Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions
Shen, John Paul, Zhao, Dongxin, Sasik, Roman, Luebeck, Jens, Birmingham, Amanda, Bojorquez-Gomez, Ana, Licon, Katherine, Klepper, Kristin +14 more·2017·Nature Methods
Cited by (359)
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- Faculty Opinions recommendation of Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens.Qiang Pan‐Hammarström, Bo Zhang · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
- Bayesian Analysis for 3D combinatorial CRISPR screensLukas Madenach, Caroline Lohoff · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
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- Data from Combinatorial CRISPR/Cas9 Screening Reveals Epistatic Networks of Interacting Tumor Suppressor Genes and Therapeutic Targets in Human Breast CancerXiaoyu Zhao, Jinyu Li, Zhimin Liu, Scott Powers · 2023
- Protein-coding potential of non-coding regions in the human genomeHitesh Kore · 2023 · Queensland University of Technology
- Meta Learning for Low-Data Prediction of Cancer-Specific Synthetic Lethality as Drug TargetsXin Liu, Siyu Tao, Jie Zheng · 2023 · IEEE International Conference on Knowledge Graph (ICKG)
- Combinatorial CRISPR screen reveals FYN and KDM4 as targets for synergistic drug combination for treating triple negative breast cancerTackhoon Kim, Byung-Sun Park, Soobeen Heo, Heeju Jeon, Jaeyeal Kim, Donghwa Kim, Sang Kook Lee, So‐Youn Jung, Sun‐Young Kong, Timothy K. Lu · 2024 · eLife
- Evaluating Chromosome Instability and Genotoxicity Through Single Cell Quantitative Imaging MicroscopyRubi Campos Gudiño, Kailee A. Rutherford, Kirk James McManus · 2024 · Methods in molecular biology
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- Multiple Heterogeneous Networks Representation with Latent Space for Synthetic Lethality PredictionXiangjin Hu, Haoran Yi, Hao Cheng, Yijing Zhao, Dongqi Zhang, Jinxin Li, Jingjing Ruan, Jin Zhang, Xinguo Lu · 2024 · IEEE Transactions on NanoBioscience
- Multidimensional variable dose analysis (mVDA) is a novel method for high-throughput mapping of genetic interactionsSonali Sengupta, Benjamin E. Housden · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Degron-modified Cas12a enhances single-cell CRISPR screeningValentina Snetkova, Carolina Galan, Romain Lopez, Antonio Rios, Takamasa Kudo, Kristel M. Dorighi, Søren Warming, Benjamin Haley · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Combinatorial CRISPR screen reveals FYN and KDM4 as targets for synergistic drug combination for treating triple negative breast cancerTackhoon Kim, Byung-Sun Park, Soobeen Heo, Heeju Jeon, Jaeyeal Kim, Donghwa Kim, Sang Kook Lee, So‐Youn Jung, Sun‐Young Kong, Timothy K. Lu · 2025 · eLife
- Cell Cycle-Based Molecular Features via Synthetic Lethality and Non-Coding RNA Interactions in CancerShizheng Xiong, Jiaming Jin, Xinmiao Zhao, Yang Zhao, Zhiheng He, Haochuan Guo, Chengjun Gong, Jiafeng Yu, Li Guo, Tingming Liang · 2025 · Genes
- Machine Learning Approaches for the Identification of Genetic InteractionsAnubha Dey, Manjari Kiran · 2025 · Methods in molecular biology
- A platform for the systematic interrogation of genetic interactions in human cells: 26 gene by genome-wide double knockout screens as a proof of conceptAndrew Chatr-aryamontri, Li Zhang, Ndeye Khady Thiombane, Vincent Archambault, Sébastien Carréno, J. D. Di Noia, I. Topisirovic, Julie A. Lessard, Philippe P. Roux, Nicolas Pilon et al. · 2025 · bioRxiv
- 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 screensYue Gu, Traver Hart, Luis G. León Novelo, John Paul Shen · 2026 · PLoS Computational Biology
- Conservation of the genetic interaction network between two yeast speciesCarles Pons · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Advancing risk gene discovery across the allele frequency spectrumMadison Caballero, Behrang Mahjani · 2026 · Human Genetics and Genomics Advances
