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A comparative encyclopedia of DNA elements in the mouse genome

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Listed:
  • Feng Yue

    (Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
    College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA.
    Present addresses: Department of Biochemistry and Molecular Biology, School of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA (F.Y.); BRCF Bioinformatics Core, University of Michigan, Ann Arbor, Michigan 48105, USA (W.W.); Division of Natural Sciences, New College of Florida, Sarasota, Florida 34243, USA (T.R.); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA (A.P.B.); Washington University in St Louis, St Louis, Missouri 63108, USA (R.L.); University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina 27599, USA (L.B.A.))

  • Yong Cheng

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Alessandra Breschi

    (Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.)

  • Jeff Vierstra

    (University of Washington)

  • Weisheng Wu

    (Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park
    Present addresses: Department of Biochemistry and Molecular Biology, School of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA (F.Y.); BRCF Bioinformatics Core, University of Michigan, Ann Arbor, Michigan 48105, USA (W.W.); Division of Natural Sciences, New College of Florida, Sarasota, Florida 34243, USA (T.R.); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA (A.P.B.); Washington University in St Louis, St Louis, Missouri 63108, USA (R.L.); University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina 27599, USA (L.B.A.))

  • Tyrone Ryba

    (319 Stadium Drive, Florida State University
    Present addresses: Department of Biochemistry and Molecular Biology, School of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA (F.Y.); BRCF Bioinformatics Core, University of Michigan, Ann Arbor, Michigan 48105, USA (W.W.); Division of Natural Sciences, New College of Florida, Sarasota, Florida 34243, USA (T.R.); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA (A.P.B.); Washington University in St Louis, St Louis, Missouri 63108, USA (R.L.); University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina 27599, USA (L.B.A.))

  • Richard Sandstrom

    (University of Washington)

  • Zhihai Ma

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Carrie Davis

    (Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.)

  • Benjamin D. Pope

    (319 Stadium Drive, Florida State University)

  • Yin Shen

    (Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.)

  • Dmitri D. Pervouchine

    (Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.)

  • Sarah Djebali

    (Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.)

  • Robert E. Thurman

    (University of Washington)

  • Rajinder Kaul

    (University of Washington)

  • Eric Rynes

    (University of Washington)

  • Anthony Kirilusha

    (California Institute of Technology)

  • Georgi K. Marinov

    (California Institute of Technology)

  • Brian A. Williams

    (California Institute of Technology)

  • Diane Trout

    (California Institute of Technology)

  • Henry Amrhein

    (California Institute of Technology)

  • Katherine Fisher-Aylor

    (California Institute of Technology)

  • Igor Antoshechkin

    (California Institute of Technology)

  • Gilberto DeSalvo

    (California Institute of Technology)

  • Lei-Hoon See

    (Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.)

  • Meagan Fastuca

    (Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.)

  • Jorg Drenkow

    (Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.)

  • Chris Zaleski

    (Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.)

  • Alex Dobin

    (Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.)

  • Pablo Prieto

    (Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.)

  • Julien Lagarde

    (Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.)

  • Giovanni Bussotti

    (Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.)

  • Andrea Tanzer

    (Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
    Faculty of Chemistry, University of Vienna, Waehringerstrasse 17/3/303, A-1090 Vienna, Austria.)

  • Olgert Denas

    (Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.)

  • Kanwei Li

    (Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.)

  • M. A. Bender

    (University of Washington
    Fred Hutchinson Cancer Research Center)

  • Miaohua Zhang

    (Fred Hutchinson Cancer Research Center)

  • Rachel Byron

    (Fred Hutchinson Cancer Research Center)

  • Mark T. Groudine

    (Fred Hutchinson Cancer Research Center
    University of Washington)

  • David McCleary

    (Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.)

  • Long Pham

    (Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.)

  • Zhen Ye

    (Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.)

  • Samantha Kuan

    (Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.)

  • Lee Edsall

    (Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.)

  • Yi-Chieh Wu

    (Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT))

  • Matthew D. Rasmussen

    (Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT))

  • Mukul S. Bansal

    (Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT))

  • Manolis Kellis

    (Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT)
    Broad Institute of MIT and Harvard)

  • Cheryl A. Keller

    (Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • Christapher S. Morrissey

    (Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • Tejaswini Mishra

    (Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • Deepti Jain

    (Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • Nergiz Dogan

    (Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • Robert S. Harris

    (Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • Philip Cayting

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Trupti Kawli

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Alan P. Boyle

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    Present addresses: Department of Biochemistry and Molecular Biology, School of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA (F.Y.); BRCF Bioinformatics Core, University of Michigan, Ann Arbor, Michigan 48105, USA (W.W.); Division of Natural Sciences, New College of Florida, Sarasota, Florida 34243, USA (T.R.); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA (A.P.B.); Washington University in St Louis, St Louis, Missouri 63108, USA (R.L.); University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina 27599, USA (L.B.A.))

  • Ghia Euskirchen

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Anshul Kundaje

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Shin Lin

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Yiing Lin

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Camden Jansen

    (University of California, Irvine, Irvine, California 92697, USA.)

