Ritesh Krishna  Ritesh Krishna photo       

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Research Staff Member for Computational Life Sciences
IBM Research Laboratory, UK

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Dr. Ritesh Krishna is an interdisciplinary scientist specializing in informatics for multi-omics based life sciences research. Ritesh obtained his PhD in Computer Science from the University of Warwick, where he developed computational methods for functional analysis of large-scale gene expression data. From there, he moved to the University of Liverpool for his Post-dcotoral research where he was associated with the Institute of Integrative Biology, Centre for Genomics Research and the Institute of Infection and Global Health. At IBM Research UK, Ritesh is responsible for leading the genomics based inititatives for UK industries.

Research Interests

Bioinformatics, Computational Biology, Next-generation Sequencing, Proteogenomics, Microarrays, Data Standardization, Exploratory data analysis, Data mining, Machine learning, Large-scale network analysis.

 

Research Grants

  • A computational cloud framework for the study of gene families, BBSRC (BB/N023145/1)

Book

Derivation of Process Algebraic Models of Biochemical Systems: pi-calculus, Stochastic Simulation of Biochemical Reactions, VDM Verlag,ISBN-13: 978-3639200188, 2009.

 

Publications

I Goodhead, F Blow, P Brownridge, M Hughes, J Kenny, R Krishna, L McLean, P Pongchaikul, R Beynon, A C Darby, Large scale and significant expression from pseudogenes in Sodalis glossinidius-a facultative bacterial endosymbiont, bioRxiv, 124388, 2017.

J Turner, R Krishna, A E V Hof, E R Sutton, K Matzen, A C Darby, The sequence of a male-specific genome region containing the sex determination switch in Aedes aegypti, bioRxiv, 122804, 2017.

J. A. Hodgson, D. W. Wallis, R. Krishna, S. J. Cornell, How to manipulate landscapes to improve the potential for range expansion, Methods in Ecology and Evolution, doi:10.1111/2041-210X.12614, 2016.

S. D. Armstrong, D. Xia, G. S. Bah, R. Krishna, H. F. Ngangyung, E. J. LaCourse, H. J. McSorley, J. A. Kengne-Ouafo, P. W. Chounna-Ndongmo, S. Wanji, P. A. Enyong, D. W. Taylor, M. L. Blaxter, J. M. Wastling, V. N. Tanya, B. L. Makepeace,Stage-specific proteomes from Onchocerca ochengi, sister species of the human river blindness parasite, uncover adaptations to a nodular lifestyle, Molecular & Cellular Proteomics, mcp.M115.055640, 2016.

R. Krishna, D. Xia, S. Sanderson, A. Shanmugasundram, S. Vermont, A. Bernal, G. Daniel-Naguib, F. Ghali, B. P. Brunk, D. S. Roos, J.M. Wastling, A.R. Jones, A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum, PROTEOMICS, doi: 10.1002/pmic.201400553, 2015.

F. Ghali, R. Krishna (joint first authors), S. Perkins, A. Collins, D. Xia, J.M. Wastling, A.R. Jones, ProteoAnnotator – Open Source Proteogenomics Annotation Software Supporting PSI Standards, PROTEOMICS, doi:10.1002/pmic.201400265, 2014.

D. Qi, R. Krishna, A. R. Jones, The jmzQuantML programming interface and validator for the mzQuantML data standard, PROTEOMICS, doi:10.1002/pmic.201300281, 2014

F. Ghali, R. Krishna, P. Lukasse, S. Martinez-Bartolome, F. Reisinger, H. Hermjakob, J. A. Vizcaino, A.R. Jones, A toolkit for the mzIdentML standard: the ProteoIDViewer, the mzidLibrary and the mzidValidator, Molecular & Cellular Proteomics, mcp.O113.029777, 2013.

(review) J.A. Medina-Aunon, R. Krishna, F. Ghali, J.P. Albar, A.R. Jones, A guide for integration of proteomics data standards into laboratory workflows, PROTEOMICS, doi: 10.1002/pmic.201200268, 2013.

(review) J.M. Wastling, S. Armstrong, R. Krishna, D. Xia, Parasites, Proteomes and Systems: has Descartes’ clock run out of time?, Parasitology, doi:10.1017/S0031182012000716 , 2012.

F. Reisinger, R. Krishna (joint first authors), F. Ghali, D. Ríos, H. Hermjakob, J. A. Vizcaíno, A. R. Jones, jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data , PROTEOMICS. doi: 10.1002/pmic.201100577 , 2012.

D. C. Wedge, R. Krishna, P. Blackhurst, J. A. Siepen, A.R. Jones and S. Hubbard, FDRAnalysis: A tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines, Journal of proteome research. doi: 10.1021/pr101157s , 2011.

R. Krishna, S. Nanda, A.Kulkarni and S. Patil, A Partial Granger Causality based Method for Analysis of Parameter Interactions in Bioreactors, Computers and Chemical Engineering . doi:10.1016/j.compchemeng.2010.07.013 , 2011.

R. Krishna, C-T. Li and V. Buchanan-Wollaston, A Temporal Precedence Based Clustering Method for Gene Expression Microarray Data, BMC Bioinformatics 11:68 . doi:10.1186/1471-2105-11-68, 2010. (Appeared as Featured article, and flagged as Highly Accessed)

J. Feng, D. Yi, R. Krishna, S. Guo and V. Buchanan-Wollaston, Listen to Genes: Dealing with Microarray Data in the Frequency Domain, PLoS ONE 4(4): e5098. doi:10.1371/journal.pone.0005098, 2009.

R. Krishna, C-T. Li and V. Buchanan-Wollaston,Interaction Based Functional Clustering of Genomic Data , in Proc. IEEE International Conference on Bioinformatics and Bioengineering, doi:10.1109/BIBE.2009.28, 2009.

R. Krishna and S. Guo, A partial granger causality approach to explore causal networks derived from multi-parameter data, Lecture notes in Computer Science, Springer Berlin / Heidelberg, vol. 5307, pp. 9--27, 2008.