Probabilistic retrieval and visualization of biologically relevant microarray experiments (2009)
Caldas, José, Gehlenborg, Nils, Faisal, Ali, Brazma, Alvis, Kaski, Samuel
No abstract available.
Visualization of large microarray experiments with space maps (2009)
Gehlenborg, Nils, Brazma, Alvis
No abstract available.
Integrating sequence, evolution and functional genomics in regulatory genomics (2009)
Vingron, Martin, Brazma, Alvis, Coulson, Richard, Van Helden, Jacques, Manke, Thomas, Palin, Kimmo, ...
Abstract With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to...
Probabilistic retrieval and visualization of biologically relevant microarray experiments (2009)
Caldas, José, Gehlenborg, Nils, Faisal, Ali, Brazma, Alvis, Kaski, Samuel
Motivation: As ArrayExpress and other repositories of genome-wide experiments are reaching a mature size, it is becoming more meaningful to search for related experiments, given a particular study....
Parkinson, Helen, Kapushesky, Misha, Kolesnikov, Nikolay, Rustici, Gabriella, Shojatalab, Mohammad, Abeygunawardena, Niran, ...
ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress...
Importing ArrayExpress datasets into R/Bioconductor (2009)
Kauffmann, Audrey, Rayner, Tim F., Parkinson, Helen, Kapushesky, Misha, Lukk, Margus, Brazma, Alvis, ...
Summary:ArrayExpress is one of the largest public repositories of microarray datasets. R/Bioconductor provides a comprehensive suite of microarray analysis and integrative bioinformatics software....
The Functional Genomics Experiment model (FuGE): (2008)
Andrew R Jones, Michael Miller, Ruedi Aebersold, Rolf Apweiler, Catherine A Ball, Alvis Brazma, ...
an extensible framework for standards in functional genomics
Taylor, Chris, Field, Dawn, Sansone, Susanna-Assunta, Apweiler, Rolf, Ashburner, Michael, Ball, Cathy, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those...
Taylor, Chris F., Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Asburner, Michael, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated...
The First RSBI (ISA-TAB) Workshop: "Can a Simple Format Work for Complex Studies?" (2008)
Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Brandizi, Marco, Brazma, Alvis, Field, Dawn, Fostel, Jennifer, ...
This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6–8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of...
Ugis Sarkans, Helen Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, ...
Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for...
Olivier Garcia, Cosmin Saveanu, Melissa Cline, Micheline Fromont-racine, Alain Jacquier, Benno Schwikowski, ...
Summary: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds...
Applications Note SEBINI: Software Environment for BIological Network Inference (2008)
Ronald C. Taylor, Anuj Shah, Charles Treatman, Meridith Blevins, Alvis Brazma
Aurora Torrente, Misha Kapushesky, Alvis Brazma
relationships between hierarchical and flat gene
ArrayExpress: A standards-based public repository for microarray data (2008)
Niran Abeygunawardena, Sergio Contrino, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, Gaurab Mukherjee, ...
ArrayExpress[1] is a public repository based at EBI that provides archive and query functions for well-annotated microarray data. As of August 2004, the data available in ArrayExpress represents...
BIOINFORMATICS ORIGINAL PAPER Systems biology (2008)
J. Vidal Rodríguez, Jaap A. Ka, Maciej Dobrzyński, Joke G. Blom, Alvis Brazma
doi:10.1093/bioinformatics/btl271 Spatial stochastic modelling of the phosphoenolpyruvatedependent phosphotransferase (PTS) pathway in Escherichia coli
The BREW workshop series: a stimulating experience in PhD education (2008)
Giegerich, Robert, Brazma, Alvis, Ukkonen, Esko, Vingron, Martin
Over recent years, five European PhD programmes have organized a series of ‘Bioinformatics Research and Education Workshops’. These workshops address the needs of first-year PhD students and have...
Deutsch, Eric W, Ball, Catherine A, Berman, Jules J, Bova, G Steven, Brazma, Alvis, Bumgarner, Roger E, ...
One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present...
4DXpress: a database for cross-species expression pattern comparisons (2008)
Haudry, Yannick, Berube, Hugo, Letunic, Ivica, Weeber, Paul-Daniel, Gagneur, Julien, Girardot, Charles, ...
In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these...
The BREW workshop series: a stimulating experience in PhD education (2008)
Giegerich, Robert, Brazma, Alvis, Jonassen, Inge, Ukkonen, Esko, Vingron, Martin
Over recent years, five European PhD programmes have organized a series of ‘Bioinformatics Research and Education Workshops’. These workshops address the needs of first-year PhD students and have...
Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David Gilbert
Approaches to the automatic discovery of patterns in biosequences.
Presentation: Invited Speaker (2007)
Name Brown, Name Brazma, Alvis Brazma, Alan Robinson
Microarray Data Annotations group was established at the first MGED meeting in November 1999, in Cambridge UK. The group has collectively developed a draft specification of the minimum information...
Jones, Andrew R, Miller, Michael, Aebersold, Ruedi, Apweiler, Rolf, Ball, Catherine A, Brazma, Alvis, ...
The Functional Genomics Experiment data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components...
Current approaches to gene regulatory network modelling (2007)
Schlitt, Thomas, Brazma, Alvis
Abstract Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists,...
Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster (2007)
Anastasia A. Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma
Understanding how sets of genes are coordinately regulated in space and time to generate the diversity of cell types that characterise complex metazoans is a major challenge in modern biology. The...
Rustici, Gabriella, Van Bakel, Harm, Lackner, Daniel H, Holstege, Frank C, Wijmenga, Cisca, Bähler, Jürg, ...
Abstract Background Recent studies in comparative genomics demonstrate that interspecies comparison represents a powerful tool for identifying both conserved and specialized biologic processes across...
PASSIM – an open source software system for managing information in biomedical studies (2007)
Viksna, Juris, Celms, Edgars, Opmanis, Martins, Podnieks, Karlis, Rucevskis, Peteris, Zarins, Andris, ...
Abstract Background One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An...
BMC Bioinformatics Review Current approaches to gene regulatory network modelling (2007)
Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB (2006)
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
Abstract Background Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the...
Deutsch, Eric W., Ball, Catherine A., Bova, G. Steven, Brazma, Alvis, Bumgarner, Roger E., Campbell, David, ...
We describe the creation process of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). Modeled after the existing minimum information...
Learning About Gene Regulatory Networks From Gene Deletion Experiments (2006)
Gene regulatory networks are a major focus of interest in molecular biology. A crucial question is how complex regulatory systems are encoded and controlled by the genome. Three recent publications...
Deutsch, Eric W., Ball, Catherine A., Bova, G. Steven, Brazma, Alvis, Bumgarner, Roger E., Campbell, David, ...
We describe the creation process of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). Modeled after the existing minimum information...
A simple spreadsheet-based, MIAME-supportive format for microarray data (2006)
Tim Rayner, Paul Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Jumin Liu, ...
{Note- this author list is not final; authors may still be added, and the list order has yet to be finalised.}
* Corresponding authors (2006)
Tim F Rayner, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, ...
A simple spreadsheet-based, MIAME-supportive format for
Blake, Jonathon, Schwager, Christian, Kapushesky, Misha, Brazma, Alvis
With the production of whole genome microarray chips the ability arises to investigate whether the regulation of particular groups of genes may be influenced by their chromosomal localization....
BIOINFORMATICS APPLICATIONS NOTE (2005)
Gene Expression, Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, ...
Vol. 21 no. 16 2005, pages 3439–3440 doi:10.1093/bioinformatics/bti525 BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
Gene Expression, Jonathon Blake, Christian Schwager, Misha Kapushesky, Alvis Brazma
ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression
David Arnosti, East Lansing, Luca Peliti Napoli, Alvis Brazma, Hinxton Nikolaus, Rajewsky New York, ...
The aim of this program is to bring together researchers and students from different backgrounds (including molecular biology, bioinformatics, biological physics) to discuss Networks and Regulation,...
Brazma A: Modelling gene networks at different organisational levels (2005)
Abstract Approaches to modelling gene regulation networks can be categorized, according to increasing detail, as network parts lists, network topology models, network control logic models, or dynamic...
Stochasticity in gene expression (2005)
Jonathon Blake, Christian Schwager, Misha Kapushesky, Alvis Brazma
ChroCoLoc: An application for calculating the probability of co-localization of
Durinck, Steffen, Moreau, Yves, Kasprzyk, Arek, Davis, Sean, De Moor, Bart, Brazma, Alvis, ...
Summary: biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers...
Fusing microarray experiments with multivariate regression (2005)
Gilks, Walter R., Tom, Brian D. M., Brazma, Alvis
Motivation: It is widely acknowledged that microarray data are subject to high noise levels and results are often platform dependent. Therefore, microarray experiments should be replicated several...
