Misha Kapushesky

According to our database, Misha Kapushesky authored at least 20 papers between 2003 and 2012.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

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, Olga Melnichuk, Robert Petryszak, Nikolay Pultsin, Gabriella Rustici, Andrew Tikhonov, Ravensara S. Travillian, Eleanor Williams, Andrey Zorin, Helen E. Parkinson, Alvis Brazma

Nucleic Acids Res., 2012

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, Gerald Papenhausen, Niall O'Connor, Mick Correll, John Quackenbush

Nucleic Acids Res., 2012

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

ontoCAT: an R package for ontology traversal and search.

Natalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris A. Swertz, Misha Kapushesky

Bioinform., 2011

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

Ângela Gonçalves, Andrew Tikhonov, Alvis Brazma, Misha Kapushesky

Bioinform., 2011

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

Modeling sample variables with an Experimental Factor Ontology.

James Malone, Ele Holloway, Tomasz Adamusiak, Misha Kapushesky, Jie Zheng, Nikolay Kolesnikov, Anna Zhukova, Alvis Brazma, Helen E. Parkinson

Bioinform., 2010

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, James Malone, Roby Mani, Ekaterina Pilicheva, Tim F. Rayner, Faisal Ibne Rezwan, Anjan Sharma, Eleanor Williams, Xiangqun Zheng Bradley, Tomasz Adamusiak, Marco Brandizi, Tony Burdett, Richard Coulson, Maria Krestyaninova, Pavel Kurnosov, Eamonn Maguire, Sudeshna Guha Neogi, Philippe Rocca-Serra, Susanna-Assunta Sansone, Nataliya Sklyar, Mengyao Zhao, Ugis Sarkans, Alvis Brazma

Nucleic Acids Res., 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

Developing an Ontology from the Application Up.

James Malone, Tomasz Adamusiak, Ele Holloway, Misha Kapushesky, Helen E. Parkinson

Proceedings of the 5th International Workshop on OWL: Experiences and Directions (OWLED 2009), 2009

2008

4D<i>Xpress</i>: 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, Thorsten Henrich

Nucleic Acids Res., 2008

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, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich

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

2007

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, Anjan Sharma, E. William, Ugis Sarkans, Alvis Brazma

Nucleic Acids Res., 2007

2006

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

Jonathon Blake, Christian Schwager, Misha Kapushesky, Alvis Brazma

Bioinform., 2006

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, Ahmet Oezcimen, Tim F. Rayner, Philippe Rocca-Serra, Anjan Sharma, Susanna-Assunta Sansone, Alvis Brazma

Nucleic Acids Res., 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

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, Susanna-Assunta Sansone, Anna Farne, Tim F. Rayner, Alvis Brazma

Bioinform., 2005

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

Supervised Learning-Aided Optimization of Expert-Driven Functional Protein Sequence Annotation.

Lev Soinov, Alexander Kanapin, Misha Kapushesky

Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

2003

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, Susanna-Assunta Sansone

Nucleic Acids Res., 2003