Evidence map›Paper›PMID 38562822›Full record

ArticlebioRxiv : the preprint server for biology2024

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

Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun and 71 more

Abstract readPreprint
PubMed Full text at PMC Publisher
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
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

81 authors.

Prashant S EmaniProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Jason J LiuProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Declan ClarkeProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Matthew JensenProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Jonathan WarrellProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.ORCID 0000-0002-1323-4602
Chirag GuptaDepartment of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Ran MengProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Che Yu LeeDepartment of Computer Science, University of California, Irvine, CA, 92697, USA.
Siwei XuDepartment of Computer Science, University of California, Irvine, CA, 92697, USA.ORCID 0000-0002-2828-3706
Cagatay DursunProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Shaoke LouProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Yuhang ChenProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Zhiyuan ChuProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Timur GaleevProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Ahyeon HwangDepartment of Computer Science, University of California, Irvine, CA, 92697, USA.
Yunyang LiDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
Pengyu NiProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Xiao ZhouProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
PsychENCODE Consortium
Trygve E BakkenAllen Institute for Brain Science, Seattle, WA, 98109, USA.ORCID 0000-0003-3373-7386
Jaroslav BendlCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Lucy BicksProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Tanima ChatterjeeProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Lijun ChengTempus Labs, Inc., Chicago, IL, 60654, USA.
Yuyan ChengProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Yi DaiDepartment of Computer Science, University of California, Irvine, CA, 92697, USA.
Ziheng DuanDepartment of Computer Science, University of California, Irvine, CA, 92697, USA.
Mary FlahertyTempus Labs, Inc., Chicago, IL, 60654, USA.
John F FullardCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Michael GanczProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Diego Garrido-MartínDepartment of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, 08028, Spain.
Sophia Gaynor-GillettTempus Labs, Inc., Chicago, IL, 60654, USA.
Jennifer GrundmanProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Natalie HawkenProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Ella HenryProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Gabriel E HoffmanCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.ORCID 0000-0002-0957-0224
Ao HuangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Yunzhe JiangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Ting JinDepartment of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Nikolas L JorstadAllen Institute for Brain Science, Seattle, WA, 98109, USA.
Riki KawaguchiProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Saniya KhullarDepartment of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Jianyin LiuProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Junhao LiuDepartment of Computer Science, University of California, Irvine, CA, 92697, USA.
Shuang LiuWaisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.
Shaojie MaDepartment of Neuroscience, Yale University, New Haven, CT, 06510, USA.
Michael MargolisProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Samantha MazariegosProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Jill MooreDepartment of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA.
Jennifer R MoranTempus Labs, Inc., Chicago, IL, 60654, USA.
Eric NguyenProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Nishigandha PhalkeDepartment of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA.
Milos PjanicCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Henry PrattDepartment of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA.
Diana QuinteroProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Ananya S RajagopalanDepartment of Computer Science, Yale University, New Haven, CT, 06520, USA.
Tiernon R RiesenmyDepartment of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA.
Nicole SheddDepartment of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA.
Manman ShiTempus Labs, Inc., Chicago, IL, 60654, USA.
Megan SpectorTempus Labs, Inc., Chicago, IL, 60654, USA.
Rosemarie TerwilligerDepartment of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA.
Kyle J TravagliniAllen Institute for Brain Science, Seattle, WA, 98109, USA.ORCID 0000-0003-3164-6448
Brie WamsleyProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Gaoyuan WangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Yan XiaProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Shaohua XiaoProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Andrew C YangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Suchen ZhengProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Michael J GandalInterdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Donghoon LeeCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.ORCID 0000-0003-0453-6059
Ed S LeinAllen Institute for Brain Science, Seattle, WA, 98109, USA.
Panos RoussosCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Nenad SestanDepartment of Neuroscience, Yale University, New Haven, CT, 06510, USA.
Zhiping WengDepartment of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA.
Kevin P WhiteYong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.
Hyejung WonDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.ORCID 0000-0003-3651-0566
Matthew J GirgentiDepartment of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA.
Jing ZhangDepartment of Computer Science, University of California, Irvine, CA, 92697, USA.
Daifeng WangDepartment of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA.ORCID 0000-0001-9190-3704
Daniel GeschwindProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Mark GersteinProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.

