Dr Misha Kapushesky

Genestack Limited
Genestack Limited

Position: Chief Executive Officer
Personal home page: http://www.linkedin.com/in/mkapushesky

PubMed journal articles - click here

Research description

Genestack was launched in 2012 with a mission to transform genomics big data computing and application engineering. We were founded by experts in bioinformatics and software architecture from the European Bioinformatics Institute with support from the world?s leading software development tools company JetBrains. Genestack?s team has a wide expertise in bioinformatics, ranging from functional genomics data analysis, algorithm design and data visualization to next-generation sequencing data processing and quality control. We are based in Cambridge, United Kingdom and St. Petersburg, Russia. We are building a universal ecosystem for bioinformatics development, aimed to reduce the chaotic clutter of inefficiency and incompatibility in today?s bioinformatics tools. Genestack's genomics operating system is a platform for developing, running and sharing big genomics datasets and applications, for pharma, biotech and healthcare.

Research Programme
Onco-Innovation
mk479
Recent publications:
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Key publications

1: Bezerra AR, Simões J, Lee W, Rung J, Weil T, Gut IG, Gut M, Bayés M, Rizzetto L, Cavalieri D, Giovannini G, Bozza S, Romani L, Kapushesky M, Moura GR, Santos MA. Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Proc Natl Acad Sci U S A. 2013 Jul 2;110(27):11079-84. doi: 10.1073/pnas.1302094110. Epub 2013 Jun 17. PubMed PMID: 23776239; PubMed Central PMCID: PMC3704024. 2: Culhane AC, Schröder MS, Sultana R, Picard SC, Martinelli EN, Kelly C, Haibe-Kains B, Kapushesky M, St Pierre AA, Flahive W, Picard KC, Gusenleitner D, Papenhausen G, O'Connor N, Correll M, Quackenbush J. GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res. 2012 Jan;40(Database issue):D1060-6. doi: 10.1093/nar/gkr901. Epub 2011 Nov 21. PubMed PMID: 22110038; PubMed Central PMCID: PMC3245038. 3: Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A. Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res. 2012 Jan;40(Database issue):D1077-81. doi: 10.1093/nar/gkr913. Epub 2011 Nov 7. PubMed PMID: 22064864; PubMed Central PMCID: PMC3245177. 4: Santamaría R, Rizzetto L, Bromley M, Zelante T, Lee W, Cavalieri D, Romani L, Miller B, Gut I, Santos M, Pierre P, Bowyer P, Kapushesky M. Systems biology of infectious diseases: a focus on fungal infections. Immunobiology. 2011 Nov;216(11):1212-27. doi: 10.1016/j.imbio.2011.08.004. Epub 2011 Aug 16. Review. PubMed PMID: 21889228. 5: Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, Kapushesky M. ontoCAT: an R package for ontology traversal and search. Bioinformatics. 2011 Sep 1;27(17):2468-70. doi: 10.1093/bioinformatics/btr375. Epub 2011 Jun 22. PubMed PMID: 21697126. 6: Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA. OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript. BMC Bioinformatics. 2011 May 29;12:218. doi: 10.1186/1471-2105-12-218. PubMed PMID: 21619703; PubMed Central PMCID: PMC3129328. 7: Goncalves A, Tikhonov A, Brazma A, Kapushesky M. A pipeline for RNA-seq data processing and quality assessment. Bioinformatics. 2011 Mar 15;27(6):867-9. doi: 10.1093/bioinformatics/btr012. Epub 2011 Jan 13. PubMed PMID: 21233166; PubMed Central PMCID: PMC3051320. 8: Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A. A global map of human gene expression. Nat Biotechnol. 2010 Apr;28(4):322-4. doi: 10.1038/nbt0410-322. PubMed PMID: 20379172; PubMed Central PMCID: PMC2974261. 9: Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H. Modeling sample variables with an Experimental Factor Ontology. Bioinformatics. 2010 Apr 15;26(8):1112-8. doi: 10.1093/bioinformatics/btq099. Epub 2010 Mar 3. PubMed PMID: 20200009; PubMed Central PMCID: PMC2853691. 10: Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res. 2009 Jan;37(Database issue):D868-72. doi: 10.1093/nar/gkn889. Epub 2008 Nov 10. PubMed PMID: 19015125; PubMed Central PMCID: PMC2686529. 11: Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T. 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Res. 2008 Jan;36(Database issue):D847-53. Epub 2007 Oct 4. PubMed PMID: 17916571; PubMed Central PMCID: PMC2238840. 12: Torrente A, Kapushesky M, Brazma A. A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings. Bioinformatics. 2005 Nov 1;21(21):3993-9. Epub 2005 Sep 1. PubMed PMID: 16141251. 13: Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A. Expression Profiler: next generation--an online platform for analysis of microarray data. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W465-70. PubMed PMID: 15215431; PubMed Central PMCID: PMC441608. 14: Soinov L, Kapushesky M. Unraveling nature's networks. Genome Biol. 2003;4(10):341. Epub 2003 Sep 16. PubMed PMID: 14519194; PubMed Central PMCID: PMC328448.