Sarkans, Ugis, Parkinson, Helen, Lara, Gonzalo Garcia, Oezcimen, Ahmet, Sharma, Anjan, Abeygunawardena, Niran, ...
Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for...
Torrente, Aurora, Kapushesky, Misha, Brazma, Alvis
Motivation: Clustering is one of the most widely used methods in unsupervised gene expression data analysis. The use of different clustering algorithms or different parameters often produces rather...
Blake, Jonathon, Schwager, Christian, Kapushesky, Misha, Brazma, Alvis
With the production of whole genome microarray chips the ability arises to investigate whether the regulation of particular groups of genes may be influenced by their chromosomal localization....
Torrente, Aurora, Kapushesky, Misha, Brazma, Alvis
Motivation: Clustering is one of the most widely used methods in unsupervised gene expression data analysis. The use of different clustering algorithms or different parameters often produces rather...
Submission of Microarray Data to Public Repositories (2004)
Catherine A. Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication.
Submission of Microarray Data to Public Repositories (2004)
Catherine A. Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, ...
Ugis Sarkans, Helen Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, ...
Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for...
Expression Profiler: next generation—an online platform for analysis of microarray data (2004)
Misha Kapushesky, Patrick Kemmeren, Aedín C. Culhane, Steffen Durinck, Jan Ihmels, Christine Körner, ...
Expression Profiler (EP,
Sarkans, Ugis, Parkinson, Helen, Lara, Gonzalo Garcia, Oezcimen, Ahmet, Sharma, Anjan, Abeygunawardena, Niran, ...
Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for...
Expression Profiler: next generation--an online platform for analysis of microarray data (2004)
Kapushesky, Misha, Kemmeren, Patrick, Culhane, Aedín C., Durinck, Steffen, Ihmels, Jan, Körner, Christine, ...
Expression Profiler (EP, http://www.ebi.ac.uk/expressionprofiler) is a web-based platform for microarray gene expression and other functional genomics-related data analysis. The new architecture,...
Sarkans, Ugis, Parkinson, Helen, Lara, Gonzalo Garcia, Oezcimen, Ahmet, Sharma, Anjan, Abeygunawardena, Niran, ...
Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for...
Reverse engineering of gene regulatory networks: a finite state linear model (2003)
Brazma, Alvis, Schlitt, Thomas
Abstract We propose a new model for describing gene regulatory networks that can capture discrete (Boolean) and continuous (differential) aspects of gene regulation. After giving some illustrations...
Towards reconstruction of gene networks from expression data by supervised learning (2003)
Soinov, Lev A, Krestyaninova, Maria A, Brazma, Alvis
Abstract Background Microarray experiments are generating datasets that can help in reconstructing gene networks. One of the most important problems in network reconstruction is finding, for each...
From Gene Networks to Gene Function (2003)
Schlitt, Thomas, Palin, Kimmo, Rung, Johan, Dietmann, Sabine, Lappe, Michael, Ukkonen, Esko, ...
We propose a novel method to identify functionally related genes based on comparisons of neighborhoods in gene networks. This method does not rely on gene sequence or protein structure homologies,...
The European Bioinformatics Institute's data resources (2003)
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
ArrayExpress--a public repository for microarray gene expression data at the EBI (2003)
Brazma, Alvis, Parkinson, Helen, Sarkans, Ugis, Shojatalab, Mohammadreza, Vilo, Jaak, Abeygunawardena, Niran, ...
ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses...
Design and implementation of microarray gene expression markup language (MAGE-ML) (2002)
Spellman, Paul T, Miller, Michael, Stewart, Jason, Troup, Charles, Sarkans, Ugis, Chervitz, Steve, ...
Abstract Background Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one...
Microarray Data Representation, Annotation and Storage (2002)
Brazma,Alvis, Sarkans,Ugis, Robinson,Allan, Jaak,Vilo, Vingron,Martin, Hoheisel,Jörg, ...
Management and analysis of the huge amounts of data produced by microarray experiments is becoming one of the major bottlenecks in the utilization of this high-throughput technology. We describe the...
Microarray Data Representation, Annotation and Storage (2002)
Brazma, Alvis, Sarkans, Ugis, Robinson, Allan, Jaak, Vilo, Vingron, Martin, Hoheisel, Jörg, ...
Management and analysis of the huge amounts of data produced by microarray experiments is becoming one of the major bottlenecks in the utilization of this high-throughput technology. We describe the...
