On the design of CRISPR-based single-cell molecular screens

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Items 101–200 of 278

1. Quantitative In Vivo Analyses Reveal a Complex Pharmacogenomic Landscape in Lung Adenocarcinoma
   Chuan Li, Wen-Yang Lin, Hira A. Rizvi, Hongchen Cai, Christopher D. McFarland, Zoë N. Rogers, Maryam Yousefi, Ian P. Winters, Charles M. Rudin, Dmitri A. Petrov et al. · 2021 · Cancer Research
2. CRISPR screening in hematology research: from bulk to single-cell level
   Sarah Meyers, Sofie Demeyer, Jan Cools · 2023 · Journal of Hematology & Oncology
3. A case of mistaken identity
   Ruth E. Hanna, John G. Doench · 2018 · Nature Biotechnology
4. Advancements in CRISPR screens for the development of cancer immunotherapy strategies
   Yan-Ruide Li, Zibai Lyu, Yanxin Tian, Ying Fang, Yichen Zhu, Yuning Chen, Lili Yang · 2023 · Molecular Therapy — Oncolytics
5. Mutational profiling of SARS-CoV-2 papain-like protease reveals requirements for function, structure, and drug escape
   Xinyu Wu, Margareta Go, Julie V. Nguyen, Nathan W. Kuchel, Bernadine G.C. Lu, Kathleen Zeglinski, Kym N. Lowes, Dale J. Calleja, Jeffrey P. Mitchell, Guillaume Lessène et al. · 2024 · Nature Communications
6. Toward mapping the human body at a cellular resolution
   Ananda L. Roy, Richard Conroy · 2018 · Molecular Biology of the Cell
7. Bioinformatics approaches to analyzing CRISPR screen data: from dropout screens to single‐cell CRISPR screens
   Yueshan Zhao, Min Zhang, Da Yang · 2022 · Quantitative Biology
8. Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s
   Sang-Yeon Seo, Seonwoo Min, Sungtae Lee, Jung Hwa Seo, Jinman Park, Hui Kwon Kim, Myungjae Song, Dawoon Baek, Sung‐Rae Cho, Seokjoong Kim · 2023 · Nature Methods
9. Spatial perturb-seq: single-cell functional genomics within intact tissue architecture
   Kimberle Shen, Wan Yi Seow, Choong Tat Keng, Michelle Gek Liang Lim, Daryl Shern Lim, Ke Guo, Amine Meliani, Muhammad Irfan Bin Hajis, Bolun Wang, Shyam Prabhakar et al. · 2026 · Nature Communications
10. Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs
    Yufeng Li, Min-Kang Tan, Almira Akkari-Henić, Limin Zhang, M. Kip, Sheng-Nan Sun, Jorian J. Sepers, Ningning Xu, Yavuz Ariyurek, S. Kloet et al. · 2024 · Nature Biomedical Engineering
11. Molecular programs guiding arealization of descending cortical pathways
    Philipp Abe, Adrien Lavalley, Ilaria Morassut, António J. Santinha, Sergi Roig‐Puiggros, Awais Javed, Esther Klingler, Natalia Baumann, Julien Prados, Randall J. Platt et al. · 2024 · Nature
12. Robust and Versatile Arrayed Libraries for Human Genome-Wide CRISPR Activation, Deletion and Silencing
    Jiang‐An Yin, Lukas D. Frick, Manuel C. Scheidmann, Tingting Liu, Chiara Trevisan, Ashutosh Dhingra, Anna Spinelli, Yancheng Wu, Longping Yao, Dalila Laura Vena et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
13. Multiomics Empowers Predictive Pancreatic Cancer Immunotherapy
    Janelle Marie Montagne, Elizabeth M. Jaffee, Elana Judith Fertig · 2023 · The Journal of Immunology
14. Systematic identification of post-transcriptional regulatory modules
    Matvei Khoroshkin, Andrey Buyan, Martin Dodel, Albertas Navickas, Johnny X. Yu, Fathima Trejo, Anthony Doty, Rithvik Baratam, Shaopu Zhou, Sean Bong Lee et al. · 2024 · Nature Communications
15. Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling
    Rachel Yan, Alba Corman, Lyla Katgara, Wang Xiao, Xinhe Xue, Zoran Z. Gajic, Richard Sam, Michael Farid, Samuel M. Friedman, Jungwook Choo et al. · 2024 · Nature Biotechnology
