Profiles Research Networking Software The University of Chicago
Keywords
Last Name
Institution

ANDREY RZHETSKY

TitlePROFESSOR
InstitutionUniversity of Chicago
DepartmentMEDICINE
AddressChicago IL 60637
Other Positions
TitlePROFESSOR
InstitutionUniversity of Chicago
DepartmentBIOLOGICAL SCIENCES COLLEGIATE DIVISION

TitlePROFESSOR
InstitutionUniversity of Chicago
DepartmentHUMAN GENETICS


 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Lykins J, Wang K, Wheeler K, Clouser F, Dixon A, El Bissati K, Zhou Y, Lyttle C, Rzhetsky A, McLeod R. Understanding Toxoplasmosis in the United States Through "Large Data" Analyses. Clin Infect Dis. 2016 Aug 15; 63(4):468-75.
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  2. Rzhetsky A, Foster JG, Foster IT, Evans JA. Choosing experiments to accelerate collective discovery. Proc Natl Acad Sci U S A. 2015 Nov 24; 112(47):14569-74.
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  3. Yao L, Li Y, Ghosh S, Evans JA, Rzhetsky A. Health ROI as a measure of misalignment of biomedical needs and resources. Nat Biotechnol. 2015 08; 33(8):807-11.
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  4. Melamed RD, Emmett KJ, Madubata C, Rzhetsky A, Rabadan R. Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes. Nat Commun. 2015 Apr 30; 6:7033.
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  5. Blair DR, Wang K, Nestorov S, Evans JA, Rzhetsky A. Quantifying the impact and extent of undocumented biomedical synonymy. PLoS Comput Biol. 2014 Sep; 10(9):e1003799.
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  6. 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. DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W137-46.
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  7. Rzhetsky A, Bagley SC, Wang K, Lyttle CS, Cook EH, Altman RB, Gibbons RD. Environmental and state-level regulatory factors affect the incidence of autism and intellectual disability. PLoS Comput Biol. 2014 Mar; 10(3):e1003518.
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  8. Maltsev N, Rzhetsky A, Conrad Gilliam T. Systems analysis of human multigene disorders. Preface. Adv Exp Med Biol. 2014; 799:v - viii.
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  9. 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. A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell. 2013 Sep 26; 155(1):70-80.
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  10. Soldatova LN, Rzhetsky A, De Grave K, King RD. Representation of probabilistic scientific knowledge. J Biomed Semantics. 2013 Apr 15; 4 Suppl 1:S7.
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  11. Balkir AS, Foster I, Rzhetsky A. A Distributed Look-up Architecture for Text Mining Applications using MapReduce. Proc Int Symp High Perform Distrib Comput. 2011 Nov; 2011.
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  12. Divoli A, Mendonça EA, Evans JA, Rzhetsky A. Conflicting biomedical assumptions for mathematical modeling: the case of cancer metastasis. PLoS Comput Biol. 2011 Oct; 7(10):e1002132.
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  13. Rzhetsky A, Evans JA. War of ontology worlds: mathematics, computer code, or Esperanto? PLoS Comput Biol. 2011 Sep; 7(9):e1002191.
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  14. Soldatova LN, Rzhetsky A. Representation of research hypotheses. J Biomed Semantics. 2011 May 17; 2 Suppl 2:S9.
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  15. Evans JA, Rzhetsky A. Advancing science through mining libraries, ontologies, and communities. J Biol Chem. 2011 Jul 08; 286(27):23659-66.
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  16. Yao L, Divoli A, Mayzus I, Evans JA, Rzhetsky A. Benchmarking ontologies: bigger or better? PLoS Comput Biol. 2011 Jan 13; 7(1):e1001055.
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  17. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep; 28(9):935-42.
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  18. Evans J, Rzhetsky A. Philosophy of science. Machine science. Science. 2010 Jul 23; 329(5990):399-400.
