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)

Items 301–359 of 359

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  2. Endogenous Reporter Systems for High-Throughput Functional Screening in Clear Cell Renal Cell Carcinoma
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  3. Combinatorial Genetic Screening in Cancer
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  7. CRISPR/Cas-based Functional Genomic Approaches to Phenotypic Screening
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  9. Network thinking applied to modeling biological evolution: from gene regulatory circuits to the transition space of genotypes.
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  10. A Genetic Interaction Screening Approach in C. elegans
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  11. Characterization of the tracrARN-DRARN genetic complex associated with the CRISPR-Cas9 system of the phytosymbiont Acholeplasma palmae: biotechnological interest
    Luis S. Moncayo, Alex Castro, Diego Arcos-Jácome, Paulo Humberto Centanaro Quiróz, Diego Vaca, Cristina Maldonado, Aleivi Pérez, Carla A. Lossada, Lenin A. González-Paz · 2021 · Revista de la Facultad de Agronomía
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  13. Uncovering Tumorigenesis Circuitry with Combinatorial CRISPR
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  14. Network thinking applied to modeling biological evolution
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  15. Faculty Opinions recommendation of Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens.
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  16. Bayesian Analysis for 3D combinatorial CRISPR screens
    Lukas Madenach, Caroline Lohoff · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  17. Combining Genetic and Mechanical Factors to Model Disease
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  18. Data from Combinatorial CRISPR/Cas9 Screening Reveals Epistatic Networks of Interacting Tumor Suppressor Genes and Therapeutic Targets in Human Breast Cancer
    Xiaoyu Zhao, Jinyu Li, Zhimin Liu, Scott Powers · 2023
  19. Protein-coding potential of non-coding regions in the human genome
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  20. Meta Learning for Low-Data Prediction of Cancer-Specific Synthetic Lethality as Drug Targets
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  21. Combinatorial CRISPR screen reveals FYN and KDM4 as targets for synergistic drug combination for treating triple negative breast cancer
    Tackhoon 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
  22. Evaluating Chromosome Instability and Genotoxicity Through Single Cell Quantitative Imaging Microscopy
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  23. High‐fidelity CRISPR/Cas12a dual‐crRNA screening reveals novel synergistic interactions in hepatocellular carcinoma
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  24. Multiple Heterogeneous Networks Representation with Latent Space for Synthetic Lethality Prediction
    Xiangjin Hu, Haoran Yi, Hao Cheng, Yijing Zhao, Dongqi Zhang, Jinxin Li, Jingjing Ruan, Jin Zhang, Xinguo Lu · 2024 · IEEE Transactions on NanoBioscience
  25. Multidimensional variable dose analysis (mVDA) is a novel method for high-throughput mapping of genetic interactions
    Sonali Sengupta, Benjamin E. Housden · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  26. Degron-modified Cas12a enhances single-cell CRISPR screening
    Valentina Snetkova, Carolina Galan, Romain Lopez, Antonio Rios, Takamasa Kudo, Kristel M. Dorighi, Søren Warming, Benjamin Haley · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  27. Combinatorial CRISPR screen reveals FYN and KDM4 as targets for synergistic drug combination for treating triple negative breast cancer
    Tackhoon 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
  28. Cell Cycle-Based Molecular Features via Synthetic Lethality and Non-Coding RNA Interactions in Cancer
    Shizheng Xiong, Jiaming Jin, Xinmiao Zhao, Yang Zhao, Zhiheng He, Haochuan Guo, Chengjun Gong, Jiafeng Yu, Li Guo, Tingming Liang · 2025 · Genes
  29. Machine Learning Approaches for the Identification of Genetic Interactions
    Anubha Dey, Manjari Kiran · 2025 · Methods in molecular biology
  30. A platform for the systematic interrogation of genetic interactions in human cells: 26 gene by genome-wide double knockout screens as a proof of concept
    Andrew 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
  31. 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
    Yue Gu, Traver Hart, Luis G. León Novelo, John Paul Shen · 2026 · PLoS Computational Biology
