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

Cited by (278)

Items 201–278 of 278

1. GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens
   Qian Yu, Paulien Van Minsel, Eva Galle, Bernard Thienpont · 2023 · Communications Biology
2. Functional genomics of psychiatric disease risk using genome engineering
   Meilín Fernández García, Samuel K. Powell, Elizabeth A. LaMarca, Michael B. Fernando, Sophie Cohen, Gang Fang, Schahram Akbarian, Kristen Brennand · 2021 · Elsevier eBooks
3. Single cell CRISPR base editor engineering and transcriptional characterization of cancer mutations
   Heon Seok Kim, Susan M. Grimes, Anuja Sathe, Billy T. Lau, Hanlee P. Ji · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
4. A multi-kingdom genetic barcoding system for precise target clone isolation
   Soh Ishiguro, Kana Ishida, Rina C. Sakata, Hideto Mori, Mamoru Takana, S. B. King, Omar S. Bashth, Minori Ichiraku, Nanami Masuyama, Ren Takimoto et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
5. Discovering chromatin dysregulation induced by protein-coding perturbations at scale
   Max P. C. Frenkel, Margaux L.A. Hujoel, Zachary Scott Morris, Srivatsan Raman · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
6. Combinatorial in vivo genome editing identifies widespread epistasis during lung tumorigenesis
   Jess D. Hebert, Yuning J. Tang, Laura Andrejka, Steven S. Lopez, Dmitri A. Petrov, Gábor Zoltán Boross, Monte M. Winslow · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
7. Inference of heterogeneous effects in single-cell genetic perturbation screens
   Zichu Fu, Lin Hou · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
8. Diversified, miniaturized and ancestral parts 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 W. Li et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
9. Functional Annotation of the Major Histocompatibility Complex Locus
   Lexi R. Bounds, Alejandro Barrera, Maria A. ter Weele, Siyan Liu, Euphy Y. Wu, Shengyu Li, Revathy Venukuttan, Ruhi Rai, W. Mu, Nahid Iglesias et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
10. Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell type specificity
    Julia Rühle, Robert Frömel, Aina Bernal, Chelsea Szu‐Tu, Joseph S. Bowness, Lars Velten · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
11. Detection of gene cis-regulatory element perturbations in single-cell transcriptomes
    Grace Hui Ting Yeo, Oscar Juez, Qing Chen, Budhaditya Banerjee, Lendy Chu, Max W. Shen, May Sabry, Ive Logister, Richard I. Sherwood, David K. Gifford · 2021 · PLoS Computational Biology
12. Single-cell exon deletion profiling reveals splicing events that shape gene expression and cell state dynamics
    Bandana Kumari, Arun Prasath Damodaran, Wilfried M. Guiblet, Mei‐Sheng Xiao, Amit K. Behera, Tyler A. On, CARL E. MCINTOSH, Maxwell Teszler, Chelsee Holloway, Sandra M. Le et al. · 2026 · Nature Communications
13. dHyperCas12a enables multiplexed CRISPRi screens
    Schuyler M. Melore, Christian D. McRoberts Amador, Marisa C. Hamilton, Charles A. Gersbach, Timothy E. Reddy · 2026 · Nature Communications
14. Challenges and opportunities in adapting high-throughput functional assays for in vivo neuroscience
    Din Selmanovic, Din Selmanovic · 2026 · Trends in Neurosciences
15. Pool-packaged AAV libraries exhibit extensive length-dependent and homology-dependent chimerism
    Jean‐Benoît Lalanne, Chau Huynh, John K. Mich, Avery C. Hunker, Troy A. McDiarmid, Haedong Kim, Boaz P. Levi, Jonathan T. Ting, Jay Shendure · 2026 · Nature Biotechnology
16. Linking GWAS risk genes to transcriptional features of major depressive disorder via in vivo Perturb-seq
    Liansheng Zhang, Xiangrui Kong, Qi Ma, Xinde Hu, Shicheng Cai, Bo Wang, Weijuan Zou, Tao Bai, Meimei Zhang, Liu Fan et al. · 2026 · Nature Genetics
17. Highly multiplexed mammalian metabolic engineering with a shotgun approach
    Julie Trolle, Sara Sessa, Aleksandra M. Wudzinska, Mark Grivainis, Katerina Rincones, Tori C. Rodrick, Drew R. Jones, David Fenyö, Sudarshan Pinglay, Jef D. Boeke · 2026 · Nature Biotechnology
18. Deciphering the Functional Long Non‐Coding RNAs Derived from MicroRNA Loci
    Weiqian Li, Yue Huo, Yue Ren, Chenxi Han, Shuo Li, Kangning Wang, Manman He, Yiying Chen, Yanran Wang, Lingjie Xu et al. · 2023 · Advanced Science
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, Adam Krejčí, Adrián Cortés, Alison Acevedo, Sunir Malla et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
20. In vivo single-cell CRISPR uncovers distinct TNF-α programs in clonal expansion and tumorigenesis
    Peter F. Renz, Umesh Ghoshdastider, Simona Baghai Sain, Fabiola Valdivia-Francia, Ameya Khandekar, Mark Ormiston, Martino Bernasconi, Jonas A. Kretz, Minkyoung Lee, Katie Hyams et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
21. Scalable single-cell pooled CRISPR screens with conventional knockout vector libraries
    Mirazul Islam, Yilin Yang, Alan J. Simmons, Yanwen Xu, Emilie L. Fisher, Wentao Deng, Brian C. Grieb, Paola Molina, Christian R. de Caestecker, Marisol A Ramirez-Solano et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
22. A scalable, high-throughput neural development platform identifies shared impact of ASD genes on cell fate and differentiation
    Xuran Wang, Matthew A. Lalli, Urvashi Thopte, Joseph D. Buxbaum · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
23. High-throughput single-cell CRISPRi screens stratify neurodevelopmental functions of schizophrenia-associated genes
    Umut Yildiz, Annique Claringbould, Mikael Marttinen, Víctor Campos-Fornés, Mantha Lamprousi, Manu Saraswat, Mathias Saver, Daria Bunina, Michael W. Dorrity, Judith B. Zaugg et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
24. Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs
    Bongmin Bae, Katherine Gu, Daniel Loftus, Amanda J. Whipple · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
25. A primer on single-cell genomics in myeloid biology
    Kyle Ferchen, Baobao Song, H. Leighton Grimes · 2020 · Current Opinion in Hematology
26. CRISPR screens identify gene targets and drug repositioning opportunities at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue, Aaron Hatzipantelis et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
27. Improved analyses of regulatory genome, transcriptome and gene function, mutation penetrance, and clinical applications
    Moyra Smith · 2021 · Elsevier eBooks
28. Single‐Cell Transcriptomics and Epigenomics for CRISPR‐Mediated Perturbation Studies
    Saumyaa Saumyaa, Ramy Elgendy, Alessandro Bonetti · 2022
29. CRISPR screens identify gene targets and drug repositioning opportunities at breast cancer risk loci
    Joseph Rosenbluh, Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2022 · Research Square
30. Faculty Opinions recommendation of A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition.
    Stephen Weiss · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
31. Faculty Opinions recommendation of Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.
    Kevin Yuk-Lap Yip · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
32. Data from 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, Zoe N. Rogers, Maryam Yousefi, Ian P. Winters, Charles M. Rudin, Dmitri A. Petrov et al. · 2023
33. Additional file 2 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
34. Additional file 7 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
35. Additional file 5 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
36. Additional file 3 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
37. Additional file 6 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
38. Additional file 8 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
39. Additional file 2 of Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen
    Qingkai Song, Ke Ni, Min Liu, Yini Li, Lixia Wang, Yingying Wang, Liu, Yingzheng, Zhenxing Yu, Yinyao Qi, Zhike Lu et al. · 2020 · Figshare
40. Additional file 5 of Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen
    Qingkai Song, Ke Ni, Min Liu, Yini Li, Lixia Wang, Yingying Wang, Liu, Yingzheng, Zhenxing Yu, Yinyao Qi, Zhike Lu et al. · 2020 · Figshare
41. Additional file 4 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
