A. Brazma

发表

Predicting gene regulatory elements in silico on a genomic scale.

I. Jonassen, A. Brazma, J. Vilo, 1998, Genome research.

The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

C. Sander, B. Steipe, P. Bork, 2004, Nature Biotechnology.

Gene expression data analysis

A. Brazma, J. Vilo, 2000, FEBS letters.

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

Jason E. Stewart, C. Ball, G. Sherlock, 2002, Genome Biology.

Microarray Data Standards: An Open Letter

C. Ball, J. Matese, M. Ringwald, 2004, Environmental Health Perspectives.

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

Jason E. Stewart, Irene F. Kim, F. Holstege, 2001, Nature Genetics.

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

P. Kemmeren, F. Holstege, A. Brazma, 2002, Molecular cell.

Global transcriptional responses of fission yeast to environmental stress.

A. Brazma, K. Kivinen, R. Lyne, 2003, Molecular biology of the cell.

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

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

Towards reconstruction of gene networks from expression data by supervised learning

A. Brazma, M. Krestyaninova, L. Soinov, 2003, Genome Biology.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

Transcriptome and genome sequencing uncovers functional variation in humans

Pedro G. Ferreira, M. Pirinen, P. Donnelly, 2013, Nature.

The European Bioinformatics Institute's data resources

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

A global map of human gene expression

H. Parkinson, A. Brazma, E. Ukkonen, 2010, Nature Biotechnology.

Efficient identification of regular expressions from representative examples

A. Brazma, 1993, COLT '93.

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

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

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

J. Harrow, A. Frankish, A. Brazma, 2013, Genome Biology.

Standards for systems biology

A. Brazma, Ugis Sarkans, M. Krestyaninova, 2006, Nature Reviews Genetics.

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

Ronald C. Taylor, Roger E Bumgarner, C. Ball, 2006, Omics : a journal of integrative biology.

Submission of Microarray Data to Public Repositories

C. Ball, J. Matese, M. Ringwald, 2004, PLoS biology.

Reuse of public genome-wide gene expression data

A. Brazma, J. Rung, 2012, Nature Reviews Genetics.

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2011, PLoS biology.

Transparency and reproducibility in artificial intelligence

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

Aberration hubs in protein interaction networks highlight actionable targets in cancer

H. Najafabadi, A. Brazma, J. Rung, 2018, Oncotarget.

International network of cancer genome projects

Gary D Bader, Benjamin J. Raphael, Joshua M. Stuart, 2010, Nature.

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

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

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 .

Periodic gene expression program of the fission yeast cell cycle

P. Lio’, A. Brazma, K. Kivinen, 2004, Nature Genetics.

The Fission Yeast Homeodomain Protein Yox1p Binds to MBF and Confines MBF-Dependent Cell-Cycle Transcription to G1-S via Negative Feedback

A. Brazma, J. Bähler, B. Wilhelm, 2009, PLoS genetics.

Pan-cancer analysis of whole genomes

Steven J. M. Jones, Nuno A. Fonseca, Icgc, 2020, Nature.

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

Fabian J Theis, D. Pe’er, A. Regev, 2020, Cell.

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

H. Parkinson, A. Brazma, J. Rung, 2010, Genome Biology.

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

Michael D. Wilson, D. Odom, J. Marioni, 2013, Cell.

Impact of Alternative Splicing on the Human Proteome

R. Aebersold, J. Marioni, A. Brazma, 2017, Cell Reports.

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

R. Bernards, A. Brazma, H. Horlings, 2013, The Journal of pathology.

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

Nuno A. Fonseca, Jonathan M. Mudge, J. Harrow, 2015, BMC Genomics.

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

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

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..

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

G. Rätsch, A. Brazma, O. Stegle, 2017, bioRxiv.

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

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

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

Bálint Antal, Alvis Brazma, Anatole Chessel, 2017 .

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

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

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 .

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

Nigel W. Hardy, Chris F. Taylor, Andrew R. Jones, 2007, Nature Biotechnology.

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

Pedro G. Ferreira, M. Rivas, R. Guigó, 2016, Scientific Reports.

The BioSample Database (BioSD) at the European Bioinformatics Institute

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

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..

From gene networks to gene function.

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

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.

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

Son K. Pham, Ian T. Fiddes, Bronwen L. Aken, 2017, bioRxiv.

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

A. Brazma, J. Bähler, S. Marguerat, 2014, RNA biology.

Tumour gene expression signature in primary melanoma predicts long-term outcomes: A prospective multicentre study

Nuno A. Fonseca, D. Bishop, A. Brazma, 2020, bioRxiv.

