ArticlebioRxiv : the preprint server for biology2024
Complete sequencing of ape genomes.
Abstract readPreprint
In one paragraph
Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
- Updated by
Authors and funding
123 authors.
DongAhn YooDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0003-0033-3721
Arang RhieGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0002-9809-8127
Prajna HebbarUC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA.
Francesca AntonacciDepartment of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy.ORCID 0000-0002-5833-6186
Glennis A LogsdonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0003-2396-0656
Steven J SolarGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0003-3051-9009
Dmitry AntipovGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0002-6087-0660
Brandon D PickettGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0001-8235-4440
Yana SafonovaComputer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA.ORCID 0000-0002-9634-4216
Francesco MontinaroDepartment of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy.
Yanting LuoDepartment of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
Joanna MalukiewiczResearch Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany.
Jessica M StorerInstitute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
Jiadong LinDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0002-8116-5901
Abigail N SequeiraDepartment of Biology, Penn State University, University Park, PA 16802, USA.
Riley J ManganComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.ORCID 0000-0003-3342-3934
Glenn HickeyUC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA.
Graciela Monfort AnezStowers Institute for Medical Research, Kansas City, MO 64110, USA.
Parithi BalachandranThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0003-3256-1403
Anton BankevichComputer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA.ORCID 0000-0003-0609-9542
Christine R BeckInstitute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.ORCID 0000-0001-7821-8489
Arjun BiddandaDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
Matthew BorchersStowers Institute for Medical Research, Kansas City, MO 64110, USA.
Gerard G BouffardNIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Emry BrannanDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
Shelise Y BrooksNIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Lucia CarboneDepartment of Medicine, KCVI, Oregon Health Sciences University, Portland, OR, USA.ORCID 0000-0002-2118-107X
Laura CarrelPSU Medical School, Penn State University School of Medicine, Hershey, PA, USA.
Agnes P ChanThe Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA.ORCID 0000-0003-2373-9580
Juyun CrawfordNIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Mark DiekhansUC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA.
Eric EngelbrechtDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA.ORCID 0000-0002-4122-3425
Cedric FeschotteDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
Giulio FormentiVertebrate Genome Laboratory, The Rockefeller University, New York, NY 10021, USA.ORCID 0000-0002-7554-5991
Gage H GarciaDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0009-0005-2383-722X
Luciana de GennaroDepartment of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy.ORCID 0009-0007-9572-7630
David GilbertSan Diego Biomedical Research Institute, San Diego, CA, USA.ORCID 0000-0001-8087-9737
Richard E GreenUniversity of California Santa Cruz, Santa Cruz, CA, USA.ORCID 0000-0003-0516-5827
Andrea GuarracinoDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.ORCID 0000-0001-9744-131X
Ishaan GuptaDepartment of Computer Science and Engineering, University of California San Diego, CA, USA.
Diana HaddadNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Junmin HanBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
Robert S HarrisDepartment of Biology, Penn State University, University Park, PA 16802, USA.
Gabrielle A HartleyInstitute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.ORCID 0000-0002-5672-2171
William T HarveyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0003-0646-7528
Michael HillerLOEWE Centre for Translational Biodiversity Genomics, Senckenberg Research Institute, Goethe University, Frankfurt, Germany.ORCID 0000-0003-3024-1449
Kendra HoekzemaDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Marlys L HouckSan Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA.
Hyeonsoo JeongDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0002-5565-2685
Kaivan KamaliDepartment of Biology, Penn State University, University Park, PA 16802, USA.
Manolis KellisComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.ORCID 0000-0001-7113-9630
Bryce KilleDepartment of Computer Science, Rice University, Houston, TX 77005, USA.ORCID 0000-0003-2946-6915
Chul LeeLaboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.ORCID 0000-0002-9403-0774
Youngho LeeLaboratory of bioinformatics and population genetics, Interdisciplinary program in bioinformatics, Seoul National University, Republic of Korea.
William LeesDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA.ORCID 0000-0001-9834-6840
Alexandra P LewisDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Qiuhui LiDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Mark LoftusDepartment of Genetics & Biochemistry, Clemson University, Clemson, SC, USA.ORCID 0000-0002-6279-6855
Yong Hwee Eddie LohNeuroscience Research Institute, University of California, Santa Barbara, CA, USA.
Hailey LoucksUC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA.ORCID 0009-0000-6956-9922
Jian MaRay and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA.ORCID 0000-0002-4202-5834
Yafei MaoBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.ORCID 0000-0002-9648-4278
Juan F I MartinezComputer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA.
Patrick MastersonNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Rajiv C McCoyDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0003-0615-146X
Barbara McGrathDepartment of Biology, Penn State University, University Park, PA 16802, USA.
Sean McKinneyStowers Institute for Medical Research, Kansas City, MO 64110, USA.
Britta S MeyerResearch Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany.ORCID 0000-0002-2549-1825
Karen H MigaUC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA.
Saswat K MohantyDepartment of Biology, Penn State University, University Park, PA 16802, USA.ORCID 0000-0002-1813-589X
Katherine M MunsonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0001-8413-6498
Karol PalDepartment of Biology, Penn State University, University Park, PA 16802, USA.ORCID 0000-0002-7726-4691
Matt PennellDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.ORCID 0000-0002-2886-3970
Pavel A PevznerDepartment of Computer Science and Engineering, University of California San Diego, CA, USA.
David PorubskyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0001-8414-8966
Tamara PotapovaStowers Institute for Medical Research, Kansas City, MO 64110, USA.ORCID 0000-0003-2761-1795
Francisca R RingelingFaculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany.
Joana L RohaDepartment of Integrative Biology, University of California, Berkeley, Berkeley, USA.ORCID 0000-0003-3266-6328
Oliver A RyderSan Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA.
Samuel SaccoUniversity of California Santa Cruz, Santa Cruz, CA, USA.
Swati SahaDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA.ORCID 0009-0004-7210-6338
Takayo SasakiSan Diego Biomedical Research Institute, San Diego, CA, USA.
Michael C SchatzDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0002-4118-4446
Nicholas J SchorkThe Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA.
Cole ShanksUC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA.
Linnéa SmedsDepartment of Biology, Penn State University, University Park, PA 16802, USA.ORCID 0000-0002-8415-9259
Dongmin R SonDepartment of Ecology, Evolution and Marine Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA.
Cynthia SteinerSan Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA.
Alexander P SweetenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0002-5316-2973
Michael G TassiaDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
Françoise Thibaud-NissenNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.ORCID 0000-0003-4957-7807
Edmundo Torres-GonzálezDepartment of Biology, Penn State University, University Park, PA 16802, USA.
Mihir TrivediDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0001-6506-2390
Wenjie WeiSchool of Life Sciences, Westlake University, Hangzhou 310024, China.ORCID 0000-0003-4105-9693
Julie WertzDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Muyu YangRay and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA.
Panpan ZhangDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
Shilong ZhangBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.ORCID 0009-0000-8844-2273
Yang ZhangRay and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA.
Zhenmiao ZhangDepartment of Computer Science and Engineering, University of California San Diego, CA, USA.ORCID 0000-0003-3748-1664
Sarah A ZhaoComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.ORCID 0009-0008-6068-5693
Yixin ZhuDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.ORCID 0000-0003-4257-462X
Erich D JarvisLaboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.ORCID 0000-0001-8931-5049
Jennifer L GertonStowers Institute for Medical Research, Kansas City, MO 64110, USA.ORCID 0000-0003-0743-3637
Iker Rivas-GonzálezDepartment of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.ORCID 0000-0002-0515-0628
Benedict PatenUC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA.ORCID 0000-0001-8863-3539
Zachary A SzpiechDepartment of Biology, Penn State University, University Park, PA 16802, USA.ORCID 0000-0001-6372-8224
Christian D HuberDepartment of Biology, Penn State University, University Park, PA 16802, USA.ORCID 0000-0002-2267-2604
Tobias L LenzResearch Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany.
Miriam K KonkelDepartment of Genetics & Biochemistry, Clemson University, Clemson, SC, USA.
Soojin V YiDepartment of Ecology, Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA.
