High-throughput functional genomics using CRISPR-Cas9

Untitled work

Bartel (2004) · doi:10.1016/s0092-8674(04)00045-5 · Cited by 34,714

A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., & Mello, C. C. (1998) · Nature · doi:10.1038/35888 · Cited by 15,429

Multiplex Genome Engineering Using CRISPR/Cas Systems

Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339

RNA-Guided Human Genome Engineering via Cas9

Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210

MicroRNAs: small RNAs with a big role in gene regulation

He, L., & Hannon, G. J. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1379 · Cited by 7,118

Development and Applications of CRISPR-Cas9 for Genome Engineering

Hsu, P. D., Lander, E. S., & Zhang, F. (2014) · Cell · doi:10.1016/j.cell.2014.05.010 · Cited by 5,762

Improved vectors and genome-wide libraries for CRISPR screening

Sanjana, N. E., Shalem, O., & Zhang, F. (2014) · Nature Methods · doi:10.1038/nmeth.3047 · Cited by 5,239

Genome-scale CRISPR-Cas9 knockout screening in human cells

Shalem, O., Sanjana, N. E., Hartenian, E., Shi, X., Scott, D. A., Mikkelsen, T. S., Heckl, D., Ebert, B. L., Root, D. E., Doench, J. G., et al. (2014) · Science · doi:10.1126/science.1247005 · Cited by 5,234

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016

DNA targeting specificity of RNA-guided Cas9 nucleases

Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741

Mutations affecting segment number and polarity in Drosophila

Nüsslein‐Volhard, C., & Wieschaus, E. F. (1980) · Nature · doi:10.1038/287795a0 · Cited by 4,370

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., Stern-Ginossar, N., Brandman, O., Whitehead, E. H., Doudna, J. A., et al. (2013) · Cell · doi:10.1016/j.cell.2013.06.044 · Cited by 3,696

One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering

Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.04.025 · Cited by 3,495

Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity

Ran, F. A., Hsu, P. D., Lin, C.-Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., Scott, D. A., Inoue, A., Matoba, S., Zhang, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.08.021 · Cited by 3,299

High-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells

Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander, J. D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2623 · Cited by 3,292

Genetic screens in human cells using the CRISPR-Cas9 system

Wang, T., Wei, J. J., Sabatini, D. M., & Lander, E. S. (2014) · Science · doi:10.1126/science.1246981 · Cited by 2,856

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., et al. (2015) · Nature · doi:10.1038/nature14136 · Cited by 2,825

Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

Gasiunas, G., Barrangou, R., Horvath, P., & Siksnys, V. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208507109 · Cited by 2,769

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., Whitehead, E. H., Guimaraes, C., Panning, B., Ploegh, H. L., Bassik, M. C., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.029 · Cited by 2,728

In vivo genome editing using Staphylococcus aureus Cas9

Ran, F. A., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., Kriz, A. J., Zetsche, B., Shalem, O., Wu, X., Makarova, K. S., et al. (2015) · Nature · doi:10.1038/nature14299 · Cited by 2,687

Mechanisms of gene silencing by double-stranded RNA

Meister, G., & Tuschl, T. (2004) · Nature · doi:10.1038/nature02873 · Cited by 2,598

CRISPR RNA Maturation by Trans-Encoded Small RNA and Host Factor RNase III

Deltcheva, E., Chylinski, K., Sharma, C. M., Gonzales, K., Chao, Y., Pirzada, Z. A., Eckert, M. R., Vogel, J., & Charpentier, E. (2011) · Nature · doi:10.1038/nature09886 · Cited by 2,563

The ENCODE (ENCyclopedia Of DNA Elements) Project

(2004) · Science · doi:10.1126/science.1105136 · Cited by 2,390

Expression profiling reveals off-target gene regulation by RNAi

Jackson, A. L., Bartz, S. R., Schelter, J., Kobayashi, S. V., Burchard, J., Mao, M., Li, B., Cavet, G., & Linsley, P. S. (2003) · Nature Biotechnology · doi:10.1038/nbt831 · Cited by 2,370

