Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 41

1.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Aug 9;174(4):1034-1035. doi: 10.1016/j.cell.2018.07.034. No abstract available.

2.

FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications.

Backenroth D, He Z, Kiryluk K, Boeva V, Pethukova L, Khurana E, Christiano A, Buxbaum JD, Ionita-Laza I.

Am J Hum Genet. 2018 May 3;102(5):920-942. doi: 10.1016/j.ajhg.2018.03.026.

3.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060. Erratum in: Cell. 2018 Aug 9;174(4):1034-1035.

4.

MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB-NFIB fusion gene.

Kim J, Geyer FC, Martelotto LG, Ng CK, Lim RS, Selenica P, Li A, Pareja F, Fusco N, Edelweiss M, Kumar R, Gularte-Merida R, Forbes AN, Khurana E, Mariani O, Badve S, Vincent-Salomon A, Norton L, Reis-Filho JS, Weigelt B.

J Pathol. 2018 Feb;244(2):143-150. doi: 10.1002/path.5006. Epub 2017 Dec 28.

PMID:
29149504
5.

Risk Factors for Cerebral Palsy in Children in Botswana.

Monokwane B, Johnson A, Gambrah-Sampaney C, Khurana E, Baier J, Baranov E, Westmoreland KD, Mazhani L, Steenhoff AP, Bearden DR.

Pediatr Neurol. 2017 Dec;77:73-77. doi: 10.1016/j.pediatrneurol.2017.07.014. Epub 2017 Aug 3.

PMID:
29074060
6.

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network.

Dhingra P, Martinez-Fundichely A, Berger A, Huang FW, Forbes AN, Liu EM, Liu D, Sboner A, Tamayo P, Rickman DS, Rubin MA, Khurana E.

Genome Biol. 2017 Jul 27;18(1):141. doi: 10.1186/s13059-017-1266-3.

7.

Health beliefs regarding pediatric cerebral palsy among caregivers in Botswana: A qualitative study.

Patel P, Baier J, Baranov E, Khurana E, Gambrah-Sampaney C, Johnson A, Monokwane B, Bearden DR.

Child Care Health Dev. 2017 Nov;43(6):861-868. doi: 10.1111/cch.12490. Epub 2017 Jul 25.

PMID:
28744889
8.

Inherited determinants of early recurrent somatic mutations in prostate cancer.

Romanel A, Garritano S, Stringa B, Blattner M, Dalfovo D, Chakravarty D, Soong D, Cotter KA, Petris G, Dhingra P, Gasperini P, Cereseto A, Elemento O, Sboner A, Khurana E, Inga A, Rubin MA, Demichelis F.

Nat Commun. 2017 Jun 29;8(1):48. doi: 10.1038/s41467-017-00046-0.

9.

Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma.

Feigin ME, Garvin T, Bailey P, Waddell N, Chang DK, Kelley DR, Shuai S, Gallinger S, McPherson JD, Grimmond SM, Khurana E, Stein LD, Biankin AV, Schatz MC, Tuveson DA.

Nat Genet. 2017 Jun;49(6):825-833. doi: 10.1038/ng.3861. Epub 2017 May 8.

10.

Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization.

Dhingra P, Fu Y, Gerstein M, Khurana E.

Curr Protoc Bioinformatics. 2017 May 2;57:15.11.1-15.11.17. doi: 10.1002/cpbi.23.

PMID:
28463398
11.

Risk Factors for Malnutrition Among Children With Cerebral Palsy in Botswana.

Johnson A, Gambrah-Sampaney C, Khurana E, Baier J, Baranov E, Monokwane B, Bearden DR.

Pediatr Neurol. 2017 May;70:50-55. doi: 10.1016/j.pediatrneurol.2017.02.003. Epub 2017 Feb 14.

PMID:
28363511
12.

Non-coding genetic variation in cancer.

Cuykendall TN, Rubin MA, Khurana E.

Curr Opin Syst Biol. 2017 Feb;1:9-15. doi: 10.1016/j.coisb.2016.12.017. Epub 2017 Mar 4.

13.

Pediatric Cerebral Palsy in Botswana: Etiology, Outcomes, and Comorbidities.

Bearden DR, Monokwane B, Khurana E, Baier J, Baranov E, Westmoreland K, Mazhani L, Steenhoff AP.

Pediatr Neurol. 2016 Jun;59:23-9. doi: 10.1016/j.pediatrneurol.2016.03.002. Epub 2016 Mar 17.

14.

Cancer genomics: Hard-to-reach repairs.

Khurana E.

Nature. 2016 Apr 14;532(7598):181-2. doi: 10.1038/532181a. No abstract available.

PMID:
27075092
15.

Role of non-coding sequence variants in cancer.

Khurana E, Fu Y, Chakravarty D, Demichelis F, Rubin MA, Gerstein M.

Nat Rev Genet. 2016 Feb;17(2):93-108. doi: 10.1038/nrg.2015.17. Epub 2016 Jan 19. Review.

PMID:
26781813
16.

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.

Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M.

Nucleic Acids Res. 2015 Sep 30;43(17):8123-34. doi: 10.1093/nar/gkv803. Epub 2015 Aug 24.

17.

