ArticleArXiv2025
FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.
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In one paragraph
Article in ArXiv, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Authors and funding
38 authors.
Rahi NavelkarDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Andrea CosoloDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Bogdan BintuShu Chien-Gene Lay, Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
Yubao ChengDepartment of Genetics, Yale University, New Haven, CT 06510, USA.
Vincent GardeuxLaboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
Silvia GutnikBiozentrum, University of Basel, Basel, BS, CH.
Taihei FujimoriDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Antonina HafnerDepartment of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
Atishay JayDepartment of Bioengineering, University of Pennsylvania.
Bojing Blair JiaBioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA; Medical Scientist Training Program, University of California San Diego, La Jolla, CA.
Adam Paul JussilaBioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
Gerard LlimosLaboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
Antonios LioutasDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Nuno M C MartinsDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA.
William J MooreDivisions of Molecular Cell and Developmental Biology and Computational Biology, University of Dundee, Dundee, UK.
Yodai TakeiDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Frances WongDivisions of Molecular Cell and Developmental Biology and Computational Biology, University of Dundee, Dundee, UK.
Kaifu YangCenter for Epigenomics, Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
Huaiying ZhangCarnegie Mellon University, Department of Biological Sciences, Pittsburgh, PA, 15213, USA.
Quan ZhuCenter for Epigenomics, Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
Magda BienkoHuman Technopole, Milan, Italy; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SciLifeLab, Stockholm, Sweden.
Lacramioara BintuDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Long CaiDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Bart DeplanckeLaboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
Marcelo NollmannCenter of Structural Biology, Univ Montpellier, CNRS, INSERM, Montpellier, France.
Susan E MangoBiozentrum, University of Basel, Basel, BS, CH.
Bing RenCenter for Epigenomics, Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
Peter J ParkDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Ahilya N SawhDepartment of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
Andrew SchroederDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Jason R SwedlowDivisions of Molecular Cell and Developmental Biology and Computational Biology, University of Dundee, Dundee, UK.
Golnaz VahediDepartment of Bioengineering, University of Pennsylvania.
Chao-Ting WuDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Sarah AufmkolkDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Alistair N BoettigerDepartment of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
Irene FarabellaIntegrative Nuclear Architecture Laboratory, Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy.
Caterina Strambio-De-CastilliaProgram in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA.
Siyuan WangDepartment of Genetics, Yale University, New Haven, CT 06510, USA.
Funding
Human Pancreas Analysis Program for Type 1 Diabetes - HPAP-T1DU01DK112217 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI MARK A. ATKINSON, KLAUS H KAESTNER · 2021 to 2026
$46.8M4D Nucleome Network Data Coordination and Integration CenterU01CA200059 · NCI · HARVARD MEDICAL SCHOOL · PI PARK, PETER J · 2015 to 2024
$24.4MPenn integrated Human Pancreas procurement and Analysis ProgramUC4DK112217 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI BETTS, MICHAEL R, FELDMAN, MICHAEL D · 2016 to 2020
$17.8MCenter for Genome ImagingRM1HG011016 · NHGRI · HARVARD MEDICAL SCHOOL · PI WU, CHAO-TING · 2021 to 2025
$12.2MCenter for 3D Structure and Physics of the GenomeUM1HG011536 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI DEKKER, JOB, MIRNY, LEONID A · 2020 to 2024
$11.8MMultiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data IntegrationUM1HG011593 · NHGRI · CARNEGIE-MELLON UNIVERSITY · PI ALBER, FRANK, BELMONT, ANDREW STEVEN · 2020 to 2024
$10.4MCenter for Integrated Multi-modal and Multi-scale Nucleome ResearchUM1HG011585 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DULAC, CATHERINE, LEIN, ED · 2020 to 2024
$6.7MLive-cell multiplex super-resolution imaging of chromatin state transitionsU01DK127419 · NIDDK · STANFORD UNIVERSITY · PI BINTU, LACRAMIOARA, BOETTIGER, ALISTAIR N. · 2020 to 2024
$5.3MThe role of the nucleolus in human genome organization in normal and disease statesU01CA260699 · NCI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI FOLTZ, DANIEL RICHARD, HUANG, SUI · 2020 to 2024
$3.3M3-Dimensional genomic architecture in innate lymphoid cells and allergic inflammationR01AI168240 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI HENAO-MEJIA, JORGE, VAHEDI, GOLNAZ · 2022 to 2025
$3.2MSingle-cell dissection of chromatin architecture mechanisms connecting pathologic instability and transcriptional silencingU01DA052715 · NIDA · UNIVERSITY OF PENNSYLVANIA · PI JAIN, RAJAN, JOYCE, ERIC F. · 2020 to 2024
$3.1MGenome Architecture in Human Germinal Center B Cell Development, Malignancy, and Somatic HypermutationU01CA260701 · NCI · YALE UNIVERSITY · PI SCHATZ, DAVID G., WANG, SIYUAN · 2020 to 2024
$3.1MNCI NIH HHS R01 CA292936NCI NIH HHS R33 CA251037NCI NIH HHS U01 CA200059NCI NIH HHS U01 CA260699NCI NIH HHS U01 CA260701NCI NIH HHS U01 CA260851NCI NIH HHS UH3 CA268202NHGRI NIH HHS R01 HG011245NHGRI NIH HHS R01 HG012969NHGRI NIH HHS RM1 HG011016NHGRI NIH HHS UM1 HG011536NHGRI NIH HHS UM1 HG011585NHGRI NIH HHS UM1 HG011593NHLBI NIH HHS R01 HL145754NIAID NIH HHS R01 AI168240NIDA NIH HHS U01 DA052715NIDDK NIH HHS U01 DK112217NIDDK NIH HHS U01 DK127419NIDDK NIH HHS U01 DK127768NIDDK NIH HHS UC4 DK112217NIGMS NIH HHS DP2 GM137414Wellcome Trust
Abstract
A key output of the NIH-Common Fund 4D Nucleome (4DN) project
Identifiers
PMID
40895078PMC
PMC12393234What OpenQuestion holds
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.