42. Additional file 3 of Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen
    Qingkai Song, Ke Ni, Min Liu, Yini Li, Lixia Wang, Yingying Wang, Liu, Yingzheng, Zhenxing Yu, Yinyao Qi, Zhike Lu et al. · 2020 · Figshare
43. 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)
44. Decoy-seq unlocks scalable genetic screening for regulatory small noncoding RNAs
    Bong Gun Choi, Sushil Sobti, Larisa M. Soto, Trey Charbonneau, Aiden M. Sababi, Albertas Navickas, Hamed Shateri Najafabadi, Hani Goodarzi · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
45. In vivo multiplexed modeling reveals diverse roles of the TBX2 subfamily and Egr1 in Kras-driven lung adenocarcinoma
    Athar Khalil, Trang Dinh, Meaghan Parks, Rebecca C. Obeng, Berkley E. Gryder, Adam M. Kresak, Yuxiang Wang, Jeff Maltas, Madeline Bedrock, Xiangzhen Wei et al. · 2025 · Genes & Diseases
46. Advances in single-cell perturbation modeling
    Xiaoning Qi, Lianhe Zhao, Runsheng Chen, Yi Chen Zhao · 2025 · Chinese Science Bulletin (Chinese Version)
47. RainBar: Optical Barcoding for Pooled Live-Cell Imaging with Single-Cell Resolution
    Ruzbeh Mosadeghi, Daniel A. Foyt, Louis Z. Sharp, Catherine A. Taylor, Neil Q. Tay, Stefan Oberlin, John Fan, Struan Bourke, Michael G. Kattah, Bo Huang et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
48. Scalable imaging-based profiling of CRISPR perturbations with protein barcodes
    Krishna Choudhary, Michael T. McManus · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
49. Additional file 6 of Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen
    Qingkai Song, Ke Ni, Liu, Min, Li, Yini, Wang, Lixia, Wang, Yingying, Liu, Yingzheng, Zhenxing Yu, Yinyao Qi, Zhike Lu et al. · 2020 · Figshare
50. Additional file 9 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Shi, Wei, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
51. Additional file 2 of SCEPTRE improves calibration and sensitivity in single-cell CRISPR screen analysis
    Timothy Barry, Wang, Xuran, John A. Morris, Roeder, Kathryn, Eugene Katsevich · 2021 · Figshare
52. Additional file 1 of SCEPTRE improves calibration and sensitivity in single-cell CRISPR screen analysis
    Timothy Barry, Wang, Xuran, John A. Morris, Roeder, Kathryn, Eugene Katsevich · 2021 · Figshare
53. Additional file 3 of In-organoid single-cell CRISPR screening reveals determinants of hepatocyte differentiation and maturation
    Liang, Junbo, Wei, Jinsong, Jun Cao, Jun Qian, Gao, Ran, Li, Xiaoyu, Wang, Dingding, Yani Gu, Dong, Lei, Yu, Jia et al. · 2024 · Figshare
54. Additional file 2 of In-organoid single-cell CRISPR screening reveals determinants of hepatocyte differentiation and maturation
    Liang, Junbo, Wei, Jinsong, Jun Cao, Jun Qian, Ran Gao, Li, Xiaoyu, Wang, Dingding, Yani Gu, Dong, Lei, Yu, Jia et al. · 2024 · Figshare
55. Additional file 1 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Shi, Wei, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
56. Additional file 1 of Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen
    Qingkai Song, Ni, Ke, Liu, Min, Li, Yini, Wang, Lixia, Wang, Yingying, Liu, Yingzheng, Zhenxing Yu, Yinyao Qi, Zhike Lu et al. · 2020 · Figshare
57. Additional file 1 of In-organoid single-cell CRISPR screening reveals determinants of hepatocyte differentiation and maturation
    Liang, Junbo, Wei, Jinsong, Jun Cao, Jun Qian, Gao, Ran, Li, Xiaoyu, Wang, Dingding, Yani Gu, Dong, Lei, Yu, Jia et al. · 2024 · Figshare
58. Multichannel genomic recording of biological information with ENGRAM
    Jenny F. Nathans, Troy A. McDiarmid, Wei Chen, Jay Shendure · 2026 · Nature Protocols
59. Preserved mitochondrial ribosomal protein gene expression marks a youthful transcriptional state in Chinese nonagenarians and centenarians
    Fu‐Hui Xiao, Haotian Wang, Long Zhao, Gong‐Hua Li, Si-Yu Ma, Li-Qin Yang, Hua Wang, Y X Zhang, Ji Li, Qing‐Peng Kong · 2026 · Cell Reports Medicine
60. HyperMap: An Efficient Framework for Transferring Perturbation Responses Across Diverse Biological Contexts
    Bhavya Dhaka, Jiahao Gao, Trey Ideker · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
61. Mosaic: Single-Cell Atlas of Stress
