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1
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84952682854
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CRISPR/Cas9 advances engineering of microbial cell factories
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This review provides an overview of the CRISPR/Cas9 tools available for model organisms E. coli and S. cerevisiae.
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1• Jakočiūnas, T., Jensen, M.K., Keasling, J.D., CRISPR/Cas9 advances engineering of microbial cell factories. Metab Eng 34 (2016), 44–59 This review provides an overview of the CRISPR/Cas9 tools available for model organisms E. coli and S. cerevisiae.
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Jakočiūnas, T.1
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2
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84964310738
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The CRISPR/Cas genome-editing tool: application in improvement of crops
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2 Khatodia, S., Bhatotia, K., Passricha, N., Khurana, S.M.P., Tuteja, N., The CRISPR/Cas genome-editing tool: application in improvement of crops. Front Plant Sci, 7, 2016, 506.
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3
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84933569948
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CasEMBLR: Cas9-facilitated multiloci genomic integration of in vivo assembled DNA parts in Saccharomyces cerevisiae
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3 Jakočiūnas, T., Rajkumar, A.S., Zhang, J., Arsovska, D., Rodriguez, A., Jendresen, C.B., Skjødt, M.L., Nielsen, A.T., Borodina, I., Jensen, M.K., et al. CasEMBLR: Cas9-facilitated multiloci genomic integration of in vivo assembled DNA parts in Saccharomyces cerevisiae. ACS Synth Biol 4 (2015), 1226–1234.
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Jakočiūnas, T.1
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Skjødt, M.L.7
Nielsen, A.T.8
Borodina, I.9
Jensen, M.K.10
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4
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84920992414
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Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds
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Here dCas9 was used for repression and activation of genes in yeast and human cells, but instead of dCas9 being fused with activating or represing domains, gRNA scaffolds were design to contain binding sites for recruitment of effector proteins.
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4•• 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. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160 (2014), 339–350 Here dCas9 was used for repression and activation of genes in yeast and human cells, but instead of dCas9 being fused with activating or represing domains, gRNA scaffolds were design to contain binding sites for recruitment of effector proteins.
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Cell
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Zalatan, J.G.1
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Tsai, J.C.7
Weissman, J.S.8
Dueber, J.E.9
Qi, L.S.10
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5
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23844505202
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Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin
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5 Bolotin, A., Quinquis, B., Sorokin, A., Dusko Ehrlich, S., Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151 (2005), 2551–2561.
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Bolotin, A.1
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6
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16444385662
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Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements
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6 Mojica, F.J.M., Díez-Villaseñor, C., García-Martínez, J., Soria, E., Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60 (2005), 174–182.
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Mojica, F.J.M.1
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7
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15844390228
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CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies
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7 Pourcel, C., Salvignol, G., Vergnaud, G., CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151 (2005), 653–663.
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Pourcel, C.1
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8
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84865070369
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A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
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8 Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., Charpentier, E., A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337, 2012.
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Jinek, M.1
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9
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84866859751
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Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria
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9 Gasiunas, G., Barrangou, R., Horvath, P., Siksnys, V., Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci 109 (2012), E2579–E2586.
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Gasiunas, G.1
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10
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84979746885
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EasyClone-MarkerFree: a vector toolkit for marker-less integration of genes into Saccharomyces cerevisiae via CRISPR-Cas9
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10 Jessop-Fabre, M.M., Jakočiūnas, T., Stovicek, V., Dai, Z., Jensen, M.K., Keasling, J.D., Borodina, I., EasyClone-MarkerFree: a vector toolkit for marker-less integration of genes into Saccharomyces cerevisiae via CRISPR-Cas9. Biotechnol J 11 (2016), 1110–1117.
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Jessop-Fabre, M.M.1
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11
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84874608929
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RNA-guided editing of bacterial genomes using CRISPR-Cas systems
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11 Jiang, W., Bikard, D., Cox, D., Zhang, F., Marraffini, L.A., RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31 (2013), 233–239.