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  19. Yao L, Evans JA, Rzhetsky A. Novel opportunities for computational biology and sociology in drug discovery. Trends Biotechnol. 2010 Apr; 28(4):161-70.
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  20. Yao L, Evans JA, Rzhetsky A. WITHDRAWN: Novel opportunities for computational biology and sociology in drug discovery. Trends Biotechnol. 2010 Feb 05.
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  21. Iossifov I, Rodriguez-Esteban R, Mayzus I, Millen KJ, Rzhetsky A. Looking at cerebellar malformations through text-mined interactomes of mice and humans. PLoS Comput Biol. 2009 Nov; 5(11):e1000559.
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  22. Yao L, Evans JA, Rzhetsky A. Novel opportunities for computational biology and sociology in drug discovery. Trends Biotechnol. 2009 Sep; 27(9):531-40.
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  23. Rzhetsky A, Seringhaus M, Gerstein MB. Getting started in text mining: part two. PLoS Comput Biol. 2009 Jul; 5(7):e1000411.
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  24. Rzhetsky A, Shatkay H, Wilbur WJ. How to get the most out of your curation effort. PLoS Comput Biol. 2009 May; 5(5):e1000391.
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  25. Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T, Al-Ahmadie HA, Tretiakova M, Camp RL, Perera-Alberto M, Rimm DL, Xu T, Rzhetsky A, White KP. Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer. Science. 2009 Feb 27; 323(5918):1218-22.
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  26. Shatkay H, Pan F, Rzhetsky A, Wilbur WJ. Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users. Bioinformatics. 2008 Sep 15; 24(18):2086-93.
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  27. Rzhetsky A, Seringhaus M, Gerstein M. Seeking a new biology through text mining. Cell. 2008 Jul 11; 134(1):9-13.
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  28. Iossifov I, Zheng T, Baron M, Gilliam TC, Rzhetsky A. Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network. Genome Res. 2008 Jul; 18(7):1150-62.
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  29. Feldman I, Rzhetsky A, Vitkup D. Network properties of genes harboring inherited disease mutations. Proc Natl Acad Sci U S A. 2008 Mar 18; 105(11):4323-8.
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  30. Rodriguez-Esteban R, Rzhetsky A. Six senses in the literature. The bleak sensory landscape of biomedical texts. EMBO Rep. 2008 Mar; 9(3):212-5.
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  31. Yao L, Rzhetsky A. Quantitative systems-level determinants of human genes targeted by successful drugs. Genome Res. 2008 Feb; 18(2):206-13.
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  32. Rzhetsky A, Wajngurt D, Park N, Zheng T. Probing genetic overlap among complex human phenotypes. Proc Natl Acad Sci U S A. 2007 Jul 10; 104(28):11694-9.
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  33. Cokol M, Iossifov I, Rodriguez-Esteban R, Rzhetsky A. How many scientific papers should be retracted? EMBO Rep. 2007 May; 8(5):422-3.
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  34. Cokol M, Rodriguez-Esteban R, Rzhetsky A. A recipe for high impact. Genome Biol. 2007; 8(5):406.
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  35. Rzhetsky A, Zheng T, Weinreb C. Self-correcting maps of molecular pathways. PLoS One. 2006 Dec 20; 1:e61.
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  36. Rodriguez-Esteban R, Iossifov I, Rzhetsky A. Imitating manual curation of text-mined facts in biomedicine. PLoS Comput Biol. 2006 Sep 08; 2(9):e118.
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  37. Wilbur WJ, Rzhetsky A, Shatkay H. New directions in biomedical text annotation: definitions, guidelines and corpus construction. BMC Bioinformatics. 2006 Jul 25; 7:356.
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  38. Rzhetsky A, Iossifov I, Loh JM, White KP. Microparadigms: chains of collective reasoning in publications about molecular interactions. Proc Natl Acad Sci U S A. 2006 Mar 28; 103(13):4940-5.
