Publications

Fu Y, Liu Z, Lu S, Bedford J, Mu X, Yip K, Khurana E^#, Gerstein M^#. 2014
FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer. Genome Biology (in press).
Talbert-Slagle K, Atkins KE, Yan KK, Khurana E, Gerstein M, Bradley EH, Berg D, Galvani AP, Townsend J. 2014
Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body. PLoS Pathogens 10(5), e1004092. Link
Khurana E^#. 2013
Learning to swim in a sea of genomic data. Genome Biology 14, 315. Link PDF
Khurana E^*, Fu Y^*, Colonna V^*, Mu X^*, 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 U, Flicek P, Fragoza R, Garrison E, Gibbs R, Gumus Z, Herreo J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin S, MacArthur D, Marth G, Muzny D, Pers T, Ritchie G, Rosenfeld J, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis E, Yu H, Rubin M, Tyler-Smith C, Gerstein M. 2013
Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 342, 84. Link (Also see FunSeq)

Research Highlight in Nature and Nature Genetics
Khurana E^*, Fu Y^*, Chen J, Gerstein M. 2013
Interpretation of genomic variants using a unified biological network approach.
PLoS Computational Biology 9(3), e1002886. Link
The 1000 Genomes Project Consortium. 2012
An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65. Link
Habegger L, Balasubramanian S, Chen D, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. 2012
VAT: A computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics 28, 2267-2269. Link
The ENCODE Project Consortium. 2012
An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature 489, 57-74. Link
Gerstein M^*, Kundaje A^*, Hariharan M^*, Landt S^*, Yan K^*, Cheng C^*, Mu X^*, Khurana E^*, Rozowsky J^*, Alexander R^*, Min R^*, Alves P^*, Abyzov A, Addleman N, Bhardwaj N, Boyle A, Cayting P, Charos A, Chen D, 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 J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge E, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy T, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip K, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham P, Myers R, Weissman S, Snyder M. 2012
Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100. Link
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. 2012
A systematic survey of loss-of-function variants in human protein-coding genes. Science 335, 823-828. Link
The ENCODE Project Consortium. 2011
A User's Guide to the Encyclopedia of DNA elements. PLoS Biology 9, e1001046. Link
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 HYK, Leng J, Li R, Li Y, Lin CY, Luo R, Mu X, 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. 2011.
Mapping copy number variation by population-scale genome sequencing. Nature 470, 59-65. Link
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, Waterson, RH, Reinke V, Gerstein M. 2011.
Prediction and characterization of non-coding RNAs in C.elegans by integrating conservation, secondary structure and high throughput sequencing and array data. Genome Res. 21, 276-285. Link
Khurana E^#, DeVane RH, Dal Peraro M, Klein ML^#. 2011.
Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus. Biochim Biophys Acta 1808(2), 530-537. Link
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. 2010.
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science 330(6012), 1775-1787. Link
1000 Genomes Project Consortium. 2010.
A map of human genome variation from population-scale sequencing. Nature 467(7319), 1061-1073. Link
Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB. 2010.
Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Res. 38(20), 6997-7007. Link
Holford ME, Khurana E, Cheung KH, Gerstein M. 2010.
Using semantic web rules to reason on an ontology of pseudogenes. Bioinformatics 26(12), i71-78. Link
Arinaminpathy Y^*, Khurana E^*,# , Engelman DM, Gerstein MB^#. 2009.
Computational Analysis of membrane proteins: the largest class of drug targets. Drug Discov Today 14(23/24), 1130-1135. Link
Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E , Robilotto R, Gerstein MB. 2009.
Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlight a recent burst of retrotranspositional activity. BMC Genomics 10, 480-492. Link
Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB. 2009.
Pseudofam: the pseudogene families database. Nucleic Acids Res. 37(Database issue), D738-D743. Link
Talbert-Slagle K, Marlatt S, Barrera FN, Khurana E, Oates JE, Gerstein M, Engelman DM, Dixon A, Dimaio D. 2009.
Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet derived growth factor {beta} receptor. J Virol. 83(19), 9773-9785. Link
Khurana E^#, Dal Peraro M^#, DeVane RH, Vemparala S, DeGrado WF^#, Klein ML. 2009.
Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from infleunza A virus. Proc. Natl. Acad. Sci. USA 106(4), 1069-1074. Link
Khurana E^#, Devane RH, Kohlmeyer A, Klein ML. 2008.
Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics. Nano Lett. 8(11), 3626-3630. Link
Khurana E^#, Nielsen SO, Ensing B, Klein ML. 2006.
Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents. J Phys Chem B. 110(38), 18965-18972 Link
Khurana E^#, Nielsen SO, Klein ML. 2006.
Gemini surfactants at the air/water interface: a fully atomistic molecular dynamics study. J Phys Chem B. 110(44), 22136-22142. Link
Dutta S, Singhal P, Agrawal P, Tomer R, Kritee K, Khurana E, Jayaram B. 2006.
A physicochemical model for analyzing DNA sequences. J Chem Inf Model. 46(1), 78-85. Link