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.

Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M.

Genome Biol. 2014;15(10):480.

18.

Cellular superspreaders: an epidemiological perspective on HIV infection inside the body.

Talbert-Slagle K, Atkins KE, Yan KK, Khurana E, Gerstein M, Bradley EH, Berg D, Galvani AP, Townsend JP.

PLoS Pathog. 2014 May 8;10(5):e1004092. doi: 10.1371/journal.ppat.1004092. eCollection 2014 May. No abstract available.

19.

Learning to swim in a sea of genomic data.

Khurana E.

Genome Biol. 2013 Dec 6;14(12):315. doi: 10.1186/gb4144.

20.

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.

Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587.

21.

Interpretation of genomic variants using a unified biological network approach.

Khurana E, Fu Y, Chen J, Gerstein M.

PLoS Comput Biol. 2013;9(3):e1002886. doi: 10.1371/journal.pcbi.1002886. Epub 2013 Mar 7.

22.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

23.

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.

Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M.

Bioinformatics. 2012 Sep 1;28(17):2267-9. Epub 2012 Jun 28.

24.

A systematic survey of loss-of-function variants in human protein-coding genes.

MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG; 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C.

Science. 2012 Feb 17;335(6070):823-8. doi: 10.1126/science.1215040. Erratum in: Science. 2012 Apr 20;336(6079):296.

25.

Mapping copy number variation by population-scale genome sequencing.

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project.

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.

26.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH.

Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Erratum in: Science. 2011 Jan 7;331(6013):30.

27.

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.

Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB.

Genome Res. 2011 Feb;21(2):276-85. doi: 10.1101/gr.110189.110. Epub 2010 Dec 22. Erratum in: Genome Res. 2011 May;21(5):811.

28.

Segmental duplications in the human genome reveal details of pseudogene formation.

Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB.

Nucleic Acids Res. 2010 Nov;38(20):6997-7007. doi: 10.1093/nar/gkq587. Epub 2010 Jul 8.

29.

Using semantic web rules to reason on an ontology of pseudogenes.

Holford ME, Khurana E, Cheung KH, Gerstein M.

Bioinformatics. 2010 Jun 15;26(12):i71-8. doi: 10.1093/bioinformatics/btq173.

30.

Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus.

Khurana E, Devane RH, Dal Peraro M, Klein ML.

Biochim Biophys Acta. 2011 Feb;1808(2):530-7. doi: 10.1016/j.bbamem.2010.03.025. Epub 2010 Apr 10.

31.

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity.

Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, Gerstein MB.

BMC Genomics. 2009 Oct 16;10:480. doi: 10.1186/1471-2164-10-480.

32.

Computational analysis of membrane proteins: the largest class of drug targets.

Arinaminpathy Y, Khurana E, Engelman DM, Gerstein MB.

Drug Discov Today. 2009 Dec;14(23-24):1130-5. doi: 10.1016/j.drudis.2009.08.006. Epub 2009 Sep 3. Review.

33.

Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor.

Talbert-Slagle K, Marlatt S, Barrera FN, Khurana E, Oates J, Gerstein M, Engelman DM, Dixon AM, Dimaio D.

J Virol. 2009 Oct;83(19):9773-85. doi: 10.1128/JVI.00946-09. Epub 2009 Jul 15.

34.

Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus.

Khurana E, Dal Peraro M, DeVane R, Vemparala S, DeGrado WF, Klein ML.

Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1069-74. doi: 10.1073/pnas.0811720106. Epub 2009 Jan 14.

35.

Pseudofam: the pseudogene families database.

Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB.

Nucleic Acids Res. 2009 Jan;37(Database issue):D738-43. doi: 10.1093/nar/gkn758. Epub 2008 Oct 28.

36.

Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics.

Khurana E, DeVane RH, Kohlmeyer A, Klein ML.

Nano Lett. 2008 Nov;8(11):3626-30. doi: 10.1021/nl801564m. Epub 2008 Oct 15.

37.

Gemini surfactants at the air/water interface: a fully atomistic molecular dynamics study.

Khurana E, Nielsen SO, Klein ML.

J Phys Chem B. 2006 Nov 9;110(44):22136-42.

PMID:
17078649
38.

Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents.

Khurana E, Nielsen SO, Ensing B, Klein ML.

J Phys Chem B. 2006 Sep 28;110(38):18965-72.

PMID:
16986891
39.

A physicochemical model for analyzing DNA sequences.

Dutta S, Singhal P, Agrawal P, Tomer R, Kritee K, Khurana E, Jayaram B.

J Chem Inf Model. 2006 Jan-Feb;46(1):78-85.

PMID:
16426042
40.

The efficacy of erythropoietin in human immunodeficiency virus-infected end-stage renal disease patients treated by maintenance hemodialysis.

Shrivastava D, Rao TK, Sinert R, Khurana E, Lundin AP, Friedman EA.

Am J Kidney Dis. 1995 Jun;25(6):904-9.

PMID:
7771487
41.

Fibrillary renal deposits and nephritis.

Duffy JL, Khurana E, Susin M, Gomez-Leon G, Churg J.

Am J Pathol. 1983 Dec;113(3):279-90.

Supplemental Content

Loading ...
Support Center