16. Efficient and multiplexed somatic genome editing with Cas12a mice
    Jess D. Hebert, Haiqing Xu, Yuning J. Tang, Paloma A. Ruiz, Colin R. Detrick, Jing Wang, Nicholas W. Hughes, Oscar Donosa, Vicky P Siah, Laura Andrejka et al. · 2025 · Nature Biomedical Engineering
17. CRISPRi screens in human astrocytes elucidate regulators of distinct inflammatory reactive states
    Kun Leng, Indigo V.L. Rose, Hyosung Kim, Wenlong Xia, Wilber Romero‐Fernandez, Brendan Rooney, Mark Koontz, Emmy Li, Yan Ao, Shinong Wang et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
18. iPro2L-PSTKNC: A Two-Layer Predictor for Discovering Various Types of Promoters by Position Specific of Nucleotide Composition
    Yinuo Lyu, Wenying He, Shuhao Li, Quan Zou, Fei Guo · 2020 · IEEE Journal of Biomedical and Health Informatics
19. Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens
    Celia Alda-Catalinas, Ximena Ibarra-Soria, Christina Flouri, Jorge Esparza Gordillo, Diana L. Cousminer, Anna Hutchinson, Bin Sun, William G. Pembroke, Sebastian Ullrich, Adam Krejčí et al. · 2024 · Genome biology
20. Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells
    Patrick Nugent, Heungwon Park, Cynthia L. Wladyka, James N. Yelland, Sayantani Sinha, Katharine Y. Chen, Christine Bynum, Grace Quarterman, Stanley Chun-Wei Lee, Andrew Caleb Hsieh et al. · 2025 · Nature Methods
21. A CRISPRi/a platform in iPSC-derived microglia uncovers regulators of disease states
    Nina M. Dräger, Sydney M. Sattler, Cindy Tzu-Ling Huang, Olivia M. Teter, Kun Leng, Sayed Hadi Hashemi, Jason Y. Hong, Giovanni Aviles, Claire Dudley Clelland, Lihong Zhan et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
22. Concepts and new developments in droplet-based single cell multi-omics
    Arthur Chow, Caleb A. Lareau · 2024 · Trends in biotechnology
23. Investigation of human aging at the single-cell level
    Yunjin Li, Qixia Wang, Yuan Xuan, Jian Zhao, Jin Li, Yuncai Tian, Geng Chen, Fei Tan · 2024 · Ageing Research Reviews
24. Myocardial reprogramming by HMGN1 underlies heart defects in trisomy 21
    Sanjeev S. Ranade, Feiya Li, Sean Whalen, Angelo Pelonero, Lin Ye, Yu Huang, Abigail Brand, Tomohiro Nishino, Rahul Mital, Ryan M. Boileau et al. · 2025 · Nature
25. A next-generation dual guide CRISPR system for genetic interaction library screening
    Thomas Burgold, Emre Karakoç, Emanuel Gonçalves, Inigo Barrio‐Hernandez, Lisa Dwane, Romina Silva, Emily Souster, Mamta Sharma, Alexandra Beck, Ching Chiek Koh et al. · 2025 · Nature Communications
26. Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi
    Fiona C. Edenhofer, Anita Térmeg, Mari Ohnuki, Jessica Jocher, Zane Kliesmete, Eva Briem, Ines Hellmann, Wolfgang Enard · 2024 · iScience
27. Trans MPRA: A framework for assaying the role of many trans -acting factors at many enhancers
    Diego Calderon, Andria Ellis, Riza M. Daza, Beth Martin, Jacob M. Tome, Wei Chen, Florence M. Chardon, Anh Leith, Choli Lee, Cole Trapnell et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
28. Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq
    Replogle, Joseph M., Xu, Albert, Norman, Thomas M., Meer, Elliott J., Terry, Jessica M., Riordan, Daniel, Srinivas, Niranjan, Mikkelsen, Tarjei S., Weissman, Jonathan S., Adamson, Britt · 2018
29. Modular vector assembly enables rapid assessment of emerging CRISPR technologies
    Abby V. McGee, Yanjing V. Liu, Audrey L Griffith, Zsofia M Szegletes, Bronte Wen, Carolyn Kraus, Nathan W. Miller, Ryan J. Steger, Berta Escude Velasco, Justin A. Bosch et al. · 2024 · Cell Genomics