    Edward Siler Monk, Bianca M. Shieu, Dhruvita Kumbhani, Liang Fu, Albert Lin, Josephine Amalia Taverna, Carrie Jo Braden, C. Jeff Uribe-Lacy, Wensheng Zhang, Casey M. Sabbag et al. · 2026 · Cells
62. Systematic mapping of chromatin dysregulation driven by viral transcriptional regulators at scale
    James E. Corban, Keelin Reilly, Jaice T. Rottenberg, Andrea Hunger, Max Frenkel, Juan I. Fuxman Bass, Srivatsan Raman · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
63. Combinatorial transcription factor interactions drive modular gene regulatory networks
    Jialei Duan, B Li, Kartik Kulkarni, Gabriela Orquera-Tornakian, Daryl Barth, L H Wang, Vrushali Pandit, Joel Liou, Nikhil V Munshi, Gary C. Hon · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
64. Multimodal temporal mapping of macrophage transcriptome remodeling during Salmonella infection
    Christophe Toussaint, Peter W. S. Hill, Bastian Klodewig, Matthew J. G. Eldridge, Fabian Joachim Theis, Sophie Hélaine, Antoine‐Emmanuel Saliba · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
65. Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity
    Julia Rühle, Robert Frömel, Aina Bernal, Chelsea Szu‐Tu, Joseph S. Bowness, Lars Velten · 2026 · Genome biology
66. Single cell CRISPR screen identifies antagonism between Nsd1-H3K36me2 and Ezh2-H3K27me3 orchestrates pluripotency transition
    Yuqing Zhu, Qingying Wang, Y J Cao, Linxiao Hou, Lin Yang, Cheng Chen, Shoudong Ye, Wei Li, Jin Zhang · 2026 · Stem Cell Reports
67. Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes
    Elena Torlai Triglia, Tyler E. Miller, Neva C. Durand, Kyung Lock Kim, Salvador Casaní-Galdón, Joshua D’Antonio, Nauman Javed, Alessandro Paz Hernandez, Ayush Raman, Anna J. Cruz et al. · 2026 · Cell Genomics
68. Enhancer-gene regulatory interactions in colorectal cancer revealed through genome-wide CRISPRi perturbations
    Philip Law, Jayaram Vijayakrishnan, James Smith, Timothy Barry, Maria Mandelia, Eugene Katsevich, Richard S. Houlston · 2026 · Wellcome Open Research
69. Combinatorial transcription factor interactions drive modular gene regulatory networks
    Jialei Duan, Boxun Li, Kartik Kulkarni, Gabriela Orquera-Tornakian, Daryl Barth, L H Wang, Vrushali Pandit, Joel Liou, Nikhil V Munshi, Gary C. Hon · 2026 · eLife
70. Combinatorial transcription factor interactions drive modular gene regulatory networks
    Jialei Duan, Boxun Li, Kartik Kulkarni, Gabriela Orquera-Tornakian, Daryl Barth, L H Wang, Vrushali Pandit, Joel Liou, Nikhil V Munshi, Gary C. Hon · 2026 · eLife
71. Allele-specific chromatin architecture shapes imprinted domains and coordinates a distal enhancer and antisense transcription at the mouse Mest-Copg2 domain
    Bongmin Bae, Katherine Gu, Daniel Loftus, Amanda J. Whipple · 2026 · Nature Communications
72. High‐Content CRISPR Screening: Methods and Applications
    Yike Zhang, Yimeng Zhang, Xudong Tang, Xinyu Deng, Yitian Zhou, Yanfeng Wu, Jianhua Luo · 2026 · MedComm
73. Benchmarking methods for inferring single-cell transcription factor activity using large-scale perturbation sequencing data
    Yuehui Zhu, Dongmei Han, Zhen Wang · 2026 · Briefings in Bioinformatics
74. Revealing therapeutic single-cell transcriptomic signatures using a simple classifier
    Xiaoli Ma, Samantha Seah, David Gfeller, Christoph A. Merten · 2026 · Cell Reports Methods
75. High-throughput identification of chromatin-opening transcription factors
    Aidan Keith, Shruti Jain, Riza M. Daza, Chengxiang Qiu, Pierre‐Luc Germain, Jay Shendure, Silvia Domcke · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
76. Emerging frontiers for AI in single-cell genomics
    Sneha Mitra, Jiaxin Li, Christina S. Leslie · 2026 · Molecular Cell
77. A Compact Regulatory Logic Governs Fibroblast Cell State Plasticity in Fibrosis
    Ada M. Zhu, Yeting Li, Haiwei Zhang, Brindha Rathinasabapathi, Bastien Cimarosti, Rangarajan D. Nadadur, Vee Xu, Yu Huang, Yuqian An, Kirsten Auclair et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
78. "GiRAFR improves gRNA detection and annotation in single cell CRISPR screens" source data
    Qian Yu, Bernard Thienpont · 2023 · Figshare