Predicting A/B compartments from histone modifications using deep learning

Autor: Zheng, Suchen, Thakkar, Nitya, Harris, Hannah L., Liu, Susanna, Zhang, Megan, Gerstein, Mark, Aiden, Erez Lieberman, Rowley, M. Jordan, Noble, William Stafford, Gürsoy, Gamze, Singh, Ritambhara

Publikováno v: In iScience 17 May 2024 27(5)

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Single-cell genomics and regulatory networks for 388 human brains.

Autor: Emani PS; 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., Liu JJ; 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., Clarke D; 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., Jensen M; 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., Warrell J; 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., Gupta C; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA.; Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA., Meng R; 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., Lee CY; Department of Computer Science, University of California, Irvine, CA, 92697, USA., Xu S; Department of Computer Science, University of California, Irvine, CA, 92697, USA., Dursun C; 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., Lou S; 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., Chen Y; 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., Chu Z; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA., Galeev T; 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., Hwang A; Department of Computer Science, University of California, Irvine, CA, 92697, USA.; Mathematical, Computational and Systems Biology, University of California, Irvine, CA, 92697, USA., Li Y; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.; Department of Computer Science, Yale University, New Haven, CT, 06520, USA., Ni P; 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., Zhou X; 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., Bakken TE; Allen Institute for Brain Science, Seattle, WA, 98109, USA., Bendl J; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA., Bicks L; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Chatterjee T; 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., Cheng L; Tempus Labs, Inc., Chicago, IL, 60654, USA., Cheng Y; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.; Department of Opthalmology, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA., Dai Y; Department of Computer Science, University of California, Irvine, CA, 92697, USA., Duan Z; Department of Computer Science, University of California, Irvine, CA, 92697, USA., Flaherty M; Tempus Labs, Inc., Chicago, IL, 60654, USA., Fullard JF; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA., Gancz M; 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., Garrido-Martín D; Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, 08028, Spain., Gaynor-Gillett S; Tempus Labs, Inc., Chicago, IL, 60654, USA.; Department of Biology, Cornell College, Mount Vernon, IA, 52314, USA., Grundman J; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Hawken N; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Henry E; 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., Hoffman GE; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA.; Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA., Huang A; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA., Jiang Y; 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., Jin T; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA.; Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA., Jorstad NL; Allen Institute for Brain Science, Seattle, WA, 98109, USA., Kawaguchi R; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.; Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA., Khullar S; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA.; Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA., Liu J; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Liu J; Department of Computer Science, University of California, Irvine, CA, 92697, USA., Liu S; Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA., Ma S; Department of Neuroscience, Yale University, New Haven, CT, 06510, USA.; Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China., Margolis M; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Mazariegos S; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Moore J; Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA., Moran JR; Tempus Labs, Inc., Chicago, IL, 60654, USA., Nguyen E; 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., Phalke N; Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA., Pjanic M; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA., Pratt H; Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA., Quintero D; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Rajagopalan AS; Department of Computer Science, Yale University, New Haven, CT, 06520, USA., Riesenmy TR; Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA., Shedd N; Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA., Shi M; Tempus Labs, Inc., Chicago, IL, 60654, USA., Spector M; Tempus Labs, Inc., Chicago, IL, 60654, USA., Terwilliger R; Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA., Travaglini KJ; Allen Institute for Brain Science, Seattle, WA, 98109, USA., Wamsley B; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Wang G; 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., Xia Y; 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., Xiao S; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Yang AC; 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., Zheng S; 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., Gandal MJ; Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.; Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.; Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA., Lee D; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA., Lein ES; Allen Institute for Brain Science, Seattle, WA, 98109, USA.; Department of Neurological Surgery, University of Washington, Seattle, WA, 98195, USA.; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA., Roussos P; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.; Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA.; Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA., Sestan N; Department of Neuroscience, Yale University, New Haven, CT, 06510, USA., Weng Z; Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA., White KP; Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore., Won H; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA., Girgenti MJ; Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA.; Wu Tsai Institute, Yale University, New Haven, CT, 06520, USA.; Clinical Neuroscience Division, National Center for Posttraumatic Stress Disorder, Veterans Affairs Connecticut Healthcare System, West Haven, CT, 06516, USA., Zhang J; Department of Computer Science, University of California, Irvine, CA, 92697, USA., Wang D; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA.; Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.; Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA., Geschwind D; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.; Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA.; Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Gerstein M; 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.; Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA.; Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT, 06520, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Mar 30. Date of Electronic Publication: 2024 Mar 30.