Integrating sequence, evolution and functional genomics in regulatory genomics

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

Urinary metabolic phenotyping for Alzheimer’s disease

N. Kurbatova, A. Brazma, H. Soininen, 2020, Scientific Reports.

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

A. Brazma, Rui Camacho, B. Cavadas, 2020, Microorganisms.

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

Nuno A. Fonseca, A. Brazma, C. Creighton, 2017, bioRxiv.

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

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

Pan-cancer study of heterogeneous RNA aberrations

Nuno A. Fonseca, Angela N. Brooks, Stefan G. Stark, 2017, bioRxiv.

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

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

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures

V. P. Collins, Matthew D. Young, N. Kurbatova, 2017, Scientific Reports.

Guidelines for reporting single-cell RNA-seq experiments

Deanne M. Taylor, S. Teichmann, J. Marioni, 2019, Nature Biotechnology.

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.

Finding transcription factor binding site combinations in the yeast genome

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

Simulating structurally variable Nuclear Pore Complexes for Microscopy

J. Ellenberg, A. Brazma, J. Hériché, 2022, bioRxiv.

On the Importance of Standardisation in Life Sciences

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

An integrated landscape of protein expression in human cancer

Andrew F. Jarnuczak, A. Brazma, I. Papatheodorou, 2019, bioRxiv.

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

A. Brazma, Mathias Wilhelm, E. Deutsch, 2021, Nature Communications.

Gene Expression Atlas at the European Bioinformatics Institute

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

Standards for microarray data: an open letter.

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

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

Nuno A. Fonseca, Angela N. Brooks, David T. W. Jones, 2020, Nature Communications.

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

A. Børresen-Dale, A. Brazma, E. Hovig, 2016, International journal of cancer.

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.

Correlating gene promoters and expression in gene disruption experiments

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

Learning a Subclass of Regular Expressions by Recognizing Periodic Repetitions

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

The underlying principles of scientific publication.

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

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

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

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.

Gene Expression Databases

A. Brazma, Ugis Sarkans, 2005 .

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

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

[Standardization of microarray experiment data].

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

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

A. Brazma, Mathias Wilhelm, E. Deutsch, 2021, Nature Communications.

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging

L. Groop, A. Brazma, J. Rung, 2015, Skeletal Muscle.

From gene expression profiling to gene regulation

Helge G. Roider, A. Brazma, E. Ukkonen, 2008 .

An open letter to the scientific journals

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

Faculty Opinions recommendation of The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

A. Brazma, 2019, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

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

Fabian J Theis, D. Pe’er, A. Regev, 2020, Nature Medicine.

Benchmarking strategies for cross-species integration of single-cell RNA sequencing data

A. Brazma, Zhichao Miao, I. Papatheodorou, 2022, bioRxiv.

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

A. Brazma, J. Vizcaíno, Mathias Walzer, 2021, Nucleic Acids Res..

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..

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

A. Brazma, J. Rung, B. Ferreira, 2019, npj Vaccines.

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

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

Efficient Algorithm for Learning Simple Regular Expressions from Noisy Examples

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

SARS-CoV-2 Receptor ACE2 is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Enriched in Specific Cell Subsets Across Tissues

Fabian J Theis, Alison Yu, Alex K. Shalek, 2020, SSRN Electronic Journal.

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

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

ArrayExpress update—simplifying data submissions

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

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

S. Teichmann, A. Brazma, Zhichao Miao, 2021, Nature Methods.

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Kyle J. Gaulton, David S. Fischer, Malte D. Luecken, 2021, Nature Medicine.

Genomic basis for RNA alterations in cancer

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

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

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

Patterns of somatic structural variation in human cancer genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature.

Power analysis of cell-type deconvolution methods across tissues

A. Brazma, Zhichao Miao, I. Papatheodorou, 2023, bioRxiv.

Pattern Discovery in Biosequences

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

Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster

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

ArrayExpress update – from bulk to single-cell expression data

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

Putative cell type discovery from single-cell gene expression data

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

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

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

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..

Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma

A. Brazma, Jean Monlong, G. Bourque, 2017, Scientific Reports.

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

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

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..

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

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

Gene Expression Data Mining and Analysis

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

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

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

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

H. Najafabadi, A. Brazma, M. Lathrop, 2018, Cell reports.

Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

A. Regev, A. Nicholson, A. Brazma, 2021, Nature Communications.

Tools for mapping high-throughput sequencing data

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

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature Communications.

