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Role of non-coding sequence variants in cancer
Role of non-coding sequence variants in cancer
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Role of non-coding sequence variants in cancer

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

Nature reviews. Genetics, 2016-02, Vol.17 (2), p.93-108 [Periódico revisado por pares]

England: Nature Publishing Group

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DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure
DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure
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DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure

Trieu, Tuan ; Martinez-Fundichely, Alexander ; Khurana, Ekta

Genome Biology, 2020-03, Vol.21 (1), p.79-79, Article 79 [Periódico revisado por pares]

England: BioMed Central Ltd

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Interpretation of genomic variants using a unified biological network approach
Interpretation of genomic variants using a unified biological network approach
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Interpretation of genomic variants using a unified biological network approach

Khurana, Ekta ; Fu, Yao ; Chen, Jieming ; Gerstein, Mark Rzhetsky, Andrey

PLoS computational biology, 2013-03, Vol.9 (3), p.e1002886-e1002886 [Periódico revisado por pares]

United States: Public Library of Science

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4
Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers
Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers
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Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers

Martinez-Fundichely, Alexander ; Dixon, Austin ; Khurana, Ekta

Nature communications, 2022-09, Vol.13 (1), p.5640-5640, Article 5640 [Periódico revisado por pares]

London: Nature Publishing Group

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5
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations
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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 research, 2015-09, Vol.43 (17), p.8123-8134 [Periódico revisado por pares]

England: Oxford University Press

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6
Loss-of-function tolerance of enhancers in the human genome
Loss-of-function tolerance of enhancers in the human genome
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Loss-of-function tolerance of enhancers in the human genome

Xu, Duo ; Gokcumen, Omer ; Khurana, Ekta Ahituv, Nadav

PLoS genetics, 2020-04, Vol.16 (4), p.e1008663-e1008663 [Periódico revisado por pares]

United States: Public Library of Science

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7
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer
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FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer

Fu, Yao ; Liu, Zhu ; Lou, Shaoke ; Bedford, Jason ; Mu, Xinmeng Jasmine ; Yip, Kevin Y ; Khurana, Ekta ; Gerstein, Mark

Genome Biology (Online Edition), 2014-01, Vol.15 (10), p.480-480, Article 480 [Periódico revisado por pares]

England: BioMed Central Ltd

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8
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences
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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, 2020-03, Vol.180 (5), p.915-927.e16 [Periódico revisado por pares]

United States: Elsevier Inc

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9
FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications
FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications
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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 ; Petukhova, Lynn ; Khurana, Ekta ; Christiano, Angela ; Buxbaum, Joseph D. ; Ionita-Laza, Iuliana

American journal of human genetics, 2018-05, Vol.102 (5), p.920-942 [Periódico revisado por pares]

United States: Elsevier Inc

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10
Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets
Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets
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Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets

Tang, Fanying ; Xu, Duo ; Wang, Shangqian ; Wong, Chen Khuan ; Martinez-Fundichely, Alexander ; Lee, Cindy J ; Cohen, Sandra ; Park, Jane ; Hill, Corinne E ; Eng, Kenneth ; Bareja, Rohan ; Han, Teng ; Liu, Eric Minwei ; Palladino, Ann ; Di, Wei ; Gao, Dong ; Abida, Wassim ; Beg, Shaham ; Puca, Loredana ; Meneses, Maximiliano ; de Stanchina, Elisa ; Berger, Michael F ; Gopalan, Anuradha ; Dow, Lukas E ; Mosquera, Juan Miguel ; Beltran, Himisha ; Sternberg, Cora N ; Chi, Ping ; Scher, Howard I ; Sboner, Andrea ; Chen, Yu ; Khurana, Ekta

Science (American Association for the Advancement of Science), 2022-05, Vol.376 (6596), p.eabe1505-eabe1505 [Periódico revisado por pares]

United States: The American Association for the Advancement of Science

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