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Jiang, W.1
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12
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84923667065
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Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway
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12 Lee, J.S., Kallehauge, T.B., Pedersen, L.E., Kildegaard, H.F., Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway. Sci Rep, 5, 2015, 8572.
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Lee, J.S.1
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13
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84923021733
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Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae
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Multiplex CRISPR/Cas9 system was established where up to 5 gRNAs were expressed on a single plasmid. System was applied for metabolic engineering purpose to increase mevalonate production in yeast.
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13• Jakočiūnas, T., Bonde, I., Herrgård, M., Harrison, S.J., Kristensen, M., Pedersen, L.E., Jensen, M.K., Keasling, J.D., Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab Eng 28C (2015), 213–222 Multiplex CRISPR/Cas9 system was established where up to 5 gRNAs were expressed on a single plasmid. System was applied for metabolic engineering purpose to increase mevalonate production in yeast.
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Metab Eng
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Jakočiūnas, T.1
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Jensen, M.K.7
Keasling, J.D.8
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14
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84937538704
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Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing
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This paper describes development of CRISPR/Cas9 system for E.coli. Genome engineering tools were used to integrate β-carotene synthetic pathway, and for optimization of both methylerythritol-phosphate (MEP) and central metabolic pathways.
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14• Li, Y., Lin, Z., Huang, C., Zhang, Y., Wang, Z., Tang, Y., Chen, T., Zhao, X., Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing. Metab Eng 31 (2015), 13–21 This paper describes development of CRISPR/Cas9 system for E.coli. Genome engineering tools were used to integrate β-carotene synthetic pathway, and for optimization of both methylerythritol-phosphate (MEP) and central metabolic pathways.
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Metab Eng
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Li, Y.1
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Chen, T.7
Zhao, X.8
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15
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84936967101
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Coupling the CRISPR/Cas9 system to lambda Red recombineering enables simplified chromosomal gene replacement in Escherichia coli
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15 Pyne, M.E., Moo-Young, M., Chung, D.A., Chou, C.P., Coupling the CRISPR/Cas9 system to lambda Red recombineering enables simplified chromosomal gene replacement in Escherichia coli. Appl Environ Microbiol 81 (2015), 5103–5114.
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Pyne, M.E.1
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16
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84940601641
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One-step generation of triple knockout CHO cell lines using CRISPR Cas9 and fluorescent enrichment
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16 Grav, L.M., Lee, J.S., Gerling, S., Beuchert Kallehauge, T., Holmgaard Hansen, A., Kol, S., Lee, G.M., Ebdrup Pedersen, L., Faustrup Kildegaard, H., One-step generation of triple knockout CHO cell lines using CRISPR Cas9 and fluorescent enrichment. Biotechnol J 10 (2015), 1446–1456.
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Grav, L.M.1
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Kol, S.6
Lee, G.M.7
Ebdrup Pedersen, L.8
Faustrup Kildegaard, H.9
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17
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84992745786
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Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells
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This paper describes a method based on Cas9 for directed evolution of proteins in mamalian cells.
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17• Hess, G.T., Frésard, L., Han, K., Lee, C.H., Li, A., Cimprich, K.A., Montgomery, S.B., Bassik, M.C., Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nat Methods 12 (2016), 1036–1042 This paper describes a method based on Cas9 for directed evolution of proteins in mamalian cells.
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Nat Methods
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Hess, G.T.1
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Bassik, M.C.8
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18
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84929135130
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Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers
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18 Hilton, I.B., D'Ippolito, A.M., Vockley, C.M., Thakore, P.I., Crawford, G.E., Reddy, T.E., Gersbach, C.A., Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol 33 (2015), 510–517.
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Hilton, I.B.1
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Gersbach, C.A.7
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19
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84986198285
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CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production
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dCas9 based method for expression balancing of mevalonate pathway to increase production of isoprenoids.
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19•• Kim, S.K., Han, G.H., Seong, W., Kim, H., Kim, S.-W., Lee, D.-H., Lee, S.-G., CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production. Metab Eng 38 (2016), 228–240 dCas9 based method for expression balancing of mevalonate pathway to increase production of isoprenoids.