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

Garneau, J. E., Dupuis, M.-È., Villion, M., Romero, D. A., Barrangou, R., Boyaval, P., Fremaux, C., Horvath, P., Magadán, A. H., & Moineau, S. (2010) · Nature · doi:10.1038/nature09523 · Cited by 2,336

Crystal structure of Cas9 in complex with guide RNA and target DNA

Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., & Nureki, O. (2014) · Cell · doi:10.1016/j.cell.2014.02.001 · Cited by 2,306

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

Tsai, S. Q., Zheng, Z., Nguyen, N. T., Liebers, M., Topkar, V. V., Thapar, V., Wyvekens, N., Khayter, C., Iafrate, A. J., Le, L. P., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3117 · Cited by 2,268

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

Platt, R. J., Chen, S., Zhou, Y., Yim, M. J., Swiech, L., Kempton, H. R., Dahlman, J. E., Parnas, O., Eisenhaure, T. M., Jovanovic, M., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.014 · Cited by 2,001

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs

Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2808 · Cited by 1,993

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

Chen, B., Gilbert, L. A., Cimini, B. A., Schnitzbauer, J., Zhang, W., Li, G., Park, J. S., Blackburn, E. H., Weissman, J. S., Qi, L. S., et al. (2013) · Cell · doi:10.1016/j.cell.2013.12.001 · Cited by 1,988

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., & Doudna, J. A. (2014) · Nature · doi:10.1038/nature13011 · Cited by 1,822

A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen

Moffat, J., Grueneberg, D. A., Yang, X., Kim, S. Y., Kloepfer, A. M., Hinkle, G., Piqani, B., Eisenhaure, T., Luo, B., Grenier, J. K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.01.040 · Cited by 1,804

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L., & Church, G. M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2675 · Cited by 1,752

The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio

Haffter, P., Granato, M., Brand, M., Mullins, M. C., Hammerschmidt, M., Kane, D. A., Odenthal, J., van Eeden, F. J. M., Jiang, Y., Heisenberg, C., et al. (1996) · Development · doi:10.1242/dev.123.1.1 · Cited by 1,691

Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation

Doench, J. G., Hartenian, E., Graham, D. B., Tothova, Z., Hegde, M., Smith, I., Sullender, M., Ebert, B. L., Xavier, R. J., & Root, D. E. (2014) · Nature Biotechnology · doi:10.1038/nbt.3026 · Cited by 1,617

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

Tanenbaum, M. E., Gilbert, L. A., Qi, L. S., Weissman, J. S., & Vale, R. D. (2014) · Cell · doi:10.1016/j.cell.2014.09.039 · Cited by 1,611

Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin

Bolotin, A., Quinquis, B., Sorokin, A., & Ehrlich, S. D. (2005) · Microbiology · doi:10.1099/mic.0.28048-0 · Cited by 1,558

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

Pattanayak, V., Lin, S., Guilinger, J. P., Ma, E., Doudna, J. A., & Liu, D. R. (2013) · Nature Biotechnology · doi:10.1038/nbt.2673 · Cited by 1,487

Gene silencing in mammals by small interfering RNAs

McManus, M. T., & Sharp, P. A. (2002) · Nature Reviews Genetics · doi:10.1038/nrg908 · Cited by 1,400

A genetic screen for mutations affecting embryogenesis in zebrafish

Driever, W., Solnica‐Krezel, L., Schier, A. F., Neuhauss, S. C. F., Malicki, J. J., Stemple, D. L., Stainier, D. Y. R., Zwartkruis, F. J. T., Abdelilah, S., Rangini, Z., et al. (1996) · Development · doi:10.1242/dev.123.1.37 · Cited by 1,338

