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1.

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.

Kumar, Sushant; Warrell, Jonathan; Li, Shantao; McGillivray, Patrick D; Meyerson, William; Salichos, Leonidas; Harmanci, Arif; Martinez-Fundichely, Alexander; Chan, Calvin W Y; Nielsen, Morten Muhlig; Lochovsky, Lucas; Zhang, Yan; Li, Xiaotong; Lou, Shaoke; Pedersen, Jakob Skou; Herrmann, Carl; Getz, Gad; Khurana, Ekta; Gerstein, Mark B.

Cell ; 180(5): 915-927.e16, 2020 03 05.

Article in English | MEDLINE | ID: mdl-32084333

2.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey, Matthew H; Tokheim, Collin; Porta-Pardo, Eduard; Sengupta, Sohini; Bertrand, Denis; Weerasinghe, Amila; Colaprico, Antonio; Wendl, Michael C; Kim, Jaegil; Reardon, Brendan; Ng, Patrick Kwok-Shing; Jeong, Kang Jin; Cao, Song; Wang, Zixing; Gao, Jianjiong; Gao, Qingsong; Wang, Fang; Liu, Eric Minwei; Mularoni, Loris; Rubio-Perez, Carlota; Nagarajan, Niranjan; Cortés-Ciriano, Isidro; Zhou, Daniel Cui; Liang, Wen-Wei; Hess, Julian M; Yellapantula, Venkata D; Tamborero, David; Gonzalez-Perez, Abel; Suphavilai, Chayaporn; Ko, Jia Yu; Khurana, Ekta; Park, Peter J; Van Allen, Eliezer M; Liang, Han; Lawrence, Michael S; Godzik, Adam; Lopez-Bigas, Nuria; Stuart, Josh; Wheeler, David; Getz, Gad; Chen, Ken; Lazar, Alexander J; Mills, Gordon B; Karchin, Rachel; Ding, Li.

Cell ; 173(2): 371-385.e18, 2018 04 05.

Article in English | MEDLINE | ID: mdl-29625053

3.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey, Matthew H; Tokheim, Collin; Porta-Pardo, Eduard; Sengupta, Sohini; Bertrand, Denis; Weerasinghe, Amila; Colaprico, Antonio; Wendl, Michael C; Kim, Jaegil; Reardon, Brendan; Kwok-Shing Ng, Patrick; Jeong, Kang Jin; Cao, Song; Wang, Zixing; Gao, Jianjiong; Gao, Qingsong; Wang, Fang; Liu, Eric Minwei; Mularoni, Loris; Rubio-Perez, Carlota; Nagarajan, Niranjan; Cortés-Ciriano, Isidro; Zhou, Daniel Cui; Liang, Wen-Wei; Hess, Julian M; Yellapantula, Venkata D; Tamborero, David; Gonzalez-Perez, Abel; Suphavilai, Chayaporn; Ko, Jia Yu; Khurana, Ekta; Park, Peter J; Van Allen, Eliezer M; Liang, Han; Lawrence, Michael S; Godzik, Adam; Lopez-Bigas, Nuria; Stuart, Josh; Wheeler, David; Getz, Gad; Chen, Ken; Lazar, Alexander J; Mills, Gordon B; Karchin, Rachel; Ding, Li.

Cell ; 174(4): 1034-1035, 2018 08 09.

Article in English | MEDLINE | ID: mdl-30096302

4.

Patterns of somatic structural variation in human cancer genomes.

Li, Yilong; Roberts, Nicola D; Wala, Jeremiah A; Shapira, Ofer; Schumacher, Steven E; Kumar, Kiran; Khurana, Ekta; Waszak, Sebastian; Korbel, Jan O; Haber, James E; Imielinski, Marcin; Weischenfeldt, Joachim; Beroukhim, Rameen; Campbell, Peter J.

Nature ; 578(7793): 112-121, 2020 02.

Article in English | MEDLINE | ID: mdl-32025012

5.

Author Correction: Patterns of somatic structural variation in human cancer genomes.

Li, Yilong; Roberts, Nicola D; Wala, Jeremiah A; Shapira, Ofer; Schumacher, Steven E; Kumar, Kiran; Khurana, Ekta; Waszak, Sebastian; Korbel, Jan O; Haber, James E; Imielinski, Marcin; Weischenfeldt, Joachim; Beroukhim, Rameen; Campbell, Peter J.

Nature ; 614(7948): E38, 2023 Feb.

Article in English | MEDLINE | ID: mdl-36697835

6.

Systems biology analysis of human genomes points to key pathways conferring spina bifida risk.

