ArticleScience (New York, N.Y.)2024
Single-cell genomics and regulatory networks for 388 human brains.
Abstract read
In one paragraph
Article in Science (New York, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers, 3 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
122citing papers in PubMed, 3 pooled it
–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
122 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Integrating cell-type-specific gene expression and genome-wide associations identifies risk genes for schizophrenia.Molecular psychiatry · 2026Pooled it
- Multi-Trait Genetic Insights Into Schizophrenia Across Ancestries: Genome-Wide Association Meta-Analyses, Machine Learning, and Drug Repurposing Study.Brain and behavior · 2026Pooled it
- A meta-analysis of single-nucleus expression quantitative trait loci linking genetic risk to brain disorders.Nature genetics · 2026Pooled it
- Predicted brain-regional gene expression patterns in individuals living with Alzheimer's disease.Neurobiology of aging · 2026Article
- Single-nucleus atlas of cell-type specific genetic regulation in the human brain.Nature genetics · 2026Article
- A single-nuclei multiomics resource across four brain regions prioritises human neural cell types influencing brain-related traits.bioRxiv : the preprint server for biology · 2026Article
- Fast, flexible analysis of differences in cellular composition with crumblr.Nature communications · 2026Article
- Personalized single-cell transcriptomics reveals molecular diversity in Alzheimer's disease.Nature communications · 2026Article
- VINE-seq and MultiVINE-seq for single-nucleus and multiome profiling of the brain vasculature.Nature protocols · 2026Review
- Developmental and cellular vulnerabilities underlie genetic architecture of schizophrenia.Molecular psychiatry · 2026Article
- Single-cell transcriptomics of human brain disorders.Molecular psychiatry · 2026Review
- Solute carrier membrane transporters: emerging targets in CNS disorders.Nature reviews. Drug discovery · 2026Review
- Article
- Cell-type-specific genetic architecture reveals neuronal and immune contributions to neuropsychiatric disorders.Molecular psychiatry · 2026Article
- Article
- Mapping genetic regulation of gene expression to cellular contexts identifies long non-coding RNAs associated with brain disorders.Nature communications · 2026Article
- Coordinated dysregulation of modular gene activity in human neuropathologies.bioRxiv : the preprint server for biology · 2026Article
- Dynamic neuro-immune regulation of psychiatric risk loci in human neurons.Nature communications · 2026Article
- Article
- Article
62 more citing papers are in PubMed but not listed here.
Corrections and comments
- Update of
Authors and funding
82 authors.
Prashant S Emani *Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-3091-5231
Jason J Liu *Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0001-7197-7319
Declan Clarke *Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-6128-7485
Matthew Jensen *Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-5153-8543
Jonathan Warrell *Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-1323-4602
Chirag Gupta *Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA.ORCID 0000-0002-6121-7065
Ran Meng *Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0003-1271-3975
Che Yu Lee *Department of Computer Science, University of California, Irvine, CA 92697, USA.ORCID 0000-0002-3039-4894
Siwei Xu *Department of Computer Science, University of California, Irvine, CA 92697, USA.ORCID 0000-0002-2828-3706
Cagatay Dursun *Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-0897-7671
Shaoke Lou *Program 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.ORCID 0000-0001-9906-4108
Zhiyuan ChuProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-3193-5031
Timur GaleevProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-6241-1011
Ahyeon HwangDepartment of Computer Science, University of California, Irvine, CA 92697, USA.ORCID 0000-0002-4686-3077
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.ORCID 0000-0001-9878-5480
Xiao ZhouProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-8933-444X
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.ORCID 0000-0001-9989-2720
Lucy BicksProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.ORCID 0000-0002-9884-0133
Tanima ChatterjeeProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0001-8956-6569
Lijun ChengTempus Labs, Chicago, IL 60654, USA.ORCID 0000-0001-7606-9563
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.ORCID 0000-0003-4696-0042
Mary FlahertyTempus Labs, Chicago, IL 60654, USA.ORCID 0009-0002-9931-7122
John F FullardCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.ORCID 0000-0001-9874-2907
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.ORCID 0000-0002-4131-4458
Sophia Gaynor-GillettTempus Labs, Chicago, IL 60654, USA.ORCID 0009-0001-7242-350X
Jennifer GrundmanProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.ORCID 0000-0003-2266-277X
Natalie HawkenProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.ORCID 0000-0002-0473-4373
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.ORCID 0000-0001-8768-0050
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.ORCID 0000-0001-7906-9470
Riki KawaguchiProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.ORCID 0000-0002-2489-4825
Saniya KhullarDepartment of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA.ORCID 0000-0002-4166-874X
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.ORCID 0009-0007-3694-7799
Shuang LiuWaisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA.