RNA-guided gene activation by CRISPR-Cas9-based transcription factors

Perez-Pinera, P., Kocak, D. D., Vockley, C. M., Adler, A. F., Kabadi, A. M., Polstein, L. R., Thakore, P. I., Glass, K. A., Ousterout, D. G., Leong, K. W., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2600 · Cited by 1,328

CRISPR RNA–guided activation of endogenous human genes

Maeder, M. L., Linder, S. J., Cascio, V. M., Fu, Y., Ho, Q. H., & Joung, J. K. (2013) · Nature Methods · doi:10.1038/nmeth.2598 · Cited by 1,249

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

Larson, M. H., Gilbert, L. A., Wang, X., Lim, W. A., Weissman, J. S., & Qi, L. S. (2013) · Nature Protocols · doi:10.1038/nprot.2013.132 · Cited by 1,241

Structures of Cas9 endonucleases reveal RNA-mediated conformational activation

Jinek, M., Jiang, F., Taylor, D. W., Sternberg, S. H., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., et al. (2014) · Science · doi:10.1126/science.1247997 · Cited by 1,230

A guide to genome engineering with programmable nucleases

Kim, S., & Kim, J. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3686 · Cited by 1,216

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., & Marraffini, L. A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt520 · Cited by 1,145

Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application

Jackson, A. L., & Linsley, P. S. (2009) · Nature Reviews Drug Discovery · doi:10.1038/nrd3010 · Cited by 1,126

A large-scale RNAi screen in human cells identifies new components of the p53 pathway

Berns, K., Hijmans, E. M., Mullenders, J., Brummelkamp, T. R., Velds, A., Heimerikx, M., Kerkhoven, R. M., Madiredjo, M., Nijkamp, W., Weigelt, B., et al. (2004) · Nature Cell Biology · doi:10.1038/nature02371 · Cited by 1,080

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library

Koike-Yusa, H., Li, Y., Tan, E.-P., Velasco-Herrera, M. D. C., & Yusa, K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2800 · Cited by 1,064

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

Wu, X., Scott, D. A., Kriz, A. J., Chiu, A. C., Hsu, P. D., Dadon, D. B., Cheng, A. W., Trevino, A. E., Konermann, S., Chen, S., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2889 · Cited by 944

Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds

Zalatan, J. G., Lee, M. E., Almeida, R., Gilbert, L. A., Whitehead, E. H., La Russa, M., Tsai, J. C., Weissman, J. S., Dueber, J. E., Qi, L. S., et al. (2015) · Cell · doi:10.1016/j.cell.2014.11.052 · Cited by 938

3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets

Birmingham, A., Anderson, E. M., Reynolds, A., Ilsley-Tyree, D., Leake, D., Fedorov, Y., Baskerville, S., Maksimova, E., Robinson, K., Karpilow, J., et al. (2006) · Nature Methods · doi:10.1038/nmeth854 · Cited by 920

siRNAs: applications in functional genomics and potential as therapeutics

Dorsett, Y., & Tuschl, T. (2004) · Nature Reviews Drug Discovery · doi:10.1038/nrd1345 · Cited by 917

The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli

Sapranauskas, R., Gasiūnas, G., Fremaux, C., Barrangou, R., Horvath, P., & Šikšnys, V. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr606 · Cited by 835

Optical control of mammalian endogenous transcription and epigenetic states

Konermann, S., Brigham, M. D., Trevino, A. E., Hsu, P. D., Heidenreich, M., Cong, L., Platt, R. J., Scott, D. A., Church, G. M., & Zhang, F. (2013) · Nature · doi:10.1038/nature12466 · Cited by 803

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

Esvelt, K. M., Mali, P., Braff, J. L., Moosburner, M., Yaung, S. J., & Church, G. M. (2013) · Nature Methods · doi:10.1038/nmeth.2681 · Cited by 786

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

Kuscu, C., Arslan, S., Singh, R., Thorpe, J., & Adli, M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2916 · Cited by 777

In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9

Swiech, L., Heidenreich, M., Banerjee, A., Habib, N., Li, Y., Trombetta, J., Sur, M., & Zhang, F. (2015) · Nature Biotechnology · doi:10.1038/nbt.3055 · Cited by 772

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

Cheng, A. W., Wang, H., Yang, H., Shi, L., Yarden Katz, A., Theunissen, T. W., Rangarajan, S., Shivalila, C., Dadon, D. B., & Jaenisch, R. (2013) · Cell Research · doi:10.1038/cr.2013.122 · Cited by 768

Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease.