Aguiar-Pulido, Vanessa; Wolujewicz, Paul; Martinez-Fundichely, Alexander; Elhaik, Eran; Thareja, Gaurav; Abdel Aleem, Alice; Chalhoub, Nader; Cuykendall, Tawny; Al-Zamer, Jamel; Lei, Yunping; El-Bashir, Haitham; Musser, James M; Al-Kaabi, Abdulla; Shaw, Gary M; Khurana, Ekta; Suhre, Karsten; Mason, Christopher E; Elemento, Olivier; Finnell, Richard H; Ross, M Elizabeth.

Proc Natl Acad Sci U S A ; 118(51)2021 12 21.

Article in English | MEDLINE | ID: mdl-34916285

7.

CNCDatabase: a database of non-coding cancer drivers.

Liu, Eric Minwei; Martinez-Fundichely, Alexander; Bollapragada, Rajesh; Spiewack, Maurice; Khurana, Ekta.

Nucleic Acids Res ; 49(D1): D1094-D1101, 2021 01 08.

Article in English | MEDLINE | ID: mdl-33095860

8.

Loss-of-function tolerance of enhancers in the human genome.

Xu, Duo; Gokcumen, Omer; Khurana, Ekta.

PLoS Genet ; 16(4): e1008663, 2020 04.

Article in English | MEDLINE | ID: mdl-32243438

9.

Role of non-coding sequence variants in cancer.

Khurana, Ekta; Fu, Yao; Chakravarty, Dimple; Demichelis, Francesca; Rubin, Mark A; Gerstein, Mark.

Nat Rev Genet ; 17(2): 93-108, 2016 Feb.

Article in English | MEDLINE | ID: mdl-26781813

10.

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

Backenroth, Daniel; He, Zihuai; Kiryluk, Krzysztof; Boeva, Valentina; Pethukova, Lynn; Khurana, Ekta; Christiano, Angela; Buxbaum, Joseph D; Ionita-Laza, Iuliana.

Am J Hum Genet ; 102(5): 920-942, 2018 05 03.

Article in English | MEDLINE | ID: mdl-29727691

11.

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

Kim, Jisun; Geyer, Felipe C; Martelotto, Luciano G; Ng, Charlotte Ky; Lim, Raymond S; Selenica, Pier; Li, Anqi; Pareja, Fresia; Fusco, Nicola; Edelweiss, Marcia; Kumar, Rahul; Gularte-Merida, Rodrigo; Forbes, Andre N; Khurana, Ekta; Mariani, Odette; Badve, Sunil; Vincent-Salomon, Anne; Norton, Larry; Reis-Filho, Jorge S; Weigelt, Britta.

J Pathol ; 244(2): 143-150, 2018 02.

Article in English | MEDLINE | ID: mdl-29149504

12.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein, Mark B; Kundaje, Anshul; Hariharan, Manoj; Landt, Stephen G; Yan, Koon-Kiu; Cheng, Chao; Mu, Xinmeng Jasmine; Khurana, Ekta; Rozowsky, Joel; Alexander, Roger; Min, Renqiang; Alves, Pedro; Abyzov, Alexej; Addleman, Nick; Bhardwaj, Nitin; Boyle, Alan P; Cayting, Philip; Charos, Alexandra; Chen, David Z; Cheng, Yong; Clarke, Declan; Eastman, Catharine; Euskirchen, Ghia; Frietze, Seth; Fu, Yao; Gertz, Jason; Grubert, Fabian; Harmanci, Arif; Jain, Preti; Kasowski, Maya; Lacroute, Phil; Leng, Jing Jane; Lian, Jin; Monahan, Hannah; O'Geen, Henriette; Ouyang, Zhengqing; Partridge, E Christopher; Patacsil, Dorrelyn; Pauli, Florencia; Raha, Debasish; Ramirez, Lucia; Reddy, Timothy E; Reed, Brian; Shi, Minyi; Slifer, Teri; Wang, Jing; Wu, Linfeng; Yang, Xinqiong; Yip, Kevin Y; Zilberman-Schapira, Gili.

Nature ; 489(7414): 91-100, 2012 Sep 06.

Article in English | MEDLINE | ID: mdl-22955619

13.

Cancer genomics: Hard-to-reach repairs.

Khurana, Ekta.

Nature ; 532(7598): 181-2, 2016 Apr 14.

Article in English | MEDLINE | ID: mdl-27075092

14.

Mapping copy number variation by population-scale genome sequencing.