30. Exponential family measurement error models for single-cell CRISPR screens
    Timothy Barry, Kathryn Roeder, Eugene Katsevich · 2024 · Biostatistics
31. Targeting T cell plasticity in kidney and gut inflammation by pooled single-cell CRISPR screening
    Leon U. B. Enk, Malte Hellmig, Kristoffer Riecken, Christoph Kilian, Paul Datlinger, Saskia-Larissa Jauch-Speer, Tobias Neben, Zeba Sultana, Varshi Sivayoganathan, Alina Borchers et al. · 2024 · Science Immunology
32. Critical cancer vulnerabilities identified by unbiased CRISPR/Cas9 screens inform on efficient cancer Immunotherapy
    Margaret A. Potts, Jackson A. McDonald, Kate D Sutherland, Marco J. Herold · 2020 · European Journal of Immunology
33. Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters
    Jean-Benoît Lalanne, Samuel G. Regalado, Silvia Domcke, Diego Calderon, B. Martin, Tony Li, Chase C. Suiter, Choli Lee, C. Trapnell, J. Shendure · 2022 · bioRxiv
34. CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias
    Travis J. Fleming, Mateusz Antoszewski, Sander Lambo, Michael C. Gundry, Riccardo Piussi, Lara Wahlster, Sanjana B. Shah, Fiona E. Reed, Kevin D. Dong, João A. Paulo et al. · 2025 · Blood
35. A one-step tRNA-CRISPR system for genome-wide genetic interaction mapping in mammalian cells
    Yulei Zhao, Kathrin Tyrishkin, Calvin P. Sjaarda, Prem Khanal, Jeff Stafford, Michael J. Rauh, Xudong Liu, Tomas Babak, Xiaolong Yang · 2019 · Scientific Reports
36. A systematic evaluation of the design, orientation, and sequence context dependencies of massively parallel reporter assays
    Jason C. Klein, Vikram Agarwal, Fumitaka Inoue, Aidan Keith, Beth Martin, Martin Kircher, Nadav Ahituv, Jay Shendure · 2020
37. Conditional resampling improves calibration and sensitivity in single-cell CRISPR screen analysis
    Timothy Barry, Xuran Wang, John A. Morris, Kathryn Roeder, Eugene Katsevich · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
38. Interrogation of genome-wide, experimentally dissected gene regulatory networks reveals mechanisms underlying dynamic cellular state control
    Xiangtian Tan, Jeremy Worley, Mikko M. Turunen, Kelly Wong, Ester Calvo Fernández, Evan Paull, Sunny J. Jones, Junqiang Wang, Heeju Noh, Beatrice Salvatori et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
39. Pooled CRISPR-activation screening coupled with single-cell RNA-seq in mouse embryonic stem cells
    Celia Alda-Catalinas, Mélanie A. Eckersley-Maslin, Wolf Reik · 2021 · STAR Protocols
40. Plant CLE peptides: functions, challenges, and future prospects
    Shuangshuang Wang, Yitao Liang, Yina Jiang · 2025 · Plant Hormones
41. Applying CRISPR-Cas9 screens to dissect hematological malignancies
    Deepak Narayanan Iyer, Aaron David Schimmer, Hong Chang · 2022 · Blood Advances
42. CRISPR interference-based platform for multimodal genetic screens in human iPSC-derived neurons
    Ruilin Tian, Mariam A. Gachechiladze, Connor Ludwig, Matthew T. Laurie, Jason Y. Hong, Diane Nathaniel, Anika V. Prabhu, Michael S. Fernandopulle, Rajan Patel, Mehrnoosh Abshari et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
43. Developmental convergence and divergence in human stem cell models of autism spectrum disorder
    Aaron Gordon, Se‐Jin Yoon, Lucy K. Bicks, Jacqueline M. Martín, Greta Pintacuda, Stephanie Arteaga, Brie Wamsley, Qiuyu Guo, Lubayna S. Elahi, Ricardo E. Dolmetsch et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
44. Extensive length and homology dependent chimerism in pool-packaged AAV libraries
