Alvis Brazma

发表

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

James C. Wright, Jonathan M. Mudge, Hendrik Weisser, 2016, Nature Communications.

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

Nuno A. Fonseca, Wojciech Bazant, Elisabet Barrera, 2017, Nucleic Acids Res..

Report on EU–USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008)

Olaf Wolkenhauer, Blaz Zupan, Ravi Iyengar, 2009, Molecular oncology.

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

Nigel W. Hardy, Chris F. Taylor, John M. Hancock, 2008, Nature Biotechnology.

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

Alvis Brazma, Katherine Lawler, Kim E. Hammond-Kosack, 2013, BMC Systems Biology.

Image Data Resource: a bioimage data integration and publication platform

Bálint Antal, Alvis Brazma, Anatole Chessel, 2017, Nature Methods.

On the Importance of Standardisation in Life Sciences

Alvis Brazma, A. Brazma, 2001, Bioinform..

ArrayExpress update—simplifying data submissions

Robert Petryszak, Maria Keays, Marco Brandizi, 2014, Nucleic Acids Res..

An open letter on microarray data from the MGED Society.

John Quackenbush, Yoshio Tateno, Helen Parkinson, 2004, Microbiology.

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

Karlis Cerans, Alvis Brazma, Juris Viksna, 2019, BMC Bioinformatics.

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

Edgars Celms, Martins Opmanis, Karlis Podnieks, 2007, BMC Bioinformatics.

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

Ibrahim Emam, Marco Brandizi, James Malone, 2010, Nucleic Acids Res..

ArrayExpress service for reviewers/editors of DNA microarray papers

Helen Parkinson, Alvis Brazma, 2006, Nature Biotechnology.

Discovering Patterns and Subfamilies in Biosequences

Esko Ukkonen, Inge Jonassen, Jaak Vilo, 1996, ISMB.

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

Alvis Brazma, Thomas Dandekar, Yevhen Vainshtein, 2010, BMC Bioinformatics.

iRAP - an integrated RNA-seq Analysis Pipeline

Nuno A. Fonseca, Robert Petryszak, John C. Marioni, 2014, bioRxiv.

Inductive Synthesis of Dot Expressions

Alvis Brazma, 1991, Baltic Computer Science.

Pattern Discovery in Biosequences

Esko Ukkonen, Inge Jonassen, Jaak Vilo, 1998, ICGI.

clustComp, a bioconductor package for the comparison of clustering results

Aurora Torrente, Alvis Brazma, 2017, Bioinform..

Current approaches to gene regulatory network modelling

Alvis Brazma, Thomas Schlitt, A. Brazma, 2007, BMC Bioinformatics.

Probabilistic retrieval and visualization of biologically relevant microarray experiments

Samuel Kaski, Ali Faisal, Alvis Brazma, 2009, Bioinform..

Algorithms for gene expression analysis

Aedín C. Culhane, Alvis Brazma, A. Brazma, 2005 .

MGED standards: work in progress.

Alvis Brazma, Catherine A Ball, C. Ball, 2006, Omics : a journal of integrative biology.

An open letter to the scientific journals

Catherine Brooksbank, Duccio Cavalieri, Paul T. Spellman, 2002, Bioinform..

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan

Satoru Miyano, Tatsuya Akutsu, Alvis Brazma, 2008, APBC.

Preface

Satoru Miyano, Tatsuya Akutsu, Alvis Brazma, 2008, APBC.

Gene Expression Atlas at the European Bioinformatics Institute

Ibrahim Emam, James Malone, Helen E. Parkinson, 2009, Nucleic Acids Res..

The BioSample Database (BioSD) at the European Bioinformatics Institute

Marco Brandizi, Helen E. Parkinson, Alvis Brazma, 2011, Nucleic Acids Res..

One-stop shop for microarray data

Graham Cameron, Michael Ashburner, Alvis Brazma, 2000, Nature.

Learning of regular expressions by pattern matching

Alvis Brazma, A. Brazma, 1995, EuroCOLT.

Modelling gene networks at different organisational levels

Alvis Brazma, Thomas Schlitt, A. Brazma, 2005, FEBS letters.

