Search filters

List of works by Alvis Brazma

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

scientific article published on 04 October 2007

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

scientific article

A General Framework for Interrogation of mRNA Stability Programs Identifies RNA-Binding Proteins that Govern Cancer Transcriptomes ⬇️

scientific article published on 01 May 2018

A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

scientific article published on 01 September 2019

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

scientific article

A call for public archives for biological image data

scientific article published on 01 November 2018

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.

scientific article

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

scientific article

A global map of human gene expression

scientific article

A guide to microarray experiments-an open letter to the scientific journals

scientific article published in The Lancet

A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings

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

A pipeline for RNA-seq data processing and quality assessment

scientific article

A proteomics sample metadata representation for multiomics integration and big data analysis

scientific article published in 2021

A public repository for DNA microarray-based gene expression data

article

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

scientific article

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

scientific article published in April 2011

Aberration hubs in protein interaction networks highlight actionable targets in cancer. ⬇️

scientific article

Abstract 389: Integrating diverse transcriptomic alterations to identify cancer-relevant genes

article

An information retrieval perspective on visualization of gene expression data with ontological annotation

article

An integrated encyclopedia of DNA elements in the human genome

scientific article

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures

scientific article published in Scientific Reports

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures

An integrated landscape of protein expression in human cancer

scientific article published on 23 April 2021

An open letter on microarray data from the MGED Society

scientific article published on November 2004

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data

scientific article

Approaches to the automatic discovery of patterns in biosequences.

scientific article

ArrayExpress service for reviewers/editors of DNA microarray papers

scientific article published in November 2006

ArrayExpress update - from bulk to single-cell expression data

scientific article published on 01 January 2019

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

scientific article

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

scientific article

ArrayExpress update--simplifying data submissions

scientific article

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

scientific article (publication date: 2013)

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

scientific article published on 28 November 2006

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

scientific article

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

scientific article (publication date: 2003)

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

scientific article

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

article

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

scientific article

Blood transcriptome profile induced by an efficacious vaccine formulated with salivary antigens from cattle ticks

scientific article published on 18 December 2019

Building and analysing genome-wide gene disruption networks.

scientific article published in January 2002

Cellular phenotype database: a repository for systems microscopy data

scientific article

Chip Technology

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression

scientific article published on 23 December 2005

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

scientific article published on 18 June 2015

Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer

article

Contributions of the EMERALD project to assessing and improving microarray data quality

scientific article

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress

scientific article

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

scientific article

Correlating gene promoters and expression in gene disruption experiments

scientific article published in January 2002

Current approaches to gene regulatory network modelling

scientific article (publication date: 27 September 2007)

Data mining for regulatory elements in yeast genome.

scientific article published on January 1997

Data storage and analysis in ArrayExpress

scientific article

Data storage and analysis in ArrayExpress and Expression Profiler

scientific article

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma

scientific article

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

scientific article

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

scientific article published on January 2006

Discovering patterns and subfamilies in biosequences

scientific article published on January 1996

Discovery of putative transcription factor binding sites from microarray-based gene expression profiles

article

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

scientific article published on 19 June 2014

Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ

scientific article published on 31 May 2019

Dysregulation at multiple points of the kynurenine pathway is a ubiquitous feature of renal cancer: implications for tumour immune evasion

scientific article published on 11 May 2020

Efficient algorithm for learning simple regular expressions from noisy examples

Efficient learning of regular expressions from good examples

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

scientific article

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

scientific article

Expression Atlas update: from tissues to single cells

scientific article published on 01 January 2020

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

scientific article

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

scientific article (publication date: July 2004)

Expression and Genetic Variation Databases for Cancer Research

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

scientific article

From ArrayExpress to BioStudies

scientific article published on 19 November 2020

From gene networks to gene function

scientific article

Funding high-throughput data sharing

scientific article

Fusing microarray experiments with multivariate regression

scientific article published in September 2005

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci

scientific article published on 06 August 2020

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

scientific article

Gene expression atlas at the European bioinformatics institute

scientific article

Gene expression data analysis

scientific article

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

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

scientific article published on August 2017

Genomic basis for RNA alterations in cancer

scientific article published on 05 February 2020

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum

scientific article

Genomic determinants of protein abundance variation in colorectal cancer cells

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

article

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

scientific article

Global transcriptional responses of fission yeast to environmental stress

scientific article

Guidelines for reporting single-cell RNA-seq experiments

scientific article published on 13 November 2020

HMGB1 binds to the rs7903146 locus in TCF7L2 in human pancreatic islets

scientific article published in February 2016

HSM - a hybrid system based approach for modelling intracellular networks

scientific article published on 21 December 2012

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

scientific article published on 05 February 2020

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

scientific article

Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression

scientific article

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

scientific article

Impact of Alternative Splicing on the Human Proteome

scientific article

Importing ArrayExpress datasets into R/Bioconductor

scientific article published on 08 June 2009

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

scientific article

Integrating sequence, evolution and functional genomics in regulatory genomics

scientific article published on 30 January 2009

International network of cancer genome projects

scientific article

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

scientific article published on 23 December 2010

Learning about gene regulatory networks from gene deletion experiments

scientific article published on January 2002

Learning of regular expressions by pattern matching

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

MGED standards: work in progress

scientific article published on January 2006

MageComet--web application for harmonizing existing large-scale experiment descriptions

scientific article published on 02 April 2012

Microarray data representation, annotation and storage

scientific article

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

scientific article (publication date: 29 May 2009)