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Kim, S.K.1
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20
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84880571335
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CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes
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Among the first ones to show that dCas9 can be fused with transcription activating or represing domains and when guided to the gene of interest can activate or repress those genes. The new tool has been tested in human and yeast cells.
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20• 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. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154 (2013), 442–451 Among the first ones to show that dCas9 can be fused with transcription activating or represing domains and when guided to the gene of interest can activate or repress those genes. The new tool has been tested in human and yeast cells.
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Cell
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Gilbert, L.A.1
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Brandman, O.8
Whitehead, E.H.9
Doudna, J.A.10
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21
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85012035006
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SWITCH: a dynamic CRISPR tool for genome engineering and metabolic pathway control for cell factory construction in Saccharomyces cerevisiae
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Have developed a Cas9/dCas9 based system that integrates both genetic engineering and transcriptional control of pathways into one system.
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21• Vanegas, K.G., Lehka, B.J., Mortensen, U.H., SWITCH: a dynamic CRISPR tool for genome engineering and metabolic pathway control for cell factory construction in Saccharomyces cerevisiae. Microb Cell Fact, 16, 2017, 25 Have developed a Cas9/dCas9 based system that integrates both genetic engineering and transcriptional control of pathways into one system.
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Vanegas, K.G.1
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22
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22 Hsu, P.D., Lander, E.S., Zhang, F., Development and applications of CRISPR-Cas9 for genome engineering. Cell 157 (2014), 1262–1278.
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23
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23 Lee, J.S., Kallehauge, T.B., Pedersen, L.E., Kildegaard, H.F., Noh, S.M., Sathyamurthy, M., Lee, G.M., Wurm, F.M., Wilson, C., Bellen, H.J., et al. Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway. Sci Rep, 5, 2015, 8572.
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24
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Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool
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24 Ronda, C., Pedersen, L.E., Hansen, H.G., Kallehauge, T.B., Betenbaugh, M.J., Nielsen, A.T., Kildegaard, H.F., Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool. Biotechnol Bioeng 111 (2014), 1604–1616.
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25
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High-efficiency multiplex genome editing of streptomyces species using an engineered CRISPR/Cas system
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25 Cobb, R.E., Wang, Y., Zhao, H., High-efficiency multiplex genome editing of streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 4 (2015), 723–728.
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26 Huang, H., Zheng, G., Jiang, W., Hu, H., Lu, Y., One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces. Acta Biochim Biophys Sin (Shanghai) 47 (2015), 231–243.
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27 Tong, Y., Charusanti, P., Zhang, L., Weber, T., Lee, S.Y., CRISPR-Cas9 based engineering of actinomycetal genomes. ACS Synth Biol 4 (2015), 1020–1029, 10.1021/acssynbio.5b00038.
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28 Wang, Y., Zhang, Z.-T., Seo, S.-O., Choi, K., Lu, T., Jin, Y.-S., Blaschek, H.P., Markerless chromosomal gene deletion in Clostridium beijerinckii using CRISPR/Cas9 system. J Biotechnol 200 (2015), 1–5.
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29
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29 Huang, H., Chai, C., Li, N., Rowe, P., Minton, N.P., Yang, S., Jiang, W., Gu, Y., CRISPR/Cas9-based efficient genome editing in Clostridium ljungdahlii, an autotrophic gas-fermenting bacterium. ACS Synth Biol 12 (2016), 1355–1361.
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30 Oh, J.-H., van Pijkeren, J.-P., CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res, 42, 2014, e131.
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31 Nødvig, C.S., Nielsen, J.B., Kogle, M.E., Mortensen, U.H., A CRISPR-Cas9 system for genetic engineering of filamentous fungi. PLoS One, 10, 2015, e0133085.
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32 Liu, R., Chen, L., Jiang, Y., Zhou, Z., Zou, G., Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system. Cell Discov, 1, 2015, 15007.