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  39. Cokol M, Iossifov I, Weinreb C, Rzhetsky A. Emergent behavior of growing knowledge about molecular interactions. Nat Biotechnol. 2005 Oct; 23(10):1243-7.
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  40. Rzhetsky A, Fitch WM. Listening to viral tongues: comparing viral trees using a stochastic context-free grammar. Mol Biol Evol. 2005 Apr; 22(4):905-13.
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  41. Krauthammer M, Kaufmann CA, Gilliam TC, Rzhetsky A. Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. Proc Natl Acad Sci U S A. 2004 Oct 19; 101(42):15148-53.
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  42. Chien M, Morozova I, Shi S, Sheng H, Chen J, Gomez SM, Asamani G, Hill K, Nuara J, Feder M, Rineer J, Greenberg JJ, Steshenko V, Park SH, Zhao B, Teplitskaya E, Edwards JR, Pampou S, Georghiou A, Chou IC, Iannuccilli W, Ulz ME, Kim DH, Geringer-Sameth A, Goldsberry C, Morozov P, Fischer SG, Segal G, Qu X, Rzhetsky A, Zhang P, Cayanis E, De Jong PJ, Ju J, Kalachikov S, Shuman HA, Russo JJ. The genomic sequence of the accidental pathogen Legionella pneumophila. Science. 2004 Sep 24; 305(5692):1966-8.
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  43. Iossifov I, Krauthammer M, Friedman C, Hatzivassiloglou V, Bader JS, White KP, Rzhetsky A. Probabilistic inference of molecular networks from noisy data sources. Bioinformatics. 2004 May 22; 20(8):1205-13.
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  44. Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboué PA, Weng W, Wilbur WJ, Hatzivassiloglou V, Friedman C. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform. 2004 Feb; 37(1):43-53.
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  45. Gomez SM, Noble WS, Rzhetsky A. Learning to predict protein-protein interactions from protein sequences. Bioinformatics. 2003 Oct 12; 19(15):1875-81.
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  46. Roth CW, Holm I, Graille M, Dehoux P, Rzhetsky A, Wincker P, Weissenbach J, Brey PT. Identification of the Anopheles gambiae ATP-binding cassette transporter superfamily genes. Mol Cells. 2003 Apr 30; 15(2):150-8.
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  47. Karev GP, Wolf YI, Rzhetsky AY, Berezovskaya FS, Koonin EV. Birth and death of protein domains: a simple model of evolution explains power law behavior. BMC Evol Biol. 2002 Oct 14; 2:18.
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  48. Christophides GK, Zdobnov E, Barillas-Mury C, Birney E, Blandin S, Blass C, Brey PT, Collins FH, Danielli A, Dimopoulos G, Hetru C, Hoa NT, Hoffmann JA, Kanzok SM, Letunic I, Levashina EA, Loukeris TG, Lycett G, Meister S, Michel K, Moita LF, Müller HM, Osta MA, Paskewitz SM, Reichhart JM, Rzhetsky A, Troxler L, Vernick KD, Vlachou D, Volz J, von Mering C, Xu J, Zheng L, Bork P, Kafatos FC. Immunity-related genes and gene families in Anopheles gambiae. Science. 2002 Oct 04; 298(5591):159-65.
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  49. Yu H, Hatzivassiloglou V, Rzhetsky A, Wilbur WJ. Automatically identifying gene/protein terms in MEDLINE abstracts. J Biomed Inform. 2002 Oct-Dec; 35(5-6):322-30.
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  50. Friedman C, Kra P, Rzhetsky A. Two biomedical sublanguages: a description based on the theories of Zellig Harris. J Biomed Inform. 2002 Aug; 35(4):222-35.
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  51. Gomez SM, Rzhetsky A. Towards the prediction of complete protein--protein interaction networks. Pac Symp Biocomput. 2002; 413-24.
