Evidence map›Paper›PMID 42393721›Full record

ArticleGenome biology2026

A one-week automated genome-wide optical pooled screen using OttoSeq.

Bryce Kirby, Matteo Di Bernardo, Iain M Cheeseman, Paul C Blainey

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

4 authors.

Bryce Kirby *Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
Matteo Di Bernardo *Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA.
Iain M CheesemanWhitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA.
Paul C BlaineyBroad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA. pblainey@broadinstitute.org.

Funding

Virology BSL4 CoreP01AI120943 · NIAID · WASHINGTON UNIVERSITY · PI Gaya K. Amarasinghe · 2016 to 2026
$30.2M
Targeting Dysregulated RNA Splicing in Neurodegenerative DiseasesRM1NS133601 · NINDS · MASSACHUSETTS GENERAL HOSPITAL · PI Clotilde Lagier-Tourenne, Michael Emmerson Ward · 2023 to 2026
$7.4M
Molecular Analysis of Kinetochore FunctionR35GM126930 · NIGMS · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI Iain McPherson Cheeseman · 2018 to 2026
$7.0M
Profiling and perturbing the inheritance of drug-induced metabolic states in cancer with Inheritance-SeqR61CA278536 · NCI · BROAD INSTITUTE, INC. · PI Paul Clark Blainey · 2024 to 2026
$621k
Chan Zuckerberg Initiative 2023-332277Chan Zuckerberg Initiative 2023-332286NCI NIH HHS R61 CA278536NIAID NIH HHS P01 AI120943NIGMS NIH HHS R35 GM126930NIH HHS P01AI120943-06A1NIH HHS R35GM126930NINDS NIH HHS RM1 NS133601
6 · The paper itself

Abstract

Optical pooled screens (OPS) are bottlenecked by labor-intensive in situ sequencing and analysis protocols. Here, we present OttoSeq, an automated OPS platform combining the Otto2 fluid handling system with the Brieflow analysis pipeline. We utilize OttoSeq to complete a genome-wide cell painting screen in eight days, sampling 5,198,240 high-quality cells across 21,732 gene knockout perturbations (224 cells per gene) and interpreting 320 functional gene clusters.

Indexed as

GenomicsSingle-Cell AnalysisHumansAI-Driven scientific discoveryAutomated in situ sequencingCell paintingCRISPR screeningHigh throughput biologyHigh throughput computingLLM automated annotationOptical pooled screeningSingle-cell genomics

Identifiers

PMID42393721
PMCPMC13621683

What OpenQuestion holds

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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.