Nature Communications (Jul 2020)
An integrative ENCODE resource for cancer genomics
- Jing Zhang,
- Donghoon Lee,
- Vineet Dhiman,
- Peng Jiang,
- Jie Xu,
- Patrick McGillivray,
- Hongbo Yang,
- Jason Liu,
- William Meyerson,
- Declan Clarke,
- Mengting Gu,
- Shantao Li,
- Shaoke Lou,
- Jinrui Xu,
- Lucas Lochovsky,
- Matthew Ung,
- Lijia Ma,
- Shan Yu,
- Qin Cao,
- Arif Harmanci,
- Koon-Kiu Yan,
- Anurag Sethi,
- Gamze Gürsoy,
- Michael Rutenberg Schoenberg,
- Joel Rozowsky,
- Jonathan Warrell,
- Prashant Emani,
- Yucheng T. Yang,
- Timur Galeev,
- Xiangmeng Kong,
- Shuang Liu,
- Xiaotong Li,
- Jayanth Krishnan,
- Yanlin Feng,
- Juan Carlos Rivera-Mulia,
- Jessica Adrian,
- James R Broach,
- Michael Bolt,
- Jennifer Moran,
- Dominic Fitzgerald,
- Vishnu Dileep,
- Tingting Liu,
- Shenglin Mei,
- Takayo Sasaki,
- Claudia Trevilla-Garcia,
- Su Wang,
- Yanli Wang,
- Chongzhi Zang,
- Daifeng Wang,
- Robert J. Klein,
- Michael Snyder,
- David M. Gilbert,
- Kevin Yip,
- Chao Cheng,
- Feng Yue,
- X. Shirley Liu,
- Kevin P. White,
- Mark Gerstein
Affiliations
- Jing Zhang
- Program in Computational Biology & Bioinformatics, Yale University
- Donghoon Lee
- Program in Computational Biology & Bioinformatics, Yale University
- Vineet Dhiman
- Department of Human Genetics, University of Chicago
- Peng Jiang
- Department of Data Science, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health
- Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University
- Patrick McGillivray
- Program in Computational Biology & Bioinformatics, Yale University
- Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University
- Jason Liu
- Program in Computational Biology & Bioinformatics, Yale University
- William Meyerson
- Program in Computational Biology & Bioinformatics, Yale University
- Declan Clarke
- Program in Computational Biology & Bioinformatics, Yale University
- Mengting Gu
- Program in Computational Biology & Bioinformatics, Yale University
- Shantao Li
- Program in Computational Biology & Bioinformatics, Yale University
- Shaoke Lou
- Program in Computational Biology & Bioinformatics, Yale University
- Jinrui Xu
- Program in Computational Biology & Bioinformatics, Yale University
- Lucas Lochovsky
- Program in Computational Biology & Bioinformatics, Yale University
- Matthew Ung
- Department of Biomedical Data Science, Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth
- Lijia Ma
- Department of Human Genetics, University of Chicago
- Shan Yu
- Department of Human Genetics, University of Chicago
- Qin Cao
- Department of Computer Science and Engineering, The Chinese University of Hong Kong
- Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston
- Koon-Kiu Yan
- Program in Computational Biology & Bioinformatics, Yale University
- Anurag Sethi
- Program in Computational Biology & Bioinformatics, Yale University
- Gamze Gürsoy
- Program in Computational Biology & Bioinformatics, Yale University
- Michael Rutenberg Schoenberg
- Program in Computational Biology & Bioinformatics, Yale University
- Joel Rozowsky
- Program in Computational Biology & Bioinformatics, Yale University
- Jonathan Warrell
- Program in Computational Biology & Bioinformatics, Yale University
- Prashant Emani
- Program in Computational Biology & Bioinformatics, Yale University
- Yucheng T. Yang
- Program in Computational Biology & Bioinformatics, Yale University
- Timur Galeev
- Program in Computational Biology & Bioinformatics, Yale University
- Xiangmeng Kong
- Program in Computational Biology & Bioinformatics, Yale University
- Shuang Liu
- Program in Computational Biology & Bioinformatics, Yale University
- Xiaotong Li
- Program in Computational Biology & Bioinformatics, Yale University
- Jayanth Krishnan
- Program in Computational Biology & Bioinformatics, Yale University
- Yanlin Feng
- Program in Computational Biology & Bioinformatics, Yale University
- Juan Carlos Rivera-Mulia
- Department of Biological Science, Florida State University
- Jessica Adrian
- Department of Genetics, School of Medicine, Stanford University
- James R Broach
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University
- Michael Bolt
- Department of Human Genetics, University of Chicago
- Jennifer Moran
- Department of Human Genetics, University of Chicago
- Dominic Fitzgerald
- Department of Human Genetics, University of Chicago
- Vishnu Dileep
- Department of Biological Science, Florida State University
- Tingting Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University
- Shenglin Mei
- Department of Biomedical Informatics, Harvard Medical School
- Takayo Sasaki
- Department of Biological Science, Florida State University
- Claudia Trevilla-Garcia
- Department of Biological Science, Florida State University
- Su Wang
- Department of Biomedical Informatics, Harvard Medical School
- Yanli Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University
- Chongzhi Zang
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia
- Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison
- Robert J. Klein
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai
- Michael Snyder
- Department of Genetics, School of Medicine, Stanford University
- David M. Gilbert
- Department of Biological Science, Florida State University
- Kevin Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong
- Chao Cheng
- Department of Biomedical Data Science, Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth
- Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University
- X. Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health
- Kevin P. White
- Department of Human Genetics, University of Chicago
- Mark Gerstein
- Program in Computational Biology & Bioinformatics, Yale University
- DOI
- https://doi.org/10.1038/s41467-020-14743-w
- Journal volume & issue
-
Vol. 11,
no. 1
pp. 1 – 11
Abstract
ENCODE is a resource comprising thousands of functional genomic datasets. Here, the authors present custom annotation within ENCODE for cancer, highlighting a workflow that can help prioritise key elements in oncogenesis.