A Simple Algorithm for Drawing Large Graphs on Small Screens

Alvis Brazma, Juris Reinfelds, Karlis Kaugars, 1994, Graph Drawing.

Tools for mapping high-throughput sequencing data

Nuno A. Fonseca, John C. Marioni, Alvis Brazma, 2012, Bioinform..

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

Sergio Contrino, Helen Parkinson, Susanna-Assunta Sansone, 2003, Comptes rendus biologies.

Orchestrating differential data access for translational research: a pilot implementation

Klaus A. Kuhn, Marco Brandizi, Mikael Linden, 2017, BMC Medical Informatics and Decision Making.

Data Storage and Analysis in ArrayExpress and Expression Profiler

Helen Parkinson, Alvis Brazma, Ugis Sarkans, 2008, Current protocols in bioinformatics.

Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq

Alvis Brazma, Mar Gonzàlez-Porta, A. Brazma, 2014, bioRxiv.

Learning a Subclass of Regular Expressions by Recognizing Periodic Repetitions

Alvis Brazma, A. Brazma, 1993, Scandinavian Conference on AI.

Genomic basis for RNA alterations in cancer

Mary Goldman, Nuno A. Fonseca, Brian Craft, 2020, Nature.

Funding high-throughput data sharing

Gavin Sherlock, Alvis Brazma, Catherine A Ball, 2004, Nature Biotechnology.

A System for Information Management in BioMedical Studies—SIMBioMS

Karlis Podnieks, Andris Zarins, Mark I. McCarthy, 2009, Bioinform..

Fusing microarray experiments with multivariate regression

Walter R. Gilks, Alvis Brazma, Brian D. M. Tom, 2005, ECCB/JBI.

Correlating gene promoters and expression in gene disruption experiments

Esko Ukkonen, Jaak Vilo, Alvis Brazma, 2002, ECCB.

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

Bálint Antal, Alvis Brazma, Anatole Chessel, 2018, Nature Methods.

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

Nuno A. Fonseca, Robert Petryszak, Maria Keays, 2013, Nucleic Acids Res..

The importance of transparency and reproducibility in artificial intelligence research

Trevor Hastie, Joelle Pineau, Robert Tibshirani, 2020, 2003.00898.

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

Helen E. Parkinson, Alvis Brazma, Ugis Sarkans, 2006, Nucleic Acids Res..

Generalized Regular Expressions-A Language for Synthesis of Programs with Braching in Loops

Efim B. Kinber, Alvis Brazma, 1986, Theor. Comput. Sci..

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

Aedín C. Culhane, Meelis Kull, Aurora Torrente, 2004, Nucleic Acids Res..

Faculty Opinions recommendation of A scalable pipeline for designing reconfigurable organisms.

Alvis Brazma, A. Brazma, 2020, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

Modeling sample variables with an Experimental Factor Ontology

Anna Zhukova, James Malone, Helen E. Parkinson, 2010, Bioinform..

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

Alvis Brazma, Misha Kapushesky, Christian Schwager, 2006, Bioinform..

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

Sergio Contrino, Helen E. Parkinson, Susanna-Assunta Sansone, 2004, Nucleic Acids Res..

One-stop shop for microarray data Is a universal, public DNA-microarray database a realistic goal?

Graham Cameron, Alvis Brazma, Michael Ashburner, 2000 .

The BREW workshop series: a stimulating experience in PhD education

Martin Vingron, Robert Giegerich, Esko Ukkonen, 2008, Briefings Bioinform..

Faculty of 1000 evaluation for A model for the generation and transmission of variations in evolution.

Alvis Brazma, 2018 .

Predicting gene regulatory elements from their expression data in the complete yeast genome

Esko Ukkonen, Inge Jonassen, Jaak Vilo, 1998, German Conference on Bioinformatics.

ArrayExpress: A Public Repository for Microarray Data

Helen Parkinson, Susanna-Assunta Sansone, Philippe Rocca-Serra, 2006 .

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

Nuno A. Fonseca, Elisabet Barrera, Robert Petryszak, 2015, Nucleic Acids Res..

ArrayExpress update – from bulk to single-cell expression data

Nuno A. Fonseca, Robert Petryszak, Anja Füllgrabe, 2018, Nucleic Acids Res..

