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Multi-tissue integrative analysis of personal epigenomes

Joel Rozowsky, Jorg Drenkow, Yucheng T Yang, Gamze Gursoy, Timur Galeev, Beatrice Borsari, Charles B Epstein, Kun Xiong, Jinrui Xu, Jiahao Gao, Keyang Yu, Ana Berthel, Zhanlin Chen, Fabio Navarro, Jason Liu, Maxwell S Sun, James Wright, Justin Chang, Christopher JF Cameron, Noam Shoresh, Elizabeth Gaskell, Jessika Adrian, Sergey Aganezov, Gabriela Balderrama-Gutierrez, Samridhi Banskota, Guillermo Barreto Corona, Sora Chee, Surya B Chhetri, Gabriel Conte Cortez Martins, Cassidy Danyko, Carrie A Davis, Daniel Farid, Nina P Farrell, Idan Gabdank, Yoel Gofin, David U Gorkin, Mengting Gu, Vivian Hecht, Benjamin C Hitz, Robbyn Issner, Melanie Kirsche, Xiangmeng Kong, Bonita R Lam, Shantao Li, Bian Li, Tianxiao Li, Xiqi Li, Khine Zin Lin, Ruibang Luo, Mark Mackiewicz, Jill E Moore, Jonathan Mudge, Nicholas Nelson, Chad Nusbaum, Ioann Popov, Henry E Pratt, Yunjiang Qiu, Srividya Ramakrishnan, Joe Raymond, Leonidas Salichos, Alexandra Scavelli, Jacob M Schreiber, Fritz J Sedlazeck, Lei Hoon See, Rachel M Sherman, Xu Shi, Minyi Shi, Cricket Alicia Sloan, J Seth Strattan, Zhen Tan, Forrest Y Tanaka, Anna Vlasova, Jun Wang, Jonathan Werner, Brian Williams, Min Xu, Chengfei Yan, Lu Yu, Christopher Zaleski, Jing Zhang, J Michael Cherry, Eric M Mendenhall, William S Noble, Zhiping Weng, Morgan E Levine, Alexander Dobin, Barbara Wold, Ali Mortazavi, Bing Ren, Jesse Gillis, Richard M Myers, Michael P Snyder, Jyoti Choudhary, Aleksandar Milosavljevic, Michael C Schatz, Roderic Guigó, Bradley E Bernstein, Thomas R Gingeras, Mark Gerstein
doi: https://doi.org/10.1101/2021.04.26.441442
Joel Rozowsky
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Jorg Drenkow
3Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Yucheng T Yang
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Gamze Gursoy
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Timur Galeev
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Beatrice Borsari
4Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
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Charles B Epstein
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Kun Xiong
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Jinrui Xu
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Jiahao Gao
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Keyang Yu
6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Ana Berthel
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Zhanlin Chen
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Fabio Navarro
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Jason Liu
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Maxwell S Sun
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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James Wright
7Institute of Cancer Research, London, UK
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Justin Chang
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Christopher JF Cameron
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Noam Shoresh
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Elizabeth Gaskell
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Jessika Adrian
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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Sergey Aganezov
9Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
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Gabriela Balderrama-Gutierrez
10Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
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Samridhi Banskota
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Guillermo Barreto Corona
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Sora Chee
11Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
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Surya B Chhetri
12Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
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Gabriel Conte Cortez Martins
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Cassidy Danyko
3Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Carrie A Davis
3Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Daniel Farid
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Nina P Farrell
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Idan Gabdank
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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Yoel Gofin
6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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David U Gorkin
11Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
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Mengting Gu
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Vivian Hecht
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Benjamin C Hitz
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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Robbyn Issner
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Melanie Kirsche
9Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
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Xiangmeng Kong
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Bonita R Lam
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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Shantao Li
