ArticleNucleic acids research2024
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes.
Erratum issuedOpen access · goldAbstract read
In one paragraph
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
22citing papers in PubMed, 1 pooled it
5.4field-weighted citation impact, top 4% of its field
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.
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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.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 35 citations in OpenAlex.
- Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR.Journal of translational medicine · 2025Pooled it
- Structural basis for target discrimination and activation by Cas13d.Science advances · 2026Article
- Stepwise DNA-unwinding gates TnpB genome-editing activity.Molecular cell · 2026Article
- Structural mining and engineering of metagenome-derived Cas12a orthologs expands the CRISPR genome editing and multiplex diagnostics toolkit.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- SIM: Discovery of novel RNA-targeting argonautes by self-iterative learning from scarce data.Acta pharmaceutica Sinica. B · 2026Article
- Structural basis of Cas8-independent Cas3 recruitment in Type I-F2 CRISPR-Cas.Nucleic acids research · 2026Article
- Customizing CRISPR-Cas PAM specificity with protein language models.Nature biotechnology · 2026Article
- Stepwise DNA unwinding gates TnpB genome-editing activity.bioRxiv : the preprint server for biology · 2026Article
- Reconstructing the complex architecture of the genome with molecular scissors: applying genome editing technology in precision medicine.Frontiers in genome editing · 2026Review
- Functional Coupling and Evolutionary Relationships Between Toxin-Antitoxin Systems and CRISPR-Cas Systems.Toxins · 2025Review
- An updated evolutionary classification of CRISPR-Cas systems including rare variants.Nature microbiology · 2025Article
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- SIMPLE: A One-Pot RPA-Cas12b Method for Single Nucleotide Variations Identification with an Expanded Scope and Clinical Applications.Phenomics (Cham, Switzerland) · 2025Article
- Engineering stimuli-responsive CRISPR-Cas systems for versatile biosensing.Analytical and bioanalytical chemistry · 2025Review
- Engineering a New Generation of Gene Editors: Integrating Synthetic Biology and AI Innovations.ACS synthetic biology · 2025Review
- DNA targeting by compact Cas9d and its resurrected ancestor.Nature communications · 2025Article
- Engineering of CRISPR-Cas PAM recognition using deep learning of vast evolutionary data.bioRxiv : the preprint server for biology · 2025Article
- Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models.Nature communications · 2024Article
- Generation of Anti-Mastitis Gene-Edited Dairy Goats with Enhancing Lysozyme Expression by Inflammatory Regulatory Sequence using ISDra2-TnpB System.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Cas12a domain flexibility guides R-loop formation and forces RuvC resetting.Molecular cell · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
53 authors at 17 institutions in 5 countries.
Benjamin A AdlerInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-7488-3040
Marena I TrinidadInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0001-7839-4642
Daniel Bellieny-RabeloInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0003-2544-7899
Elaine ZhangInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0009-0002-9578-8971
Hannah M KarpInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-1619-5901
Petr SkopintsevInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-6043-157X
Brittney W ThorntonInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Rachel F WeissmanInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-1806-6564
Peter H YoonInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-9156-1393
LinXing ChenInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0003-2774-1952
Tomas HesslerInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-2024-8615
Amy R EggersInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0001-5249-4872
David ColognoriInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0001-6995-7079
Ron BogerInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-4467-271X
Erin E DohertyInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-1555-4124
Connor A TsuchidaInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Ryan V TranDepartment of Chemistry, University of California, Berkeley, CA 94720, USA.
Laura HofmanInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-6206-681X
Honglue ShiInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0003-3847-1652
Kevin M WaskoInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Zehan ZhouInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Chenglong XiaInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-5895-6342
Muntathar J Al-ShimaryInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-7021-2565
Jaymin R PatelInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-4380-4805
Vienna C J X ThomasInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Rithu PattaliInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Matthew J KanInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0003-4840-2917
Anna VardapetyanInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Alana YangInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Arushi LahiriDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
Micaela F MaxwellDepartment of Chemistry and Biochemistry, Hampton University, Hampton, VA 23668, USA.
Andrew G MurdockInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Glenn C RamitInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Hope R HendersonInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Roland W CalvertMonash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia.
Rebecca S BamertMonash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia.
Gavin J KnottMonash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia.ORCID 0000-0002-9007-6273
Audrone LapinaiteSchool of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA.ORCID 0000-0002-9427-9342
Patrick PauschLSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania.ORCID 0000-0001-8947-9107
Joshua C CofskyDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.ORCID 0000-0001-5403-8555
Erik J SontheimerRNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.ORCID 0000-0002-0881-0310
Blake WiedenheftDepartment of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA.ORCID 0000-0001-9297-5304
Peter C FineranDepartment of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.ORCID 0000-0002-4639-6704
Stan J J BrounsDepartment of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands.ORCID 0000-0002-9573-1724
Dipali G SashitalRoy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0001-7681-6987
Brian C ThomasMetagenomi, Inc., Emeryville, CA 94608, USA.
Christopher T BrownMetagenomi, Inc., Emeryville, CA 94608, USA.ORCID 0000-0002-7758-6447
Daniela S A GoltsmanMetagenomi, Inc., Emeryville, CA 94608, USA.
Rodolphe BarrangouInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-0648-3504
Virginius SiksnysInstitute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania.ORCID 0000-0003-1983-2096
Jillian F BanfieldInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0001-8203-8771
David F SavageInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0003-0042-2257
Jennifer A DoudnaInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.ORCID 0000-0001-9161-999X
Innovative Genomics Institute · USQB3 · USHoward Hughes Medical Institute · USMonash University · AUPlanetary Science Institute · USUniversity of California, Berkeley · USUniversity of California, San Francisco · USVilnius University · LTArizona State University · USDelft University of Technology · NLHampton University · USHarvard University · USIowa State University · USMaurice Wilkins Centre · NZMontana State University · USNorth Carolina State University · USUniversity of Massachusetts Chan Medical School · US
Funding
Targeting Viroporins and Coronavirus M ProteinU19AI171110 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI James Solomon Fraser · 2022 to 2026
$103.4MPediatric Scientist Development Program (PSDP) [K12]K12HD000850 · NICHD · YALE UNIVERSITY · PI Sallie R. Permar · 1987 to 2026
$44.1MStructural and functional understanding of bacterial defense and viral counter defenseR35GM134867 · NIGMS · MONTANA STATE UNIVERSITY - BOZEMAN · PI Blake A Wiedenheft · 2020 to 2026
$3.8MDefining Mechanisms of Diverse CRISPR-Cas ComplexesR35GM140876 · NIGMS · IOWA STATE UNIVERSITY · PI Dipali Gurudutt Sashital · 2021 to 2026
$2.7MBiology and Biotechnology of Cell and Gene TherapyT32GM139780 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Amy Elizabeth Herr, Dirk Hockemeyer · 2021 to 2026
$2.4MEngineering Novel Precision Genome Editing ToolsDP2GM149550 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI LAPINAITE, AUDRONE · 2022 to 2025
$2.3MExpanding CRISPR-Cas editing technology through exploration of novel Cas proteins and DNA repair systemsU01AI142817 · NIAID · UNIVERSITY OF CALIFORNIA BERKELEY · PI BANFIELD, JILLIAN, DOUDNA, JENNIFER A · 2018 to 2022
$2.0MCharacterization and engineering of a compact genome editor for adeno-associated virus delivery to correct mutations causing cystic fibrosisF31HL156468 · NHLBI · UNIVERSITY OF CALIFORNIA BERKELEY · PI TSUCHIDA, CONNOR ANDREW · 2021 to 2022
$77kEuropean Research Council 101003229Howard Hughes Medical InstituteNHLBI NIH HHS F31 HL156468NIAID NIH HHS U19 AI171110NICHD NIH HHS K12 HD000850NIGMS NIH HHS DP2 GM149550NIGMS NIH HHS GM140876NIGMS NIH HHS R35 GM134867NIGMS NIH HHS R35 GM140876NIGMS NIH HHS T32 GM139780NIH HHS DP2GM149550NIH HHS R35GM134867NIH HHS U01AI142817
Abstract
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.
Indexed as
CRISPR-Associated ProteinsCRISPR-Cas SystemsDatabases, GeneticEndodeoxyribonucleasesEncyclopedias as TopicPhylogenyCRISPR-Associated ProteinsEndodeoxyribonucleases
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