Evidence map›Paper›PMID 42288725›Full record

ArticleBMC bioinformatics2026

CRISPRessoSea: streamlined analysis and comparison of pooled amplicon CRISPR screens.

Samuel Coleman, Jacob Tye, Daxton Furniss, Robert Sainsbury, Abhay Rastogi, Xincen Xi, Balazs Murnyak, Jason Bell, Joseph Skeate, Minjing Wang and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 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

13 authors.

Samuel Coleman *Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
Jacob Tye *Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
Daxton FurnissDepartment of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
Robert SainsburyDepartment of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
Abhay RastogiDepartment of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
Xincen XiDepartment of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
Balazs MurnyakDepartment of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
Jason BellDepartment of Pediatrics, Masonic Cancer Center, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
Joseph SkeateDepartment of Pediatrics, Masonic Cancer Center, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
Minjing WangDepartment of Pediatrics, Masonic Cancer Center, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
Beau WebberDepartment of Pediatrics, Masonic Cancer Center, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
Branden MoriarityDepartment of Pediatrics, Masonic Cancer Center, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
Kendell ClementDepartment of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA. k.clement@utah.edu.

Funding

Women's CancerP30CA077598 · NCI · UNIVERSITY OF MINNESOTA TWIN CITIES · PI Douglas Yee · 1998 to 2026
$100.4M
Use of microfluidic tumor cultures to enable clinical trials of therapies for ovarian cancerP50CA136393 · NCI · MAYO CLINIC ROCHESTER · PI Zhenkun Lou · 2009 to 2026
$37.0M
UNIVERSITY OF UTAH MEDICAL INFORMATICS TRAININGT15LM007124 · NLM · UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH · PI Karen Louise Eilbeck · 1997 to 2026
$22.0M
Project 4:Targeting M2-like Macrophages and MDSC with Myelolytic-VirotherapyU54CA232561 · NCI · RESEARCH INST NATIONWIDE CHILDREN'S HOSP · PI CASSADY, KEVIN A, CRIPE, TIMOTHY P · 2019 to 2023
$12.1M
TRAINING IN HEMOGLOBIN &CELL MEMBRANE RESEARCHT32HL007062 · NHLBI · UNIVERSITY OF MINNESOTA TWIN CITIES · PI Jeffrey S. Miller, Gregory M Vercellotti · 1985 to 2026
$10.3M
Project 3P01CA254849 · NCI · UNIVERSITY OF MINNESOTA · PI LARGAESPADA, DAVID ANDREW, MASOPUST, DAVID · 2021 to 2025
$9.4M
TECH CoreU54CA268069 · NCI · UNIVERSITY OF MINNESOTA · PI Kevin William Eliceiri, Paolo Provenzano · 2022 to 2026
$8.2M
SCGE Disease Models Studies Supplement: Evaluation of prime editing for the amelioration of alpha-1-antitrypsin deficiency in murine and porcine models.U24OD026641 · OD · RECOMBINETICS, INC. · PI CARLSON, DANIEL FRED · 2018 to 2022
$4.1M
Activated NK CAR Cells to Cure HIVR01AI161017 · NIAID · UNIVERSITY OF MINNESOTA · PI MORIARITY, BRANDEN S, SKINNER, PAMELA J · 2021 to 2025
$3.8M
Engineered B Cells as a Universal Platform for the Treatment of EnzymopathiesR01AI146009 · NIAID · UNIVERSITY OF MINNESOTA · PI MORIARITY, BRANDEN S · 2020 to 2024
$1.9M
Pan-disease characterization of DNA methylation dysregulationR00HG011658 · NHGRI · UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH · PI CLEMENT, KENDELL · 2023 to 2025
$747k
Multiplex Engineered Human Lymphocytes for Therapeutic Protein DeliveryR21AI163731 · NIAID · UNIVERSITY OF MINNESOTA · PI WEBBER, BEAU RICHARD · 2021 to 2022
$426k
NCI NIH HHS P01 CA254849NCI NIH HHS P30 CA077598NCI NIH HHS P50 CA136393NCI NIH HHS R21 CA237789NCI NIH HHS U54 CA232561NCI NIH HHS U54 CA268069NHGRI NIH HHS R00 HG011658NHLBI NIH HHS T32 HL007062NIAID NIH HHS R01 AI146009NIAID NIH HHS R01 AI161017NIAID NIH HHS R21 AI163731NIH HHS R00HG011658NIH HHS R01AI146009, R01AI161017, P01CA254849, P50CA136393, U24OD026641, U54CA232561, P30CA077598, U54CA268069NIH HHS R21CA237789, R21AI163731, P01CA254849, P50CA136393, U54CA268069, R01AI146009NIH HHS T15LM007124NIH HHS T32HL007062NIH HHS U24 OD026641NLM NIH HHS T15 LM007124
6 · The paper itself

Abstract

backgroundCRISPR genome editing enables precise modification of genomic targets but may also induce unintended edits at off-target sites with similar sequences. Pooled amplicon sequencing can assess on- and off-target editing across many samples, yet analyzing, aggregating, and visualizing results from multiple pooled experiments remains challenging. Tools to simplify and standardize these analyses are needed to provide reproducible and comparable interpretation of editing data.

resultsWe developed CRISPRessoSea, a software package that processes, compares, and visualizes genome editing rates from pooled amplicon sequencing experiments. The tool provides standardized workflows for analyzing editing across multiple targets and samples, supports both nuclease- and base-editing modalities, and generates clear, data-rich summaries suitable for downstream interpretation.

conclusionsCRISPRessoSea facilitates reproducible, scalable analysis of CRISPR editing outcomes across diverse experimental designs, enabling more efficient and transparent assessment of genome editing specificity. The software is freely available at https://github.com/clementlab/CRISPRessoSea .

Indexed as

Clustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Cas SystemsGene EditingSoftwareHigh-Throughput Nucleotide SequencingCRISPRGenome editingOff-targetsPooled amplicon sequencing analysis

Identifiers

PMID42288725
PMCPMC13543416

What OpenQuestion holds

Textmetadata
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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.