression profiles

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

Periodic gene expression program of the fission yeast cell cycle.

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression

ArrayExpress update--trends in database growth and links to data analysis tools

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

A global map of human gene expression

ArrayExpress--a public repository for microarray gene expression data at the EBI

Modeling sample variables with an Experimental Factor Ontology

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Design and implementation of microarray gene expression markup language (MAGE-ML)

A CD8+ T cell transcription signature predicts prognosis in autoimmune disease

Reuse of public genome-wide gene expression data

Gene expression data analysis

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

Gene expression atlas at the European bioinformatics institute

Predicting gene regulatory elements in silico on a genomic scale

Protein interaction verification and functional annotation by integrated analysis of genome-scale data.

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Tools for mapping high-throughput sequencing data

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome

From gene networks to gene function

Expression Atlas: gene and protein expression across multiple studies and organisms.

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges

Standards for microarray data

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

Current approaches to gene regulatory network modelling

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

Variation in genomic landscape of clear cell renal cell carcinoma across Europe

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

One-stop shop for microarray data

Standards for systems biology

Large scale comparison of global gene expression patterns in human and mouse.

Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications