Evidence map›Paper›PMID 40597657›Full record

ArticleBMC genomics2025

CRISPRware: a software package for contextual gRNA library design.

Eric Malekos, Christy Montano, Susan Carpenter

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. 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

5 · Who and what money

Authors and funding

3 authors.

Eric MalekosDepartment of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA. emalekos@ucsc.edu.ORCID http://orcid.org/0000-0003-3084-2930
Christy MontanoDepartment of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA.ORCID http://orcid.org/0009-0009-7027-8458
Susan CarpenterDepartment of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA. sucarpen@ucsc.edu.ORCID http://orcid.org/0000-0002-5600-5404

Funding

High throughput functional characterization of lncRNAs in macrophage biologyR35GM137801 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI CARPENTER, SUSAN · 2020 to 2024
$2.2M
Identification and characterization of small open reading frames translated during inflammationF31AI179201 · NIAID · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI MALEKOS, ERIC · 2023 to 2025
$134k
National Institute of Allergy and Infectious Diseases F31AI179201NIAID NIH HHS F31 AI179201NIGMS NIH HHS R35 GM137801NIGMS NIH HHS R35GM137801
6 · The paper itself

Abstract

We present CRISPRware, an efficient method for generating guide RNA (gRNA) libraries against transcribed, translated, and noncoding regions. CRISPRware leverages next-generation sequencing data to design context-specific gRNAs and can account for genetic variation, which allows allele-specific guide design on a genome-wide scale. As a demonstration of use and to create a publicly available resource, we use CRISPRware to identify and score gRNAs against coding sequences in six model organisms for Cas9 and Cas12A and host these in a publicly available session on the UCSC Genome Browser.

Indexed as

CRISPR-Cas SystemsGene LibraryRNA, Guide, CRISPR-Cas SystemsSoftwareAnimalsHigh-Throughput Nucleotide SequencingHumansRNA, Guide, CRISPR-Cas SystemsCRISPR screenGuide RNANext generation sequencing

Identifiers

PMID40597657
PMCPMC12210694

What OpenQuestion holds

Textmetadata
LicenceCC BY
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 OpenQuestion graph.