Evidence map›Paper›PMID 42039528›Full record

ArticlebioRxiv : the preprint server for biology2026

Genome-scale functional mapping of the mammalian whole brain with in vivo Perturb-seq.

Tuo Shi, Maria Korshunova, Seoyeon Kim, David DeTomaso, Xinhe Zheng, Lavanya Vishvanath, Thokozile Nyasulu, Nhan Huynh, Alexander Sun, Patrick C Thompson and 20 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

30 authors.

Tuo ShiHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID 0000-0002-5268-0146
Maria KorshunovaNVIDIA, Santa Clara, CA, USA.
Seoyeon KimHoward Hughes Medical Institute, Chevy Chase, MD, USA.
David DeTomasoPerturbAI, San Francisco, CA, USA.
Xinhe ZhengHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID 0000-0002-4388-6724
Lavanya VishvanathHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID 0009-0007-9351-6792
Thokozile NyasuluHoward Hughes Medical Institute, Chevy Chase, MD, USA.
Nhan HuynhHoward Hughes Medical Institute, Chevy Chase, MD, USA.
Alexander SunHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID 0009-0006-7243-9700
Patrick C ThompsonHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID 0009-0006-2755-2819
Yifan ZhangHoward Hughes Medical Institute, Chevy Chase, MD, USA.
Emilie M WigdorInstitute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK.ORCID 0000-0002-2370-0128
Narjes RohaniInstitute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK.
Salma AliInstitute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK.
Huixian QiuHoward Hughes Medical Institute, Chevy Chase, MD, USA.
Michael GeraltHoward Hughes Medical Institute, Chevy Chase, MD, USA.
Ziyan ZhaoHoward Hughes Medical Institute, Chevy Chase, MD, USA.
Sara RabhiNVIDIA, Santa Clara, CA, USA.
Zizhen YaoAllen Institute for Brain Science, Seattle, WA, USA.ORCID 0000-0002-9361-5607
Cindy Tj van VelthovenAllen Institute for Brain Science, Seattle, WA, USA.ORCID 0000-0001-5120-4546
Joseph R NeryGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID 0000-0003-0153-5659
Rosa Gomez CastanonGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Severin DicksNVIDIA, Santa Clara, CA, USA.ORCID 0000-0002-0370-1983
Tiffany J ChenNVIDIA, Santa Clara, CA, USA.
Joseph R EckerHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID 0000-0001-5799-5895
Hongkui ZengAllen Institute for Brain Science, Seattle, WA, USA.ORCID 0000-0002-0326-5878
Grace Xy ZhengPerturbAI, San Francisco, CA, USA.
Stephan J SandersInstitute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK.ORCID 0000-0001-9112-5148
Laksshman SundaramNVIDIA, Santa Clara, CA, USA.ORCID 0000-0002-8953-3940
Xin JinHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID 0000-0003-2344-992X

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Functional genomics studies have provided critical insights into cell type-specific gene regulatory programs, but to date most have been conducted in wild-type tissues or cell cultures. Here, we present a gene expression functional atlas across the mouse brain. We use an enhanced in vivo Perturb-seq platform to analyze transcriptome-wide responses to loss of 1,947 disease-associated genes, profiling over 7.7 million cells spanning major brain regions and neuronal populations. We find striking cell-type-specific essentiality and transcriptional programs and show that closely related disease genes such as two NMDA receptor subunits can drive opposing transcriptional programs. Together, this work reveals insights into the genetics and mechanisms of neurodevelopmental, psychiatric, and neurodegenerative diseases in vivo, paving the way for the design of future genetic medicine.

Identifiers

PMID42039528
PMCPMC13108593

What OpenQuestion holds

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Registered trials

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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.