    Jean‐Benoît Lalanne, John K. Mich, Chau Huynh, Avery C. Hunker, Troy A. McDiarmid, Boaz P. Levi, Jonathan T. Ting, Jay Shendure · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
45. Analysis of single-cell CRISPR perturbations indicates that enhancers predominantly act multiplicatively
    Jessica Zhou, Karthik Guruvayurappan, Shushan Toneyan, Hsiuyi V. Chen, Aaron R. Chen, Peter K. Koo, Graham McVicker · 2024 · Cell Genomics
46. EML4−ALK Variant-Specific Genetic Interactions Shape Lung Tumorigenesis
    Alberto Diaz-Jimenez, Emily G. Shuldiner, Kálmán Somogyi, Karen Y. Shih, Óscar González-Velasco, Mulham Najajreh, Stewart J. Kim, Filiz Akkas, Christopher W. Murray, Laura Andrejka et al. · 2025 · Cancer Discovery
47. Transgene integration in mammalian cells: The tools, the challenges, and the future
    John H.C. Fong, Francesca Ceroni · 2025 · Cell Systems
48. The use of base editing technology to characterize single nucleotide variants
    Sophia McDaniel, Alexis C. Komor, Alon Goren · 2022 · Computational and Structural Biotechnology Journal
49. Mapping gene regulatory networks of primary CD4 + T cells using single-cell genomics and genome engineering
    Rachel E. Gate, Min Cheol Kim, Andrew C. Lu, David S. Lee, Eric Shifrut, Meena Subramaniam, Alexander Marson, Chun Ye · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
50. High-throughput single-cell functional elucidation of neurodevelopmental disease-associated genes reveals convergent mechanisms altering neuronal differentiation
    Matthew A. Lalli, Denis R. Avey, Joseph D. Dougherty, Jeffrey Milbrandt, Robi David Mitra · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
51. Mapping variation in the morphological landscape of human cells with optical pooled CRISPRi screening
    Ramon Lorenzo D. Labitigan, Adrian L. Sanborn, Cynthia V. Hao, Caleb K. Chan, Nathan M. Belliveau, Eva M. Brown, Mansi Mehrotra, Julie A. Theriot · 2024 · eLife
52. Defining cis-regulatory elements and transcription factors that control human cortical interneuron development
    Gareth Chapman, Julianna J. Determan, Haley Jetter, Komal Kaushik, Ramachandran Prakasam, Kristen L. Kroll · 2024 · iScience
53. Finding needles in a haystack: dissecting tumor heterogeneity with single-cell transcriptomic and chromatin accessibility profiling
    Sarah E. Pierce, Samuel H. Kim, William James Greenleaf · 2021 · Current Opinion in Genetics & Development
54. Experimental and Computational Approaches for Single-Cell Enhancer Perturbation Assay
    Shiqi Xie, Gary C. Hon · 2019 · Methods in molecular biology
55. CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer’s disease
    Nicole F. Oldham Green, Gavin J. Sutton, Javier Pérez‐Burillo, Juli Wang, Samuel Bagot, Hannah G Danon, Kieran Walsh, Akira Gokoolparsadh, Samantha A. Miles, Guang Yang et al. · 2025 · Nature Neuroscience
56. Splice isoform-perturbation coupled to single cell transcriptome profiling reveals functions of microexons in neurogenesis and autism-linked pathways
    Steven J. Dupas, Guillermo E. Parada, Jack Daiyang Li, Kevin R. Brown, Jason Moffat, Benjamin J. Blencowe · 2026 · Nature Communications
57. Directed evolution of small RNA-stabilizing motifs that improve prime-editing efficiency
    Holt A. Sakai, Sarah E. Pierce, Allen Yujie Jiang, Ana Cristian, Meirui An, Chae Rin Kim, Nouraiz Ahmed, Colin F. Hemez, Y. Allen Tao, Emily Zhang et al. · 2026 · Nature Biotechnology