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33 Jacobs, J.Z., Ciccaglione, K.M., Tournier, V., Zaratiegui, M., Implementation of the CRISPR-Cas9 system in fission yeast. Nat Commun 5 (2014), 1–5.
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Synthetic RNA polymerase III promoters facilitate high-efficiency CRISPR–Cas9-mediated genome editing in Yarrowia lipolytica
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34 Schwartz, C.M., Hussain, M.S., Blenner, M., Wheeldon, I., Synthetic RNA polymerase III promoters facilitate high-efficiency CRISPR–Cas9-mediated genome editing in Yarrowia lipolytica. ACS Synth Biol 5 (2016), 356–359.
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Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast Pichia pastoris
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35 Weninger, A., Hatzl, A.-M., Schmid, C., Vogl, T., Glieder, A., Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast Pichia pastoris. J Biotechnol 235 (2016), 139–149.
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36
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36 Wendt, K.E., Ungerer, J., Cobb, R.E., Zhao, H., Pakrasi, H.B., CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973. Microb Cell Fact, 15, 2016, 115.
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Li, H.1
Shen, C.R.2
Huang, C.-H.3
Sung, L.-Y.4
Wu, M.-Y.5
Hu, Y.-C.6
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38
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84908352138
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Resource genome-scale CRISPR-mediated control of gene repression and activation
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Among the first ones to show genome-wide screening with dCas9 for activating and repressing genes in mamalian cells.
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38•• Gilbert, L.A., Horlbeck, M.A., Adamson, B., Villalta, J.E., Chen, Y., Whitehead, E.H., Guimaraes, C., Panning, B., Ploegh, H.L., Resource genome-scale CRISPR-mediated control of gene repression and activation. Cell 159 (2014), 647–661 Among the first ones to show genome-wide screening with dCas9 for activating and repressing genes in mamalian cells.
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(2014)
Cell
, vol.159
, pp. 647-661
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Gilbert, L.A.1
Horlbeck, M.A.2
Adamson, B.3
Villalta, J.E.4
Chen, Y.5
Whitehead, E.H.6
Guimaraes, C.7
Panning, B.8
Ploegh, H.L.9
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39
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84986586549
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Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening
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39 Kiessling, M.K., Schuierer, S., Stertz, S., Beibel, M., Bergling, S., Knehr, J., Carbone, W., de Vallière, C., Tchinda, J., Bouwmeester, T., et al. Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening. BMC Genomics, 17, 2016, 723.
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(2016)
BMC Genomics
, vol.17
, pp. 723
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Kiessling, M.K.1
Schuierer, S.2
Stertz, S.3
Beibel, M.4
Bergling, S.5
Knehr, J.6
Carbone, W.7
de Vallière, C.8
Tchinda, J.9
Bouwmeester, T.10
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40
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84947039940
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A genome-wide CRISPR library for high-throughput genetic screening in Drosophila cells
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40 Bassett, A.R., Kong, L., Liu, J.-L., A genome-wide CRISPR library for high-throughput genetic screening in Drosophila cells. J Genet Genomics 42 (2015), 301–309.
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(2015)
J Genet Genomics
, vol.42
, pp. 301-309
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Bassett, A.R.1
Kong, L.2
Liu, J.-L.3
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41
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84898665052
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Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library
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Among the first ones to perform genome-wide knock-out screen in mammalian cells by using CRISPR/Cas9. The screen identified 27 known and 4 unknown genes that play a role in resistance to Clostridium septicum alpha-toxin or 6-thioguanine.
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41•• Koike-Yusa, H., Li, Y., Tan, E.-P., Velasco-Herrera, M.D.C., Yusa, K., Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol 32 (2013), 267–373 Among the first ones to perform genome-wide knock-out screen in mammalian cells by using CRISPR/Cas9. The screen identified 27 known and 4 unknown genes that play a role in resistance to Clostridium septicum alpha-toxin or 6-thioguanine.