Stefan CanzarFaculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany.
Corey T WatsonDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA.ORCID 0000-0001-7248-8787
Peter H SudmantDepartment of Integrative Biology, University of California, Berkeley, Berkeley, USA.ORCID 0000-0002-9573-8248
Erin MolloyDepartment of Computer Science, University of Maryland, College Park, MD 20742, USA.ORCID 0000-0001-5553-3312
Erik GarrisonDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
Craig B LoweDepartment of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.ORCID 0000-0002-6838-1976
Mario VenturaDepartment of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy.ORCID 0000-0001-7762-8777
Rachel J O'NeillInstitute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.ORCID 0000-0002-1525-6821
Sergey KorenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Kateryna D MakovaDepartment of Biology, Penn State University, University Park, PA 16802, USA.ORCID 0000-0002-6212-9526
Adam M PhillippyGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0003-2983-8934
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0002-8246-4014
Funding
Upgrade of confocal microscopy at the Oregon National Primate Research CenterP51OD011092 · OD · OREGON HEALTH & SCIENCE UNIVERSITY · PI Bonnie J. Nagel · 2012 to 2026
$203.9MSystems BiologyU19AG023122 · NIA · TRANSLATIONAL GENOMICS RESEARCH INST · PI JODI A LAPIDUS · 2004 to 2026
$102.6MImplementing the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)U24HG010263 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI Enis Afgan, VINCENT JAMES CAREY · 2018 to 2026
$23.8MTRAINING PROGRAM IN COMPUTATIONAL BIOLOGY AND MEDICINET15LM007093 · NLM · RICE UNIVERSITY · PI Lydia E. Kavraki · 1992 to 2026
$20.8MGENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MIdentifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human GenomesU24HG007497 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Evan Eichler, Jan Oliver Korbel · 2019 to 2026
$17.2MSequence and Assembly of Segmental DuplicationsR01HG002385 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2001 to 2026
$13.3MProject 3: Functional Microbiome and Host Signatures in Transition from Commensal to pathogenP01AI152999 · NIAID · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI ARIAS, CESAR AUGUSTO, SAVIDGE, TOR C. · 2020 to 2025
$12.0MStatistical Methods for Gene Regulatory Analysis From Single Cell Genomics DataP20GM139769 · NIGMS · CLEMSON UNIVERSITY · PI ALEXANDROV, ANDREI · 2021 to 2025
$10.8MSequence-resolved structural variation of human genomesR01HG010169 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2018 to 2026
$4.5MGenomic and Physiological Impact of Transposable Elements.R35GM122550 · NIGMS · CORNELL UNIVERSITY · PI Cedric Feschotte · 2017 to 2026
$4.4MDissecting the role of NOTCH2NL genes in human brain development and neurological disorders associated with chromosome 1q21.1 distal duplications and deletions.R01MH120295 · NIMH · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI SALAMA, SOFIE REDA · 2020 to 2024
$3.7MNHGRI NIH HHS R01 HG002385NHGRI NIH HHS R01 HG010169NHGRI NIH HHS R01 HG010329NHGRI NIH HHS R01 HG013017NHGRI NIH HHS R35 HG011332NHGRI NIH HHS U01 HG013760NHGRI NIH HHS U24 HG007497NHGRI NIH HHS U24 HG010263NHGRI NIH HHS U41 HG007234NIAID NIH HHS P01 AI152999NIA NIH HHS R01 AG056169NIA NIH HHS R56 AG056169NIA NIH HHS U19 AG023122NIA NIH HHS UH3 AG064706NIGMS NIH HHS P20 GM139769NIGMS NIH HHS R01 GM123312NIGMS NIH HHS R35 GM122550NIGMS NIH HHS R35 GM133600NIGMS NIH HHS R35 GM133747NIGMS NIH HHS R35 GM142916NIGMS NIH HHS R35 GM146886NIGMS NIH HHS R35 GM146926NIGMS NIH HHS R35 GM151945NIH HHS P51 OD011092NIMH NIH HHS R01 MH120295NLM NIH HHS T15 LM007093
Abstract
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390
Registered trials
None linked
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.