58. Requirements for the neurodevelopmental disorder-associated gene ZNF292 in human cortical interneuron development and function
    Komal Kaushik, Gareth Chapman, Ramachandran Prakasam, Faiza Batool, Maamoon Saleh, Julianna J. Determan, James E. Huettner, Kristen L. Kroll · 2025 · Cell Reports
59. A multi-kingdom genetic barcoding system for precise clone isolation
    Soh Ishiguro, Kana Ishida, Rina C. Sakata, Minori Ichiraku, Ren Takimoto, Rina Yogo, Yusuke Kijima, Hideto Mori, Mamoru Tanaka, S. B. King et al. · 2025 · Nature Biotechnology
60. Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing
    Tianzi Wei, Jiaxuan Li, Xiang Lei, Risheng Lin, Qingyan Wu, Zhenfeng Zhang, Shimin Shuai, Ruilin Tian · 2025 · Cell Reports
61. Genomic and Transcriptomic Profiling of High-risk Bladder Cancer Reveals Diverse Molecular and Microenvironment Ecosystems
    Khyati A. Meghani, Yanni Yu, Noah Frydenlund, Erik Z. Li, Bonnie Choy, Sarki Abba Abdulkadir, Joshua J. Meeks · 2025 · European Urology
62. Computational Methods for Analysis of Large-Scale CRISPR Screens
    Xueqiu Lin, Augustine G. Chemparathy, Marie F. La Russa, Timothy Daley, Lei S. Qi · 2020 · Annual Review of Biomedical Data Science
63. Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay
    Eleni P. Mimitou, Anthony Youzhi Cheng, Antonino Montalbano, Stephanie Hao, Marlon Stoeckius, Mateusz Legut, Timothy Roush, Alberto M. Herrera, Efthymia Papalexi, Zeping Ouyang et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
64. Mapping variation in the morphological landscape of human cells with optical pooled CRISPRi screening
    Ramon Lorenzo D. Labitigan, Adrian L. Sanborn, Cynthia V. Hao, Caleb K. Chan, Nathan M. Belliveau, Eva M. Brown, Mansi Mehrotra, Julie A. Theriot · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
65. PerturbSci-Kinetics : Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens
    Zihan Xu, Andras Sziraki, Jasper Lee, Wei You Zhou, Junyue Cao · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
66. Multiplex, multimodal mapping of variant effects in secreted proteins
    Nicholas A. Popp, Rachel L. Powell, Melinda K. Wheelock, Kristen J. Holmes, Brendan D. Zapp, Kathryn M. Sheldon, Shelley Nakaya Fletcher, Xiaoping Wu, Shawn Fayer, Alan F. Rubin et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
67. Genome-wide single-cell perturbation screens with VIPerturb-seq
    Alexandra Bradu, John D. Blair, Erin M. Cumming, Isabella Mascio, Isabella Mascio, Junsuk Lee, Carl M. McCormick, Radhika Rathi, Benan N. Nalbant, Chao Dong et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
68. Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic loci
    Ke Zhao, Yao Zhou, Xueqi Wang, Zhao Wang, Xinran Xu, Yichen Chen, Lin Zhao, Chengyue Wu, Jianhua Wang, Hongcheng Yao et al. · 2025 · Cell Genomics
69. Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors
    Jiakai Hou, Shaoheng Liang, Chunyu Xu, Yanjun Wei, Yunfei Wang, Yukun Tan, Nidhi Sahni, Daniel James McGrail, Chantale Bernatchez, Michael A. Davies et al. · 2022 · NAR Cancer
70. Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network
    Marin Truchi, Caroline Lacoux, Cyprien Gille, Julien Fassy, Virginie Magnone, Rafael Lopez-Goncalvez, Cédric Girard-Riboulleau, Iris Manosalva, Marine Gautier‐Isola, Kévin Lebrigand et al. · 2024 · Frontiers in Bioinformatics
71. Large-scale discovery of chromatin dysregulation induced by oncofusions and other protein-coding variants
    Max P. C. Frenkel, James E. Corban, Margaux L.A. Hujoel, Zachary Scott Morris, Srivatsan Raman · 2024 · Nature Biotechnology