  32. Conservation of the genetic interaction network between two yeast species
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  33. Advancing risk gene discovery across the allele frequency spectrum
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  34. Boundary issues: SWI/SNF shapes chromatin patterns in and around centromeres
    Karen A. Lane, Alison Harrod, Jessica A. Downs · 2025 · Open Biology
  35. Targeting synthetic lethality: an effective therapeutic approach in ovarian and endometrial cancers
    Alizée Lebeau, Athanasios Kakkos, Natacha Leroi, Vincent Bours, Katty Delbecque, Frédéric Goffin, Elodie Gonne, Christine Gennigens · 2025 · Therapeutic Advances in Medical Oncology
  36. Additional file 1 of Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screens
    Merve Dede, Megan E. McLaughlin, Eiru Kim, Traver Hart · 2020 · Figshare
  37. Additional file 6 of Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screens
    Merve Dede, Megan E. McLaughlin, Eiru Kim, Traver Hart · 2020 · Figshare
  38. Zero-shot biological reasoning with open-weights large language models reproduces CRISPR screen based prediction of synthetic lethal interactions
    A. Prosz, Z. Sztupinszki, M. Dióssy, O. Kilim, Bogumił Zimoń, I. Csabai, Z. Szallasi · 2026 · bioRxiv
  39. High-throughput Genome Wide CRISPR Knock Out mechanical sort identifies genes driving metastatic cancer cell softening
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  40. PARP inhibitor synthetic lethality reveals homologous recombination sub-pathway architecture
    Ki 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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  42. Identification et caractérisation de facteurs impliqués dans la réponse cellulaire aux ARN double brin
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  43. Laboratory yeast crosses reveal limited epistasis in the genetic basis of complex traits
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  44. Mapping the genetic landscape of HNF1B-dependent cell growth
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    Masroor Bayati, Jigyansa Mishra, Laura Luhari, Maria Farina-Morillas, Jüri Reimand · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  46. Mapping the genetic landscape of the DNA damage response with Cas12a-based combinatorial knockout screens
    Samuel 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)
  47. FORGE-CRISPR: Reusable Modules for Focused CRISPR Library Construction
    Ji-Ann Lee, D. Conklin, M. Palazzolo, Jay M. Lee, S. Dubinett · 2026 · bioRxiv
  48. CRISPRing through time: How cutting-edge technology is revolutionizing life sciences and medicine
    Ishani Banik, Jean‐Philippe Coppé · 2026 · Molecular Therapy — Nucleic Acids
  49. SLAMR: LLM-Augmented Multimodal Learning for Cold-Start Synthetic Lethality Recommendation in Cancer Cell Lines
    Siyu Tao, Yingfan Rui, Jie Zheng · 2026 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
  50. Patient‐Derived Organoid‐Based CRISPR Screens in Cancer Research: Applications, Advances, and Challenges
    Julianne du Plessis, Aadilah Omar · 2026 · Cancer Medicine
  51. Advances in combinatorial CRISPRi screening and applications: Decoding higher-order interactions for next-generation microbial cell factories in synthetic biology
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  52. A high-throughput co-culture CRISPR array for rapid fitness hypothesis testing and growth engineering in CHO cells
    Jannis Marzluf, Lea Huckfeldt, Dominik Haidas, Christoph Zehe, Ann‐Cathrin Leroux · 2026 · iScience
  53. Using Biological Networks to Guide Biomedical Prediction
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  54. Synthetic Lethality in Cancer Therapy
    Satya Swaroop Nune, Swagata Halder · 2026 · Elsevier eBooks
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  56. Host chromatin architecture in HPV-driven cervical cancer: molecular mechanisms and therapeutic resistance
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  57. Niche-dependent epistasis within the cancer genome shapes metastatic fitness
    Xiyu Liu, Le He, Min Zhao, Samantha M. Golomb, Wei Ma, Xinrui Yang, Emilija Aleksandrovic, Hazel M. Borges, Kevin M. Dean, Lei Wang et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  58. DRAGON-3D: an electron-density-aware generative model for dual-target drug molecule generation
    Zhong-Xing Zhou, Hong-Xing Zhang, Shi Feng, Yan Zhao, Zhenyang Liu, Jun-Bao Huang, Qing-Chuan Zheng · 2026 · Physical Chemistry Chemical Physics
  59. FAIRsharing record for: BioGRID Open Repository of CRISPR Screens
    FAIRsharing Team · 2018 · FAIRsharing.org