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(2013)
Nat Biotechnol
, vol.32
, pp. 267-373
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Koike-Yusa, H.1
Li, Y.2
Tan, E.-P.3
Velasco-Herrera, M.D.C.4
Yusa, K.5
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42
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84892765883
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Genome-scale CRISPR-Cas9 knockout screening in human cells
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42 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. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science, 343, 2014.
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(2014)
Science
, vol.343
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Shalem, O.1
Sanjana, N.E.2
Hartenian, E.3
Shi, X.4
Scott, D.A.5
Mikkelsen, T.S.6
Heckl, D.7
Ebert, B.L.8
Root, D.E.9
Doench, J.G.10
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43
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84960094162
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Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design
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This paper determines rules for choosing efficient guiding gRNAs. Employing dCas9 and modelling approach authors identify that guides targeting low nucleosome occupancy regions and regions between the transcription start site (TSS) and 200 bp upstream of the TSS are most effective.
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43•• Smith, J.D., Suresh, S., Schlecht, U., Wu, M., Wagih, O., Peltz, G., Davis, R.W., Steinmetz, L.M., Parts, L., St. Onge, R.P., et al. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biol, 17, 2016, 45 This paper determines rules for choosing efficient guiding gRNAs. Employing dCas9 and modelling approach authors identify that guides targeting low nucleosome occupancy regions and regions between the transcription start site (TSS) and 200 bp upstream of the TSS are most effective.
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(2016)
Genome Biol
, vol.17
, pp. 45
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Smith, J.D.1
Suresh, S.2
Schlecht, U.3
Wu, M.4
Wagih, O.5
Peltz, G.6
Davis, R.W.7
Steinmetz, L.M.8
Parts, L.9
St. Onge, R.P.10
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44
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84970002343
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Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli
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CRISPR array system based on dCas9 for down regulation of genes in E.coli. Authors show that down-regulating novel and computationally predicted metabolic engineering targets can improve the yield of certain compound.
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44•• Cress, B.F., Jones, J.A., Kim, D.C., Leitz, Q.D., Englaender, J.A., Collins, S.M., Linhardt, R.J., Koffas, M.A.G., Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res 44 (2016), 4472–4485 CRISPR array system based on dCas9 for down regulation of genes in E.coli. Authors show that down-regulating novel and computationally predicted metabolic engineering targets can improve the yield of certain compound.
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(2016)
Nucleic Acids Res
, vol.44
, pp. 4472-4485
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Cress, B.F.1
Jones, J.A.2
Kim, D.C.3
Leitz, Q.D.4
Englaender, J.A.5
Collins, S.M.6
Linhardt, R.J.7
Koffas, M.A.G.8
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45
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85006488344
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Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens
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Has developed a method called Perturb-seq, which combines single-cell RNA sequencing (RNA-seq) and CRISPR-based perturbations to perform many pooled assays.
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45•• Dixit, A., Parnas, O., Li, B., Chen, J., Fulco, C.P., Jerby-Arnon, L., Marjanovic, N.D., Dionne, D., Burks, T., Raychowdhury, R., et al. Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167 (2016), 1853–1866 Has developed a method called Perturb-seq, which combines single-cell RNA sequencing (RNA-seq) and CRISPR-based perturbations to perform many pooled assays.
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(2016)
Cell
, vol.167
, pp. 1853-1866
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Dixit, A.1
Parnas, O.2
Li, B.3
Chen, J.4
Fulco, C.P.5
Jerby-Arnon, L.6
Marjanovic, N.D.7
Dionne, D.8
Burks, T.9
Raychowdhury, R.10
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46
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85006269827
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Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-Seq
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Has developed a method called CRISP-seq, which integrates single-cell RNA sequencing and CRISPR-pooled screens.
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46•• Jaitin, D.A., Weiner, A., Yofe, I., Lara-Astiaso, D., Keren-Shaul, H., David, E., Salame, T.M., Tanay, A., Oudenaarden van, A., Amit, I., Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-Seq. Cell 167 (2016), 1883–1896 Has developed a method called CRISP-seq, which integrates single-cell RNA sequencing and CRISPR-pooled screens.