Transparency and reproducibility in artificial intelligence

Trevor Hastie, Joelle Pineau, Robert Tibshirani, 2020, Nature.

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

Samuel Kaski, Jaakko Peltonen, Helena Aidos, 2010, 2010 IEEE International Conference on Acoustics, Speech and Signal Processing.

Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster

Mahesan Niranjan, Alvis Brazma, Steven Russell, 2007, PLoS Comput. Biol..

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

Bart De Moor, Yves Moreau, Steffen Durinck, 2005, Bioinform..

The European Bioinformatics Institute's data resources

Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler, 2003, Nucleic Acids Res..

Putative cell type discovery from single-cell gene expression data

Irene Papatheodorou, Alvis Brazma, Pablo Moreno, 2020, Nature Methods.

Data Mining and Visualisation in Molecular Biology Databases

Alan J. Robinson, Peter Maccallum, Alvis Brazma, 1997, German Conference on Bioinformatics.

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

Sergio Contrino, Helen E. Parkinson, Susanna-Assunta Sansone, 2005, Bioinform..

Minimum Information About a Microarray Experiment (MIAME) – Successes, Failures, Challenges

Alvis Brazma, A. Brazma, 2009, TheScientificWorldJournal.

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

Paul T. Spellman, Rafael A. Irizarry, John Quackenbush, 2006, BMC Bioinformatics.

Faculty Opinions recommendation of Tempo and mode of genome evolution in a 50,000-generation experiment.

Alvis Brazma, 2017 .

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

Samuel Kaski, Sohan Seth, Alvis Brazma, 2015, Bioinform..

Data Mining for Regulatory Elements in Yeast Genome

Esko Ukkonen, Jaak Vilo, Alvis Brazma, 1997, ISMB.

MoDa-A Data Warehouse for Multi-"Omics" Data

Ibrahim Emam, Alvis Brazma, Ugis Sarkans, 2013 .

Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract)

Esko Ukkonen, Jaak Vilo, Alvis Brazma, 1996, ISAAC.

Reconstruction of gene regulatory networks under the finite state linear model.

Alvis Brazma, Juris Viksna, Dace Ruklisa, 2005, Genome informatics. International Conference on Genome Informatics.

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

Martin Eisenacher, Johannes Griss, Juan Antonio Vizcaíno, 2018, Nucleic Acids Res..

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

Mark I. McCarthy, Alvis Brazma, Johan Rung, 2010, Bioinform..

Building and analysing genome-wide gene disruption networks

Jaak Vilo, Alvis Brazma, Johan Rung, 2002, ECCB.

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

Helen E. Parkinson, Tony Burdett, Alvis Brazma, 2012, Bioinform..

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

Aurora Torrente, Alvis Brazma, Leo Lahti, 2012, Nucleic acids research.

Approaches to the Automatic Discovery of Patterns in Biosequences

David R. Gilbert, Inge Jonassen, Alvis Brazma, 1998, J. Comput. Biol..

Microarray data representation, annotation and storage.

Martin Vingron, Alvis Brazma, Ugis Sarkans, 2002, Advances in biochemical engineering/biotechnology.

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

Audrey Kauffmann, Martin Kuiper, James Malone, 2011, BioTechniques.

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

Johanna R. McEntyre, Alvis Brazma, Ugis Sarkans, 2017, Nucleic Acids Res..

Models of Inductive Synthesis

Efim B. Kinber, Alvis Brazma, 1990, J. Log. Program..

Expression and Genetic Variation Databases for Cancer Research

Alvis Brazma, Johan Rung, 2011 .

Cellular phenotype database: a repository for systems microscopy data

Alvis Brazma, Ugis Sarkans, Gabriella Rustici, 2015, Bioinform..

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

Nigel W. Hardy, Chris F. Taylor, Marco Brandizi, 2008, Omics : a journal of integrative biology.

Modeling and Analysis of Qualitative Behavior of Gene Regulatory Networks

Karlis Cerans, Alvis Brazma, Juris Viksna, 2014, HSB.

Noise-tolerant efficient inductive synthesis of regular expressions from good examples

Karlis Cerans, Alvis Brazma, A. Brazma, 1997, New Generation Computing.

Efficient Learning of Regular Expressions from Good Examples

Karlis Cerans, Alvis Brazma, A. Brazma, 1994, AII/ALT.