Rouet, P., Smih, F., & Jasin, M. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.12.8096 · Cited by 739

High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells

Zhou, Y., Zhu, S., Cai, C., Yuan, P., Li, C., Huang, Y., & Wei, W. (2014) · Nature · doi:10.1038/nature13166 · Cited by 733

Defining functional DNA elements in the human genome

Kellis, M., Wold, B. J., Snyder, M. P., Bernstein, B., Kundaje, A. B., Marinov, G. K., Ward, L. D., Birney, E., Crawford, G. E., Dekker, J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1318948111 · Cited by 724

Genome-Wide RNAi Analysis of Growth and Viability in Drosophila Cells

Boutros, M., Kiger, A. A., Armknecht, S., Kerr, K., Hild, M., Koch, B., Haas, S. A., Paro, R., & Perrimon, N. (2004) · Science · doi:10.1126/science.1091266 · Cited by 702

A resource for large-scale RNA-interference-based screens in mammals

Paddison, P. J., Silva, J. M., Conklin, D. S., Schlabach, M., Li, M. Z., Aruleba, S., Balija, V. S., O'Shaughnessy, A., Gnoj, L., Scobie, K., et al. (2004) · Nature Cell Biology · doi:10.1038/nature02370 · Cited by 695

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases

Frock, R. L., Hu, J., Meyers, R. M., Ho, Y.-J., Kii, E., & Alt, F. W. (2015) · Nature Biotechnology · doi:10.1038/nbt.3101 · Cited by 673

Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2

Frank, F., Sonenberg, N., & Nagar, B. (2010) · Nature · doi:10.1038/nature09039 · Cited by 666

Determination of Anteroposterior Polarity in Drosophila

Nüsslein‐Volhard, C., Frohnhöfer, H. G., & Lehmann, R. (1987) · Science · doi:10.1126/science.3686007 · Cited by 649

The art and design of genetic screens: Drosophila melanogaster

St Johnston, D. (2002) · Nature Reviews Genetics · doi:10.1038/nrg751 · Cited by 644

CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences

Lin, Y., Cradick, T. J., Brown, M. T., Deshmukh, H., Ranjan, P., Sarode, N., Wile, B. M., Vertino, P. M., Stewart, F. J., & Bao, G. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku402 · Cited by 634

Second-generation shRNA libraries covering the mouse and human genomes

Silva, J. M., Li, M. Z., Chang, K. C. N., Ge, W., Golding, M. C., Rickles, R. J., Siolas, D., Hu, G., Paddison, P. J., Schlabach, M. R., et al. (2005) · Nature Genetics · doi:10.1038/ng1650 · Cited by 625

Statistical methods for analysis of high-throughput RNA interference screens

Birmingham, A., Selfors, L. M., Forster, T., Wrobel, D., Kennedy, C. J., Shanks, E., Santoyo-Lopez, J., Dunican, D. J., Long, A., Kelleher, D., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1351 · Cited by 586

A public genome-scale lentiviral expression library of human ORFs

Yang, X., Boehm, J. S., Yang, X., Salehi-Ashtiani, K., Hao, T., Shen, Y., Lubonja, R., Thomas, S. R., Alkan, O., Bhimdi, T., et al. (2011) · Nature Methods · doi:10.1038/nmeth.1638 · Cited by 570