Mills, Ryan E; Walter, Klaudia; Stewart, Chip; Handsaker, Robert E; Chen, Ken; Alkan, Can; Abyzov, Alexej; Yoon, Seungtai Chris; Ye, Kai; Cheetham, R Keira; Chinwalla, Asif; Conrad, Donald F; Fu, Yutao; Grubert, Fabian; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Iakoucheva, Lilia M; Iqbal, Zamin; Kang, Shuli; Kidd, Jeffrey M; Konkel, Miriam K; Korn, Joshua; Khurana, Ekta; Kural, Deniz; Lam, Hugo Y K; Leng, Jing; Li, Ruiqiang; Li, Yingrui; Lin, Chang-Yun; Luo, Ruibang; Mu, Xinmeng Jasmine; Nemesh, James; Peckham, Heather E; Rausch, Tobias; Scally, Aylwyn; Shi, Xinghua; Stromberg, Michael P; Stütz, Adrian M; Urban, Alexander Eckehart; Walker, Jerilyn A; Wu, Jiantao; Zhang, Yujun; Zhang, Zhengdong D; Batzer, Mark A; Ding, Li; Marth, Gabor T; McVean, Gil; Sebat, Jonathan; Snyder, Michael; Wang, Jun.

Nature ; 470(7332): 59-65, 2011 Feb 03.

Article in English | MEDLINE | ID: mdl-21293372

15.

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

Lochovsky, Lucas; Zhang, Jing; Fu, Yao; Khurana, Ekta; Gerstein, Mark.

Nucleic Acids Res ; 43(17): 8123-34, 2015 Sep 30.

Article in English | MEDLINE | ID: mdl-26304545

16.

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

Lu, Zhi John; Yip, Kevin Y; Wang, Guilin; Shou, Chong; Hillier, Ladeana W; Khurana, Ekta; Agarwal, Ashish; Auerbach, Raymond; Rozowsky, Joel; Cheng, Chao; Kato, Masaomi; Miller, David M; Slack, Frank; Snyder, Michael; Waterston, Robert H; Reinke, Valerie; Gerstein, Mark B.

Genome Res ; 21(2): 276-85, 2011 Feb.

Article in English | MEDLINE | ID: mdl-21177971

17.

Interpretation of genomic variants using a unified biological network approach.

Khurana, Ekta; Fu, Yao; Chen, Jieming; Gerstein, Mark.

PLoS Comput Biol ; 9(3): e1002886, 2013.

Article in English | MEDLINE | ID: mdl-23505346

18.

TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer.

Wong, Elissa W P; Sahin, Merve; Yang, Rui; Lee, UkJin; Zhan, Yingqian A; Misra, Rohan; Tomas, Fanny; Alomran, Nawaf; Polyzos, Alexander; Lee, Cindy J; Trieu, Tuan; Fundichely, Alexander M; Wiesner, Thomas; Rosowicz, Andrew; Cheng, Shuyuan; Liu, Christina; Lallo, Morgan; Merghoub, Taha; Hamard, Pierre-Jacques; Koche, Richard; Khurana, Ekta; Apostolou, Effie; Zheng, Deyou; Chen, Yu; Leslie, Christina S; Chi, Ping.

bioRxiv ; 2024 Jun 03.

Article in English | MEDLINE | ID: mdl-38895201

19.

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

Habegger, Lukas; Balasubramanian, Suganthi; Chen, David Z; Khurana, Ekta; Sboner, Andrea; Harmanci, Arif; Rozowsky, Joel; Clarke, Declan; Snyder, Michael; Gerstein, Mark.

Bioinformatics ; 28(17): 2267-9, 2012 Sep 01.

Article in English | MEDLINE | ID: mdl-22743228

20.

Impulsivity and Risk-Taking Behavior in School-Going Adolescents.

Soni, Ujjwal; Sharma, Rahul; Sharma, Marisha; Khurana, Ekta; Chopra, Jayesh; Julka, Dhawani; Gaur, Nikhil.

Cureus ; 15(6): e40728, 2023 Jun.

Article in English | MEDLINE | ID: mdl-37485185

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Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Patterns of somatic structural variation in human cancer genomes.

Author Correction: Patterns of somatic structural variation in human cancer genomes.

Systems biology analysis of human genomes points to key pathways conferring spina bifida risk.

CNCDatabase: a database of non-coding cancer drivers.

Loss-of-function tolerance of enhancers in the human genome.

Role of non-coding sequence variants in cancer.

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

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

Architecture of the human regulatory network derived from ENCODE data.

Cancer genomics: Hard-to-reach repairs.

Mapping copy number variation by population-scale genome sequencing.

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

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

Interpretation of genomic variants using a unified biological network approach.

TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer.

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

Impulsivity and Risk-Taking Behavior in School-Going Adolescents.