Relation Patterns and their Automatic Discovery in Biosequences

Esko Ukkonen, Inge Jonassen, Alvis Brazma, 1997 .

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

Aurora Torrente, Alvis Brazma, Misha Kapushesky, 2005, Bioinform..

A pipeline for RNA-seq data processing and quality assessment

Alvis Brazma, Andrew Tikhonov, Misha Kapushesky, 2011, Bioinform..

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

Ravi Shankar, Michael Miller, Helen E. Parkinson, 2010, Bioinform..

Visualization of large microarray experiments with space maps

Alvis Brazma, Nils Gehlenborg, A. Brazma, 2009, BMC Bioinformatics.

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data

Nuno A. Fonseca, Robert Petryszak, Anja Füllgrabe, 2017, Bioinform..

Efficient Algorithm for Learning Simple Regular Expressions from Noisy Examples

Alvis Brazma, A. Brazma, 1994, AII/ALT.

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

Ibrahim Emam, Marco Brandizi, Faisal Ibne Rezwan, 2008, Nucleic Acids Res..

Faculty Opinions recommendation of Clinical-grade computational pathology using weakly supervised deep learning on whole slide images.

Alvis Brazma, 2019 .

Importing ArrayExpress datasets into R/Bioconductor

Audrey Kauffmann, Helen E. Parkinson, Wolfgang Huber, 2009, Bioinform..

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

Aedín C. Culhane, Robert Petryszak, James Malone, 2011, Nucleic Acids Res..

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

Thorsten Henrich, Joachim Wittbrodt, Peer Bork, 2007, Nucleic Acids Res..

Updates to BioSamples database at European Bioinformatics Institute

Marco Brandizi, Helen E. Parkinson, Tony Burdett, 2014, Nucleic Acids Res..

Microarray gene expression data analysis - a beginner's guide

John Quackenbush, Alvis Brazma, Helen C. Causton, 2003 .

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

Helen E. Parkinson, Susanna-Assunta Sansone, Philippe Rocca-Serra, 2003, Nucleic Acids Res..

A call for public archives for biological image data

Ardan Patwardhan, Ewan Birney, Charles E. Cook, 2018, Nature Methods.

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

Maria Keays, Ibrahim Emam, Marco Brandizi, 2012, Nucleic Acids Res..

Finding transcription factor binding site combinations in the yeast genome

Esko Ukkonen, Jaak Vilo, Alvis Brazma, 1997, German Conference on Bioinformatics.

Probabilistic retrieval and visualization of biologically relevant microarray experiments

Samuel Kaski, Ali Faisal, Alvis Brazma, 2009, BMC Bioinformatics.

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

Bálint Antal, Alvis Brazma, Ugis Sarkans, 2016, bioRxiv.

Lack of correct data format and comparability limits future integrative microarray research

Helen Parkinson, Alvis Brazma, 2006 .

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

Thorsten Henrich, Mirana Ramialison, John Quackenbush, 2008, Nature Biotechnology.

Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data

Esko Ukkonen, Alan J. Robinson, Inge Jonassen, 2000, ISMB.

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

Samuel Kaski, Ali Faisal, Eeva Kettunen, 2011, Bioinform..

Data storage and analysis in ArrayExpress.

Helen Parkinson, Alvis Brazma, Ugis Sarkans, 2006, Methods in enzymology.

Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress

Xi Wang, Thorsten Henrich, Joachim Wittbrodt, 2008, APBC.

From ArrayExpress to BioStudies

Irene Papatheodorou, Alvis Brazma, Ugis Sarkans, 2020, Nucleic Acids Res..

Learning About Gene Regulatory Networks From Gene Deletion Experiments

Alvis Brazma, Thomas Schlitt, A. Brazma, 2002, Comparative and functional genomics.

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

Masahiro Yoshida, Fabian J. Theis, Oliver Eickelberg, 2020, Nature Medicine.

Gene Expression Data Mining and Analysis

Jaak Vilo, Alvis Brazma, A. Brazma, 2001 .

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

Gunnar Rätsch, Nuno A. Fonseca, André Kahles, 2019, Cell.