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  52. Krauthammer M, Kra P, Iossifov I, Gomez SM, Hripcsak G, Hatzivassiloglou V, Friedman C, Rzhetsky A. Of truth and pathways: chasing bits of information through myriads of articles. Bioinformatics. 2002; 18 Suppl 1:S249-57.
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  53. Yu H, Hatzivassiloglou V, Friedman C, Rzhetsky A, Wilbur WJ. Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. Proc AMIA Symp. 2002; 919-23.
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  54. Gomez SM, Lo SH, Rzhetsky A. Probabilistic prediction of unknown metabolic and signal-transduction networks. Genetics. 2001 Nov; 159(3):1291-8.
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  55. Rzhetsky A, Gomez SM. Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics. 2001 Oct; 17(10):988-96.
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  56. Tammur J, Prades C, Arnould I, Rzhetsky A, Hutchinson A, Adachi M, Schuetz JD, Swoboda KJ, Ptácek LJ, Rosier M, Dean M, Allikmets R. Two new genes from the human ATP-binding cassette transporter superfamily, ABCC11 and ABCC12, tandemly duplicated on chromosome 16q12. Gene. 2001 Jul 25; 273(1):89-96.
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  57. Dean M, Rzhetsky A, Allikmets R. The human ATP-binding cassette (ABC) transporter superfamily. Genome Res. 2001 Jul; 11(7):1156-66.
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  58. Scott K, Brady R, Cravchik A, Morozov P, Rzhetsky A, Zuker C, Axel R. A chemosensory gene family encoding candidate gustatory and olfactory receptors in Drosophila. Cell. 2001 Mar 09; 104(5):661-73.
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  59. Annilo T, Tammur J, Hutchinson A, Rzhetsky A, Dean M, Allikmets R. Human and mouse orthologs of a new ATP-binding cassette gene, ABCG4. Cytogenet Cell Genet. 2001; 94(3-4):196-201.
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  60. Hatzivassiloglou V, Duboué PA, Rzhetsky A. Disambiguating proteins, genes, and RNA in text: a machine learning approach. Bioinformatics. 2001; 17 Suppl 1:S97-106.
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  61. Friedman C, Kra P, Yu H, Krauthammer M, Rzhetsky A. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics. 2001; 17 Suppl 1:S74-82.
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  62. Rzhetsky A, Morozov P. Markov chain Monte Carlo computation of confidence intervals for substitution-rate variation in proteins. Pac Symp Biocomput. 2001; 203-14.
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  63. Koike T, Rzhetsky A. A graphic editor for analyzing signal-transduction pathways. Gene. 2000 Dec 23; 259(1-2):235-44.
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  64. Krauthammer M, Rzhetsky A, Morozov P, Friedman C. Using BLAST for identifying gene and protein names in journal articles. Gene. 2000 Dec 23; 259(1-2):245-52.
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  65. Rzhetsky A, Koike T, Kalachikov S, Gomez SM, Krauthammer M, Kaplan SH, Kra P, Russo JJ, Friedman C. A knowledge model for analysis and simulation of regulatory networks. Bioinformatics. 2000 Dec; 16(12):1120-8.
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  66. Migliazza A, Cayanis E, Bosch-Albareda F, Komatsu H, Martinotti S, Toniato E, Kalachikov S, Bonaldo MF, Jelene P, Ye X, Rzhetsky A, Qu X, Chien M, Inghirami G, Gaidano G, Vitolo U, Saglio G, Resegotti L, Zhang P, Soares MB, Russo J, Fischer SG, Edelman IS, Efstratiadis A, Dalla-Favera R. Molecular pathogenesis of B-cell chronic lymphocytic leukemia: analysis of 13q14 chromosomal deletions. Curr Top Microbiol Immunol. 2000; 252:275-84.
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  67. Tilson MD, Rzhetsky A. A novel hypothesis regarding the evolutionary origins of the immunoglobulin fold. Curr Med Res Opin. 2000; 16(2):88-93.