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
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Bian Li
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Tianxiao Li
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Xiqi Li
6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Khine Zin Lin
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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Ruibang Luo
13Department of Computer Science, The University of Hong Kong, Hong Kong, CHN
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Mark Mackiewicz
14HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
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Jill E Moore
15Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
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Jonathan Mudge
16European Bioinformatics Institute, Cambridge, Cambridgeshire, GB
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Nicholas Nelson
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Chad Nusbaum
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Ioann Popov
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Henry E Pratt
15Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
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Yunjiang Qiu
11Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
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Srividya Ramakrishnan
9Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
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Joe Raymond
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Leonidas Salichos
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
17Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, NY, USA
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Alexandra Scavelli
3Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Jacob M Schreiber
18Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Fritz J Sedlazeck
9Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
19Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
20Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
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Lei Hoon See
3Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Rachel M Sherman
9Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
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Xu Shi
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Minyi Shi
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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Cricket Alicia Sloan
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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J Seth Strattan
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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Zhen Tan
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Forrest Y Tanaka
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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Anna Vlasova
4Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
21Comparative Genomics Group, Life Science Programme, Barcelona Supercomputing Centre, Barcelona, Spain
22Institute of Research in Biomedicine, Barcelona, Spain
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Jun Wang
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Jonathan Werner
3Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Brian Williams
23Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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Min Xu
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Chengfei Yan
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Lu Yu
7Institute of Cancer Research, London, UK
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Christopher Zaleski
3Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Jing Zhang
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
24Department of Computer Science, University of California, Irvine, CA, USA
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J Michael Cherry
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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Eric M Mendenhall
12Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
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William S Noble
18Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Zhiping Weng
15Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
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Morgan E Levine
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
25Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
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Alexander Dobin
3Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Barbara Wold
23Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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Ali Mortazavi
10Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
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Bing Ren
11Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
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Jesse Gillis
3Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Richard M Myers
14HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
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Michael P Snyder
8Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
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Jyoti Choudhary
7Institute of Cancer Research, London, UK
