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Bonev, B. ; Gonçalo, C.B.* ; Chen, F.* ; Codeluppi, S.* ; Corces, M.R.* ; Fan, J.* ; Heiman, M.* ; Harris, K.* ; Inoue, F.* ; Kellis, M.* ; Levine, A.P.* ; Lotfollahi, M. ; Luo, C.* ; Maynard, K.R.* ; Nitzan, M.* ; Ramani, V.* ; Satijia, R.* ; Schirmer, L.* ; Shen, Y.* ; Sun, N.* ; Green, G.S.* ; Theis, F.* ; Wang, X.* ; Welch, J.D.* ; Gokce, O.* ; Konopka, G.* ; Liddelow, S.A.* ; Macosko, E.* ; Bayraktar, O.* ; Habib, N.* ; Nowakowski, T.J.*

Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.

Nat. Neurosci. 27, 2292-2309 (2024)
Publ. Version/Full Text Postprint DOI PMC
Open Access Green
Over the past decade, single-cell genomics technologies have allowed scalable profiling of cell-type-specific features, which has substantially increased our ability to study cellular diversity and transcriptional programs in heterogeneous tissues. Yet our understanding of mechanisms of gene regulation or the rules that govern interactions between cell types is still limited. The advent of new computational pipelines and technologies, such as single-cell epigenomics and spatially resolved transcriptomics, has created opportunities to explore two new axes of biological variation: cell-intrinsic regulation of cell states and expression programs and interactions between cells. Here, we summarize the most promising and robust technologies in these areas, discuss their strengths and limitations and discuss key computational approaches for analysis of these complex datasets. We highlight how data sharing and integration, documentation, visualization and benchmarking of results contribute to transparency, reproducibility, collaboration and democratization in neuroscience, and discuss needs and opportunities for future technology development and analysis.
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Publication type Article: Journal article
Document type Review
Keywords Regulatory Network Inference; Chromatin Accessibility; Gene-expression; Mouse Cortex; Rna-analysis; Dynamics; Seq; Transcription; Organization; Methylation
Language english
Publication Year 2024
HGF-reported in Year 2024
ISSN (print) / ISBN 1097-6256
e-ISSN 1546-1726
Journal Nature Neuroscience
Quellenangaben Volume: 27, Issue: 12, Pages: 2292-2309 Article Number: , Supplement: ,
Publisher Nature Publishing Group
Publishing Place Heidelberger Platz 3, Berlin, 14197, Germany
Reviewing status Peer reviewed
Institute(s) Helmholtz Pioneer Campus (HPC)
Institute of Computational Biology (ICB)
POF-Topic(s) 30204 - Cell Programming and Repair
30205 - Bioengineering and Digital Health
Research field(s) Pioneer Campus
Enabling and Novel Technologies
PSP Element(s) G-510004-001
G-503800-001
Grants Swedish Research Council
HHMI Emerging Pathogens Initiative
Sontag Foundation
James S. McDonnell Foundation 21st Century Science Initiative in Understanding Human Cognition
Carol and Gene Ludwig Family Foundation
Simons Foundation
NHGRI
NINDS
NIMH
JPB Foundation Picower Institute Innovation Fund
Helmholtz Center Munich, DFG priority program
ERA-NET Neuron (MOSAIC)
Shurl and Kay Curci Foundation
Esther A & Joseph Klingenstein Fund
Knut and Alice Wallenberg Foundation
Swedish Brain Foundation
Swedish Society for Medical Research (SSMF)
Goran Gustafsson Foundation for Research in Natural Sciences and Medicine
National Institutes of Health (NIH)
NIH
European Research Council Consolidator grant
Israel Science Foundation
Belfer Neurodegeneration Consortium
Cure Alzheimer's Fund
European Research Council
European Union (ERC)
Wellcome Sanger core
Wellcome LEAP funding
National Institute of General Medical Sciences of the NIH
NINDS Intramural funds
Lieber Institute for Brain Development
European Research Council (ERC)
National Multiple Sclerosis Society
German Research Foundation through collaborative research projects
Heisenberg Fellowship
DOI 10.1038/s41593-024-01806-0
WOS ID 001369839700019
Scopus ID 85211137231
PubMed ID 39627587
Erfassungsdatum 2024-12-06
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