ArticleNature methods2017
Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.
Open access · greenAbstract read
In one paragraph
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 223 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
223citing papers in PubMed, 1 pooled it
21.9field-weighted citation impact, top 1% 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.
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.
Who cites it
223 citing papers in PubMed, 1 synthesis or guideline pooled it, 365 citations in OpenAlex.
- Synthetic lethal gene pairs: Experimental approaches and predictive models.Frontiers in genetics · 2022Pooled it
- CRISPR/Cas Systems: Biological Basis and Genome Editing Applications.Methods in molecular biology (Clifton, N.J.) · 2027Review
- Host chromatin architecture in HPV-driven cervical cancer: molecular mechanisms and therapeutic resistance.Medical oncology (Northwood, London, England) · 2026Review
- A high-throughput co-culture CRISPR array for rapid fitness hypothesis testing and growth engineering in CHO cells.iScience · 2026Article
- CRISPRing through time: How cutting-edge technology is revolutionizing life sciences and medicine.Molecular therapy. Nucleic acids · 2026Review
- Patient-Derived Organoid-Based CRISPR Screens in Cancer Research: Applications, Advances, and Challenges.Cancer medicine · 2026Review
- Advancing risk gene discovery across the allele frequency spectrum.HGG advances · 2026Review
- Article
- A tunable Cas12a platform for single-cell perturbation screening and CRISPRi.Nature communications · 2026Article
- Laboratory yeast crosses reveal limited epistasis in the genetic basis of complex traits.bioRxiv : the preprint server for biology · 2026Article
- Double-CRISPR Knockout Simulation (DKOsim): A Monte-Carlo randomization system to model cell growth behavior and infer the optimal library design for growth-based double knockout screens.PLoS computational biology · 2026Article
- Article
- High-throughput Genome Wide CRISPR Knock Out mechanical sort identifies genes driving metastatic cancer cell softening.bioRxiv : the preprint server for biology · 2026Article
- Scaling perturbations: beyond genome-scale CRISPR screens.bioRxiv : the preprint server for biology · 2026Article
- Quantitative analysis of genetic interactions in human cells from genome-wide CRISPR-Cas9 screens.bioRxiv : the preprint server for biology · 2026Article
- Using Biological Networks to Guide Biomedical Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Synthetic lethality in cancer drug discovery: challenges and opportunities.Nature reviews. Drug discovery · 2026Review
- Functional modules predict cancer-relevant genetic interactions in mammalian cells.bioRxiv : the preprint server for biology · 2025Article
- A next-generation dual guide CRISPR system for genetic interaction library screening.Nature communications · 2025Article
- Applications of Genome-wide Screening of CRISPR/Cas9 Knockout Library in Identifying Novel Molecular Targets for Xenobiotics.Environment & health (Washington, D.C.) · 2025Review
163 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
22 authors at 4 institutions in 1 country.
John Paul ShenDepartment of Medicine, Division of Genetics, University of California, San Diego, La Jolla, California, USA.ORCID http://orcid.org/0000-0003-4588-2775
Dongxin ZhaoThe Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California, USA.
Roman SasikCenter for Computational Biology &Bioinformatics, University of California, San Diego, La Jolla, California, USA.
Jens LuebeckBioinformatics &Systems Biology Program, University of California, San Diego, La Jolla, California, USA.
Amanda BirminghamCenter for Computational Biology &Bioinformatics, University of California, San Diego, La Jolla, California, USA.
Ana Bojorquez-GomezDepartment of Medicine, Division of Genetics, University of California, San Diego, La Jolla, California, USA.
Katherine LiconDepartment of Medicine, Division of Genetics, University of California, San Diego, La Jolla, California, USA.
Kristin KlepperDepartment of Medicine, Division of Genetics, University of California, San Diego, La Jolla, California, USA.
Daniel PekinDepartment of Medicine, Division of Genetics, University of California, San Diego, La Jolla, California, USA.
Alex N BeckettDepartment of Medicine, Division of Genetics, University of California, San Diego, La Jolla, California, USA.
