GE Journal Club (genome engineering/gene editing)

CURRENT SCHEDULE

DATE PRESENTERS PAPERS
05/20/2019 NO MEETING – – – – – – – –
05/27/2019 NO MEETING
(Memorial Day)
– – – – – – – –
06/03/2019 Stephanie Mohr
Shannon Knight
TBD
06/10/2019 Josh Li 
Zhenfei Xie
TBD
06/17/2019 NO MEETING – – – – – – – –
06/24/2019 Claire Hu
Ricky Brathwaite
TBD
07/01/2019 TBD TBD
07/08/2019 TBD TBD
07/15/2019 TBD TBD
07/22/2019 TBD TBD
07/29/2019 TBD TBD

PAST MEETINGS

DATE PRESENTERS PAPERS
05/13/2019 Julian Grunewald
Clarita Ingaramo
1) Grunewald J, et al. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature. 2019 Apr 17. 
2) Pan et al.
Near-infrared upconversion-activated CRISPR-Cas9 system: A remote-controlled gene editing platform. Sci Adv. 2019 Apr 3;5(4):eaav7199. 
05/06/2019 Jonathan Zirin
Ben Ewen-Campen
1) Hoffmann MD, et al. Cell-specific CRISPR-Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins. Nucleic Acids Res. 2019 Apr 15. pii: gkz271.
2) Guichard A, et al.
Efficient allelic-drive in Drosophila. Nat Commun. 2019 Apr 9;10(1):1640.
04/29/2019 Justin Bosch
Chiao-Lin Chen
1) Kocak DD, et al. Increasing the specificity of CRISPR systems with engineered RNA secondary structures. Nat Biotechnol. 2019 Apr 15.
2) Bian WP, et al.
A knock-in strategy for editing human and zebrafish mitochondrial DNA using mito-CRISPR/Cas9 system. ACS Synth Biol. 2019 Apr 10.
04/22/2019 NO MEETING – – – – – – – –
04/15/2019 Baolong Xia
Tracy Zhang
1) Ma Z, et al. PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components. Nature. 2019 Apr 3.
2) El-Brolosy MA, et al.
Genetic compensation triggered by mutant mRNA degradation. Nature. 2019 Apr 3.
3) Iyer S, et al.
Precise therapeutic gene correction by a simple nuclease-induced double-stranded break. Nature. 2019 Apr 3.
04/08/2019 Cory Smith
Ankita Singh
1) Smith CJ, et al. Enabling large-scale genome editing by reducing DNA nicking. bioRxiv. Mar. 15, 2019.
2) Tuladhar R, et al. 
CRISPR/Cas9-based mutagenesis frequently provokes on-target mRNA misregulation. bioRxiv. Mar. 20, 2019.
04/01/2019 Pedro Saavedra
Ram Viswanatha

1) Min YL, et al. CRISPR-Cas9 corrects Duchenne muscular dystrophy exon 44 deletion mutations in mice and human cells. Sci Adv. 2019 Mar 6;5(3):eaav4324.
2) Hwang B, et al.
Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements. Nat Commun. 2019 Mar 15;10(1):1234

03/25/2019 Kendell Clement
Afroditi Petsakou
1) Clement K, et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol. 2019 Feb 26.
2) Katrekar D, et al. 
In vivo RNA editing of point mutations via RNA-guided adenosine deaminases. Nat Methods. 2019 Feb 8.
03/18/2019 NO MEETING – – – – – – – –
03/11/2019 Benjamin Kleinstiver
Henrique Camara
1) Kleinstiver BP, et al. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol. 2019 Feb 11.   
2) Wang XW, et al. 
A microRNA-inducible CRISPR-Cas9 platform serves as a microRNA sensor and cell-type-specific genome regulation tool. Nat Cell Biol. 2019 Feb 25.
03/04/2019   NO MEETING – – – – – – – –
02/25/2019 NO MEETING – – – – – – – –
02/18/2019 NO MEETING – – – – – – – –
02/11/2019 Julio Sainz de Aja
Sarah Bowling
1) Grunwald HA, et al. Super-Mendelian inheritance mediated by CRISPR-Cas9 in the female mouse germline. Nature. 2019 Jan 23.
2) Salvador-Martinez I, et al. 
Is it possible to reconstruct an accurate cell lineage using CRISPR recorders? Elife. 2019 Jan 28;8. pii: e40292.
02/04/2019 NO MEETING – – – – – – – –
01/28/2019 Ah-Ram Kim
Enzo Mameli

