ArrayExpress - a public repository for microarray gene expression data at the EBI. - Alvis Brazma; Helen E. Parkinson; Ugis Sarkans; Mohammadreza Shojatalab; Jaak Vilo; Niran Abeygunawardena; Ele Holloway; Misha Kapushesky; Patrick Kemmeren; Gonzalo Garcia Lara; Ahmet Oezcimen; Philippe Rocca-Serra; et al. (Nucleic Acids Res., 2003)

Supervised Learning-Aided Optimization of Expert-Driven Functional Protein Sequence Annotation. - Lev Soinov; Alexander Kanapin; Misha Kapushesky (WABI, 2004)

Expression Profiler: next generation - an online platform for analysis of microarray data. - Misha Kapushesky; Patrick Kemmeren; Aedín C. Culhane; Steffen Durinck; Jan Ihmels; Christine Körner; Meelis Kull; Aurora Torrente; Ugis Sarkans; Jaak Vilo; Alvis Brazma (Nucleic Acids Res., 2004)

The ArrayExpress gene expression database: a software engineering and implementation perspective. - Ugis Sarkans; Helen E. Parkinson; Gonzalo Garcia Lara; Ahmet Oezcimen; Anjan Sharma; Niran Abeygunawardena; Sergio Contrino; Ele Holloway; Philippe Rocca-Serra; Gaurab Mukherjee; Mohammadreza Shojatalab; Misha Kapushesky; et al. (Bioinform., 2005)

A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings. - Aurora Torrente; Misha Kapushesky; Alvis Brazma (Bioinform., 2005)

ArrayExpress - a public repository for microarray gene expression data at the EBI. - Helen E. Parkinson; Ugis Sarkans; Mohammadreza Shojatalab; Niran Abeygunawardena; Sergio Contrino; Richard Coulson; Anna Farne; Gonzalo Garcia Lara; Ele Holloway; Misha Kapushesky; P. Lilja; Gaurab Mukherjee; et al. (Nucleic Acids Res., 2005)

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression. - Jonathon Blake; Christian Schwager; Misha Kapushesky; Alvis Brazma (Bioinform., 2006)

ArrayExpress - a public database of microarray experiments and gene expression profiles. - Helen E. Parkinson; Misha Kapushesky; Mohammadreza Shojatalab; Niran Abeygunawardena; Richard Coulson; Anna Farne; Ele Holloway; Nikolay Kolesnykov; P. Lilja; Margus Lukk; Roby Mani; Tim F. Rayner; et al. (Nucleic Acids Res., 2007)

Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress. - Yannick Haudry; Chuang Kee Ong; Laurence Ettwiller; Hugo Bérubé; Ivica Letunic; Misha Kapushesky; Paul-Daniel Weeber; Xi Wang; Julien Gagneur; Charles Girardot; Detlev Arendt; Peer Bork; et al. (APBC, 2008)

4DXpress: a database for cross-species expression pattern comparisons. - Yannick Haudry; Hugo Bérubé; Ivica Letunic; Paul-Daniel Weeber; Julien Gagneur; Charles Girardot; Misha Kapushesky; Detlev Arendt; Peer Bork; Alvis Brazma; Eileen E. M. Furlong; Joachim Wittbrodt; et al. (Nucleic Acids Res., 2008)

Developing an Ontology from the Application Up. - James Malone; Tomasz Adamusiak; Ele Holloway; Misha Kapushesky; Helen E. Parkinson (OWLED, 2009)

Importing ArrayExpress datasets into R/Bioconductor. - Audrey Kauffmann; Tim F. Rayner; Helen E. Parkinson; Misha Kapushesky; Margus Lukk; Alvis Brazma; Wolfgang Huber (Bioinform., 2009)

ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. - Helen E. Parkinson; Misha Kapushesky; Nikolay Kolesnikov; Gabriella Rustici; Mohammadreza Shojatalab; Niran Abeygunawardena; Hugo Bérubé; Miroslaw Dylag; Ibrahim Emam; Anna Farne; Ele Holloway; Margus Lukk; et al. (Nucleic Acids Res., 2009)

Modeling sample variables with an Experimental Factor Ontology. - James Malone; Ele Holloway; Tomasz Adamusiak; Misha Kapushesky; Jie Zheng 001; Nikolay Kolesnikov; Anna Zhukova; Alvis Brazma; Helen E. Parkinson (Bioinform., 2010)

Gene Expression Atlas at the European Bioinformatics Institute. - Misha Kapushesky; Ibrahim Emam; Ele Holloway; Pavel Kurnosov; Andrey Zorin; James Malone; Gabriella Rustici; Eleanor Williams; Helen E. Parkinson; Alvis Brazma (Nucleic Acids Res., 2010)

A pipeline for RNA-seq data processing and quality assessment. - Ângela Gonçalves; Andrew Tikhonov; Alvis Brazma; Misha Kapushesky (Bioinform., 2011)

ontoCAT: an R package for ontology traversal and search. - Natalja Kurbatova; Tomasz Adamusiak; Pavel Kurnosov; Morris A. Swertz; Misha Kapushesky (Bioinform., 2011)

OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript. - Tomasz Adamusiak; Tony Burdett; Natalja Kurbatova; K. Joeri van der Velde; Niran Abeygunawardena; Despoina Antonakaki; Misha Kapushesky; Helen E. Parkinson; Morris A. Swertz (BMC Bioinform., 2011)

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. - Aedín C. Culhane; Markus S. Schröder; Razvan Sultana; Shaita C. Picard; Enzo N. Martinelli; Caroline Kelly; Benjamin Haibe-Kains; Misha Kapushesky; Anne-Alyssa St Pierre; William Flahive; Kermshlise C. Picard; Daniel Gusenleitner; et al. (Nucleic Acids Res., 2012)

Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments. - Misha Kapushesky; Tomasz Adamusiak; Tony Burdett; Aedín C. Culhane; Anna Farne; Alexey Filippov; Ele Holloway; Andrey Klebanov; Nataliya Kryvych; Natalja Kurbatova; Pavel Kurnosov; James Malone; et al. (Nucleic Acids Res., 2012)