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

scientific article (publication date: December 2001)

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

scientific article

Mining for putative regulatory elements in the yeast genome using gene expression data

scientific article

Modeling and Analysis of Qualitative Behavior of Gene Regulatory Networks

article

Modeling sample variables with an Experimental Factor Ontology

scientific article

Modelling gene networks at different organisational levels

scientific article

Modelling in molecular biology: describing transcription regulatory networks at different scales

scientific article (publication date: 29 March 2006)

Modelling-based experiment retrieval: a case study with gene expression clustering ⬇️

scientific article published on 6 January 2016

On the Importance of Standardisation in Life Sciences

scientific article published on 01 February 2001

One-stop shop for microarray data

scientific article published in February 2000

Orchestrating differential data access for translational research: a pilot implementation

scientific article

PASSIM--an open source software system for managing information in biomedical studies

scientific article published on 9 February 2007

Periodic gene expression program of the fission yeast cell cycle.

scientific article published on 13 June 2004

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress

scientific article (publication date: October 2005)

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

scientific article

Predicting gene regulatory elements in silico on a genomic scale

scientific article

Prediction of gene expression in embryonic structures of Drosophila melanogaster

scientific article

Probabilistic retrieval and visualization of biologically relevant microarray experiments

scientific article published on June 2009

Probabilistic retrieval and visualization of biologically relevant microarray experiments

scientific article published on 19 October 2009

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

scientific article (publication date: August 2008)

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

scientific article

Publisher Correction: Image Data Resource: a bioimage data integration and publication platform

scholarly article by Eleanor Williams published in October 2018

Putative cell type discovery from single-cell gene expression data

scientific article published on 18 May 2020

REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology

scientific article published on 21 May 2021

RNA-Seq gene profiling--a systematic empirical comparison

scientific article

Reconstruction of gene regulatory networks under the finite state linear model

scientific article published in January 2005

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System

scientific article published on 4 September 2015

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

scientific article published on 21 March 2018

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008)

scientific article

Report on the thirteenth international workshop on the identification and functional, evolutionary and expression analysis of transcribed sequences: comparative and functional genomics workshop.

scientific article published in January 2004

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

scientific article published on 15 September 2013

Reuse of public genome-wide gene expression data

scientific article (publication date: 27 December 2012)

SAIL--a software system for sample and phenotype availability across biobanks and cohorts.

scientific article

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

scientific article published on 12 September 2016

Standardization of microarray experiment data

scientific article

Standards for microarray data

scientific article

Standards for microarray data: an open letter

scientific article

Standards for systems biology

scientific article published on August 2006

Submission of microarray data to public repositories

scientific article

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

scientific article

Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants

scientific article published in 2014

The ArrayExpress gene expression database: a software engineering and implementation perspective

scientific article published on 25 November 2004

The BREW workshop series: a stimulating experience in PhD education

scientific article published on 23 January 2008

The BioSample Database (BioSD) at the European Bioinformatics Institute

scientific article

The BioStudies database

scientific article

The BioStudies database-one stop shop for all data supporting a life sciences study.

scientific article published on 23 October 2017

The European Bioinformatics Institute's data resources.

scientific article

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article

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

scientific article (publication date: February 2004)

The Image Data Resource: A Bioimage Data Integration and Publication Platform

scientific article

The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays

scientific article

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

scientific article

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

scientific article published on 01 January 2022

The RNASeq-er API - a gateway to systematically updated analysis of public RNA-Seq data.

scientific article

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

scientific article

The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback

scientific article

The underlying principles of scientific publication.

scientific article published in November 2002

Tools for mapping high-throughput sequencing data

scientific article

Top-down standards will not serve systems biology

scientific article published in Nature

Towards reconstruction of gene networks from expression data by supervised learning

scientific article

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

scientific article

Transcriptome and genome sequencing uncovers functional variation in humans

scientific article

Transparency and reproducibility in artificial intelligence

scientific article published on 14 October 2020

Tumour gene expression signature in primary melanoma predicts long-term outcomes

scientific article published on 18 February 2021

Updates to BioSamples database at European Bioinformatics Institute

scientific article

Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes

scientific article

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

scientific article published on 29 October 2014

Visualization of large microarray experiments with space maps

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

article

Wrestling with SUMO and bio-ontologies

scientific article

clustComp, a Bioconductor package for the comparison of clustering results

scientific article published on 23 August 2017

Paulina is supported by:

About Paulina

Help