Brain Regeneration Resembles Brain Cancer at Its Early Wound Healing Stage and Diverges From Cancer Later at Its Proliferation and Differentiation Stages

A. Brazma, I. Papatheodorou, G. Ozhan, 2022, Frontiers in Cell and Developmental Biology.

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

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

Modelling gene networks at different organisational levels

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

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

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

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.

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..

Modeling sample variables with an Experimental Factor Ontology

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

Resource Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

James C. Wright, Emanuel J. V. Gonçalves, A. Brazma, 2018 .

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

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

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

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

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

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

Gene expression data analysis.

A. Brazma, J. Vilo, 2001, FEBS letters.

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System

D. Odom, J. Marioni, A. Brazma, 2015, PloS one.

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

Nuno A. Fonseca, A. Brazma, C. Creighton, 2022, Nature communications.

One-stop shop for microarray data

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

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

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

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

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

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

Alvis Brazma, A. Brazma, 2009, TheScientificWorldJournal.

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.

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..

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

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

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

A. Brazma, M. Lathrop, S. Bhattarai, 2020, British Journal of Cancer.

A pan cancer analysis of promoter activity highlights the regulatory role of alternative transcription start sites and their association with noncoding mutations

Nuno A. Fonseca, Angela N. Brooks, G. Rätsch, 2017, bioRxiv.

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

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

Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses

A. Brazma, Zhichao Miao, P. Moreno, 2021, Scientific Reports.

Meta-analysis reveals consistent immune response patterns in COVID-19 infected patients at single-cell resolution

A. Brazma, Zhichao Miao, P. Moreno, 2021, bioRxiv.

Importing ArrayExpress datasets into R/Bioconductor

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

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

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

An open letter on microarray data from the MGED Society.

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

Standards for Microarray Data

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

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

A. Brazma, J. Rung, B. Ferreira, 2019, npj Vaccines.

L. M. Voortman, E. Birney, J. Ellenberg, 2021, Nature Methods.

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..

Top-down standards will not serve systems biology

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

From ArrayExpress to BioStudies

Irene Papatheodorou, Alvis Brazma, Ugis Sarkans, 2020, 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..

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

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

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.

Current approaches to gene regulatory network modelling

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

Learning About Gene Regulatory Networks From Gene Deletion Experiments

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

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

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

Image Data Resource: a bioimage data integration and publication platform

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

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

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

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

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

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

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

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

Nuno A. Fonseca, G. Rätsch, A. Brazma, 2018 .

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

A. Brazma, A. Harris, M. Lathrop, 2020, British Journal of Cancer.

Expression Atlas update: gene and protein expression in multiple species

J. Marioni, A. Brazma, M. Tello-Ruiz, 2021, Nucleic Acids Res..

Using Deep Learning to Extrapolate Protein Expression Measurements

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

Algorithms for gene expression analysis

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

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

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

Approaches to the Automatic Discovery of Patterns in Biosequences

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

Learning of regular expressions by pattern matching

Alvis Brazma, A. Brazma, 1995, EuroCOLT.

Efficient Learning of Regular Expressions from Good Examples

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

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

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

LOMAR: LOcalization Microscopy Analysis in R

A. Brazma, J. Hériché, V. Uhlmann, 2022, bioRxiv.

A pipeline for RNA-seq data processing and quality assessment

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

Data Mining for Regulatory Elements in Yeast Genome

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

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

F. Holstege, C. Wijmenga, A. Brazma, 2007, Genome Biology.

Wnt and BMP signaling enhance melanocyte regeneration and suppress melanoma cell migration

A. Brazma, I. Papatheodorou, G. Ozhan, 2022 .

Visualization of large microarray experiments with space maps

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

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

L. Groop, A. Brazma, J. Rung, 2016, Molecular and Cellular Endocrinology.

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

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

Single-Cell Analysis Reveals the Immune Characteristics of Myeloid Cells and Memory T Cells in Recovered COVID-19 Patients With Different Severities

A. Brazma, Zhichao Miao, I. Papatheodorou, 2022, Frontiers in Immunology.

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

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

The BioStudies database

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

Comprehensive molecular characterization of mitochondrial genomes in human cancers

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2017, bioRxiv.

Data storage and analysis in ArrayExpress.

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

Author Correction: Pan-cancer analysis of whole genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2023, Nature.

Orchestrating differential data access for translational research: a pilot implementation

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

Sex differences in oncogenic mutational processes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2019, Nature Communications.

iRAP - an integrated RNA-seq Analysis Pipeline

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

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

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

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.

Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing

Roger E Bumgarner, John Quackenbush, A. Brazma, 2021, bioRxiv.

Simulating structurally variable nuclear pore complexes for microscopy

J. Ellenberg, A. Brazma, J. Hériché, 2023, bioRxiv.

The BioImage Archive - building a home for life-sciences microscopy data.

A. Brazma, J. Swedlow, G. Kleywegt, 2022, Journal of molecular biology.

The BioImage Archive - building a home for life-sciences microscopy data

A. Brazma, J. Swedlow, G. Kleywegt, 2021, bioRxiv.

A call for public archives for biological image data

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

MGED standards: work in progress.

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

A call for public archives for biological image data

Charles E. Cook, E. Birney, J. Ellenberg, 2018, Nature Methods.

The importance of transparency and reproducibility in artificial intelligence research

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

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

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

Fusing microarray experiments with multivariate regression

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

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

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

Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

L. Egevad, A. Brazma, G. Bourque, 2023, Clinical Cancer Research.

A System for Information Management in BioMedical Studies—SIMBioMS

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

Microarray data representation, annotation and storage.

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

Building and analysing genome-wide gene disruption networks

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

Benchmarking strategies for cross-species integration of single-cell RNA sequencing data

A. Brazma, Zhichao Miao, I. Papatheodorou, 2023, bioRxiv.

Canonical Wnt and TGF-β/BMP signaling enhance melanocyte regeneration and suppress invasiveness, migration, and proliferation of melanoma cells

A. Brazma, I. Papatheodorou, G. Ozhan, 2023, bioRxiv.

Probabilistic retrieval and visualization of biologically relevant microarray experiments

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

Funding high-throughput data sharing

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

Microarray gene expression data analysis - a beginner's guide

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

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.

Data Storage and Analysis in ArrayExpress and Expression Profiler

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

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

B. Moor, S. Durinck, A. Brazma, 2005, Bioinform..

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

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

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

B. Moor, S. Durinck, A. Brazma, 2005 .

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

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

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Nuno A. Fonseca, Benjamin J. Raphael, Allison P. Heath, 2020, Nature Communications.

Impact of Alternative Splicing on the Human Proteome

R. Aebersold, J. Marioni, A. Brazma, 2017, Cell reports.

Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

A. Regev, A. Nicholson, A. Brazma, 2020, Nature Communications.

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.

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

Nuno A. Fonseca, J. Marioni, A. Brazma, 2014, bioRxiv.

Cellular phenotype database: a repository for systems microscopy data

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

Faculty Opinions recommendation of Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis.

A. Brazma, 2018, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

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

I. Jonassen, A. Brazma, J. Vilo, 1999, Nature Genetics.

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

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

Pol III binding in six mammalian genomes shows high conservation among amino acid isotypes, despite divergence in tRNA gene usage

D. Odom, A. Brazma, C. Kutter, 2011, Nature Genetics.

Pol III binding in six mammalian genomes shows high conservation among amino acid isotypes, despite divergence in tRNA gene usage

A. Brazma, C. Kutter, Gordon D. Brown, 2012 .

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

Ronald C. Taylor, Roger E Bumgarner, C. Ball, 2008, Nature Biotechnology.

SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways

Fabian J Theis, D. Pe’er, A. Regev, 2020, Nature Medicine.

A CD8 T cell transcription signature predicts prognosis in autoimmune disease

A. Brazma, P. MacAry, E. McKinney, 2010, Nature Medicine.

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

J. Harrow, A. Frankish, A. Brazma, 2013, Genome Biology.

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

M. Bihoreau, S. Heath, A. Brazma, 2014, Nature Communications.

A pan cancer analysis of promoter activity highlights the regulatory role of alternative transcription start sites and their association with noncoding mutations

Angela N. Brooks, G. Rätsch, A. Brazma, 2017 .

Image Data Resource: a bioimage data integration and publication platform

Richard K. Ferguson, A. Brazma, J. Swedlow, 2017, Nature Methods.

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

Helen Parkinson, Alvis Brazma, Thomas Schlitt, 2008 .

A pipeline for RNA-seq data processing and quality assessment

A. Brazma, M. Kapushesky, Andrew Tikhonov, 2011, Bioinform..

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

Tim F. Rayner, C. Ball, G. Sherlock, 2006 .

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

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

Databases and ontologies Advance Access publication March 3, 2010 Modeling sample variables with an Experimental Factor Ontology

A. Brazma, M. Kapushesky, T. Adamusiak, 2009 .

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

Nuno A. Fonseca, D. Bishop, A. Brazma, 2021, Nature Communications.

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

A. Børresen-Dale, A. Brazma, E. Hovig, 2016, International journal of cancer.

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

A. Brazma, M. Kapushesky, Aurora Torrente, 2005, Bioinform..