Shaojie MaDepartment of Neuroscience, Yale University, New Haven, CT 06510, USA.ORCID 0000-0002-8782-3047
Michael MargolisORCID 0000-0002-3706-8960
Samantha MazariegosProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.ORCID 0009-0000-1762-6454
Jill MooreDepartment of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA.ORCID 0000-0002-3023-0806
Jennifer R MoranTempus Labs, Chicago, IL 60654, USA.ORCID 0009-0000-1294-2079
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.ORCID 0000-0003-3980-6450
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.ORCID 0000-0001-9413-834X
Diana QuinteroProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.ORCID 0000-0002-6364-4183
Ananya S RajagopalanDepartment of Computer Science, Yale University, New Haven, CT 06520, USA.ORCID 0009-0008-2390-4738
Tiernon R RiesenmyDepartment of Statistics and Data Science, Yale University, New Haven, CT 06520, USA.ORCID 0009-0006-2048-0744
Nicole SheddDepartment of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA.ORCID 0000-0003-2272-5398
Manman ShiTempus Labs, Chicago, IL 60654, USA.
Megan SpectorTempus Labs, Chicago, IL 60654, USA.ORCID 0009-0001-4525-4413
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.ORCID 0000-0002-4454-9834
Gaoyuan WangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0003-4039-748X
Yan XiaProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0001-6432-9911
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.ORCID 0000-0003-3703-1970
Michael J GandalInterdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles CA, 90095, USA.ORCID 0000-0001-5800-5128
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.ORCID 0000-0001-9012-6552
Panos RoussosCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.ORCID 0000-0002-4640-6239
Nenad SestanDepartment of Neuroscience, Yale University, New Haven, CT 06510, USA.ORCID 0000-0003-0966-9619
Zhiping WengDepartment of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA.ORCID 0000-0002-3032-7966
Kevin P WhiteYong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore.ORCID 0000-0001-6934-5793
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.ORCID 0000-0003-1647-326X
Jing ZhangDepartment of Computer Science, University of California, Irvine, CA 92697, USA.ORCID 0000-0002-5970-0509
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.ORCID 0000-0003-2896-3450
Mark GersteinProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-9746-3719
PsychENCODE Consortium
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
$83.6MResearch Education ComponentP30AG066514 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI NIKOLAOS K ROBAKIS · 2020 to 2026
$31.0MUCLA-Caltech Medical Scientist Training ProgramT32GM008042 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AJIJOLA, OLUJIMI A, DAWSON, DAVID WAYNE · 1985 to 2023
$29.9MA multimodal atlas of human brain cell typesU01MH114812 · NIMH · ALLEN INSTITUTE · PI LEIN, ED · 2017 to 2021
$19.2MUnderstanding 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
$11.8MHigher Order Chromatin and Genetic Risk for Alzheimer's DiseaseR01AG050986 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ROUSSOS, PANAGIOTIS · 2015 to 2025
$11.2MUnderstanding 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
$9.9MWaisman Center Intellectual and Developmental Disabilities Research CenterP50HD105353 · NICHD · UNIVERSITY OF WISCONSIN-MADISON · PI Qiang Chang · 2021 to 2026
$8.5M Functional Genomics of Human Brain DevelopmentP50MH106934 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD · 2014 to 2019
$7.9MCis-Regulatory Epigenome Mappings in SchizophreniaU01MH103392 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, SKLAR, PAMELA · 2014 to 2017
$7.6MMolecular Profiling of SchizophreniaR01MH110921 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI CHESS, ANDREW J, ROUSSOS, PANAGIOTIS · 2016 to 2020
$6.9MTranscriptional and Epigenetic Signatures of Human Brain Development and AutismU01MH103339 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD, STATE, MATTHEW W. · 2014 to 2017
$6.5MBLRD VA I01 BX002395BLRD VA I01 BX005160NHGRI NIH HHS R01 HG012572NIA NIH HHS P30 AG066514NIA 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 MH122681NIMH 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 R01 MH137578NIMH 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 NS128761
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, multiomics datasets into a resource comprising >2.8 million 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 >550,000 cell type-specific regulatory elements and >1.4 million 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.
Indexed as
BrainGene Regulatory NetworksMental DisordersSingle-Cell AnalysisAgingCell CommunicationChromatinGenomicsHumansPrefrontal CortexQuantitative Trait LociChromatin
Identifiers
What Socratic holds
Textmetadata
LicenceTDM
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 Socratic graph.