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CRISPR/Cas Collection

CRISPR in Nucleic Acids Research

Read the Editorial by Senior Executive Editors, Barry Stoddard and Keith Fox.

Basic Studies of Genomics, Mechanism, and Structure

The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli.
Sapranauskas, R., Gasiunas, G., Fremaux, C., Barrangou, R., Horvath, P. and Siksnys, V.
Nucl. Acids Res. (2011), 39 (21) 9275-9282.
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Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus.
Deng, L., Kenchappa, C.S., Peng, X., She, Q. and Garrett, R.A.
Nucl. Acids Res. (2012), 40 (6) 2470-2480.
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Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli.
Yosef, I., Goren, M.G. and Qimron, U.
Nucl. Acids Res. (2012), 40 (12) 5569-5576.
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Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis.
Richter, H., Zoephel, J., Schermuly, J., Maticzka, D., Backofen, R. and Randau, L.
Nucl. Acids Res. (2012), 40 (19) 9887-9896.
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Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2.
Kenchappa, C.S., Heidarsson, P.O., Kragelund, B.B., Garrett, R.A. and Poulsen, F.M.
Nucl. Acids Res. (2013), 41 (5) 3424-3435.
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Crass: identification and reconstruction of CRISPR from unassembled metagenomic data.
Skennerton, C.T., Imelfort, M. and Tyson, G.W.
Nucl. Acids Res. (2013), 41 (10) e105.
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RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri.
Su, A.A., Tripp, V. and Randau, L.
Nucl. Acids Res. (2013), 41 (12) 6250-6258.
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Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2.
Arslan, Z., Wurm, R., Brener, O., Ellinger, P., Nagel-Steger, L., Oesterhelt, F., Schmitt, L., Willbold, D., Wagner, R., Gohlke, H., Smits S.H.J. and Pul U.
Nucl. Acids Res. (2013), 41 (12) 6347-6359.
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Unexpectedly broad target recognition of the CRISPR-mediated virus defence system in the archaeon Sulfolobus solfataricus.
Manica, A., Zebec, Z., Steinkellner, J. and Schleper, C.
Nucl. Acids Res. (2013), 41 (22) 10509-10517.
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Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases.
Niewoehner, O., Jinek, M. and Doudna, J.A.
Nucl. Acids Res. (2014), 42 (2) 1341-1353.
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Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process.
Li, M., Wang, R., Zhao, D. and Xiang, H.
Nucl. Acids Res. (2014), 42 (4) 2483-2492.
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Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems.
Fonfara, I., Le Rhun, A., Chylinski, K., Makarova, K.S., Lecrivain, A.L., Bzdrenga, J., Koonin, E.V. and Charpentier, E.
Nucl. Acids Res. (2014), 42 (4) 2577-2590.
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Active site plasticity enables metal-dependent tuning of Cas5d nuclease activity in CRISPR-Cas type I-C system.
Punetha, A., Sivathanu, R. and Anand, B.
Nucl. Acids Res. (2014), 42 (6) 3846-3856.
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In vitro assembly and activity of an archaeal CRISPR-Cas type I-A Cascade interference complex.
Plagens, A., Tripp, V., Daume, M., Sharma, K., Klingl, A., Hrle, A., Conti, E., Urlaub, H. and Randau, L.
Nucl. Acids Res. (2014), 42 (8) 5125-5138.
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CRISPR-mediated targeted mRNA degradation in the archaeon Sulfolobus solfataricus.
Zebec, Z., Manica, A., Zhang, J., White, M.F. and Schleper, C.
Nucl. Acids Res. (2014), 42 (8) 5280-5288.
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Pervasive generation of oppositely oriented spacers during CRISPR adaptation.
Shmakov, S., Savitskaya, E., Semenova, E., Logacheva, M.D., Datsenko, K.A. and Severinov, K.
Nucl. Acids Res. (2014), 42 (9) 5907-5916.
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Cas6 specificity and CRISPR RNA loading in a complex CRISPR-Cas system.
Sokolowski, R.D., Graham, S. and White, M.F.
Nucl. Acids Res. (2014), 42 (10) 6532-6541.
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Haloarcula hispanica CRISPR authenticates PAM of a target sequence to prime discriminative adaptation.
Li, M., Wang, R. and Xiang, H.
Nucl. Acids Res. (2014), 42 (11) 7226-7235.
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Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system.
Arslan, Z., Hermanns, V., Wurm, R., Wagner, R. and Pul, U.
Nucl. Acids Res. (2014), 42 (12) 7884-7893.
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Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer.
Richter, C., Dy, R.L., McKenzie, R.E., Watson, B.N., Taylor, C., Chang, J.T., McNeil, M.B., Staals, R.H. and Fineran, P.C.
Nucl. Acids Res. (2014), 42 (13) 8516-8526.
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The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity.
Lemak, S., Nocek, B., Beloglazova, N., Skarina, T., Flick, R., Brown, G., Joachimiak, A., Savchenko, A. and Yakunin, A.F.
Nucl. Acids Res. (2014), 42 (17) 11144-11155.
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An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference.
Peng, W., Feng, M., Feng, X., Liang, Y.X. and She, Q.
Nucl. Acids Res. (2015), 43 (1) 406-417.
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CRISPR RNA binding and DNA target recognition by purified Cascade complexes from Escherichia coli.
Beloglazova, N., Kuznedelov, K., Flick, R., Datsenko, K.A., Brown, G., Popovic, A., Lemak, S., Semenova, E., Severinov, K. and Yakunin, A.F.
Nucl. Acids Res. (2015), 43 (1) 530-543.
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Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition.
Liu, T., Li, Y., Wang, X., Ye, Q., Li, H., Liang, Y., She, Q. and Peng, N.
Nucl. Acids Res. (2015), 43 (2) 1044-1055.
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Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus.
Wei, Y., Chesne, M.T., Terns, R.M. and Terns, M.P.
Nucl. Acids Res. (2015), 43 (3) 1749-1758.
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Mechanism of foreign DNA recognition by a CRISPR RNA-guided surveillance complex from Pseudomonas aeruginosa.
Rollins, M.F., Schuman, J.T., Paulus, K., Bukhari, H.S. and Wiedenheft, B.
Nucl. Acids Res. (2015), 43 (4) 2216-2222.
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Regulation of the Type I-F CRISPR-Cas system by CRP-cAMP and GalM controls spacer acquisition and interference.
Patterson, A.G., Chang, J.T., Taylor, C. and Fineran, P.C.
Nucl. Acids Res. (2015), 43 (12) 6038-6048.
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The Cas6e ribonuclease is not required for interference and adaptation by the E. coli type I-E CRISPR-Cas system.
Semenova, E., Kuznedelov, K., Datsenko, K.A., Boudry, P.M., Savitskaya, E.E., Medvedeva, S., Beloglazova, N., Logacheva, M., Yakunin, A.F. and Severinov, K.
Nucl. Acids Res. (2015), 43 (12) 6049-6061.
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Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli.
van Erp, P.B., Jackson, R.N., Carter, J., Golden, S.M., Bailey, S. and Wiedenheft, B.
Nucl. Acids Res. (2015), 43 (17) 8381-8391.
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Interference activity of a minimal Type I CRISPR-Cas system from Shewanella putrefaciens.
Dwarakanath, S., Brenzinger, S., Gleditzsch, D., Plagens, A., Klingl, A., Thormann, K. and Randau, L.
Nucl. Acids Res. (2015), 43 (18) 8913-8923.
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DNA targeting by the type I-G and type I-A CRISPR-Cas systems of Pyrococcus furiosus.
Elmore, J., Deighan, T., Westpheling, J., Terns, R.M. and Terns, M.P.
Nucl. Acids Res. (2015), 43 (21) 10353-10363.
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Different genome stability proteins underpin primed and naive adaptation in E. coli CRISPR-Cas immunity.
Ivancic-Bace, I., Cass, S.D., Wearne, S.J. and Bolt, E.L.
Nucl. Acids Res. (2015), 43 (22) 10821-10830.
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CRISPR interference and priming varies with individual spacer sequences.
Xue, C., Seetharam, A.S., Musharova, O., Severinov, K., Brouns, S.J., Severin, A.J. and Sashital, D.G.
Nucl. Acids Res. (2015), 43 (22) 10831-10847.
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Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery.
Vorontsova, D., Datsenko, K.A., Medvedeva, S., Bondy-Denomy, J., Savitskaya, E.E., Pougach, K., Logacheva, M., Wiedenheft, B., Davidson, A.R., Severinov, K. and Semenova E..
Nucl. Acids Res. (2015), 43 (22) 10848-10860.
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Multiple nucleic acid cleavage modes in divergent type III CRISPR systems.
Zhang, J., Graham, S., Tello, A., Liu, H. and White, M.F.
Nucl. Acids Res. (2016), 44 (4) 1789-1799.
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Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3'-terminal segment of guide RNA.
Mekler, V., Minakhin, L., Semenova, E., Kuznedelov, K. and Severinov, K.
Nucl. Acids Res. (2016), 44 (6) 2837-2845.
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Applications for Targeted Genome Engineering and Gene Modification

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems.
DiCarlo, J.E., Norville, J.E., Mali, P., Rios, X., Aach, J. and Church, G.M.
Nucl. Acids Res. (2013), 41 (7) 4336-4343.
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Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish.
Xiao, A., Wang, Z., Hu, Y., Wu, Y., Luo, Z., Yang, Z., Zu, Y., Li, W., Huang, P., Tong, X. et al.
Nucl. Acids Res. (2013), 41 (14) e141.
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Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system.
Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F. and Marraffini, L.A.
Nucl. Acids Res. (2013), 41 (15) 7429-7437.
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CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity.
Cradick, T.J., Fine, E.J., Antico, C.J. and Bao, G.
Nucl. Acids Res. (2013), 41 (20) 9584-9592.
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Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice.
Jiang, W., Zhou, H., Bi, H., Fromm, M., Yang, B. and Weeks, D.P.
Nucl. Acids Res. (2013), 41 (20) e188.
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Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination.
Chen, C., Fenk, L.A. and de Bono, M.
Nucl. Acids Res. (2013), 41 (20) e193.
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High-efficiency genome editing via 2A-coupled co-expression of fluorescent proteins and zinc finger nucleases or CRISPR/Cas9 nickase pairs.
Duda, K., Lonowski, L.A., Kofoed-Nielsen, M., Ibarra, A., Delay, C.M., Kang, Q., Yang, Z., Pruett-Miller, S.M., Bennett, E.P., Wandall, H.H. et al.
Nucl. Acids Res. (2014), 42 (10) e84.
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Efficient chromosomal gene modification with CRISPR/cas9 and PCR-based homologous recombination donors in cultured Drosophila cells.
Bottcher, R., Hollmann, M., Merk, K., Nitschko, V., Obermaier, C., Philippou-Massier, J., Wieland, I., Gaul, U. and Forstemann, K.
Nucl. Acids Res. (2014), 42 (11) e89.
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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. and Bao, G.
Nucl. Acids Res. (2014), 42 (11) 7473-7485.
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CRISPR-Cas: an efficient tool for genome engineering of virulent bacteriophages.
Martel, B. and Moineau, S.
Nucl. Acids Res. (2014), 42 (14) 9504-9513.
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CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri.
Oh, J.H. and van Pijkeren, J.P.
Nucl. Acids Res. (2014), 42 (17) e131.
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Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice.
Zhou, H., Liu, B., Weeks, D.P., Spalding, M.H. and Yang, B.
Nucl. Acids Res. (2014), 42 (17) 10903-10914.
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Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector.
Kabadi, A.M., Ousterout, D.G., Hilton, I.B. and Gersbach, C.A.
Nucl. Acids Res. (2014), 42 (19) e147.
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Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers.
Gao, X., Tsang, J.C., Gaba, F., Wu, D., Lu, L. and Liu, P.
Nucl. Acids Res. (2014), 42 (20) e155.
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Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression.
Luo, M.L., Mullis, A.S., Leenay, R.T. and Beisel, C.L.
Nucl. Acids Res. (2015), 43 (1) 674-681.
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CRISPR-based self-cleaving mechanism for controllable gene delivery in human cells.
Moore, R., Spinhirne, A., Lai, M.J., Preisser, S., Li, Y., Kang, T. and Bleris, L.
Nucl. Acids Res. (2015), 43 (2) 1297-1303.
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Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines.
Ho, T.T., Zhou, N., Huang, J., Koirala, P., Xu, M., Fung, R., Wu, F. and Mo, Y.Y.
Nucl. Acids Res. (2015), 43 (3) e17.
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Efficient CRISPR-rAAV engineering of endogenous genes to study protein function by allele-specific RNAi.
Kaulich, M., Lee, Y.J., Lonn, P., Springer, A.D., Meade, B.R. and Dowdy, S.F.
Nucl. Acids Res. (2015), 43 (7) e45.
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Highly efficient CRISPR/Cas9-mediated TAR cloning of genes and chromosomal loci from complex genomes in yeast.
Lee, N.C., Larionov, V. and Kouprina, N.
Nucl. Acids Res. (2015), 43 (8) e55.
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Functional validation of mouse tyrosinase non-coding regulatory DNA elements by CRISPR-Cas9-mediated mutagenesis.
Seruggia, D., Fernandez, A., Cantero, M., Pelczar, P. and Montoliu, L.
Nucl. Acids Res. (2015), 43 (10) 4855-4867.
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Nuclear domain 'knock-in' screen for the evaluation and identification of small molecule enhancers of CRISPR-based genome editing.
Pinder, J., Salsman, J. and Dellaire, G.
Nucl. Acids Res. (2015), 43 (19) 9379-9392.
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Enriching CRISPR-Cas9 targeted cells by co-targeting the HPRT gene.
Liao, S., Tammaro, M. and Yan, H.
Nucl. Acids Res. (2015), 43 (20) e134.
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CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity.
Carrington, B., Varshney, G.K., Burgess, S.M. and Sood, R.
Nucl. Acids Res. (2015), 43 (22) e157.
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CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis.
McCaffrey, J., Sibert, J., Zhang, B., Zhang, Y., Hu, W., Riethman, H. and Xiao, M.
Nucl. Acids Res. (2016), 44 (2) e11.
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Harnessing Type I and Type III CRISPR-Cas systems for genome editing.
Li, Y., Pan, S., Zhang, Y., Ren, M., Feng, M., Peng, N., Chen, L., Liang, Y.X. and She, Q.
Nucl. Acids Res. (2016), 44 (4) e34.
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Programmable control of bacterial gene expression with the combined CRISPR and antisense RNA system.
Lee, Y.J., Hoynes-O'Connor, A., Leong, M.C. and Moon, T.S.
Nucl. Acids Res. (2016), 44 (5) 2462-2473.
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Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci.
Chen, B., Hu, J., Almeida, R., Liu, H., Balakrishnan, S., Covill-Cooke, C., Lim, W.A. and Huang, B.
Nucl. Acids Res. (2016), 44 (8) e75.
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In vivo blunt-end cloning through CRISPR/Cas9-facilitated non-homologous end-joining.
Geisinger, J.M., Turan, S., Hernandez, S., Spector, L.P. and Calos, M.P.
Nucl. Acids Res. (2016), 44 (8) e76.
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Effective knockdown of Drosophila long non-coding RNAs by CRISPR interference.
Ghosh, S., Tibbit, C. and Liu, J.L.
Nucl. Acids Res. (2016), 44 (9) e84.
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Knock-in of large reporter genes in human cells via CRISPR/Cas9-induced homology-dependent and independent DNA repair.
He, X., Tan, C., Wang, F., Wang, Y., Zhou, R., Cui, D., You, W., Zhao, H., Ren, J. and Feng, B.
Nucl. Acids Res. (2016), 44 (9) e85.
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Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system.
Shao, S., Zhang, W., Hu, H., Xue, B., Qin, J., Sun, C., Sun, Y., Wei, W. and Sun, Y.
Nucl. Acids Res. (2016), 44 (9) e86.
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Repurposing the CRISPR-Cas9 system for targeted DNA methylation.
Vojta, A., Dobrinic, P., Tadic, V., Bockor, L., Korac, P., Julg, B., Klasic, M. and Zoldos, V.
Nucl. Acids Res. (2016) Ahead of Print.
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Computational and Online Tools