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(2016)
Cell
, vol.167
, pp. 1883-1896
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Jaitin, D.A.1
Weiner, A.2
Yofe, I.3
Lara-Astiaso, D.4
Keren-Shaul, H.5
David, E.6
Salame, T.M.7
Tanay, A.8
Oudenaarden van, A.9
Amit, I.10
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47
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85006345820
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A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response
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47 Adamson, B., Norman, T.M., Jost, M., Cho, M.Y., Nuñez, J.K., Chen, Y., Villalta, J.E., Gilbert, L.A., Horlbeck, M.A., Hein, M.Y., et al. A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell 167 (2016), 1867–1882.
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(2016)
Cell
, vol.167
, pp. 1867-1882
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Adamson, B.1
Norman, T.M.2
Jost, M.3
Cho, M.Y.4
Nuñez, J.K.5
Chen, Y.6
Villalta, J.E.7
Gilbert, L.A.8
Horlbeck, M.A.9
Hein, M.Y.10
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48
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85011034228
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Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
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Has developed CRISPR based method for trackable genome engineering (CREATE) and reverse engineered all 645 nonsynonymous mutations identified in an evolved thermotolerant E. coli strain.
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48•• Garst, A.D., Bassalo, M.C., Pines, G., Lynch, S.A., Halweg-Edwards, A.L., Liu, R., Liang, L., Wang, Z., Zeitoun, R., Alexander, W.G., et al. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nat Biotechnol 35 (2016), 48–55 Has developed CRISPR based method for trackable genome engineering (CREATE) and reverse engineered all 645 nonsynonymous mutations identified in an evolved thermotolerant E. coli strain.
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(2016)
Nat Biotechnol
, vol.35
, pp. 48-55
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Garst, A.D.1
Bassalo, M.C.2
Pines, G.3
Lynch, S.A.4
Halweg-Edwards, A.L.5
Liu, R.6
Liang, L.7
Wang, Z.8
Zeitoun, R.9
Alexander, W.G.10
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49
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84856258903
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The molecular diversity of adaptive convergence
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49 Tenaillon, O., Rodríguez-Verdugo, A., Gaut, R.L., McDonald, P., Bennett, A.F., Long, A.D., Gaut, B.S., The molecular diversity of adaptive convergence. Science, 335, 2012.
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(2012)
Science
, vol.335
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Tenaillon, O.1
Rodríguez-Verdugo, A.2
Gaut, R.L.3
McDonald, P.4
Bennett, A.F.5
Long, A.D.6
Gaut, B.S.7
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50
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84988911466
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Enhanced protein and biochemical production using CRISPRi-based growth switches
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Have showed that CRISPR/Cas9 can be used to regulate expression of genes that are responsible for groth and by slowing the groth increase production proteins and chemicals.
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50• Li, S., Jendresen, C.B., Grünberger, A., Ronda, C., Jensen, S.I., Noack, S., Nielsen, A.T., Enhanced protein and biochemical production using CRISPRi-based growth switches. Metab Eng 38 (2016), 274–284 Have showed that CRISPR/Cas9 can be used to regulate expression of genes that are responsible for groth and by slowing the groth increase production proteins and chemicals.
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(2016)
Metab Eng
, vol.38
, pp. 274-284
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Li, S.1
Jendresen, C.B.2
Grünberger, A.3
Ronda, C.4
Jensen, S.I.5
Noack, S.6
Nielsen, A.T.7
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51
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85013830067
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Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae
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This paper describes a method for systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae.
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51• Deaner, M., Alper, H.S., Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae. Metab Eng 40 (2017), 14–22, 10.1016/j.ymben.2017.01.012 This paper describes a method for systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae.
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(2017)
Metab Eng
, vol.40
, pp. 14-22
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Deaner, M.1
Alper, H.S.2
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52
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77954590959
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OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions
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52 Ranganathan, S., Suthers, P.F., Maranas, C.D., OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput Biol, 6, 2010, e1000744.
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(2010)
PLoS Comput Biol
, vol.6
, pp. e1000744
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Ranganathan, S.1
Suthers, P.F.2
Maranas, C.D.3
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53
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84930971149
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CRISPathBrick: modular combinatorial assembly of type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli
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CRISPR array system based on dCas9 for down regulation of genes in E. coli. Authors show that down-regulating novel and computationally predicted metabolic engineering targets can improve the yield of certain compound.
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53•• Cress, B.F., Toparlak ÖD, Guleria, S., Lebovich, M., Stieglitz, J.T., Englaender, J.A., Jones, J.A., Linhardt, R.J., Koffas, M.A.G., CRISPathBrick: modular combinatorial assembly of type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli. ACS Synth Biol 4 (2015), 987–1000 CRISPR array system based on dCas9 for down regulation of genes in E. coli. Authors show that down-regulating novel and computationally predicted metabolic engineering targets can improve the yield of certain compound.
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(2015)
ACS Synth Biol
, vol.4
, pp. 987-1000
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Cress, B.F.1
Toparlak ÖD2
Guleria, S.3
Lebovich, M.4
Stieglitz, J.T.5
Englaender, J.A.6
Jones, J.A.7
Linhardt, R.J.8
Koffas, M.A.G.9
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54
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84929504676
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Metabolic engineering of cyanobacteria for the synthesis of commodity products
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54 Angermayr, S.A., Gorchs Rovira, A., Hellingwerf, K.J., Ducat, D.C., Wijffels, R.H., Keasling, J.D., Berg, J.J., et al. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends Biotechnol 33 (2015), 352–361.
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(2015)
Trends Biotechnol
, vol.33
, pp. 352-361
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Angermayr, S.A.1
Gorchs Rovira, A.2
Hellingwerf, K.J.3
Ducat, D.C.4
Wijffels, R.H.5
Keasling, J.D.6
Berg, J.J.7
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55
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84961794371
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Multiple gene repression in Cyanobacteria using CRISPRi
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55 Yao, L., Cengic, I., Anfelt, J., Hudson, E.P., Multiple gene repression in Cyanobacteria using CRISPRi. ACS Synth Biol 5 (2016), 207–212.
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(2016)
ACS Synth Biol
, vol.5
, pp. 207-212
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Yao, L.1
Cengic, I.2
Anfelt, J.3
Hudson, E.P.4
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56
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84982860066
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CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002
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This study shows usability of dCas9 for gene repression in cyanobacteria to increase central carbon flux. Such experimental design provides 2-fold increase in lactate production.
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56• Gordon, G.C., Korosh, T.C., Cameron, J.C., Markley, A.L., Begemann, M.B., Pfleger, B.F., CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng 38 (2016), 170–179 This study shows usability of dCas9 for gene repression in cyanobacteria to increase central carbon flux. Such experimental design provides 2-fold increase in lactate production.
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(2016)
Metab Eng
, vol.38
, pp. 170-179
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Gordon, G.C.1
Korosh, T.C.2
Cameron, J.C.3
Markley, A.L.4
Begemann, M.B.5
Pfleger, B.F.6
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57
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85027956141
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CRISPRi engineering E. coli for morphology diversification
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57 Elhadi, D., Lv, L., Jiang, X.-R., Wu, H., Chen, G.-Q., CRISPRi engineering E. coli for morphology diversification. Metab Eng 38 (2016), 358–369.
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(2016)
Metab Eng
, vol.38
, pp. 358-369
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Elhadi, D.1
Lv, L.2
Jiang, X.-R.3
Wu, H.4
Chen, G.-Q.5
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58
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84962052932
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Stability of ensemble models predicts productivity of enzymatic systems
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58 Theisen, M.K., Lafontaine Rivera, J.G., Liao, J.C., Stability of ensemble models predicts productivity of enzymatic systems. PLOS Comput Biol, 12, 2016, e1004800.
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(2016)
PLOS Comput Biol
, vol.12
, pp. e1004800
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Theisen, M.K.1
Lafontaine Rivera, J.G.2
Liao, J.C.3
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