Alvis Brazma

According to our database1, Alvis Brazma authored at least 83 papers between 1986 and 2022.

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Bibliography

2022
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.
Nucleic Acids Res., 2022

Expression Atlas update: gene and protein expression in multiple species.
Nucleic Acids Res., 2022

2021
From ArrayExpress to BioStudies.
Nucleic Acids Res., 2021

2020
Genomic basis for RNA alterations in cancer.
Nat., 2020

Expression Atlas update: from tissues to single cells.
Nucleic Acids Res., 2020

2019
The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Nucleic Acids Res., 2019

ArrayExpress update - from bulk to single-cell expression data.
Nucleic Acids Res., 2019

Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ.
BMC Bioinform., 2019

2018
The BioStudies database - one stop shop for all data supporting a life sciences study.
Nucleic Acids Res., 2018

Expression Atlas: gene and protein expression across multiple studies and organisms.
Nucleic Acids Res., 2018

2017
Orchestrating differential data access for translational research: a pilot implementation.
BMC Medical Informatics Decis. Mak., 2017

clustComp, a bioconductor package for the comparison of clustering results.
Bioinform., 2017

The RNASeq-er API - a gateway to systematically updated analysis of public RNA-seq data.
Bioinform., 2017

2016
Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants.
Nucleic Acids Res., 2016

Modelling-based experiment retrieval: a case study with gene expression clustering.
Bioinform., 2016

2015
ArrayExpress update - simplifying data submissions.
Nucleic Acids Res., 2015

Cellular phenotype database: a repository for systems microscopy data.
Bioinform., 2015

2014
Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Nucleic Acids Res., 2014

Updates to BioSamples database at European Bioinformatics Institute.
Nucleic Acids Res., 2014

Modeling and Analysis of Qualitative Behavior of Gene Regulatory Networks.
Proceedings of the Hybrid Systems Biology, 2014

2013
ArrayExpress update - trends in database growth and links to data analysis tools.
Nucleic Acids Res., 2013

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.
BMC Syst. Biol., 2013

2012
Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments.
Nucleic Acids Res., 2012

The BioSample Database (BioSD) at the European Bioinformatics Institute.
Nucleic Acids Res., 2012

Fully scalable online-preprocessing algorithm for short oligonucleotide microarray atlases
CoRR, 2012

MageComet - web application for harmonizing existing large-scale experiment descriptions.
Bioinform., 2012

Tools for mapping high-throughput sequencing data.
Bioinform., 2012

Data-driven information retrieval in heterogeneous collections of transcriptomics data links <i>SIM2s</i> to malignant pleural mesothelioma.
Bioinform., 2012

2011
ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments.
Nucleic Acids Res., 2011

SAIL - a software system for sample and phenotype availability across biobanks and cohorts.
Bioinform., 2011

A pipeline for RNA-seq data processing and quality assessment.
Bioinform., 2011

2010
Gene Expression Atlas at the European Bioinformatics Institute.
Nucleic Acids Res., 2010

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.
BMC Bioinform., 2010

Annotare - a tool for annotating high-throughput biomedical investigations and resulting data.
Bioinform., 2010

Modeling sample variables with an Experimental Factor Ontology.
Bioinform., 2010

An information retrieval perspective on visualization of gene expression data with ontological annotation.
Proceedings of the IEEE International Conference on Acoustics, 2010

2009
ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression.
Nucleic Acids Res., 2009

Visualization of large microarray experiments with space maps.
BMC Bioinform., 2009

Probabilistic retrieval and visualization of biologically relevant microarray experiments.
BMC Bioinform., 2009

A System for Information Management in BioMedical Studies - SIMBioMS.
Bioinform., 2009

Importing ArrayExpress datasets into R/Bioconductor.
Bioinform., 2009

2008
4D<i>Xpress</i>: a database for cross-species expression pattern comparisons.
Nucleic Acids Res., 2008

The BREW workshop series: a stimulating experience in PhD education.
Briefings Bioinform., 2008

Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

Preface.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

2007
Prediction of Gene Expression in Embryonic Structures of <i>Drosophila melanogaster</i>.
PLoS Comput. Biol., 2007

ArrayExpress - a public database of microarray experiments and gene expression profiles.
Nucleic Acids Res., 2007

PASSIM - an open source software system for managing information in biomedical studies.
BMC Bioinform., 2007

Current approaches to gene regulatory network modelling.
BMC Bioinform., 2007

2006
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
BMC Bioinform., 2006

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.
Bioinform., 2006

2005
ArrayExpress - a public repository for microarray gene expression data at the EBI.
Nucleic Acids Res., 2005

A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.
Bioinform., 2005

The ArrayExpress gene expression database: a software engineering and implementation perspective.
Bioinform., 2005

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
Bioinform., 2005

Fusing microarray experiments with multivariate regression.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

2004
Expression Profiler: next generation - an online platform for analysis of microarray data.
Nucleic Acids Res., 2004

2003
The European Bioinformatics Institute's data resources.
Nucleic Acids Res., 2003

ArrayExpress - a public repository for microarray gene expression data at the EBI.
Nucleic Acids Res., 2003

Microarray gene expression data analysis - a beginner's guide.
Blackwell, ISBN: 978-1-40510-682-5, 2003

2002
An open letter to the scientific journals.
Bioinform., 2002

Building and analysing genome-wide gene disruption networks.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

Correlating gene promoters and expression in gene disruption experiments.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

2001
On the Importance of Standardisation in Life Sciences.
Bioinform., 2001

2000
Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

1998
Approaches to the Automatic Discovery of Patterns in Biosequences.
J. Comput. Biol., 1998

Pattern Discovery in Biosequences.
Proceedings of the Grammatical Inference, 4th International Colloquium, 1998

Predicting gene regulatory elements from their expression data in the complete yeast genome.
Proceedings of the German Conference on Bioinformatics, 1998

1997
Noise-Tolerant Efficient Inductive Synthesis of Regular Expressions from Good Examples.
New Gener. Comput., 1997

Data Mining for Regulatory Elements in Yeast Genome.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

Finding transcription factor binding site combinations in the yeast genome.
Proceedings of the German Conference on Bioinformatics, 1997

Data Mining and Visualisation in Molecular Biology Databases.
Proceedings of the German Conference on Bioinformatics, 1997

1996
Discovering Patterns and Subfamilies in Biosequences.
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract).
Proceedings of the Algorithms and Computation, 7th International Symposium, 1996

1995
Learning of regular expressions by pattern matching.
Proceedings of the Computational Learning Theory, Second European Conference, 1995

1994
A Simple Algorithm for Drawing Large Graphs on Small Screens.
Proceedings of the Graph Drawing, DIMACS International Workshop, 1994

Efficient Learning of Regular Expressions from Good Examples.
Proceedings of the Algorithmic Learning Theory, 1994

Efficient Algorithm for Learning Simple Regular Expressions from Noisy Examples.
Proceedings of the Algorithmic Learning Theory, 1994

1993
Learning a Subclass of Regular Expressions by Recognizing Periodic Repetitions.
Proceedings of the Fourth Scandinavian Conference on Artificial Intelligence, 1993

Efficient Identification of Regular Expressions from Representative Examples.
Proceedings of the Sixth Annual ACM Conference on Computational Learning Theory, 1993

1991
Inductive Synthesis of Dot Expressions.
Proceedings of the Baltic Computer Science, Selected Papers, 1991

1990
Models of Inductive Synthesis.
J. Log. Program., 1990

1986
Generalized Regular Expressions-A Language for Synthesis of Programs with Braching in Loops.
Theor. Comput. Sci., 1986


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