- Boundary issues: SWI/SNF shapes chromatin patterns in and around centromeresKaren A. Lane, Alison Harrod, Jessica A. Downs · 2025 · Open Biology
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- Additional file 1 of Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screensMerve Dede, Megan E. McLaughlin, Eiru Kim, Traver Hart · 2020 · Figshare
- Additional file 6 of Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screensMerve Dede, Megan E. McLaughlin, Eiru Kim, Traver Hart · 2020 · Figshare
- Zero-shot biological reasoning with open-weights large language models reproduces CRISPR screen based prediction of synthetic lethal interactionsA. Prosz, Z. Sztupinszki, M. Dióssy, O. Kilim, Bogumił Zimoń, I. Csabai, Z. Szallasi · 2026 · bioRxiv
- High-throughput Genome Wide CRISPR Knock Out mechanical sort identifies genes driving metastatic cancer cell softeningKatherine M Young, Curtis N. Dobrowolski, Nicholas E. Stone, Kalina Paunovska, Sydney Bules, Kelly Ahkee, James Hankish, Alex Chapman, James E. Dahlman, Todd Sulchek et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- PARP inhibitor synthetic lethality reveals homologous recombination sub-pathway architectureKi Choi Chan, Anastasiia Kovina, Johanna Ertl da Costa, Anke Busch, Ratna Nuria Cordoni, Björn Stratenwerth, Markus Löbrich · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
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- Laboratory yeast crosses reveal limited epistasis in the genetic basis of complex traitsMisha Gupta, Caroline M. Holmes, Jenya Belousova, Shreyas Gopalakrishnan, Artur Rego‐Costa, Michael M. Desai · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Mapping the genetic landscape of HNF1B-dependent cell growthDeborah Gaglioti · 2024
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- Mapping the genetic landscape of the DNA damage response with Cas12a-based combinatorial knockout screensSamuel B. Hayward, Alina Vaitsiankova, Tomás Lama-Díaz, Juihsuan Chou, Angelo Taglialatela, Jen‐Wei Huang, Yodharaudshani Wijesekarahanthi, Joshua R. Heyza, Giuseppe Leuzzi, Chuanyuan Chen et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- FORGE-CRISPR: Reusable Modules for Focused CRISPR Library ConstructionJi-Ann Lee, D. Conklin, M. Palazzolo, Jay M. Lee, S. Dubinett · 2026 · bioRxiv
- CRISPRing through time: How cutting-edge technology is revolutionizing life sciences and medicineIshani Banik, Jean‐Philippe Coppé · 2026 · Molecular Therapy — Nucleic Acids
- SLAMR: LLM-Augmented Multimodal Learning for Cold-Start Synthetic Lethality Recommendation in Cancer Cell LinesSiyu Tao, Yingfan Rui, Jie Zheng · 2026 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
- Patient‐Derived Organoid‐Based CRISPR Screens in Cancer Research: Applications, Advances, and ChallengesJulianne du Plessis, Aadilah Omar · 2026 · Cancer Medicine
- Advances in combinatorial CRISPRi screening and applications: Decoding higher-order interactions for next-generation microbial cell factories in synthetic biology朱晓菲, Weiwen Zhang, Tao Sun, Lei Chen · 2026 · Microbiological Research
- A high-throughput co-culture CRISPR array for rapid fitness hypothesis testing and growth engineering in CHO cellsJannis Marzluf, Lea Huckfeldt, Dominik Haidas, Christoph Zehe, Ann‐Cathrin Leroux · 2026 · iScience
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- Synthetic Lethality in Cancer TherapySatya Swaroop Nune, Swagata Halder · 2026 · Elsevier eBooks
- CRISPR/Cas Systems: Biological Basis and Genome Editing ApplicationsEce Çakıroğlu, Serif Senturk · 2026 · Methods in molecular biology
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- DRAGON-3D: an electron-density-aware generative model for dual-target drug molecule generationZhong-Xing Zhou, Hong-Xing Zhang, Shi Feng, Yan Zhao, Zhenyang Liu, Jun-Bao Huang, Qing-Chuan Zheng · 2026 · Physical Chemistry Chemical Physics
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