An integrated view of the structure and function of the human 4D nucleome
Year: 2025
Type: article
Language: en
Topic: Genomics and Chromatin Dynamics
Authors and affiliations:
raw_author_name: Job Dekker
raw_affiliation_strings: Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA. job.dekker@umassmed.edu
Howard Hughes Medical Institute, Chevy Chase, MD, USA. job.dekker@umassmed.edu
Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
raw_author_name: Betul Akgol Oksuz
raw_affiliation_strings: Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
raw_author_name: Yang Zhang
raw_affiliation_strings: Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
raw_author_name: Ye Wang
raw_affiliation_strings: Department of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
raw_author_name: Miriam K. Minsk
raw_affiliation_strings: Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
raw_author_name: Shuzhen Kuang
raw_affiliation_strings: Gladstone Institutes, San Francisco, CA, USA
raw_author_name: Liyan Yang
raw_affiliation_strings: Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
raw_author_name: Johan H. Gibcus
raw_affiliation_strings: Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
raw_author_name: Nils Krietenstein
raw_affiliation_strings: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
raw_author_name: Oliver J. Rando
raw_affiliation_strings: Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
raw_author_name: Jie Xu
raw_affiliation_strings: Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
raw_author_name: Derek H. Janssens
raw_affiliation_strings: Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
raw_author_name: Steven Henikoff
raw_affiliation_strings: Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
Howard Hughes Medical Institute, Chevy Chase, MD, USA
raw_author_name: Alexander Kukalev
raw_affiliation_strings: Epigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
raw_author_name: Willemin Andréa
raw_affiliation_strings: Epigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
raw_author_name: Warren Winick-Ng
raw_affiliation_strings: Epigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
raw_author_name: Rieke Kempfer
raw_affiliation_strings: Epigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
raw_author_name: Ana Pombo
raw_affiliation_strings: Epigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
raw_author_name: Miao Yu
raw_affiliation_strings: Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
State Key Laboratory of Genetics and Development of Complex Phenotypes, School of Life Sciences, Fudan University, Shanghai, China
raw_author_name: Pradeep Kumar
raw_affiliation_strings: Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
raw_author_name: Liguo Zhang
raw_affiliation_strings: Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
raw_author_name: Andrew S. Belmont
raw_affiliation_strings: Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
raw_author_name: Takayo Sasaki
raw_affiliation_strings: San Diego Biomedical Research Institute, San Diego, CA, USA
raw_author_name: Tom van Schaik
raw_affiliation_strings: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
Oncode Institute, Utrecht, The Netherlands
raw_author_name: Laura Brueckner
raw_affiliation_strings: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
raw_author_name: Daan Peric-Hupkes
raw_affiliation_strings: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
Oncode Institute, Utrecht, The Netherlands
raw_author_name: Bas van Steensel
raw_affiliation_strings: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
Oncode Institute, Utrecht, The Netherlands
raw_author_name: Ping Wang
raw_affiliation_strings: Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
raw_author_name: Haoxi Chai
raw_affiliation_strings: Life Sciences Institute, Zhejiang University, Hangzhou, P.R. China
raw_author_name: Minji Kim
raw_affiliation_strings: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
raw_author_name: Yijun Ruan
raw_affiliation_strings: Life Sciences Institute, Zhejiang University, Hangzhou, P.R. China
raw_author_name: Ran Zhang
raw_affiliation_strings: Department of Genome Sciences, University of Washington, Seattle, WA, USA
Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
raw_author_name: Sofia A. Quinodoz
raw_affiliation_strings: Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
raw_author_name: Prashant Bhat
raw_affiliation_strings: David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
raw_author_name: Mitchell Guttman
raw_affiliation_strings: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
raw_author_name: Wenxin Zhao
raw_affiliation_strings: Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
raw_author_name: Shu Chien
raw_affiliation_strings: Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
raw_author_name: Yuan Liu
raw_affiliation_strings: Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
raw_author_name: Sergey V. Venev
raw_affiliation_strings: Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
raw_author_name: Dariusz Plewczynski
raw_affiliation_strings: Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
raw_author_name: Ibai Irastorza Azcarate
raw_affiliation_strings: Epigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
raw_author_name: Dominik Szabó
raw_affiliation_strings: Epigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
raw_author_name: Christoph J. Thieme
raw_affiliation_strings: Epigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
raw_author_name: Teresa Szczepińska
raw_affiliation_strings: Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Warsaw, Poland
Epigenetic Regulation and Chromatin Architecture Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
raw_author_name: Mateusz Chiliński
raw_affiliation_strings: Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
raw_author_name: Kaustav Sengupta
raw_affiliation_strings: Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
raw_author_name: Mattia Conte
raw_affiliation_strings: Department of Physics, University of Naples "Federico II", and INFN, Naples, Italy
raw_author_name: Andrea Esposito
raw_affiliation_strings: Department of Physics, University of Naples "Federico II", and INFN, Naples, Italy