Haploid Genetic Screens in Human Cells Identify Host Factors Used by Pathogens

Carette, J. E., Guimarães, C. P., Varadarajan, M., Park, A. S., Wüthrich, I., Godarova, A., Kotecki, M., Cochran, B., Spooner, E., Ploegh, H. L., et al. (2009) · Science · doi:10.1126/science.1178955 · Cited by 499

The art and design of genetic screens: RNA interference

Boutros, M., & Ahringer, J. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2364 · Cited by 489

Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system

Dupuy, A. J., Akagi, K., Largaespada, D. A., Copeland, N. G., & Jenkins, N. A. (2005) · Nature · doi:10.1038/nature03691 · Cited by 482

Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing

Veres, A., Gosis, B. S., Ding, Q., Collins, R., Ragavendran, A., Brand, H., Erdin, S., Cowan, C. A., Talkowski, M. E., & Musunuru, K. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.04.020 · Cited by 474

Synthetic lethal screen identification of chemosensitizer loci in cancer cells

Whitehurst, A. W., Bodemann, B. O., Cardenas, J., Ferguson, D., Girard, L., Peyton, M., Minna, J. D., Michnoff, C. H., Hao, W., Roth, M. G., et al. (2007) · Nature · doi:10.1038/nature05697 · Cited by 471

The art and design of genetic screens: Caenorhabditis elegans

Jørgensen, E. M., & Mango, S. E. (2002) · Nature Reviews Genetics · doi:10.1038/nrg794 · Cited by 440

The art and design of genetic screens: zebrafish

Patton, E. E., & Zon, L. I. (2001) · Nature Reviews Genetics · doi:10.1038/35103567 · Cited by 433

An Oncogenomics-Based In Vivo RNAi Screen Identifies Tumor Suppressors in Liver Cancer

Zender, L., Xue, W., Zuber, J. A., Semighini, C. P., Krasnitz, A., Ma, B., Zender, P., Kubicka, S., Luk, J. M., Schirmacher, P., et al. (2008) · Cell · doi:10.1016/j.cell.2008.09.061 · Cited by 428

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

Cheung, H. W., Cowley, G. S., Weir, B. A., Boehm, J. S., Rusin, S., Scott, J. A., East, A., Ali, L. D., Lizotte, P. H., Wong, T. C., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1109363108 · Cited by 423

Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers

Hoffman, G. R., Rahal, R., Buxton, F., Xiang, K., McAllister, G., Frias, E., Bagdasarian, L., Huber, J., Lindeman, A., Chen, D., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1316793111 · Cited by 421

Antiviral RNA Interference in Mammalian Cells

Maillard, P. V., Ciaudo, C., Marchais, A., Li, Y., Jay, F., Ding, S., & Voinnet, O. (2013) · Science · doi:10.1126/science.1241930 · Cited by 409

High-throughput RNAi screening in cultured cells: a user's guide

Echeverri, C. J., & Perrimon, N. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1836 · Cited by 380

Microhomology-based choice of Cas9 nuclease target sites

Bae, S., Kweon, J., Kim, H. S., & Kim, J. (2014) · Nature Methods · doi:10.1038/nmeth.3015 · Cited by 380

High-throughput RNAi screening by time-lapse imaging of live human cells

Neumann, B., Held, M., Liebel, U., Erfle, H., Rogers, P., Pepperkok, R., & Ellenberg, J. (2006) · Nature Methods · doi:10.1038/nmeth876 · Cited by 380

A Genome-Scale RNA Interference Screen Implicates NF1 Loss in Resistance to RAF Inhibition

Whittaker, S. R., Theurillat, J.-P. P., Allen, E. M. V., Wagle, N., Hsiao, J., Cowley, G. S., Schadendorf, D., Root, D. E., & Garraway, L. A. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0470 · Cited by 369

RNA Interference Functions as an Antiviral Immunity Mechanism in Mammals

Li, Y., Lü, J., Han, Y., Fan, X., & Ding, S. (2013) · Science · doi:10.1126/science.1241911 · Cited by 365