  • Venkat S. Malladi

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Melissa S. Cline

    (Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC))

  • Drew T. Erickson

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Vanessa M. Kirkup

    (Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC))

  • Katrina Learned

    (Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC))

  • Cricket A. Sloan

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Kate R. Rosenbloom

    (Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC))

  • Beatriz Lacerda de Sousa

    (and Center for Reproductive Sciences, University of California San Francisco)

  • Kathryn Beal

    (European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.)

  • Miguel Pignatelli

    (European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.)

  • Paul Flicek

    (European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.)

  • Jin Lian

    (Yale University, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA.)

  • Tamer Kahveci

    (Computer & Information Sciences & Engineering, University of Florida)

  • Dongwon Lee

    (Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA.)

  • W. James Kent

    (Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC))

  • Miguel Ramalho Santos

    (and Center for Reproductive Sciences, University of California San Francisco)

  • Javier Herrero

    (European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
    Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK.)

  • Cedric Notredame

    (Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.)

  • Audra Johnson

    (University of Washington)

  • Shinny Vong

    (University of Washington)

  • Kristen Lee

    (University of Washington)

  • Daniel Bates

    (University of Washington)

  • Fidencio Neri

    (University of Washington)

  • Morgan Diegel

    (University of Washington)

  • Theresa Canfield

    (University of Washington)

  • Peter J. Sabo

    (University of Washington)

  • Matthew S. Wilken

    (University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA.)

  • Thomas A. Reh

    (University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA.)

  • Erika Giste

    (University of Washington)

  • Anthony Shafer

    (University of Washington)

  • Tanya Kutyavin

    (University of Washington)

  • Eric Haugen

    (University of Washington)

  • Douglas Dunn

    (University of Washington)

  • Alex P. Reynolds

    (University of Washington)

  • Shane Neph

    (University of Washington)

  • Richard Humbert

    (University of Washington)

  • R. Scott Hansen

    (University of Washington)

  • Marella De Bruijn

    (MRC Molecular Haemotology Unit, University of Oxford, Oxford OX3 9DS, UK.)

  • Licia Selleri

    (Weill Cornell Medical College)

  • Alexander Rudensky

    (HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter)

  • Steven Josefowicz

    (HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter)

  • Robert Samstein

    (HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter)

  • Evan E. Eichler

    (University of Washington)

  • Stuart H. Orkin

    (Dana Farber Cancer Institute, Harvard Medical School)

  • Dana Levasseur

    (University of Iowa Carver College of Medicine)

  • Thalia Papayannopoulou

    (University of Washington)

  • Kai-Hsin Chang

    (University of Iowa Carver College of Medicine)

  • Arthur Skoultchi

    (Albert Einstein College of Medicine)

  • Srikanta Gosh

    (Albert Einstein College of Medicine)

  • Christine Disteche

    (University of Washington)

  • Piper Treuting

    (University of Washington)

  • Yanli Wang

    (Bioinformatics and Genomics program, The Pennsylvania State University, University Park)

  • Mitchell J. Weiss

    (St Jude Children’s Research Hospital, Memphis)

  • Gerd A. Blobel

    (The Children’s Hospital of Philadelphia
    Perelman School of Medicine at the University of Pennsylvania)

  • Xiaoyi Cao

    (University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.)

  • Sheng Zhong

    (University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.)

  • Ting Wang

    (Center for Genome Sciences and Systems Biology, Washington University School of Medicine)

  • Peter J. Good

    (NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.)

  • Rebecca F. Lowdon

    (NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
    Present addresses: Department of Biochemistry and Molecular Biology, School of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA (F.Y.); BRCF Bioinformatics Core, University of Michigan, Ann Arbor, Michigan 48105, USA (W.W.); Division of Natural Sciences, New College of Florida, Sarasota, Florida 34243, USA (T.R.); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA (A.P.B.); Washington University in St Louis, St Louis, Missouri 63108, USA (R.L.); University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina 27599, USA (L.B.A.))

  • Leslie B. Adams

    (NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
    Present addresses: Department of Biochemistry and Molecular Biology, School of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA (F.Y.); BRCF Bioinformatics Core, University of Michigan, Ann Arbor, Michigan 48105, USA (W.W.); Division of Natural Sciences, New College of Florida, Sarasota, Florida 34243, USA (T.R.); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA (A.P.B.); Washington University in St Louis, St Louis, Missouri 63108, USA (R.L.); University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina 27599, USA (L.B.A.))

  • Xiao-Qiao Zhou

    (NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.)

  • Michael J. Pazin

    (NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.)

  • Elise A. Feingold

    (NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.)

  • Barbara Wold

    (California Institute of Technology)

  • James Taylor

    (Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.)

  • Ali Mortazavi

    (University of California, Irvine, Irvine, California 92697, USA.)

  • Sherman M. Weissman

    (Yale University, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA.)

  • John A. Stamatoyannopoulos

    (University of Washington)

  • Michael P. Snyder

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.)

  • Roderic Guigo

    (Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.)