Pages S172–S180 Correlating gene promoters and expression in gene disruption experiments (2002)
Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo
Motivation: Finding putative transcription factor binding sites in the upstream sequences of similarly expressed genes has recently become a subject of intensive studies. In this paper we investigate...
DOI: 10.1093/nar/gkg066 The European Bioinformatics Institute’s data resources (2002)
Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola Mulder, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
© 2002 Spellman et al., licensee BioMed Central Ltd (2002)
Paul T Spellman, Michael Miller, Jason Stewart, Charles Troup, Steve Chervitz, Derek Bernhart, ...
The electronic version of this article is the complete one and can be found online at
Correlating gene promoters and expression in gene disruption experiments (2002)
Palin, Kimmo, Ukkonen, Esko, Brazma, Alvis, Vilo, Jaak
Motivation: Finding putative transcription factor binding sites in the upstream sequences of similarly expressed genes has recently become a subject of intensive studies. In this paper we investigate...
Learning about Gene Regulatory Networks from Gene Deletion Experiments (2002)
Gene regulatory networks are a major focus of interest in molecular biology. A crucial question is how complex regulatory systems are encoded and controlled by the genome. Three recent publications...
An open letter to the scientific journals (2002)
Ball, Catherine A., Sherlock, Gavin, Parkinson, Helen, Rocca-Sera, Philippe, Brooksbank, Catherine, Causton, Helen C., ...
Gene expression data analysis (2000)
Abstract Microarrays are one of the latest breakthroughs in experimental molecular biology, which allow monitoring of gene expression for tens of thousands of genes in parallel and are already...
Gene Expression Data Analysis (2000)
Alvis Brazma, Jaak Vilo, Edited Gianni Cesareni
Microarrays are one of the latest breakthroughs in experimental molecular biology, which allow monitoring of gene expression for tens of thousands of genes in parallel and are already producing huge...
Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data (2000)
Jaak Vilo, Alvis Brazma, Embl Outstation, Embl Outstation, Inge Jonasson, N Bergen, ...
We have developed a set of methods and tools for automatic discovery of putative regulatory signals in genome sequences. The analysis pipeline consists of gene expression data clustering, sequence...
Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data (2000)
Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan Robinson, Esko Ukkonen
We have developed a method for discovering signals in large sets of genomic sequences.
Predicting Gene Regulatory Elements in Silico on a Genomic Scale (1998)
Brazma, Alvis, Jonassen, Inge, Vilo, Jaak, Ukkonen, Esko
We performed a systematic analysis of gene upstream regions in the yeast genome for occurrences of regular expression-type patterns with the goal of identifying potential regulatory elements. To...
Predicting Gene Regulatory Elements in Silico on a Genomic Scale (1998)
Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen
We performed a systematic analysis of gene upstream regions in the yeast genome for occurrences of regular expression-type patterns with the goal of identifying potential regulatory elements. To...
Approaches to the Automatic Discovery of Patterns in Biosequences (1997)
Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David Gilbert
This paper surveys approaches to the discovery of patterns in biosequences and places these approaches within a formal framework that systematises the types of patterns and the discovery algorithms....
Relation Patterns and their Automatic Discovery in Biosequences (1997)
Alvis Brazma, Inge Jonassen, Inge Jonassen, Ingvar Eidhammer, Ingvar Eidhammer, Esko Ukkonen, ...
We have extended the pattern language used in PROSITE to enable it to describe dependencies between amino acid residues. We have developed a minimum description length principle based fitness measure...
A Simple Algorithm for Drawing Large Graphs on Small Screens (1995)
Kaugars, Karlis, Reinfelds, Juris, Brazma, Alvis
Viewing a large graph in limited display space has traditionally been accomplished using either reduced scale rendering of the graph or by attaching scrollbars to a view window which shows only a...
A Simple Algorithm for Drawing Large Graphs on Small Screens (1995)
Kaugars, Karlis, Reinfelds, Juris, Brazma, Alvis
Viewing a large graph in limited display space has traditionally been accomplished using either reduced scale rendering of the graph or by attaching scrollbars to a view window which shows only a...
A Simple Algorithm for Drawing Large Graphs on Small Screens (1995)
Kaugars, Karlis, Reinfelds, Juris, Brazma, Alvis
Viewing a large graph in limited display space has traditionally been accomplished using either reduced scale rendering of the graph or by attaching scrollbars to a view window which shows only a...
A Pattern Language for Molecular Biology (1995)
In this paper we have formalised and studied a language for describing constrained patterns in biosequences. We have developed an efficient and elegant algorithm for finding a given pattern in a...
