Ekta Khurana

Ekta Khurana

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Ekta Khurana

Ekta Khurana

Publications by authors named "Ekta Khurana"

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36Publications

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Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.

Cell Syst 2019 May 8;8(5):446-455.e8. Epub 2019 May 8.

Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.04.001DOI Listing
May 2019

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

Curr Protoc Bioinformatics 2017 05 2;57:15.11.1-15.11.17. Epub 2017 May 2.

Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York.

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http://dx.doi.org/10.1002/cpbi.23DOI Listing
May 2017

Non-coding genetic variation in cancer.

Curr Opin Syst Biol 2017 Feb 4;1:9-15. Epub 2017 Mar 4.

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, 10065, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S24523100173000
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http://dx.doi.org/10.1016/j.coisb.2016.12.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203332PMC
February 2017

Cancer genomics: Hard-to-reach repairs.

Authors:
Ekta Khurana

Nature 2016 Apr;532(7598):181-2

Meyer Cancer Center and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.

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http://dx.doi.org/10.1038/532181aDOI Listing
April 2016

Role of non-coding sequence variants in cancer.

Nat Rev Genet 2016 Feb 19;17(2):93-108. Epub 2016 Jan 19.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.

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http://www.nature.com/articles/nrg.2015.17
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http://dx.doi.org/10.1038/nrg.2015.17DOI Listing
February 2016

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

Genome Biol 2014 ;15(10):480

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/s13059-014-0480-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203974PMC
October 2015

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

Nucleic Acids Res 2015 Sep 24;43(17):8123-34. Epub 2015 Aug 24.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA Department of Computer Science, Yale University, New Haven, CT 06520, USA

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787796PMC
September 2015

Learning to swim in a sea of genomic data.

Authors:
Ekta Khurana

Genome Biol 2013 Dec 6;14(12):315. Epub 2013 Dec 6.

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http://dx.doi.org/10.1186/gb4144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053704PMC
December 2013

Interpretation of genomic variants using a unified biological network approach.

PLoS Comput Biol 2013 7;9(3):e1002886. Epub 2013 Mar 7.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002886DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3591262PMC
November 2013

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

Biochim Biophys Acta 2011 Feb 10;1808(2):530-7. Epub 2010 Apr 10.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1016/j.bbamem.2010.03.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975046PMC
February 2011

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

Authors:
Mark B Gerstein Zhi John Lu Eric L Van Nostrand Chao Cheng Bradley I Arshinoff Tao Liu Kevin Y Yip Rebecca Robilotto Andreas Rechtsteiner Kohta Ikegami Pedro Alves Aurelien Chateigner Marc Perry Mitzi Morris Raymond K Auerbach Xin Feng Jing Leng Anne Vielle Wei Niu Kahn Rhrissorrakrai Ashish Agarwal Roger P Alexander Galt Barber Cathleen M Brdlik Jennifer Brennan Jeremy Jean Brouillet Adrian Carr Ming-Sin Cheung Hiram Clawson Sergio Contrino Luke O Dannenberg Abby F Dernburg Arshad Desai Lindsay Dick Andréa C Dosé Jiang Du Thea Egelhofer Sevinc Ercan Ghia Euskirchen Brent Ewing Elise A Feingold Reto Gassmann Peter J Good Phil Green Francois Gullier Michelle Gutwein Mark S Guyer Lukas Habegger Ting Han Jorja G Henikoff Stefan R Henz Angie Hinrichs Heather Holster Tony Hyman A Leo Iniguez Judith Janette Morten Jensen Masaomi Kato W James Kent Ellen Kephart Vishal Khivansara Ekta Khurana John K Kim Paulina Kolasinska-Zwierz Eric C Lai Isabel Latorre Amber Leahey Suzanna Lewis Paul Lloyd Lucas Lochovsky Rebecca F Lowdon Yaniv Lubling Rachel Lyne Michael MacCoss Sebastian D Mackowiak Marco Mangone Sheldon McKay Desirea Mecenas Gennifer Merrihew David M Miller Andrew Muroyama John I Murray Siew-Loon Ooi Hoang Pham Taryn Phippen Elicia A Preston Nikolaus Rajewsky Gunnar Rätsch Heidi Rosenbaum Joel Rozowsky Kim Rutherford Peter Ruzanov Mihail Sarov Rajkumar Sasidharan Andrea Sboner Paul Scheid Eran Segal Hyunjin Shin Chong Shou Frank J Slack Cindie Slightam Richard Smith William C Spencer E O Stinson Scott Taing Teruaki Takasaki Dionne Vafeados Ksenia Voronina Guilin Wang Nicole L Washington Christina M Whittle Beijing Wu Koon-Kiu Yan Georg Zeller Zheng Zha Mei Zhong Xingliang Zhou Julie Ahringer Susan Strome Kristin C Gunsalus Gos Micklem X Shirley Liu Valerie Reinke Stuart K Kim LaDeana W Hillier Steven Henikoff Fabio Piano Michael Snyder Lincoln Stein Jason D Lieb Robert H Waterston

Science 2010 Dec 22;330(6012):1775-87. Epub 2010 Dec 22.

Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/science.1196914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569PMC
December 2010

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

Nucleic Acids Res 2010 Nov 8;38(20):6997-7007. Epub 2010 Jul 8.

Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1093/nar/gkq587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978362PMC
November 2010

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

Bioinformatics 2010 Jun;26(12):i71-8

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881358PMC
June 2010

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

Drug Discov Today 2009 Dec 3;14(23-24):1130-5. Epub 2009 Sep 3.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.

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http://dx.doi.org/10.1016/j.drudis.2009.08.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796609PMC
December 2009

Pseudofam: the pseudogene families database.

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

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1093/nar/gkn758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686518PMC
January 2009

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

Proc Natl Acad Sci U S A 2009 Jan 14;106(4):1069-74. Epub 2009 Jan 14.

Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.

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http://dx.doi.org/10.1073/pnas.0811720106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2626606PMC
January 2009

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

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

Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://pubs.acs.org/doi/abs/10.1021/nl801564m
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http://dx.doi.org/10.1021/nl801564mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2696305PMC
November 2008

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

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

Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.

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http://dx.doi.org/10.1021/jp063343dDOI Listing
November 2006

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

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

Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.

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http://dx.doi.org/10.1021/jp057471yDOI Listing
September 2006

A physicochemical model for analyzing DNA sequences.

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

Department of Chemistry and Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi.

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http://dx.doi.org/10.1021/ci050119xDOI Listing
April 2006