  • Thomas R. Gingeras

    (Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.)

  • David M. Gilbert

    (319 Stadium Drive, Florida State University)

  • Ross C. Hardison

    (Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • Michael A. Beer

    (Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA.)

  • Bing Ren

    (Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.)

Abstract

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.

Suggested Citation

  • Feng Yue & Yong Cheng & Alessandra Breschi & Jeff Vierstra & Weisheng Wu & Tyrone Ryba & Richard Sandstrom & Zhihai Ma & Carrie Davis & Benjamin D. Pope & Yin Shen & Dmitri D. Pervouchine & Sarah Djeb, 2014. "A comparative encyclopedia of DNA elements in the mouse genome," Nature, Nature, vol. 515(7527), pages 355-364, November.
    • Handle: RePEc:nat:nature:v:515:y:2014:i:7527:d:10.1038_nature13992
    DOI: 10.1038/nature13992
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    Cited by:

    1. Orshay Gabay & Yoav Shoshan & Eli Kopel & Udi Ben-Zvi & Tomer D. Mann & Noam Bressler & Roni Cohen‐Fultheim & Amos A. Schaffer & Shalom Hillel Roth & Ziv Tzur & Erez Y. Levanon & Eli Eisenberg, 2022. "Landscape of adenosine-to-inosine RNA recoding across human tissues," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Yue Yuan & Qiang Huo & Ziru Zhang & Qun Wang & Juanxia Wang & Shuaikang Chang & Peng Cai & Karen M. Song & David W. Galbraith & Weixiao Zhang & Long Huang & Rentao Song & Zeyang Ma, 2024. "Decoding the gene regulatory network of endosperm differentiation in maize," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    3. Yaqi Su & Zhejian Yu & Siqian Jin & Zhipeng Ai & Ruihong Yuan & Xinyi Chen & Ziwei Xue & Yixin Guo & Di Chen & Hongqing Liang & Zuozhu Liu & Wanlu Liu, 2024. "Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    4. Liang-Yu Fu & Tao Zhu & Xinkai Zhou & Ranran Yu & Zhaohui He & Peijing Zhang & Zhigui Wu & Ming Chen & Kerstin Kaufmann & Dijun Chen, 2022. "ChIP-Hub provides an integrative platform for exploring plant regulome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    5. Ravneet Jaura & Ssu-Yu Yeh & Kaitlin N. Montanera & Alyssa Ialongo & Zobia Anwar & Yiming Lu & Kavindu Puwakdandawa & Ho Sung Rhee, 2022. "Extended intergenic DNA contributes to neuron-specific expression of neighboring genes in the mammalian nervous system," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    6. Adriana Arneson & Amin Haghani & Michael J. Thompson & Matteo Pellegrini & Soo Bin Kwon & Ha Vu & Emily Maciejewski & Mingjia Yao & Caesar Z. Li & Ake T. Lu & Marco Morselli & Liudmilla Rubbi & Bret B, 2022. "A mammalian methylation array for profiling methylation levels at conserved sequences," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Hongchun Lin & Hui Peng & Yuxiang Sun & Meijun Si & Jiao Wu & Yanlin Wang & Sandhya S. Thomas & Zheng Sun & Zhaoyong Hu, 2023. "Reprogramming of cis-regulatory networks during skeletal muscle atrophy in male mice," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    8. Abrar Aljahani & Peng Hua & Magdalena A. Karpinska & Kimberly Quililan & James O. J. Davies & A. Marieke Oudelaar, 2022. "Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    9. Alan Y. Du & Jason D. Chobirko & Xiaoyu Zhuo & Cédric Feschotte & Ting Wang, 2024. "Regulatory transposable elements in the encyclopedia of DNA elements," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    10. Jiacheng Wu & Xiaoqing Xu & Jiaqi Duan & Yangyang Chai & Jiaying Song & Dongsheng Gong & Bingjing Wang & Ye Hu & Taotao Han & Yuanyuan Ding & Yin Liu & Jingnan Li & Xuetao Cao, 2024. "EFHD2 suppresses intestinal inflammation by blocking intestinal epithelial cell TNFR1 internalization and cell death," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    11. Jin Woo Oh & Michael A. Beer, 2024. "Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    12. Tulsi Patel & Jennifer Hammelman & Siaresh Aziz & Sumin Jang & Michael Closser & Theodore L. Michaels & Jacob A. Blum & David K. Gifford & Hynek Wichterle, 2022. "Transcriptional dynamics of murine motor neuron maturation in vivo and in vitro," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    13. Joern Pezoldt & Carolin Wiechers & Mangge Zou & Maria Litovchenko & Marjan Biocanin & Michael Beckstette & Katarzyna Sitnik & Martina Palatella & Guido Mierlo & Wanze Chen & Vincent Gardeux & Stefan F, 2022. "Postnatal expansion of mesenteric lymph node stromal cells towards reticular and CD34+ stromal cell subsets," Nature Communications, Nature, vol. 13(1), pages 1-19, December.

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