High-content genome-wide RNAi screens identify regulators of parkin upstream of mitophagy

Hasson, S. A., Kane, L. A., Yamano, K., Huang, C.-H., Sliter, D. A., Buehler, E., Wang, C., Heman-Ackah, S. M., Hessa, T., Guha, R., et al. (2013) · Nature · doi:10.1038/nature12748 · Cited by 365

A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility

Bassik, M. C., Kampmann, M., Lebbink, R. J., Wang, S., Hein, M. Y., Poser, I., Weibezahn, J., Horlbeck, M. A., Chen, S., Mann, M., et al. (2013) · Cell · doi:10.1016/j.cell.2013.01.030 · Cited by 365

Genome-scale loss-of-function screening with a lentiviral RNAi library

Root, D. E., Hacohen, N., Hahn, W. C., Lander, E. S., & Sabatini, D. M. (2006) · Nature Methods · doi:10.1038/nmeth924 · Cited by 364

Introduction of Double-Strand Breaks into the Genome of Mouse Cells by Expression of a Rare-Cutting Endonuclease

Rouet, P., Smih, F., & Jasin, M. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.12.8096-8106.1994 · Cited by 363

Saturation editing of genomic regions by multiplex homology-directed repair

Findlay, G. M., Boyle, E. A., Hause, R. J., Klein, J. C., & Shendure, J. (2014) · Nature · doi:10.1038/nature13695 · Cited by 362

The Many Faces of RNAi

Ketting, R. F. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.01.012 · Cited by 353

A genetic screen for mutations affecting embryogenesis in zebrafish.

Driever, W., Solnica‐Krezel, L., Schier, A. F., Neuhauss, S. C. F., Malicki, J. J., Stemple, D. L., Stainier, D. Y. R., Zwartkruis, F. J. T., Abdelilah, S., Rangini, Z., et al. (1996) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-215 · Cited by 349

RNAi screening comes of age: improved techniques and complementary approaches

Mohr, S. E., Smith, J. A., Shamu, C. E., Neumüller, R. A., & Perrimon, N. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3860 · Cited by 344

Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs

Smith, C., Gore, A., Yan, W., Abalde-Atristain, L., Li, Z., He, C., Wang, Y., Brodsky, R. A., Zhang, K., Cheng, L., et al. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.06.011 · Cited by 342

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

LeProust, E. M., Peck, B. J., Spirin, K., McCuen, H. B., Moore, B., Namsaraev, E., & Caruthers, M. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq163 · Cited by 326

The Loop Position of shRNAs and Pre-miRNAs Is Critical for the Accuracy of Dicer Processing In Vivo

Gu, S., Jin, L., Zhang, Y., Huang, Y., Zhang, F., Valdmanis, P. N., & Kay, M. A. (2012) · Cell · doi:10.1016/j.cell.2012.09.042 · Cited by 291

In vivo RNAi screening identifies a mechanism of sorafenib resistance in liver cancer

Rudalska, R., Dauch, D., Longerich, T., McJunkin, K., Wuestefeld, T., Kang, T.-W., Hohmeyer, A., Pesic, M., Leibold, J., von Thun, A., et al. (2014) · Nature Medicine · doi:10.1038/nm.3679 · Cited by 282

Lessons from Nature: microRNA-based shRNA libraries

Chang, K., Elledge, S. J., & Hannon, G. J. (2006) · Nature Methods · doi:10.1038/nmeth923 · Cited by 280

A computational study of off-target effects of RNA interference

Qiu, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki324 · Cited by 276

Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of Squamous Cell Carcinomas

Schramek, D., Sendoel, A., Segal, J. P., Beronja, S., Heller, E., Oristian, D., Reva, B. A., & Fuchs, E. V. (2014) · Science · doi:10.1126/science.1248627 · Cited by 269

