A citation-based method for searching scientific literature

Maximilian Haeussler, Kai Schönig, Hélène Eckert, Alexis Eschstruth, Joffrey Mianné, Jean-Baptiste Renaud, Sylvie Schneider-Maunoury, Alena Shkumatava, Lydia Teboul, Jim Kent, Jean-Stephane Joly, Jean-Paul Concordet. Genome Biol 2016
Times Cited: 756







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



Times Cited
  Times     Co-cited
Similarity


Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.
John G Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W Vaimberg, Katherine F Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard,[...]. Nat Biotechnol 2016
24

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

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases.
Shengdar Q Tsai, Zongli Zheng, Nhu T Nguyen, Matthew Liebers, Ved V Topkar, Vishal Thapar, Nicolas Wyvekens, Cyd Khayter, A John Iafrate, Long P Le,[...]. Nat Biotechnol 2015
20

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
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
16

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.
Miguel A Moreno-Mateos, Charles E Vejnar, Jean-Denis Beaudoin, Juan P Fernandez, Emily K Mis, Mustafa K Khokha, Antonio J Giraldez. Nat Methods 2015
570
15

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
14


DeepCRISPR: optimized CRISPR guide RNA design by deep learning.
Guohui Chuai, Hanhui Ma, Jifang Yan, Ming Chen, Nanfang Hong, Dongyu Xue, Chi Zhou, Chenyu Zhu, Ke Chen, Bin Duan,[...]. Genome Biol 2018
115
12

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
11

Genome editing. The new frontier of genome engineering with CRISPR-Cas9.
Jennifer A Doudna, Emmanuelle Charpentier. Science 2014
11

Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells.
Daesik Kim, Sangsu Bae, Jeongbin Park, Eunji Kim, Seokjoong Kim, Hye Ryeong Yu, Jinha Hwang, Jong-Il Kim, Jin-Soo Kim. Nat Methods 2015
577
11

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells.
Yanfang Fu, Jennifer A Foden, Cyd Khayter, Morgan L Maeder, Deepak Reyon, J Keith Joung, Jeffry D Sander. Nat Biotechnol 2013
11

Sequence determinants of improved CRISPR sgRNA design.
Han Xu, Tengfei Xiao, Chen-Hao Chen, Wei Li, Clifford A Meyer, Qiu Wu, Di Wu, Le Cong, Feng Zhang, Jun S Liu,[...]. Genome Res 2015
287
11

Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning.
Daqi Wang, Chengdong Zhang, Bei Wang, Bin Li, Qiang Wang, Dong Liu, Hongyan Wang, Yan Zhou, Leming Shi, Feng Lan,[...]. Nat Commun 2019
70
15


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
10

E-CRISP: fast CRISPR target site identification.
Florian Heigwer, Grainne Kerr, Michael Boutros. Nat Methods 2014
447
10

Rationally engineered Cas9 nucleases with improved specificity.
Ian M Slaymaker, Linyi Gao, Bernd Zetsche, David A Scott, Winston X Yan, Feng Zhang. Science 2016
10

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets.
Shengdar Q Tsai, Nhu T Nguyen, Jose Malagon-Lopez, Ved V Topkar, Martin J Aryee, J Keith Joung. Nat Methods 2017
339
10

WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system.
Nathan Wong, Weijun Liu, Xiaowei Wang. Genome Biol 2015
150
10

Easy quantitative assessment of genome editing by sequence trace decomposition.
Eva K Brinkman, Tao Chen, Mario Amendola, Bas van Steensel. Nucleic Acids Res 2014
10

CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool.
Manuel Stemmer, Thomas Thumberger, Maria Del Sol Keyer, Joachim Wittbrodt, Juan L Mateo. PLoS One 2015
429
9

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
9

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

Genetic screens in human cells using the CRISPR-Cas9 system.
Tim Wang, Jenny J Wei, David M Sabatini, Eric S Lander. Science 2014
9

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells.
Xuebing Wu, David A Scott, Andrea J Kriz, Anthony C Chiu, Patrick D Hsu, Daniel B Dadon, Albert W Cheng, Alexandro E Trevino, Silvana Konermann, Sidi Chen,[...]. Nat Biotechnol 2014
578
9

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
9

Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells.
Ayal Hendel, Rasmus O Bak, Joseph T Clark, Andrew B Kennedy, Daniel E Ryan, Subhadeep Roy, Israel Steinfeld, Benjamin D Lunstad, Robert J Kaiser, Alec B Wilkens,[...]. Nat Biotechnol 2015
566
8

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
8

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
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

Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach.
Raj Chari, Prashant Mali, Mark Moosburner, George M Church. Nat Methods 2015
223
8

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity.
Vikram Pattanayak, Steven Lin, John P Guilinger, Enbo Ma, Jennifer A Doudna, David R Liu. Nat Biotechnol 2013
915
7

Predicting the mutations generated by repair of Cas9-induced double-strand breaks.
Felicity Allen, Luca Crepaldi, Clara Alsinet, Alexander J Strong, Vitalii Kleshchevnikov, Pietro De Angeli, Petra Páleníková, Anton Khodak, Vladimir Kiselev, Michael Kosicki,[...]. Nat Biotechnol 2018
190
7

CRISPR-Cas9 Structures and Mechanisms.
Fuguo Jiang, Jennifer A Doudna. Annu Rev Biophys 2017
596
7

SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with high generalization performance.
Hui Kwon Kim, Younggwang Kim, Sungtae Lee, Seonwoo Min, Jung Yoon Bae, Jae Woo Choi, Jinman Park, Dongmin Jung, Sungroh Yoon, Hyongbum Henry Kim. Sci Adv 2019
40
17

CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens.
Jean-Paul Concordet, Maximilian Haeussler. Nucleic Acids Res 2018
274
7

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
7

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
7

A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells.
Christopher A Vakulskas, Daniel P Dever, Garrett R Rettig, Rolf Turk, Ashley M Jacobi, Michael A Collingwood, Nicole M Bode, Matthew S McNeill, Shuqi Yan, Joab Camarena,[...]. Nat Med 2018
308
6

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
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

CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters.
Ferhat Alkan, Anne Wenzel, Christian Anthon, Jakob Hull Havgaard, Jan Gorodkin. Genome Biol 2018
44
13

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
6

Mapping the genomic landscape of CRISPR-Cas9 cleavage.
Peter Cameron, Chris K Fuller, Paul D Donohoue, Brittnee N Jones, Matthew S Thompson, Matthew M Carter, Scott Gradia, Bastien Vidal, Elizabeth Garner, Euan M Slorach,[...]. Nat Methods 2017
181
6

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks.
Megan van Overbeek, Daniel Capurso, Matthew M Carter, Matthew S Thompson, Elizabeth Frias, Carsten Russ, John S Reece-Hoyes, Christopher Nye, Scott Gradia, Bastien Vidal,[...]. Mol Cell 2016
219
6


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
6

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
6


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.