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  68. Morozov P, Sitnikova T, Churchill G, Ayala FJ, Rzhetsky A. A new method for characterizing replacement rate variation in molecular sequences. Application of the Fourier and wavelet models to Drosophila and mammalian proteins. Genetics. 2000 Jan; 154(1):381-95.
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  69. Vosshall LB, Amrein H, Morozov PS, Rzhetsky A, Axel R. A spatial map of olfactory receptor expression in the Drosophila antenna. Cell. 1999 Mar 05; 96(5):725-36.
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  70. Rzhetsky A, Kalachikov S, Ye X, Zhang P, Russo JJ. Tools for visualization and integration of intermediate sequencing results in large disease gene discovery projects. Gene. 1998 Feb 16; 208(1):31-5.
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  71. Yoshida A, Rzhetsky A, Hsu LC, Chang C. Human aldehyde dehydrogenase gene family. Eur J Biochem. 1998 Feb 01; 251(3):549-57.
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  72. Ayala FJ, Rzhetsky A, Ayala FJ. Origin of the metazoan phyla: molecular clocks confirm paleontological estimates. Proc Natl Acad Sci U S A. 1998 Jan 20; 95(2):606-11.
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  73. Qu XY, Hauptschein RS, Rzhetsky A, Scotto L, Chien MC, Ye X, Frigeri F, Rao PH, Pasqualucci L, Gamberi B, Deaven LL, Zhang P, Chaganti RS, Dalla-Favera R, Russo JJ. Analysis of a 69-kb contiguous genomic sequence at a putative tumor suppressor gene locus on human chromosome 6q27. DNA Seq. 1998; 9(4):189-204.
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  74. Rzhetsky A, Ayala FJ, Hsu LC, Chang C, Yoshida A. Exon/intron structure of aldehyde dehydrogenase genes supports the "introns-late" theory. Proc Natl Acad Sci U S A. 1997 Jun 24; 94(13):6820-5.
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  75. Rzhetsky A, Dopazo J, Snyder E, Dangler CA, Ayala FJ. Assessing dissimilarity of genes by comparing their RNAse A mismatch cleavage patterns. Genetics. 1996 Dec; 144(4):1975-83.
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  76. Rzhetsky A, Sitnikova T. When is it safe to use an oversimplified substitution model in tree-making? Mol Biol Evol. 1996 Nov; 13(9):1255-65.
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  77. Kumar S, Rzhetsky A. Evolutionary relationships of eukaryotic kingdoms. J Mol Evol. 1996 Feb; 42(2):183-93.
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  78. Rzhetsky A. Estimating substitution rates in ribosomal RNA genes. Genetics. 1995 Oct; 141(2):771-83.
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  79. Takezaki N, Rzhetsky A, Nei M. Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol. 1995 Sep; 12(5):823-33.
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  80. Sitnikova T, Rzhetsky A, Nei M. Interior-branch and bootstrap tests of phylogenetic trees. Mol Biol Evol. 1995 Mar; 12(2):319-33.
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  81. Rzhetsky A, Nei M. Tests of applicability of several substitution models for DNA sequence data. Mol Biol Evol. 1995 Jan; 12(1):131-51.
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  82. Rzhetsky A, Kumar S, Nei M. Four-cluster analysis: a simple method to test phylogenetic hypotheses. Mol Biol Evol. 1995 Jan; 12(1):163-7.
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  83. Rzhetsky A, Nei M. METREE: a program package for inferring and testing minimum-evolution trees. Comput Appl Biosci. 1994 Jul; 10(4):409-12.
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  84. Rzhetsky A, Nei M. Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites. J Mol Evol. 1994 Mar; 38(3):295-9.
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  85. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol. 1993 Sep; 10(5):1073-95.
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  86. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol. 1992 Oct; 35(4):367-75.
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