72. Analysis of single-cell CRISPR perturbations indicates that enhancers act multiplicatively and provides limited evidence for epistatic-like interactions
    Jessica Zhou, Karthik Guruvayurappan, Shushan Toneyan, Hsiuyi V. Chen, Aaron R. Chen, Peter K. Koo, Graham McVicker · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
73. scEMB: Learning context representation of genes based on large-scale single-cell transcriptomics
    Kang‐Lin Hsieh, Yan Chu, Xiaoyang Li, Patrick Glen Pilie, Yulin Dai · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
74. Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens
    Samuel G. Regalado, Chengxiang Qiu, Jean‐Benoît Lalanne, Beth Martin, Madeleine Duran, Cole Trapnell, Aidan Keith, Silvia Domcke, Jay Shendure · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
75. CRISPR GENome and epigenome engineering improves loss-of-function genetic-screening approaches
    Jannis Stadager, Chiara Bernardini, Laura Hartmann, Henrik May, Jessica Wiepcke, Monika Kuban, Z. Najafova, Steven A. Johnsen, Stefan Legewie, Franziska R. Traube et al. · 2025 · Cell Reports Methods
76. A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording
    Troy A. McDiarmid, Megan L. Taylor, Wei Chen, Florence M. Chardon, Junhong Choi, Hanna Liao, Xiaoyi Li, Haedong Kim, Jean‐Benoît Lalanne, Tony Yi‐Wei Li et al. · 2025 · Nature Biotechnology
77. Single cell transcriptional perturbome in pluripotent stem cell models
    Elisa Balmas, Maria Luisa Ratto, Kirsten E Snijders, Silvia Becca, Carla Liaci, Irene Ricca, Giorgio Roberto Merlo, Raffaele Calogero, Luca Alessandrì, Sasha Mendjan et al. · 2025 · Molecular Systems Biology
78. Awakening the Genome: CRISPR Activation to Unravel the Origin and Vulnerabilities of Cancer
    John E. La Marca, Sarah T. Diepstraten, Gemma L. Kelly, Marco J. Herold · 2024 · Annual Review of Cancer Biology
79. Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions
    Adelaide Tovar, Yasuhiro Kyono, Kirsten Nishino, Maya Bose, Arushi Varshney, Stephen C.J. Parker, Jacob Otto Kitzman · 2026 · Human Genetics and Genomics Advances
80. Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas
    Udit Parekh, Daniella McDonald, Amir Dailamy, Yan Wu, Thekla Cordes, Kun Zhang, Ann M. Ponsford Tipps, Christian M. Metallo, Prashant Mali · 2021 · iScience
81. Genetically Encoded Fluorescence Barcodes Allow for Single-Cell Analysis via Spectral Flow Cytometry
    Xiaoming Lu, Daniel J. Pritko, Megan Abravanel, Jonah R. Huggins, Oluwaferanmi Ogunleye, Tirthankar Biswas, Katia C. Ashy, Semaj K. Woods, Mariclaire W.T. Livingston, Mark Blenner et al. · 2025 · ACS Synthetic Biology
82. Generation of barcoded plasmid libraries for massively parallel analysis of chromatin position effects
    Mikhail O. Lebedev, Lyubov A. Yarinich, Anton V. Ivankin, Alexey V. Pindyurin · 2019 · Vavilov Journal of Genetics and Breeding
83. Mapping Genetic Interactions in Human Cancer Cells Using a One-Step tRNA-CRISPR System
    Derek Yisen Zhang, Xiong Gui, Xiaolong Yang · 2021 · Methods in molecular biology
84. crisprQTL mapping as a genome-wide association framework for cellular genetic screens
    Molly J. Gasperini, Andrew J. Hill, José L. McFaline‐Figueroa, Beth Martin, Cole Trapnell, Nadav Ahituv, Jay Shendure · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
85. Decoding Heterogenous Single-cell Perturbation Responses
    Bicna Song, Dingyu Liu, Weiwei Dai, Natalie F. McMyn, Qingyang Wang, Dapeng Yang, Adam Krejčí, Anatoly Vasilyev, Nicole Untermoser, Anke Loregger et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
