Professor, Department of Medicine Section of Genetic Medicine and Department of Human Genetics
Senior Fellow, Institute for Genomics and Systems Biology at the University of Chicago and Argonne National Laboratory
Senior Fellow, Computation Institute at the University of Chicago and Argonne National Laboratory
M.S. (Mathematical Biology) Novosibirsk State University, Novosibirsk, Russia, 1985
Ph.D. (Genetics) Institute of Cytology and Genetics, Novosibirsk, Russia, 1990
The University of Chicago Knapp Center for Biomedical Discovery (KCBD) 900 E. 57th St. Room 10160A Chicago, IL 60637
Phone: (773) 834-7367
Fax: (773) 834-2877
 

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

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

 

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)

 

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)

 

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)

 

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)

 

A recipe for high impact.
Cokol M, Rodriguez-Esteban R, Rzhetsky A
(2007) Genome Biol. 2007;8(5):406. 17493291 (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)