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Items: 1 to 50 of 95

1.

Human Organoids Share Structural and Genetic Features with Primary Pancreatic Adenocarcinoma Tumors.

Romero-Calvo I, Weber C, Ray M, Brown M, Kirby K, Nandi RK, Long TM, Sparrow SM, Ugolkov A, Qiang W, Zhang Y, Brunetti T, Kindler H, Segal JP, Rzhetsky A, Mazar AP, Buschmann MM, Weichselbaum R, Roggin K, White KP.

Mol Cancer Res. 2018 Aug 31. pii: molcanres.0531.2018. doi: 10.1158/1541-7786.MCR-18-0531. [Epub ahead of print]

PMID:
30171177
2.

Comprehensive modeling reveals proximity, seasonality, and hygiene practices as key determinants of MRSA colonization in exposed households.

Mork RL, Hogan PG, Muenks CE, Boyle MG, Thompson RM, Morelli JJ, Sullivan ML, Gehlert SJ, Ross DG, Yn A, Bubeck Wardenburg J, Rzhetsky A, Burnham CD, Fritz SA.

Pediatr Res. 2018 Jul 19. doi: 10.1038/s41390-018-0113-x. [Epub ahead of print]

PMID:
30135590
3.

Associations between environmental quality and adult asthma prevalence in medical claims data.

Gray CL, Lobdell DT, Rappazzo KM, Jian Y, Jagai JS, Messer LC, Patel AP, DeFlorio-Barker SA, Lyttle C, Solway J, Rzhetsky A.

Environ Res. 2018 Oct;166:529-536. doi: 10.1016/j.envres.2018.06.020. Epub 2018 Jun 27.

PMID:
29957506
4.

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning.

Kim JS, Gao X, Rzhetsky A.

PLoS Comput Biol. 2018 Apr 26;14(4):e1006106. doi: 10.1371/journal.pcbi.1006106. eCollection 2018 Apr.

5.

Conjunction of factors triggering waves of seasonal influenza.

Chattopadhyay I, Kiciman E, Elliott JW, Shaman JL, Rzhetsky A.

Elife. 2018 Feb 27;7. pii: e30756. doi: 10.7554/eLife.30756.

6.

Preexisting Type 2 Immune Activation Protects against the Development of Sepsis.

Krishack PA, Wang K, Rzhetsky A, Solway J, Sperling AI, Verhoef PA.

Am J Respir Cell Mol Biol. 2017 Nov;57(5):628-630. doi: 10.1165/rcmb.2017-0277LE. No abstract available.

PMID:
29090959
7.

Classification of common human diseases derived from shared genetic and environmental determinants.

Wang K, Gaitsch H, Poon H, Cox NJ, Rzhetsky A.

Nat Genet. 2017 Sep;49(9):1319-1325. doi: 10.1038/ng.3931. Epub 2017 Aug 7.

8.

Understanding Toxoplasmosis in the United States Through "Large Data" Analyses.

Lykins J, Wang K, Wheeler K, Clouser F, Dixon A, El Bissati K, Zhou Y, Lyttle C, Rzhetsky A, McLeod R.

Clin Infect Dis. 2016 Aug 15;63(4):468-75. doi: 10.1093/cid/ciw356. Epub 2016 Jun 26.

9.

Choosing experiments to accelerate collective discovery.

Rzhetsky A, Foster JG, Foster IT, Evans JA.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14569-74. doi: 10.1073/pnas.1509757112. Epub 2015 Nov 9.

10.

Health ROI as a measure of misalignment of biomedical needs and resources.

Yao L, Li Y, Ghosh S, Evans JA, Rzhetsky A.

Nat Biotechnol. 2015 Aug;33(8):807-11. doi: 10.1038/nbt.3276. No abstract available.

11.

Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes.

Melamed RD, Emmett KJ, Madubata C, Rzhetsky A, Rabadan R.

Nat Commun. 2015 Apr 30;6:7033. doi: 10.1038/ncomms8033.

12.

Quantifying the impact and extent of undocumented biomedical synonymy.

Blair DR, Wang K, Nestorov S, Evans JA, Rzhetsky A.

PLoS Comput Biol. 2014 Sep 25;10(9):e1003799. doi: 10.1371/journal.pcbi.1003799. eCollection 2014 Sep.

13.

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.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W137-46. doi: 10.1093/nar/gku412. Epub 2014 Jun 3.