Kyle Salinas SanchezDepartment of Medicine, Division of Genetics, University of California, San Diego, La Jolla, California, USA.
Alex ThomasBioinformatics &Systems Biology Program, University of California, San Diego, La Jolla, California, USA.
Chih-Chung KuoDepartment of Bioengineering, University of California, San Diego, La Jolla, California, USA.
Dan DuThe Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California, USA.ORCID http://orcid.org/0000-0002-3470-2890
Assen RoguevThe Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California, USA.
Nathan E LewisNovo Nordisk Center for Biosustainability at the University of California, San Diego, La Jolla, California, USA.
Aaron N ChangCenter for Computational Biology &Bioinformatics, University of California, San Diego, La Jolla, California, USA.
Jason F KreisbergDepartment of Medicine, Division of Genetics, University of California, San Diego, La Jolla, California, USA.
Nevan KroganThe Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California, USA.
Lei QiThe Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California, USA.ORCID http://orcid.org/0000-0002-3965-3223
Trey IdekerDepartment of Medicine, Division of Genetics, University of California, San Diego, La Jolla, California, USA.
Prashant MaliMoores UCSD Cancer Center, La Jolla, California, USA.
University of California San Diego · USUniversity of California, San Francisco · USBroad Center · USStanford University · US
Funding
UC San Diego Clinical and Translational Research InstituteUL1TR001442 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FIRESTEIN, GARY S, HOGARTH, MICHAEL · 2015 to 2024
$88.3MX-ray Screening and Rapid Structure DeterminationP50GM082250 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KROGAN, NEVAN J · 2007 to 2018
$48.8MSYNTHETIC SYSTEMSP50GM085764 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WINZELER, ELIZABETH A · 2010 to 2018
$23.3MUsing Networks to Seed Hierarchical Whole-cell Models of CancerU54CA209891 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI IDEKER, TREY, KROGAN, NEVAN J · 2017 to 2021
$10.9MA Systems Approach to Mapping the DNA Damage ResponseR01ES014811 · NIEHS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IDEKER, TREY · 2005 to 2021
$8.6MGRADUATE TRAINING PROGRAM IN BIONFORMATICST32GM008806 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET, REN, BING · 2001 to 2020
$6.2MUnraveling the mammalian secretory pathway through systems biology and algorithm developmentR35GM119850 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LEWIS, NATHAN ENOCH · 2016 to 2025
$4.3MComparative Analysis of Genetic Interaction NetworksR01GM084279 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IDEKER, TREY, KROGAN, NEVAN J · 2008 to 2017
$3.9MHarnessing CRISPR for Targeted and Inducible Epigenomic ReprogrammingR01DA036858 · NIDA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LIM, WENDELL A, QI, LEI STANLEY · 2013 to 2017
$2.9MGenome-wide Analysis of Heparan Sulfate using CRISPR/Cas9R21CA199292 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ESKO, JEFFREY D · 2015 to 2016
$371kHSRD VA CDA 16-150NCATS NIH HHS UL1 TR001442NCI NIH HHS L30 CA171000NCI NIH HHS R21 CA199292NCI NIH HHS U54 CA209891NIDA NIH HHS R01 DA036858NIEHS NIH HHS R01 ES014811NIGMS NIH HHS P50 GM082250NIGMS NIH HHS P50 GM085764NIGMS NIH HHS R01 GM084279NIGMS NIH HHS R35 GM119850NIGMS NIH HHS T32 GM008806
Abstract
We developed a systematic approach to map human genetic networks by combinatorial CRISPR-Cas9 perturbations coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with dual guide RNAs in three cell lines, comprising 141,912 tests of interaction. Numerous therapeutically relevant interactions were identified, and these patterns replicated with combinatorial drugs at 75% precision. From these results, we anticipate that cellular context will be critical to synthetic-lethal therapies.
Indexed as
Combinatorial Chemistry TechniquesA549 CellsCell Line, TumorChromosome MappingClustered Regularly Interspaced Short Palindromic RepeatsEpistasis, GeneticHeLa CellsHigh-Throughput Nucleotide SequencingHumansNeoplasm ProteinsNeoplasm Proteins
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
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.