Finding a Good Collection of Patterns Covering a Set of Sequences (1995)
Alvis Brazma, Alvis Brazma, Esko Ukkonen, Esko Ukkonen, Jaak Vilo, Jaak Vilo
. We consider a problem of learning of unions of pattern languages from positive examples. We consider three different classes of patterns - regular patterns, substring patterns and the so called...
Approaches to the Automatic Discovery of Patterns in Biosequences (1995)
Alvis Brazma, Inge Jonassen, Inge Jonassen, Ingvar Eidhammer, Ingvar Eidhammer, David Gilbert, ...
This paper is a survey of approaches and algorithms used for the automatic discovery of patterns in biosequences. Patterns with the expressive power in the class of regular languages are considered,...
Learning Regular Expressions by Pattern Matching (1994)
We are considering the problem of restoring regular expressions from representative examples. We describe a natural learning algorithm for obtaining a "plausible" regular expression from...
Design and implementation of microarray gene expression markup language (MAGE-ML)
Spellman, Paul T, Miller, Michael, Stewart, Jason, Troup, Charles, Sarkans, Ugis, Chervitz, Steve, ...
Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to...
Global Transcriptional Responses of Fission Yeast to Environmental Stress
Chen, Dongrong, Toone, W. Mark, Mata, Juan, Lyne, Rachel, Burns, Gavin, Kivinen, Katja, ...
We explored transcriptional responses of the fission yeast Schizosaccharomyces pombe to various environmental stresses. DNA microarrays were used to characterize changes in expression profiles of all...
Towards reconstruction of gene networks from expression data by supervised learning
Soinov, Lev A, Krestyaninova, Maria A, Brazma, Alvis
One of the most important problems in gene network reconstruction is finding, for each gene in the network, which genes can affect it. A supervised learning approach was used to address this question...
The European Bioinformatics Institute's data resources
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
ArrayExpress—a public repository for microarray gene expression data at the EBI
Brazma, Alvis, Parkinson, Helen, Sarkans, Ugis, Shojatalab, Mohammadreza, Vilo, Jaak, Abeygunawardena, Niran, ...
ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses...
From Gene Networks to Gene Function
Schlitt, Thomas, Palin, Kimmo, Rung, Johan, Dietmann, Sabine, Lappe, Michael, Ukkonen, Esko, ...
We propose a novel method to identify functionally related genes based on comparisons of neighborhoods in gene networks. This method does not rely on gene sequence or protein structure homologies,...
Expression Profiler: next generation—an online platform for analysis of microarray data
Kapushesky, Misha, Kemmeren, Patrick, Culhane, Aedín C., Durinck, Steffen, Ihmels, Jan, Körner, Christine, ...
Expression Profiler (EP, http://www.ebi.ac.uk/expressionprofiler) is a web-based platform for microarray gene expression and other functional genomics-related data analysis. The new architecture,...
Submission of Microarray Data to Public Repositories
Ball, Catherine A, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication
Microarray Data Standards: An Open Letter
Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
Mukherjee, Gaurab, Abeygunawardena, Niran, Parkinson, Helen, Contrino, Sergio, Durinck, Steffen, Farne, Anna, ...
ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data. Plant-based data...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
Design and implementation of microarray gene expression markup language (MAGE-ML)
Spellman, Paul T, Miller, Michael, Stewart, Jason, Troup, Charles, Sarkans, Ugis, Chervitz, Steve, ...
Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to...
Global Transcriptional Responses of Fission Yeast to Environmental Stress
Chen, Dongrong, Toone, W. Mark, Mata, Juan, Lyne, Rachel, Burns, Gavin, Kivinen, Katja, ...
We explored transcriptional responses of the fission yeast Schizosaccharomyces pombe to various environmental stresses. DNA microarrays were used to characterize changes in expression profiles of all...
Towards reconstruction of gene networks from expression data by supervised learning
Soinov, Lev A, Krestyaninova, Maria A, Brazma, Alvis
One of the most important problems in gene network reconstruction is finding, for each gene in the network, which genes can affect it. A supervised learning approach was used to address this question...
The European Bioinformatics Institute's data resources
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
ArrayExpress—a public repository for microarray gene expression data at the EBI
Brazma, Alvis, Parkinson, Helen, Sarkans, Ugis, Shojatalab, Mohammadreza, Vilo, Jaak, Abeygunawardena, Niran, ...
ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses...