14.

Systems analysis of human multigene disorders. Preface.

Maltsev N, Rzhetsky A, Conrad Gilliam T.

Adv Exp Med Biol. 2014;799:v - viii. No abstract available.

PMID:
24678533
15.

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.

PLoS Comput Biol. 2014 Mar 13;10(3):e1003518. doi: 10.1371/journal.pcbi.1003518. eCollection 2014 Mar.

16.

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.

Cell. 2013 Sep 26;155(1):70-80. doi: 10.1016/j.cell.2013.08.030.

17.

Representation of probabilistic scientific knowledge.

Soldatova LN, Rzhetsky A, De Grave K, King RD.

J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S7. doi: 10.1186/2041-1480-4-S1-S7. Epub 2013 Apr 15.

18.

A Distributed Look-up Architecture for Text Mining Applications using MapReduce.

Balkir AS, Foster I, Rzhetsky A.

Proc Int Symp High Perform Distrib Comput. 2011 Nov;2011. doi: 10.1145/1996130.1996174.

19.

Conflicting biomedical assumptions for mathematical modeling: the case of cancer metastasis.

Divoli A, Mendonça EA, Evans JA, Rzhetsky A.

PLoS Comput Biol. 2011 Oct;7(10):e1002132. doi: 10.1371/journal.pcbi.1002132. Epub 2011 Oct 6. Review.

20.

War of ontology worlds: mathematics, computer code, or Esperanto?

Rzhetsky A, Evans JA.

PLoS Comput Biol. 2011 Sep;7(9):e1002191. doi: 10.1371/journal.pcbi.1002191. Epub 2011 Sep 29.

21.

Representation of research hypotheses.

Soldatova LN, Rzhetsky A.

J Biomed Semantics. 2011 May 17;2 Suppl 2:S9. doi: 10.1186/2041-1480-2-S2-S9.

22.

Advancing science through mining libraries, ontologies, and communities.

Evans JA, Rzhetsky A.

J Biol Chem. 2011 Jul 8;286(27):23659-66. doi: 10.1074/jbc.R110.176370. Epub 2011 May 12. Review.

23.

Benchmarking ontologies: bigger or better?

Yao L, Divoli A, Mayzus I, Evans JA, Rzhetsky A.

PLoS Comput Biol. 2011 Jan 13;7(1):e1001055. doi: 10.1371/journal.pcbi.1001055.

24.

The BioPAX community standard for pathway data sharing.

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, 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.

Nat Biotechnol. 2010 Sep;28(9):935-42. doi: 10.1038/nbt.1666. Epub 2010 Sep 9. Erratum in: Nat Biotechnol. 2010 Dec;28(12):1308. Nat Biotechnol. 2012 Apr;30(4):365. Reubenacker, Oliver [corrected to Ruebenacker, Oliver].

25.

Philosophy of science. Machine science.

Evans J, Rzhetsky A.

Science. 2010 Jul 23;329(5990):399-400. doi: 10.1126/science.1189416. No abstract available.

26.

Novel opportunities for computational biology and sociology in drug discovery.

Yao L, Evans JA, Rzhetsky A.

Trends Biotechnol. 2010 Apr;28(4):161-70. Review.

27.

WITHDRAWN: Novel opportunities for computational biology and sociology in drug discovery.

Yao L, Evans JA, Rzhetsky A.

Trends Biotechnol. 2010 Feb 5. pii: S0167-7799(10)00013-2. doi: 10.1016/j.tibtech.2010.01.003. [Epub ahead of print]

PMID:
26642912
28.

Looking at cerebellar malformations through text-mined interactomes of mice and humans.

Iossifov I, Rodriguez-Esteban R, Mayzus I, Millen KJ, Rzhetsky A.

PLoS Comput Biol. 2009 Nov;5(11):e1000559. doi: 10.1371/journal.pcbi.1000559. Epub 2009 Nov 6.

29.

Novel opportunities for computational biology and sociology in drug discovery.

Yao L, Evans JA, Rzhetsky A.

Trends Biotechnol. 2009 Sep;27(9):531-40. doi: 10.1016/j.tibtech.2009.06.003. Epub 2009 Aug 10. Review. Corrected and republished in: Trends Biotechnol. 2010 Apr;28(4):161-70.

30.

Getting started in text mining: part two.

Rzhetsky A, Seringhaus M, Gerstein MB.