raw_author_name: Alex Abraham
raw_affiliation_strings: Department of Physics, University of Naples "Federico II", and INFN, Naples, Italy
raw_author_name: Ruochi Zhang
raw_affiliation_strings: Department of Genome Sciences, University of Washington, Seattle, WA, USA
Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
raw_author_name: Yuchuan Wang
raw_affiliation_strings: Department of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
raw_author_name: Xingzhao Wen
raw_affiliation_strings: Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
raw_author_name: Qiuyang Wu
raw_affiliation_strings: Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
raw_author_name: Yang Yang
raw_affiliation_strings: Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
raw_author_name: Jie Liu
raw_affiliation_strings: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
raw_author_name: Lorenzo Boninsegna
raw_affiliation_strings: Department of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
raw_author_name: Asli Yildirim
raw_affiliation_strings: Department of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
raw_author_name: Yuxiang Zhan
raw_affiliation_strings: Department of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
raw_author_name: Andrea Maria Chiariello
raw_affiliation_strings: Department of Physics, University of Naples "Federico II", and INFN, Naples, Italy
raw_author_name: Simona Bianco
raw_affiliation_strings: Department of Physics, University of Naples "Federico II", and INFN, Naples, Italy
raw_author_name: Lindsay Lee
raw_affiliation_strings: Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
raw_author_name: Ming Hu
raw_affiliation_strings: Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
raw_author_name: Yun Li
raw_affiliation_strings: Department of Biostatistics, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
raw_author_name: R. Jordan Barnett
raw_affiliation_strings: Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
raw_author_name: Ashley L. Cook
raw_affiliation_strings: Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
raw_author_name: Daniel J. Emerson
raw_affiliation_strings: Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
raw_author_name: Claire Marchal
raw_affiliation_strings: In silichrom Ltd, Newbury, UK
raw_author_name: Peiyao Zhao
raw_affiliation_strings: San Diego Biomedical Research Institute, San Diego, CA, USA
raw_author_name: Peter J. Park
raw_affiliation_strings: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
raw_author_name: Burak H. Alver
raw_affiliation_strings: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
raw_author_name: Andrew J. Schroeder
raw_affiliation_strings: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
raw_author_name: Rahi Navelkar
raw_affiliation_strings: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
raw_author_name: Clara Bakker
raw_affiliation_strings: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
raw_author_name: William Ronchetti
raw_affiliation_strings: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
raw_author_name: Shannon Ehmsen
raw_affiliation_strings: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
raw_author_name: Alexander D. Veit
raw_affiliation_strings: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
raw_author_name: Nils Gehlenborg
raw_affiliation_strings: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
raw_author_name: Ting Wang
raw_affiliation_strings: Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
raw_author_name: Daofeng Li
raw_affiliation_strings: Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
raw_author_name: Xiaotao Wang
raw_affiliation_strings: Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA. wangxiaotao@fudan.edu.cn
Institute of Reproduction and Development, Shanghai Key Laboratory of Reproduction and Development, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China. wangxiaotao@fudan.edu.cn
Institute of Reproduction and Development, Shanghai Key Laboratory of Reproduction and Development, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
raw_author_name: Mario Nicodemi
raw_affiliation_strings: Department of Physics, University of Naples "Federico II", and INFN, Naples, Italy. mario.nicodemi@na.infn.it
Department of Physics, University of Naples "Federico II", and INFN, Naples, Italy
raw_author_name: Bing Ren
raw_affiliation_strings: Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA. bren@nygenome.org
Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
raw_author_name: Sheng Zhong
raw_affiliation_strings: Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. szhong@ucsd.edu
Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
raw_author_name: Jennifer E. Phillips-Cremins
raw_affiliation_strings: Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA. jennifer.cremins@wustl.edu
Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
raw_author_name: David M. Gilbert
raw_affiliation_strings: San Diego Biomedical Research Institute, San Diego, CA, USA. gilbert@sdbri.org
San Diego Biomedical Research Institute, San Diego, CA, USA
raw_author_name: Katherine S. Pollard
raw_affiliation_strings: Gladstone Institutes, San Francisco, CA, USA. katherine.pollard@gladstone.ucsf.edu
Gladstone Institutes, San Francisco, CA, USA
raw_author_name: Frank Alber
raw_affiliation_strings: Department of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA. falber@g.ucla.edu
Department of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
raw_author_name: Jian Ma
raw_affiliation_strings: Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA. jianma@cs.cmu.edu
Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
raw_author_name: William S. Noble
raw_affiliation_strings: Department of Genome Sciences, University of Washington, Seattle, WA, USA. william-noble@uw.edu
Department of Genome Sciences, University of Washington, Seattle, WA, USA
raw_author_name: Feng Yue
raw_affiliation_strings: Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA. Yue@northwestern.edu
Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA. Yue@northwestern.edu
Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA