F Ann Ran, Patrick D Hsu, Jason Wright, Vineeta Agarwala, David A Scott, Feng Zhang. Nat Protoc 2013
Times Cited: 5542
Times Cited: 5542
Times Cited
Times Co-cited
Similarity
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
Prashant Mali, Luhan Yang, Kevin M Esvelt, John Aach, Marc Guell, James E DiCarlo, Julie E Norville, George M Church. Science 2013
9
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
8
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
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
8
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
Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A Doudna, Emmanuelle Charpentier. Science 2012
7
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
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
7
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
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
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
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
5
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
Yanfang Fu, Jennifer A Foden, Cyd Khayter, Morgan L Maeder, Deepak Reyon, J Keith Joung, Jeffry D Sander. Nat Biotechnol 2013
5
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
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
5
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
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
5
Improved vectors and genome-wide libraries for CRISPR screening.
Neville E Sanjana, Ophir Shalem, Feng Zhang. Nat Methods 2014
Neville E Sanjana, Ophir Shalem, Feng Zhang. Nat Methods 2014
5
NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
5
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
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
4
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases.
Sangsu Bae, Jeongbin Park, Jin-Soo Kim. Bioinformatics 2014
Sangsu Bae, Jeongbin Park, Jin-Soo Kim. Bioinformatics 2014
4
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
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
4
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
Alexis C Komor, Yongjoo B Kim, Michael S Packer, John A Zuris, David R Liu. Nature 2016
4
Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity.
F Ann Ran, Patrick D Hsu, Chie-Yu Lin, Jonathan S Gootenberg, Silvana Konermann, Alexandro E Trevino, David A Scott, Azusa Inoue, Shogo Matoba, Yi Zhang,[...]. Cell 2013
F Ann Ran, Patrick D Hsu, Chie-Yu Lin, Jonathan S Gootenberg, Silvana Konermann, Alexandro E Trevino, David A Scott, Azusa Inoue, Shogo Matoba, Yi Zhang,[...]. Cell 2013
4
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
4
Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
Heng Li, Richard Durbin. Bioinformatics 2009
4
BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
4
Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
4
4
Easy quantitative assessment of genome editing by sequence trace decomposition.
Eva K Brinkman, Tao Chen, Mario Amendola, Bas van Steensel. Nucleic Acids Res 2014
Eva K Brinkman, Tao Chen, Mario Amendola, Bas van Steensel. Nucleic Acids Res 2014
4
RNA targeting with CRISPR-Cas13.
Omar O Abudayyeh, Jonathan S Gootenberg, Patrick Essletzbichler, Shuo Han, Julia Joung, Joseph J Belanto, Vanessa Verdine, David B T Cox, Max J Kellner, Aviv Regev,[...]. Nature 2017
Omar O Abudayyeh, Jonathan S Gootenberg, Patrick Essletzbichler, Shuo Han, Julia Joung, Joseph J Belanto, Vanessa Verdine, David B T Cox, Max J Kellner, Aviv Regev,[...]. Nature 2017
4
CRISPR/Cas, the immune system of bacteria and archaea.
Philippe Horvath, Rodolphe Barrangou. Science 2010
Philippe Horvath, Rodolphe Barrangou. Science 2010
4
Cerebral organoids model human brain development and microcephaly.
Madeline A Lancaster, Magdalena Renner, Carol-Anne Martin, Daniel Wenzel, Louise S Bicknell, Matthew E Hurles, Tessa Homfray, Josef M Penninger, Andrew P Jackson, Juergen A Knoblich. Nature 2013
Madeline A Lancaster, Magdalena Renner, Carol-Anne Martin, Daniel Wenzel, Louise S Bicknell, Matthew E Hurles, Tessa Homfray, Josef M Penninger, Andrew P Jackson, Juergen A Knoblich. Nature 2013
3
E-CRISP: fast CRISPR target site identification.
Florian Heigwer, Grainne Kerr, Michael Boutros. Nat Methods 2014
Florian Heigwer, Grainne Kerr, Michael Boutros. Nat Methods 2014
3
CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences.
Yanni Lin, Thomas J Cradick, Matthew T Brown, Harshavardhan Deshmukh, Piyush Ranjan, Neha Sarode, Brian M Wile, Paula M Vertino, Frank J Stewart, Gang Bao. Nucleic Acids Res 2014
Yanni Lin, Thomas J Cradick, Matthew T Brown, Harshavardhan Deshmukh, Piyush Ranjan, Neha Sarode, Brian M Wile, Paula M Vertino, Frank J Stewart, Gang Bao. Nucleic Acids Res 2014
3
Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy.
Leonela Amoasii, John C W Hildyard, Hui Li, Efrain Sanchez-Ortiz, Alex Mireault, Daniel Caballero, Rachel Harron, Thaleia-Rengina Stathopoulou, Claire Massey, John M Shelton,[...]. Science 2018
Leonela Amoasii, John C W Hildyard, Hui Li, Efrain Sanchez-Ortiz, Alex Mireault, Daniel Caballero, Rachel Harron, Thaleia-Rengina Stathopoulou, Claire Massey, John M Shelton,[...]. Science 2018
3
Off-target Effects in CRISPR/Cas9-mediated Genome Engineering.