86. FAST-STEM: A human pluripotent stem cell engineering toolkit for rapid design-build-test-learn development of human cell-based therapeutic devices
    Aaron H. Rosenstein, Rangarajan Sambathkumar, Brandon M. Murareanu, Navroop K. Dhaliwal, Fumao Sun, Xinyaun Zhao, Abolfazl Dadvar, Rasha Al-attar, Andrew Chai, Nitya Gulati et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
87. An expanded role for single-cell chemical genomics profiling in drug discovery
    Adeya Wyatt, Kevin Hoffer-Hawlik, Ross M. Giglio, Elham Azizi, José L. McFaline‐Figueroa · 2026 · Biochemical Journal
88. Disordered protein LAT encodes relative levels of signaling pathways in T cell activation
    Adam J. Rubin, Tyler T. Dao, Amelia V. Schueppert, Saehyun Choi, Jay T. Groves, Aviv Regev, Alex K. Shalek · 2026 · Science
89. Combinatorial In Vivo Genome Editing Identifies Widespread Epistasis and an Accessible Fitness Landscape During Lung Tumorigenesis
    Jess D. Hebert, Yuning J. Tang, Márton Szamecz, Laura Andrejka, Steven S. Lopez, Dmitri A. Petrov, Gábor Zoltán Boross, Monte M. Winslow · 2025 · Molecular Biology and Evolution
90. CRISPR Screening in Single Cells
    Johan Henriksson · 2019 · Methods in molecular biology
91. Selenocysteine metabolism is a targetable vulnerability in MYCN -amplified cancers
    Hamed Alborzinia, Zhiyi Chen, Umut Yildiz, Florêncio Porto Freitas, Felix C. E. Vogel, Julianna Patricia Varga, Jasmin Batani, Christoph Bartenhagen, Werner Schmitz, Gabriele Büchel et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
92. memento: Generalized differential expression analysis of single-cell RNA-seq with method of moments estimation and efficient resampling
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93. Endogenous fine-mapping of functional regulatory elements in complex genetic loci
    Ke Zhao, Yao Zhou, Chengyue Wu, Jianhua Wang, Hongcheng Yao, Xin Cheng, Lin Zhao, Wei Wang, Xinlei Chu, Xianfu Yi et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
94. Mapping variation in the morphological landscape of human cells with optical pooled CRISPRi screening
    Ramon Lorenzo D. Labitigan, Adrian L. Sanborn, Cynthia V. Hao, Caleb K. Chan, Nathan M. Belliveau, Eva M. Brown, Mansi Mehrotra, Julie A. Theriot · 2024 · eLife
95. HyperCas12a enables multiplexed CRISPRi screens
    Schuyler M. Melore, Christian McRoberts Amador, Marisa C. Hamilton, Charles A. Gersbach, Timothy E. Reddy · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
96. Functional mapping of epigenetic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes
    Yuning J. Tang, Haiqing Xu, Nicholas W. Hughes, Samuel H. Kim, Paloma A. Ruiz, Emily G. Shuldiner, Steven S. Lopez, Jess D. Hebert, Saswati Karmakar, Laura Andrejka et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
97. Dissecting cellular ecosystem with single-cell CRISPR screens
    Zhirui Liu, Zilin Lan, Xiaoli Kang, Yao Yao, Shuquan Rao · 2025 · Blood Science
98. Next-generation CRISPR screens enable causal systems immunology
    Hao Shi, Hongbo Chi · 2026 · The Journal of Experimental Medicine
99. Integrative analyses elucidate transcriptional regulatory functions of risk alleles for metabolic liver disease
    Biying Zhu, Na He, Yang Xiao, Bin Chen, C Li, Ravi Mandla, Yifan Liu, Jiayu Zhang, Xiao Chang, Fulong Yu et al. · 2026 · Nature Genetics
100. Editing the Epigenome in Neurodegenerative Diseases
     Anna S. Vetchinova, E. Yu. Fedotova, Sergey Nikolaevich Illarioshkin · 2021 · Neurochemical Journal