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.
Grissa, I., Vergnaud, G. and Pourcel, C.
Nucl. Acids Res. (2007), 35 (Web Server issue) W52-57.
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CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.
Grissa, I., Vergnaud, G. and Pourcel, C.
Nucl. Acids Res. (2008), 36 (Web Server issue) W145-148.
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CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems.
Lange, S.J., Alkhnbashi, O.S., Rose, D., Will, S. and Backofen, R.
Nucl. Acids Res. (2013), 41 (17) 8034-8044.
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CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing.
Montague, T.G., Cruz, J.M., Gagnon, J.A., Church, G.M. and Valen, E.
Nucl. Acids Res. (2014), 42 (Web Server issue) W401-407.
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Cas9-chromatin binding information enables more accurate CRISPR off-target prediction.
Singh, R., Kuscu, C., Quinlan, A., Qi, Y. and Adli, M.
Nucl. Acids Res. (2015), 43 (18) e118.
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CRISPRz: a database of zebrafish validated sgRNAs.
Varshney, G.K., Zhang, S., Pei, W., Adomako-Ankomah, A., Fohtung, J., Schaffer, K., Carrington, B., Maskeri, A., Slevin, C., Wolfsberg, T. et al.
Nucl. Acids Res. (2016), 44 (D1) D822-826.
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Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes.
Oliveros J.C., Franch M., Tabas-Madrid D., San-León D., Montoliu L., Cubas P., Pazos F.
Nucl. Acids Res. (2016) Ahead of Print.
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CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering.
Labun K., Montague T.G., Gagnon J.A., Thyme S.B., Valen E.
Nucl. Acids Res. (2016) Ahead of Print.
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Surveys & Summaries

Classification and evolution of type II CRISPR-Cas systems.
Chylinski, K., Makarova, K.S., Charpentier, E. and Koonin, E.V.
Nucl. Acids Res. (2014), 42 (10) 6091-6105.
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Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference.
Barrangou, R., Birmingham, A., Wiemann, S., Beijersbergen, R.L., Hornung, V. and Smith, A.
Nucl. Acids Res. (2015), 43 (7) 3407-3419.
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