A citation-based method for searching scientific literature

John G Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W Vaimberg, Katherine F Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard, Herbert W Virgin, Jennifer Listgarten, David E Root. Nat Biotechnol 2016
Times Cited: 1532







List of co-cited articles
520 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A Doudna, Emmanuelle Charpentier. Science 2012
22

DNA targeting specificity of RNA-guided Cas9 nucleases.
Patrick D Hsu, David A Scott, Joshua A Weinstein, F Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli J Fine, Xuebing Wu, Ophir Shalem,[...]. Nat Biotechnol 2013
20

Improved vectors and genome-wide libraries for CRISPR screening.
Neville E Sanjana, Ophir Shalem, Feng Zhang. Nat Methods 2014
19

Multiplex genome engineering using CRISPR/Cas systems.
Le Cong, F Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D Hsu, Xuebing Wu, Wenyan Jiang, Luciano A Marraffini,[...]. Science 2013
18

Genome-scale CRISPR-Cas9 knockout screening in human cells.
Ophir Shalem, Neville E Sanjana, Ella Hartenian, Xi Shi, David A Scott, Tarjei Mikkelson, Dirk Heckl, Benjamin L Ebert, David E Root, John G Doench,[...]. Science 2014
15

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Wei Li, Han Xu, Tengfei Xiao, Le Cong, Michael I Love, Feng Zhang, Rafael A Irizarry, Jun S Liu, Myles Brown, X Shirley Liu. Genome Biol 2014
721
14

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities.
Kendall R Sanson, Ruth E Hanna, Mudra Hegde, Katherine F Donovan, Christine Strand, Meagan E Sullender, Emma W Vaimberg, Amy Goodale, David E Root, Federica Piccioni,[...]. Nat Commun 2018
203
14

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12

RNA-guided human genome engineering via Cas9.
Prashant Mali, Luhan Yang, Kevin M Esvelt, John Aach, Marc Guell, James E DiCarlo, Julie E Norville, George M Church. Science 2013
12

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing.
Kornel Labun, Tessa G Montague, Maximilian Krause, Yamila N Torres Cleuren, Håkon Tjeldnes, Eivind Valen. Nucleic Acids Res 2019
337
11

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
11

Genetic screens in human cells using the CRISPR-Cas9 system.
Tim Wang, Jenny J Wei, David M Sabatini, Eric S Lander. Science 2014
11

Genome engineering using the CRISPR-Cas9 system.
F Ann Ran, Patrick D Hsu, Jason Wright, Vineeta Agarwala, David A Scott, Feng Zhang. Nat Protoc 2013
10

Search-and-replace genome editing without double-strand breaks or donor DNA.
Andrew V Anzalone, Peyton B Randolph, Jessie R Davis, Alexander A Sousa, Luke W Koblan, Jonathan M Levy, Peter J Chen, Christopher Wilson, Gregory A Newby, Aditya Raguram,[...]. Nature 2019
9

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage.
Alexis C Komor, Yongjoo B Kim, Michael S Packer, John A Zuris, David R Liu. Nature 2016
9


High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects.
Benjamin P Kleinstiver, Vikram Pattanayak, Michelle S Prew, Shengdar Q Tsai, Nhu T Nguyen, Zongli Zheng, J Keith Joung. Nature 2016
8

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening.
Julia Joung, Silvana Konermann, Jonathan S Gootenberg, Omar O Abudayyeh, Randall J Platt, Mark D Brigham, Neville E Sanjana, Feng Zhang. Nat Protoc 2017
390
8

Highly efficient Cas9-mediated transcriptional programming.
Alejandro Chavez, Jonathan Scheiman, Suhani Vora, Benjamin W Pruitt, Marcelle Tuttle, Eswar P R Iyer, Shuailiang Lin, Samira Kiani, Christopher D Guzman, Daniel J Wiegand,[...]. Nat Methods 2015
752
8

Rationally engineered Cas9 nucleases with improved specificity.
Ian M Slaymaker, Linyi Gao, Bernd Zetsche, David A Scott, Winston X Yan, Feng Zhang. Science 2016
8

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
8

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
8

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage.
Nicole M Gaudelli, Alexis C Komor, Holly A Rees, Michael S Packer, Ahmed H Badran, David I Bryson, David R Liu. Nature 2017
8

Enhanced proofreading governs CRISPR-Cas9 targeting accuracy.
Janice S Chen, Yavuz S Dagdas, Benjamin P Kleinstiver, Moira M Welch, Alexander A Sousa, Lucas B Harrington, Samuel H Sternberg, J Keith Joung, Ahmet Yildiz, Jennifer A Doudna. Nature 2017
548
8

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR.
Wei Li, Johannes Köster, Han Xu, Chen-Hao Chen, Tengfei Xiao, Jun S Liu, Myles Brown, X Shirley Liu. Genome Biol 2015
143
7

CRISPResso2 provides accurate and rapid genome editing sequence analysis.
Kendell Clement, Holly Rees, Matthew C Canver, Jason M Gehrke, Rick Farouni, Jonathan Y Hsu, Mitchel A Cole, David R Liu, J Keith Joung, Daniel E Bauer,[...]. Nat Biotechnol 2019
291
7