Using Deep Learning to Extrapolate Protein Expression Measurements

Edgars Celms, Juan Antonio Vizcaíno, Lelde Lace, 2020, Proteomics.

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

Edgars Celms, Martins Opmanis, Andris Zarins, 2014, Nature Communications.

Integrating sequence, evolution and functional genomics in regulatory genomics

Martin Vingron, Esko Ukkonen, Thomas Manke, 2009, Genome Biology.

[Standardization of microarray experiment data].

Kazuho Ikeo, Yoshio Tateno, Alvis Brazma, 2003, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

A CD8 T cell transcription signature predicts prognosis in autoimmune disease

Alvis Brazma, Afzal N. Chaudhry, Paul A. Lyons, 2010, Nature Medicine.

Expression Atlas update: from tissues to single cells

Nuno A. Fonseca, Robert Petryszak, Irene Papatheodorou, 2019, Nucleic Acids Res..

HSM - a hybrid system based approach for modelling intracellular networks.

Karlis Cerans, Alvis Brazma, Juris Viksna, 2013, Gene.

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

Nuno A. Fonseca, John C. Marioni, Alvis Brazma, 2014, bioRxiv.

The underlying principles of scientific publication.

Duccio Cavalieri, John Quackenbush, Terry Gaasterland, 2002, Bioinformatics.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

Rodrigo Dienstmann, Justin Guinney, Julio Saez-Rodriguez, 2016, bioRxiv.

Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress

Sergio Contrino, Yves Moreau, Helen Parkinson, 2005, Plant Physiology.

Standards for microarray data: an open letter.

Paul T. Spellman, John Quackenbush, Yoshio Tateno, 2004, Environmental health perspectives.

Standards for Microarray Data

Duccio Cavalieri, John Quackenbush, Terry Gaasterland, 2002, Science.

Cellular phenotype database with ontology assisted data browsing

Simon Jupp, Alvis Brazma, Ugis Sarkans, 2014 .

Wrestling with SUMO and bio-ontologies

Robert Stevens, John Quackenbush, Gilberto Fragoso, 2006, Nature Biotechnology.

Pol Iii Binding in Six Mammalian Genomes Shows High Conservation among Amino Acid Isotypes, despite Divergence in Trna Gene Usage Ukpmc Funders Group Author Manuscript Introduction

Alvis Brazma, Michael D. Wilson, Stephen Watt, 2022 .

The Image Data Resource : A Bioimage Data Integration and Publication Platform 1 2 3 4

Bálint Antal, Alvis Brazma, Anatole Chessel, 2017 .

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

Gunnar Rätsch, Junjun Zhang, Nuno A. Fonseca, 2017 .

A quick introduction to elements of biology - cells, molecules, genes, functional genomics, microarrays

Helen Parkinson, Alvis Brazma, Thomas Schlitt, 2008 .

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

Nuno A. Fonseca, Alvis Brazma, Liliana Greger, 2017, bioRxiv.

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

Aurora Torrente, Helen Parkinson, Alvis Brazma, 2016, PloS one.

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

Mark Gerstein, Benedict Paten, Paul Flicek, 2017, bioRxiv.

Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies

Christian J. Stoeckert, Alvis Brazma, Catherine A. Ball, 2004 .

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

Gunnar Rätsch, Mark Gerstein, Li Ding, 2017, bioRxiv.

Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants

Alvis Brazma, Emmanouil T. Dermitzakis, Johan Rung, 2014, PloS one.

The BioStudies database

Alvis Brazma, Ugis Sarkans, Jo McEntyre, 2015, Molecular Systems Biology.

Reverse engineering of gene regulatory networks: a finite state linear model

Alvis Brazma, Thomas Schlitt, A. Brazma, 2003, Genome Biology.

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

Nuno A. Fonseca, Alvis Brazma, John Marioni, 2014, bioRxiv.

Top-down standards will not serve systems biology

Robert Gentleman, John Quackenbush, Wolfgang Huber, 2006, Nature.

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

Alvis Brazma, Thomas Schlitt, A. Brazma, 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

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

Paul Flicek, Alvis Brazma, Klara Stefflova, 2012, Genome research.

From gene networks to gene function.

Michael Lappe, Esko Ukkonen, Alvis Brazma, 2003, Genome research.