Research Description
My main interest is in (asymptotic) understanding how phenotypes, such as human healthy diversity and maladies, are implemented at the level of genes and networks of interacting molecules. To harvest as much information about known molecular interactions as possible, my group runs a large-scale text-mining effort aiming at analysis of a vast corpus of biomedical publications. Currently we can extract from text automatically about 500 distinct flavors of relations among biomedical entities (such as bind, activate, merystilate, and transport). To sharpen our text-mining axes, we are actively designing related models and computational applications. Furthermore, in cooperation with our experimentally talented colleagues, we are striving to use text-mined networks to understand, interpret and refine high- or low-throughput experimental data. We are also computationally generating biological hypotheses that our generous collaborators are attempting to test experimentally. My older (still smoldering) passion is in developing and applying computational methods related to phylogenetics and evolutionary biology. Research interests include: (1) Bioinformatics and phylogenetics applied to analysis of genes, proteins, molecular pathways, and human disease. (2) Application of statistics to sequence analysis and analysis of molecular networks. (3) Development of algorithms and programs for pathway/sequence analysis, pathway/sequence comparison and phylogeny reconstruction.
Selected Publications
Choosing experiments to accelerate collective discovery.
Rzhetsky A, Foster JG, Foster IT, Evans JA
(2015 Nov) Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14569-74. doi: 10.1073/pnas.1509757112. Epub 2015 Nov 9. 26554009 (Full Text)
Health ROI as a measure of misalignment of biomedical needs and resources.
Yao L, Li Y, Ghosh S, Evans JA, Rzhetsky A
(2015 Aug) Nat Biotechnol. 2015 Aug;33(8):807-11. doi: 10.1038/nbt.3276.26252133
Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes.
Melamed RD, Emmett KJ, Madubata C, Rzhetsky A, Rabadan R
(2015) Nat Commun. 2015 Apr 30;6:7033. doi: 10.1038/ncomms8033. 25926297(Full Text)
Quantifying the impact and extent of undocumented biomedical synonymy.
Blair DR, Wang K, Nestorov S, Evans JA, Rzhetsky A
(2014 Sep) PLoS Comput Biol. 2014 Sep 25;10(9):e1003799. doi: 10.1371/journal.pcbi.1003799. eCollection 2014 Sep. 25255227 (Full Text)
DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.
Liu CC, Tseng YT, Li W, Wu CY, Mayzus I, Rzhetsky A, Sun F, Waterman M, Chen JJ, Chaudhary PM, Loscalzo J, Crandall E, Zhou XJ
(2014 Jul) Nucleic Acids Res. 2014 Jul;42(Web Server issue):W137-46. doi: 10.1093/nar/gku412. Epub 2014 Jun 3. 24895436 (Full Text)
Environmental and state-level regulatory factors affect the incidence of autism and intellectual disability.
Rzhetsky A, Bagley SC, Wang K, Lyttle CS, Cook EH Jr, Altman RB, Gibbons RD
(2014 Mar) PLoS Comput Biol. 2014 Mar 13;10(3):e1003518. doi: 10.1371/journal.pcbi.1003518. eCollection 2014 Mar. 24625521 (Full Text)
A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.
Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A
(2013 Sep) Cell. 2013 Sep 26;155(1):70-80. doi: 10.1016/j.cell.2013.08.030.24074861 (Full Text)
Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network.
Iossifov I, Zheng T, Baron M, Gilliam TC, Rzhetsky A
(2008 Jul) Genome Res. 2008 Jul;18(7):1150-62. doi: 10.1101/gr.075622.107. Epub 2008 Apr 16. 18417725 (Full Text)
Eurocan plus report: feasibility study for coordination of national cancer research activities.
(2008) Ecancermedicalscience. 2008;2:84. doi: 10.3332/ecancer.2011.84. Epub 2008 May 20. 22274749 (Full Text)
Six senses in the literature. The bleak sensory landscape of biomedical texts.
Rodriguez-Esteban R, Rzhetsky A
(2008 Mar) EMBO Rep. 2008 Mar;9(3):212-5. doi: 10.1038/embor.2008.15.18311168 (Full Text)
Network properties of genes harboring inherited disease mutations.
Feldman I, Rzhetsky A, Vitkup D
(2008 Mar) Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4323-8. doi: 10.1073/pnas.0701722105. Epub 2008 Mar 7. 18326631 (Full Text)
Quantitative systems-level determinants of human genes targeted by successful drugs.
Yao L, Rzhetsky A
(2008 Feb) Genome Res. 2008 Feb;18(2):206-13. Epub 2007 Dec 14. 18083776(Full Text)
Probing genetic overlap among complex human phenotypes.
Rzhetsky A, Wajngurt D, Park N, Zheng T
(2007 Jul) Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11694-9. Epub 2007 Jul 3. 17609372 (Full Text)
How many scientific papers should be retracted?
Cokol M, Iossifov I, Rodriguez-Esteban R, Rzhetsky A
(2007 May) EMBO Rep. 2007 May;8(5):422-3. 17471252 (Full Text)
A recipe for high impact.
Cokol M, Rodriguez-Esteban R, Rzhetsky A
(2007) Genome Biol. 2007;8(5):406. 17493291 (Full Text)