The art and design of genetic screens: yeast

Forsburg, S. L. (2001) · Nature Reviews Genetics · doi:10.1038/35088500 · Cited by 265

Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast

Trcek, T., Larson, D. R., Moldón, A., Query, C. C., & Singer, R. H. (2011) · Cell · doi:10.1016/j.cell.2011.11.051 · Cited by 261

The art and design of genetic screens: Arabidopsis thaliana

Page, D. R., & Grossniklaus, U. (2002) · Nature Reviews Genetics · doi:10.1038/nrg730 · Cited by 240

In vivo discovery of immunotherapy targets in the tumour microenvironment

Zhou, P., Shaffer, D. R., Alvarez Arias, D. A., Nakazaki, Y., Pos, W., Torres, A. J., Cremasco, V., Dougan, S. K., Cowley, G. S., Elpek, K., et al. (2014) · Nature · doi:10.1038/nature12988 · Cited by 237

Using next-generation sequencing to isolate mutant genes from forward genetic screens

Schneeberger, K. (2014) · Nature reviews genetics · doi:10.1038/nrg3745 · Cited by 233

PiggyBac Transposon Mutagenesis: A Tool for Cancer Gene Discovery in Mice

Rad, R., Rad, L., Wang, W., Cadiñanos, J., Vassiliou, G. S., Rice, S., Campos, L. S., Yusa, K., Banerjee, R., Li, M. A., et al. (2010) · Science · doi:10.1126/science.1193004 · Cited by 230

Building mammalian signalling pathways with RNAi screens

Moffat, J., & Sabatini, D. M. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1860 · Cited by 204

The love–hate relationship between Ras and NotchPreprint

Sundaram, M. V. (2005) · Genes & Development · doi:10.1101/gad.1330605 · Cited by 191

Promoter Elements Regulate Cytoplasmic mRNA Decay

Bregman, A., Avraham‐Kelbert, M., Barkai, O., Duek, L., Guterman, A., & Choder, M. (2011) · Cell · doi:10.1016/j.cell.2011.12.005 · Cited by 181

RNAi screens in mice identify physiological regulators of oncogenic growth

Beronja, S., Janki, P., Heller, E., Lien, W., Keyes, B. E., Oshimori, N., & Fuchs, E. V. (2013) · Nature · doi:10.1038/nature12464 · Cited by 162

Harnessing transposons for cancer gene discovery

Copeland, N. G., & Jenkins, N. A. (2010) · Nature reviews. Cancer · doi:10.1038/nrc2916 · Cited by 155

Isolation and Characterization of a Near-Haploid Human Cell Line

Kotecki, M. (1999) · Experimental Cell Research · doi:10.1006/excr.1999.4656 · Cited by 155

Mismatch repair genes identified using genetic screens in Blm-deficient embryonic stem cells

Guo, G., Wang, W., & Bradley, A. (2004) · Nature · doi:10.1038/nature02653 · Cited by 135

Repurposing CRISPR/Cas9 for in situ functional assaysPreprint

Malina, A., Mills, J. R., Cencic, R., Yan, Y., Fraser, J., Nederveen-Schippers, L. M., Paquet, M., Dostie, J., & Pelletier, J. (2013) · Genes & Development · doi:10.1101/gad.227132.113 · Cited by 132

Harnessing transposons for cancer gene discovery

Neal, Copeland, Nancy, N., & Jenkins (2007) · 南京医科大学学报：英文版 · Cited by 128

Quantifying Genome-Editing Outcomes at Endogenous Loci with SMRT Sequencing

Hendel, A., Kildebeck, E., Fine, E. J., Clark, J. T., Punjya, N., Sebastiano, V., Bao, G., & Porteus, M. H. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.02.040 · Cited by 124

Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis

Cleary, M. A., Kilian, K. A., Wang, Y., Bradshaw, J., Cavet, G., Ge, W., Kulkarni, A., Paddison, P. J., Chang, K., Sheth, N. U., et al. (2004) · Nature Methods · doi:10.1038/nmeth724 · Cited by 108