Funding

Topographic, cell type and molecular pathway characterization ofAlzheimer's disease using single cell transcriptomics and epigenomicsU19AG060909 · NIA · ALLEN INSTITUTE · PI Ed Lein · 2020 to 2026
$83.6M
UCLA-Caltech Medical Scientist Training ProgramT32GM008042 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AJIJOLA, OLUJIMI A, DAWSON, DAVID WAYNE · 1985 to 2023
$29.9M
Research Training for Computation and Informatics in Biology and MedicineT15LM007359 · NLM · UNIVERSITY OF WISCONSIN-MADISON · PI Mark W. Craven, Colin Noel Dewey · 2002 to 2026
$22.6M
A multimodal atlas of human brain cell typesU01MH114812 · NIMH · ALLEN INSTITUTE · PI LEIN, ED · 2017 to 2021
$19.2M
Understanding the molecular mechanisms that contribute to neuropsychiatric symptoms in Alzheimer DiseaseR01AG067025 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI FINKBEINER, STEVEN M, HAROUTUNIAN, VAHRAM · 2019 to 2023
$11.8M
Higher Order Chromatin and Genetic Risk for Alzheimer's DiseaseR01AG050986 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ROUSSOS, PANAGIOTIS · 2015 to 2025
$11.2M
Understanding the protective and neuroinflammatory role of human brain immune cells in Alzheimer DiseaseR01AG065582 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI HAROUTUNIAN, VAHRAM, ROUSSOS, PANAGIOTIS · 2020 to 2024
$9.9M
Waisman Center Intellectual and Developmental Disabilities Research CenterP50HD105353 · NICHD · UNIVERSITY OF WISCONSIN-MADISON · PI Brittany Gail Travers · 2021 to 2026
$8.5M
Functional Genomics of Human Brain DevelopmentP50MH106934 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD · 2014 to 2019
$7.9M
Cis-Regulatory Epigenome Mappings in SchizophreniaU01MH103392 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, SKLAR, PAMELA · 2014 to 2017
$7.6M
Molecular Profiling of SchizophreniaR01MH110921 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI CHESS, ANDREW J, ROUSSOS, PANAGIOTIS · 2016 to 2020
$6.9M
Transcriptional and Epigenetic Signatures of Human Brain Development and AutismU01MH103339 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD, STATE, MATTHEW W. · 2014 to 2017
$6.5M
BLRD VA I01 BX002395NHGRI NIH HHS R01 HG012572NIA NIH HHS R01 AG050986NIA NIH HHS R01 AG065582NIA NIH HHS R01 AG067025NIA NIH HHS U19 AG060909NICHD NIH HHS P50 HD105353NIDA NIH HHS U01 DA048279NIGMS NIH HHS T32 GM008042NIMH NIH HHS P50 MH106934NIMH NIH HHS R01 MH094714NIMH NIH HHS R01 MH105472NIMH NIH HHS R01 MH105898NIMH NIH HHS R01 MH109677NIMH NIH HHS R01 MH109715NIMH NIH HHS R01 MH109897NIMH NIH HHS R01 MH110905NIMH NIH HHS R01 MH110920NIMH NIH HHS R01 MH110921NIMH NIH HHS R01 MH110926NIMH NIH HHS R01 MH110927NIMH NIH HHS R01 MH110928NIMH NIH HHS R01 MH111721NIMH NIH HHS R01 MH116529NIMH NIH HHS R01 MH117291NIMH NIH HHS R01 MH117292NIMH NIH HHS R01 MH117293NIMH NIH HHS R01 MH117406NIMH NIH HHS R01 MH121521NIMH NIH HHS R01 MH123922NIMH NIH HHS R01 MH125246NIMH NIH HHS R01 MH125516NIMH NIH HHS R01 MH126393NIMH NIH HHS R01 MH126459NIMH NIH HHS R01 MH129301NIMH NIH HHS R21 MH102791NIMH NIH HHS R21 MH103877NIMH NIH HHS R21 MH105853NIMH NIH HHS R21 MH105881NIMH NIH HHS R21 MH109956NIMH NIH HHS R21 MH129817NIMH NIH HHS R56 MH114899NIMH NIH HHS R56 MH114901NIMH NIH HHS R56 MH114911NIMH NIH HHS RF1 MH128695NIMH NIH HHS RF1 MH128970NIMH NIH HHS U01 MH103339NIMH NIH HHS U01 MH103340NIMH NIH HHS U01 MH103346NIMH NIH HHS U01 MH103365NIMH NIH HHS U01 MH103392NIMH NIH HHS U01 MH114812NIMH NIH HHS U01 MH116438NIMH NIH HHS U01 MH116441NIMH NIH HHS U01 MH116442NIMH NIH HHS U01 MH116487NIMH NIH HHS U01 MH116488NIMH NIH HHS U01 MH116489NIMH NIH HHS U01 MH116492NIMH NIH HHS U01 MH122509NIMH NIH HHS U01 MH122590NIMH NIH HHS U01 MH122591NIMH NIH HHS U01 MH122592NIMH NIH HHS U01 MH122678NIMH NIH HHS U01 MH122681NIMH NIH HHS U01 MH122849NINDS NIH HHS R01 NS128523NINDS NIH HHS R21 NS127432NINDS NIH HHS R21 NS128761NLM NIH HHS T15 LM007359
6 · The paper itself

Abstract

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.

Identifiers

PMID38562822
PMCPMC10983939

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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.