PLoS Comput Biol. 2009 Jul;5(7):e1000411. doi: 10.1371/journal.pcbi.1000411. Epub 2009 Jul 31. No abstract available.

31.

How to get the most out of your curation effort.

Rzhetsky A, Shatkay H, Wilbur WJ.

PLoS Comput Biol. 2009 May;5(5):e1000391. doi: 10.1371/journal.pcbi.1000391. Epub 2009 May 22.

32.

Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer.

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.

Science. 2009 Feb 27;323(5918):1218-22. doi: 10.1126/science.1157669. Epub 2009 Jan 22.

33.

Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users.

Shatkay H, Pan F, Rzhetsky A, Wilbur WJ.

Bioinformatics. 2008 Sep 15;24(18):2086-93. doi: 10.1093/bioinformatics/btn381. Epub 2008 Aug 20.

34.

Seeking a new biology through text mining.

Rzhetsky A, Seringhaus M, Gerstein M.

Cell. 2008 Jul 11;134(1):9-13. doi: 10.1016/j.cell.2008.06.029.

35.

Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network.

Iossifov I, Zheng T, Baron M, Gilliam TC, Rzhetsky A.

Genome Res. 2008 Jul;18(7):1150-62. doi: 10.1101/gr.075622.107. Epub 2008 Apr 16.

36.

Network properties of genes harboring inherited disease mutations.

Feldman I, Rzhetsky A, Vitkup D.

Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4323-8. doi: 10.1073/pnas.0701722105. Epub 2008 Mar 7.

37.

Six senses in the literature. The bleak sensory landscape of biomedical texts.

Rodriguez-Esteban R, Rzhetsky A.

EMBO Rep. 2008 Mar;9(3):212-5. doi: 10.1038/embor.2008.15. No abstract available.

38.

Quantitative systems-level determinants of human genes targeted by successful drugs.

Yao L, Rzhetsky A.

Genome Res. 2008 Feb;18(2):206-13. Epub 2007 Dec 14.

39.

Probing genetic overlap among complex human phenotypes.

Rzhetsky A, Wajngurt D, Park N, Zheng T.

Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11694-9. Epub 2007 Jul 3.

40.

A recipe for high impact.

Cokol M, Rodriguez-Esteban R, Rzhetsky A.

Genome Biol. 2007;8(5):406.

41.

How many scientific papers should be retracted?

Cokol M, Iossifov I, Rodriguez-Esteban R, Rzhetsky A.

EMBO Rep. 2007 May;8(5):422-3. No abstract available.

42.

Self-correcting maps of molecular pathways.

Rzhetsky A, Zheng T, Weinreb C.

PLoS One. 2006 Dec 20;1:e61.

43.

Imitating manual curation of text-mined facts in biomedicine.

Rodriguez-Esteban R, Iossifov I, Rzhetsky A.

PLoS Comput Biol. 2006 Sep 8;2(9):e118. Epub 2006 Jul 27.

44.

New directions in biomedical text annotation: definitions, guidelines and corpus construction.

Wilbur WJ, Rzhetsky A, Shatkay H.

BMC Bioinformatics. 2006 Jul 25;7:356.

45.

Microparadigms: chains of collective reasoning in publications about molecular interactions.

Rzhetsky A, Iossifov I, Loh JM, White KP.

Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4940-5. Epub 2006 Mar 16.

46.

Emergent behavior of growing knowledge about molecular interactions.

Cokol M, Iossifov I, Weinreb C, Rzhetsky A.

Nat Biotechnol. 2005 Oct;23(10):1243-7. No abstract available.

PMID:
16211067
47.

Listening to viral tongues: comparing viral trees using a stochastic context-free grammar.

Rzhetsky A, Fitch WM.

Mol Biol Evol. 2005 Apr;22(4):905-13. Epub 2004 Dec 29.

PMID:
15626684
48.

Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease.

Krauthammer M, Kaufmann CA, Gilliam TC, Rzhetsky A.

Proc Natl Acad Sci U S A. 2004 Oct 19;101(42):15148-53. Epub 2004 Oct 7.

49.

The genomic sequence of the accidental pathogen Legionella pneumophila.

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.

Science. 2004 Sep 24;305(5692):1966-8.

50.

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.

Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboué PA, Weng W, Wilbur WJ, Hatzivassiloglou V, Friedman C.

J Biomed Inform. 2004 Feb;37(1):43-53.

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