Xiao-Hui Zhang, Louis Y Tee, Xiao-Gang Wang, Qun-Shan Huang, Shi-Hua Yang. Mol Ther Nucleic Acids 2015
Xiao-Hui Zhang, Louis Y Tee, Xiao-Gang Wang, Qun-Shan Huang, Shi-Hua Yang. Mol Ther Nucleic Acids 2015
3
The Molecular Signatures Database (MSigDB) hallmark gene set collection.
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, Pablo Tamayo. Cell Syst 2015
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, Pablo Tamayo. Cell Syst 2015
3
Bacteria-autophagy interplay: a battle for survival.
Ju Huang, John H Brumell. Nat Rev Microbiol 2014
Ju Huang, John H Brumell. Nat Rev Microbiol 2014
3
Defining a Cancer Dependency Map.
Aviad Tsherniak, Francisca Vazquez, Phil G Montgomery, Barbara A Weir, Gregory Kryukov, Glenn S Cowley, Stanley Gill, William F Harrington, Sasha Pantel, John M Krill-Burger,[...]. Cell 2017
Aviad Tsherniak, Francisca Vazquez, Phil G Montgomery, Barbara A Weir, Gregory Kryukov, Glenn S Cowley, Stanley Gill, William F Harrington, Sasha Pantel, John M Krill-Burger,[...]. Cell 2017
3
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences.
Charlotte Soneson, Michael I Love, Mark D Robinson. F1000Res 2015
Charlotte Soneson, Michael I Love, Mark D Robinson. F1000Res 2015
3
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
3
Genetic screens in human cells using the CRISPR-Cas9 system.
Tim Wang, Jenny J Wei, David M Sabatini, Eric S Lander. Science 2014
Tim Wang, Jenny J Wei, David M Sabatini, Eric S Lander. Science 2014
3
JASPAR 2020: update of the open-access database of transcription factor binding profiles.
Oriol Fornes, Jaime A Castro-Mondragon, Aziz Khan, Robin van der Lee, Xi Zhang, Phillip A Richmond, Bhavi P Modi, Solenne Correard, Marius Gheorghe, Damir Baranašić,[...]. Nucleic Acids Res 2020
Oriol Fornes, Jaime A Castro-Mondragon, Aziz Khan, Robin van der Lee, Xi Zhang, Phillip A Richmond, Bhavi P Modi, Solenne Correard, Marius Gheorghe, Damir Baranašić,[...]. Nucleic Acids Res 2020
3
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.
Elphège P Nora, Anton Goloborodko, Anne-Laure Valton, Johan H Gibcus, Alec Uebersohn, Nezar Abdennur, Job Dekker, Leonid A Mirny, Benoit G Bruneau. Cell 2017
Elphège P Nora, Anton Goloborodko, Anne-Laure Valton, Johan H Gibcus, Alec Uebersohn, Nezar Abdennur, Job Dekker, Leonid A Mirny, Benoit G Bruneau. Cell 2017
3
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
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
3
A protein-tagging system for signal amplification in gene expression and fluorescence imaging.
Marvin E Tanenbaum, Luke A Gilbert, Lei S Qi, Jonathan S Weissman, Ronald D Vale. Cell 2014
Marvin E Tanenbaum, Luke A Gilbert, Lei S Qi, Jonathan S Weissman, Ronald D Vale. Cell 2014
3
Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
3
Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6.
Jonathan S Gootenberg, Omar O Abudayyeh, Max J Kellner, Julia Joung, James J Collins, Feng Zhang. Science 2018
Jonathan S Gootenberg, Omar O Abudayyeh, Max J Kellner, Julia Joung, James J Collins, Feng Zhang. Science 2018
3
Nucleic acid detection with CRISPR-Cas13a/C2c2.
Jonathan S Gootenberg, Omar O Abudayyeh, Jeong Wook Lee, Patrick Essletzbichler, Aaron J Dy, Julia Joung, Vanessa Verdine, Nina Donghia, Nichole M Daringer, Catherine A Freije,[...]. Science 2017
Jonathan S Gootenberg, Omar O Abudayyeh, Jeong Wook Lee, Patrick Essletzbichler, Aaron J Dy, Julia Joung, Vanessa Verdine, Nina Donghia, Nichole M Daringer, Catherine A Freije,[...]. Science 2017
3
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
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
3
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
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
3
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
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
3
Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering.
Addison V Wright, James K Nuñez, Jennifer A Doudna. Cell 2016
Addison V Wright, James K Nuñez, Jennifer A Doudna. Cell 2016
3
Early positive exercise test and extensive coronary disease: effect of antianginal therapy.
J Mukharji, M Kremers, K Lipscomb, C G Blomqvist. Am J Cardiol 1985
J Mukharji, M Kremers, K Lipscomb, C G Blomqvist. Am J Cardiol 1985
5
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
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
3
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.