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants.
Russell T Walton, Kathleen A Christie, Madelynn N Whittaker, Benjamin P Kleinstiver. Science 2020
277
7

Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis.
Sidi Chen, Neville E Sanjana, Kaijie Zheng, Ophir Shalem, Kyungheon Lee, Xi Shi, David A Scott, Jun Song, Jen Q Pan, Ralph Weissleder,[...]. Cell 2015
476
7

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.
Traver Hart, Megha Chandrashekhar, Michael Aregger, Zachary Steinhart, Kevin R Brown, Graham MacLeod, Monika Mis, Michal Zimmermann, Amelie Fradet-Turcotte, Song Sun,[...]. Cell 2015
740
7

Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs.
Jennifer Listgarten, Michael Weinstein, Benjamin P Kleinstiver, Alexander A Sousa, J Keith Joung, Jake Crawford, Kevin Gao, Luong Hoang, Melih Elibol, John G Doench,[...]. Nat Biomed Eng 2018
104
7

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.
Luke A Gilbert, Max A Horlbeck, Britt Adamson, Jacqueline E Villalta, Yuwen Chen, Evan H Whitehead, Carla Guimaraes, Barbara Panning, Hidde L Ploegh, Michael C Bassik,[...]. Cell 2014
7

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library.
Hiroko Koike-Yusa, Yilong Li, E-Pien Tan, Martin Del Castillo Velasco-Herrera, Kosuke Yusa. Nat Biotechnol 2014
641
7

CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.
Luke A Gilbert, Matthew H Larson, Leonardo Morsut, Zairan Liu, Gloria A Brar, Sandra E Torres, Noam Stern-Ginossar, Onn Brandman, Evan H Whitehead, Jennifer A Doudna,[...]. Cell 2013
7

Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.
Lei S Qi, Matthew H Larson, Luke A Gilbert, Jennifer A Doudna, Jonathan S Weissman, Adam P Arkin, Wendell A Lim. Cell 2013
7

E-CRISP: fast CRISPR target site identification.
Florian Heigwer, Grainne Kerr, Michael Boutros. Nat Methods 2014
447
7

Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation.
John G Doench, Ella Hartenian, Daniel B Graham, Zuzana Tothova, Mudra Hegde, Ian Smith, Meagan Sullender, Benjamin L Ebert, Ramnik J Xavier, David E Root. Nat Biotechnol 2014
842
7

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.
Isaac B Hilton, Anthony M D'Ippolito, Christopher M Vockley, Pratiksha I Thakore, Gregory E Crawford, Timothy E Reddy, Charles A Gersbach. Nat Biotechnol 2015
965
6

Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.
Fiona M Behan, Francesco Iorio, Gabriele Picco, Emanuel Gonçalves, Charlotte M Beaver, Giorgia Migliardi, Rita Santos, Yanhua Rao, Francesco Sassi, Marika Pinnelli,[...]. Nature 2019
409
6

Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.
Robin M Meyers, Jordan G Bryan, James M McFarland, Barbara A Weir, Ann E Sizemore, Han Xu, Neekesh V Dharia, Phillip G Montgomery, Glenn S Cowley, Sasha Pantel,[...]. Nat Genet 2017
668
6


Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury,[...]. Cell 2016
528
6

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
6

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system.
Bernd Zetsche, Jonathan S Gootenberg, Omar O Abudayyeh, Ian M Slaymaker, Kira S Makarova, Patrick Essletzbichler, Sara E Volz, Julia Joung, John van der Oost, Aviv Regev,[...]. Cell 2015
6

Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR.
Maximilian Haeussler, Kai Schönig, Hélène Eckert, Alexis Eschstruth, Joffrey Mianné, Jean-Baptiste Renaud, Sylvie Schneider-Maunoury, Alena Shkumatava, Lydia Teboul, Jim Kent,[...]. Genome Biol 2016
756
6

In vivo genome editing using Staphylococcus aureus Cas9.
F Ann Ran, Le Cong, Winston X Yan, David A Scott, Jonathan S Gootenberg, Andrea J Kriz, Bernd Zetsche, Ophir Shalem, Xuebing Wu, Kira S Makarova,[...]. Nature 2015
6

Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.
Baohui Chen, Luke A Gilbert, Beth A Cimini, Joerg Schnitzbauer, Wei Zhang, Gene-Wei Li, Jason Park, Elizabeth H Blackburn, Jonathan S Weissman, Lei S Qi,[...]. Cell 2013
6

Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors.
Andrew V Anzalone, Luke W Koblan, David R Liu. Nat Biotechnol 2020
437
6

A highly specific SpCas9 variant is identified by in vivo screening in yeast.
Antonio Casini, Michele Olivieri, Gianluca Petris, Claudia Montagna, Giordano Reginato, Giulia Maule, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Francesca Demichelis,[...]. Nat Biotechnol 2018
208
6


GUIDES: sgRNA design for loss-of-function screens.
Joshua A Meier, Feng Zhang, Neville E Sanjana. Nat Methods 2017
33
18


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.