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Aleksandar Milosavljevic
6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Michael C Schatz
9Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
19Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Roderic Guigó
4Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
26Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
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Bradley E Bernstein
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
27Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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Thomas R Gingeras
3Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Mark Gerstein
1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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  • For correspondence: pi@gersteinlab.org
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Abstract

Evaluating the impact of genetic variants on transcriptional regulation is a central goal in biological science that has been constrained by reliance on a single reference genome. To address this, we constructed phased, diploid genomes for four cadaveric donors (using long-read sequencing) and systematically charted noncoding regulatory elements and transcriptional activity across more than 25 tissues from these donors. Integrative analysis revealed over a million variants with allele-specific activity, coordinated, locus-scale allelic imbalances, and structural variants impacting proximal chromatin structure. We relate the personal genome analysis to the ENCODE encyclopedia, annotating allele- and tissue-specific elements that are strongly enriched for variants impacting expression and disease phenotypes. These experimental and statistical approaches, and the corresponding EN-TEx resource, provide a framework for personalized functional genomics.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Multi-tissue integrative analysis of personal epigenomes
Joel Rozowsky, Jorg Drenkow, Yucheng T Yang, Gamze Gursoy, Timur Galeev, Beatrice Borsari, Charles B Epstein, Kun Xiong, Jinrui Xu, Jiahao Gao, Keyang Yu, Ana Berthel, Zhanlin Chen, Fabio Navarro, Jason Liu, Maxwell S Sun, James Wright, Justin Chang, Christopher JF Cameron, Noam Shoresh, Elizabeth Gaskell, Jessika Adrian, Sergey Aganezov, Gabriela Balderrama-Gutierrez, Samridhi Banskota, Guillermo Barreto Corona, Sora Chee, Surya B Chhetri, Gabriel Conte Cortez Martins, Cassidy Danyko, Carrie A Davis, Daniel Farid, Nina P Farrell, Idan Gabdank, Yoel Gofin, David U Gorkin, Mengting Gu, Vivian Hecht, Benjamin C Hitz, Robbyn Issner, Melanie Kirsche, Xiangmeng Kong, Bonita R Lam, Shantao Li, Bian Li, Tianxiao Li, Xiqi Li, Khine Zin Lin, Ruibang Luo, Mark Mackiewicz, Jill E Moore, Jonathan Mudge, Nicholas Nelson, Chad Nusbaum, Ioann Popov, Henry E Pratt, Yunjiang Qiu, Srividya Ramakrishnan, Joe Raymond, Leonidas Salichos, Alexandra Scavelli, Jacob M Schreiber, Fritz J Sedlazeck, Lei Hoon See, Rachel M Sherman, Xu Shi, Minyi Shi, Cricket Alicia Sloan, J Seth Strattan, Zhen Tan, Forrest Y Tanaka, Anna Vlasova, Jun Wang, Jonathan Werner, Brian Williams, Min Xu, Chengfei Yan, Lu Yu, Christopher Zaleski, Jing Zhang, J Michael Cherry, Eric M Mendenhall, William S Noble, Zhiping Weng, Morgan E Levine, Alexander Dobin, Barbara Wold, Ali Mortazavi, Bing Ren, Jesse Gillis, Richard M Myers, Michael P Snyder, Jyoti Choudhary, Aleksandar Milosavljevic, Michael C Schatz, Roderic Guigó, Bradley E Bernstein, Thomas R Gingeras, Mark Gerstein
bioRxiv 2021.04.26.441442; doi: https://doi.org/10.1101/2021.04.26.441442
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Multi-tissue integrative analysis of personal epigenomes
Joel Rozowsky, Jorg Drenkow, Yucheng T Yang, Gamze Gursoy, Timur Galeev, Beatrice Borsari, Charles B Epstein, Kun Xiong, Jinrui Xu, Jiahao Gao, Keyang Yu, Ana Berthel, Zhanlin Chen, Fabio Navarro, Jason Liu, Maxwell S Sun, James Wright, Justin Chang, Christopher JF Cameron, Noam Shoresh, Elizabeth Gaskell, Jessika Adrian, Sergey Aganezov, Gabriela Balderrama-Gutierrez, Samridhi Banskota, Guillermo Barreto Corona, Sora Chee, Surya B Chhetri, Gabriel Conte Cortez Martins, Cassidy Danyko, Carrie A Davis, Daniel Farid, Nina P Farrell, Idan Gabdank, Yoel Gofin, David U Gorkin, Mengting Gu, Vivian Hecht, Benjamin C Hitz, Robbyn Issner, Melanie Kirsche, Xiangmeng Kong, Bonita R Lam, Shantao Li, Bian Li, Tianxiao Li, Xiqi Li, Khine Zin Lin, Ruibang Luo, Mark Mackiewicz, Jill E Moore, Jonathan Mudge, Nicholas Nelson, Chad Nusbaum, Ioann Popov, Henry E Pratt, Yunjiang Qiu, Srividya Ramakrishnan, Joe Raymond, Leonidas Salichos, Alexandra Scavelli, Jacob M Schreiber, Fritz J Sedlazeck, Lei Hoon See, Rachel M Sherman, Xu Shi, Minyi Shi, Cricket Alicia Sloan, J Seth Strattan, Zhen Tan, Forrest Y Tanaka, Anna Vlasova, Jun Wang, Jonathan Werner, Brian Williams, Min Xu, Chengfei Yan, Lu Yu, Christopher Zaleski, Jing Zhang, J Michael Cherry, Eric M Mendenhall, William S Noble, Zhiping Weng, Morgan E Levine, Alexander Dobin, Barbara Wold, Ali Mortazavi, Bing Ren, Jesse Gillis, Richard M Myers, Michael P Snyder, Jyoti Choudhary, Aleksandar Milosavljevic, Michael C Schatz, Roderic Guigó, Bradley E Bernstein, Thomas R Gingeras, Mark Gerstein
bioRxiv 2021.04.26.441442; doi: https://doi.org/10.1101/2021.04.26.441442

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