From Gene Networks to Gene Function
Schlitt, Thomas, Palin, Kimmo, Rung, Johan, Dietmann, Sabine, Lappe, Michael, Ukkonen, Esko, ...
We propose a novel method to identify functionally related genes based on comparisons of neighborhoods in gene networks. This method does not rely on gene sequence or protein structure homologies,...
Expression Profiler: next generation—an online platform for analysis of microarray data
Kapushesky, Misha, Kemmeren, Patrick, Culhane, Aedín C., Durinck, Steffen, Ihmels, Jan, Körner, Christine, ...
Expression Profiler (EP, http://www.ebi.ac.uk/expressionprofiler) is a web-based platform for microarray gene expression and other functional genomics-related data analysis. The new architecture,...
Submission of Microarray Data to Public Repositories
Ball, Catherine A, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication
Mukherjee, Gaurab, Abeygunawardena, Niran, Parkinson, Helen, Contrino, Sergio, Durinck, Steffen, Farne, Anna, ...
ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data. Plant-based data...
Microarray Data Standards: An Open Letter
Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
PASSIM – an open source software system for managing information in biomedical studies
Viksna, Juris, Celms, Edgars, Opmanis, Martins, Podnieks, Karlis, Rucevskis, Peteris, Zarins, Andris, ...
Rustici, Gabriella, Van Bakel, Harm, Lackner, Daniel H, Holstege, Frank C, Wijmenga, Cisca, Bähler, Jürg, ...
Analysis of genome-wide responses to changing copper and iron levels in budding and fission yeast reveals conservation of only a small core set of genes and remarkable differences in the responses of...
Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster
Samsonova, Anastasia A, Niranjan, Mahesan, Russell, Steven, Brazma, Alvis
Understanding how sets of genes are coordinately regulated in space and time to generate the diversity of cell types that characterise complex metazoans is a major challenge in modern biology. The...
Current approaches to gene regulatory network modelling
Schlitt, Thomas, Brazma, Alvis
Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network...
Modelling in molecular biology: describing transcription regulatory networks at different scales
Schlitt, Thomas, Brazma, Alvis
Approaches to describe gene regulation networks can be categorized by increasing detail, as network parts lists, network topology models, network control logic models or dynamic models. We discuss...
4DXpress: a database for cross-species expression pattern comparisons
Haudry, Yannick, Berube, Hugo, Letunic, Ivica, Weeber, Paul-Daniel, Gagneur, Julien, Girardot, Charles, ...
In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these...
Learning About Gene Regulatory Networks From Gene Deletion Experiments
Schlitt, Thomas, Brazma, Alvis
Gene regulatory networks are a major focus of interest in molecular biology. A crucial question is how complex regulatory systems are encoded and controlled by the genome. Three recent publications...
Integrating sequence, evolution and functional genomics in regulatory genomics
Vingron, Martin, Brazma, Alvis, Coulson, Richard, Van Helden, Jacques, Manke, Thomas, Palin, Kimmo, ...
Finding transcription factor binding sites in regulatory regions of the genome
Parkinson, Helen, Kapushesky, Misha, Kolesnikov, Nikolay, Rustici, Gabriella, Shojatalab, Mohammad, Abeygunawardena, Niran, ...
ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress...
Probabilistic retrieval and visualization of biologically relevant microarray experiments
Caldas, José, Gehlenborg, Nils, Faisal, Ali, Brazma, Alvis, Kaski, Samuel
Motivation: As ArrayExpress and other repositories of genome-wide experiments are reaching a mature size, it is becoming more meaningful to search for related experiments, given a particular study....
Importing ArrayExpress datasets into R/Bioconductor
Kauffmann, Audrey, Rayner, Tim F., Parkinson, Helen, Kapushesky, Misha, Lukk, Margus, Brazma, Alvis, ...
Summary:ArrayExpress is one of the largest public repositories of microarray datasets. R/Bioconductor provides a comprehensive suite of microarray analysis and integrative bioinformatics software....
Aligianni, Sofia, Lackner, Daniel H., Klier, Steffi, Rustici, Gabriella, Wilhelm, Brian T., Marguerat, Samuel, ...
The regulation of the G1- to S-phase transition is critical for cell-cycle progression. This transition is driven by a transient transcriptional wave regulated by transcription factor complexes...
A System for Information Management in BioMedical Studies—SIMBioMS
Krestyaninova, Maria, Zarins, Andris, Viksna, Juris, Kurbatova, Natalja, Rucevskis, Peteris, Neogi, Sudeshna Guha, ...
Summary: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of...