The art and design of genetic screens: mammalian culture cells

Grimm, S. (2004) · Nature reviews genetics · doi:10.1038/nrg1291 · Cited by 107

The art and design of genetic screens: mouse

Kile, B. T., & Hilton, D. J. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1636 · Cited by 104

Rapid creation and quantitative monitoring of high coverage shRNA libraries

Bassik, M. C., Lebbink, R. J., Churchman, L. S., Ingolia, N. T., Patena, W., LeProust, E. M., Schuldiner, M., Weissman, J. S., & McManus, M. T. (2009) · Nature Methods · doi:10.1038/nmeth.1330 · Cited by 99

The art and design of genetic screens: Escherichia coli

Shuman, H. A., & Silhavy, T. J. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1087 · Cited by 99

Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens

Franceschini, A., Meier, R., Casanova, A., Kreibich, S., Daga, N., Andritschke, D., Dilling, S., Rämö, P., Emmenlauer, M., Kaufmann, A. M., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1402353111 · Cited by 70

siRNA off-target effects in genome-wide screens identify signaling pathway members

Buehler, E., Khan, A. A., Marine, S. D., Rajaram, M., Bahl, A., Burchard, J., & Ferrer, M. (2012) · Scientific Reports · doi:10.1038/srep00428 · Cited by 69

A dynamic perspective of RNAi library development

Pan, Q., van der Laan, L. J. W., Janssen, H. L. A., & Peppelenbosch, M. P. (2012) · Trends in biotechnology · doi:10.1016/j.tibtech.2012.01.002 · Cited by 28

Computational detection and suppression of sequence-specific off-target phenotypes from whole genome RNAi screens

Zhong, R., Kim, J., Kim, H. S., Kim, M., Lum, L., Levine, B., Xiao, G., White, M. A., & Xie, Y. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku306 · Cited by 22

Antiviral RNAi in mammals

Burgess, D. J. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3616 · Cited by 5

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

Anzalone, A. V., Koblan, L. W., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0561-9 · Cited by 2,237

The Biogenesis, Functions, and Challenges of Circular RNAs

Li, X., Yang, L. C., & Chen, L. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.034 · Cited by 2,060

CRISPR–Cas9 Structures and Mechanisms

Jiang, F., & Doudna, J. A. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-062215-010822 · Cited by 2,029

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions

Oughtred, R., Rust, J., Chang, C., Breitkreutz, B., Stark, C., Willems, A., Boucher, L., Leung, G., Kolas, N., Zhang, F., et al. (2021) · Protein Science · doi:10.1002/pro.3978 · Cited by 1,858

Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects

Li, H., Yang, Y., Hong, W., Huang, M., Wu, M., & Zhao, X. (2020) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-019-0089-y · Cited by 1,829

Genetic screens and functional genomics using CRISPR /Cas9 technology

Hartenian, E., & Doench, J. G. (2015) · FEBS Journal · doi:10.1111/febs.13248 · Cited by 100

High‐throughput screens in mammalian cells using the CRISPR‐Cas9 system

Peng, J., Zhou, Y., Zhu, S., & Wei, W. (2015) · FEBS Journal · doi:10.1111/febs.13251 · Cited by 60

Genome-scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening

Joung, J., Konermann, S., Gootenberg, J. S., Abudayyeh, O. O., Platt, R. J., Brigham, M. D., Sanjana, N. E., & Zhang, F. (2017) · Nature Protocols · doi:10.1038/nprot.2017.016 · Cited by 1,243

The Current Situation and Development Prospect of Whole-Genome Screening

Yang, C., Lei, Y., Ren, T., & Yao, M. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25010658 · Cited by 12

Prion Diseases

Pagel, M. D. (1996) · Trends in Neurosciences · doi:10.1016/s0166-2236(96)60033-2