1) Matharu N, et al. CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency. Science. 2019 Jan 18;363(6424). pii: eaau0629.
2) Oakes BL, et al.
CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell. 2019 Jan 10;176(1-2):254-267.e16

  NO MEETING 2018: 12/17, 12/24, 12/31
2019: 01/07, 01/14, 01/21
12/10/2018 Henrique Camara
Maria Clara Ingaramo
1) Garcia-Marques J, et al. Unlimited genetic switches for cell-type specific manipulation. bioRxiv [Internet]. Nov. 14, 2018.
2) Farzadfard F, et al.
Single-Nucleotide-Resolution Computing and Memory in Living Cells. bioRxiv [Internet]. Feb. 16, 2018.
12/03/2018 Stephanie Mohr
Justin Bosch
1) Chong Z-S, et al. Pooled extracellular receptor-ligand interaction screening using CRISPR activation. Genome Biol. 2018 Nov 26;19(1):205. 
2) Fueller J, et al.
CRISPR/Cas12a-assisted PCR tagging of mammalian genes. bioRxiv [Internet]. Nov. 20, 2018.
11/26/2018 Baolong Xia
Tracy Zhang
1) Sanson KR, et al. Up, down, and out: optimized libraries for CRISPRa, CRISPRi, and CRISPR-knockout genetic screens. bioRxiv [Internet]. July 2, 2018.
2) Shen MW, et al.
Predictable and precise template-free CRISPR editing of pathogenic variants. Nature. 2018 Nov 7. 
11/19/2018 Johana Vásquez
Chiao-Lin Chen

1) Haney MS, et al. Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. Nat Genet. 2018 Nov 5. 
2) Harrington LB, et al. 
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 18 Oct 2018: eaav4294.

11/12/2018 NO MEETING – – – – – – – –
11/05/2018 Pedro Saavedra
Ram Viswanatha

1) Wroblewska A, et al. Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens. Cell. 2018 Oct 18.
2) Nishimasu H, et al.
Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science. 2018 Aug 30.

10/29/2018 Afroditi Petsakou
Ben Ewen-Campen

1) Schmidt F, et al. Transcriptional recording by CRISPR spacer acquisition from RNA. Nature. 2018 Oct 3.
2) Zafra MP, et al. 
Optimized base editors enable efficient editing in cells, organoids and mice. Nat Biotechnol. 2018 Oct;36(9):888-893. 

10/22/2018 Justin Bosch
Stephanie Mohr

1) Akcakaya P, et al. In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature. 2018 Sep 12.
2) Findlay GM, et al.
Accurate classification of BRCA1 variants with saturation genome editing. Nature. 2018 Sep 12.

10/15/2018

Baolong Xia
Charles Xu

1) Sharon E,  et al. Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing. Cell. 2018 Sep 18. pii: S0092-8674(18)31118-8.
2) Alemany A, et al.
Whole-organism clone tracing using single-cell sequencing. Nature. 2018 Apr 5;556(7699):108-112.

10/08/2018 NO MEETING – – – – – – – –
10/01/2018

Ankita Singh
Chiao-Lin Chen

1) Swings T, et al. CRISPR-FRT targets shared sites in a knock-out collection for off-the-shelf genome editing. Nat Commun. 2018 Jun 8;9(1):2231.
2)  Allen FR, et al. 
Mutations generated by repair of Cas9-induced double strand breaks are predictable from surrounding sequence. bioRxiv [Internet]. Aug. 25, 2018.

  NO MEETING 09/04, 09/10, 09/17, 09/24

08/27/2018

Pedro Saavedra
Ram Viswanatha

1) Horlbeck MA, et al. Mapping the Genetic Landscape of Human Cells. Cell. 2018 Aug 9;174(4):953-967.e22. 
2) Roche PJR, et al. 
Homology Directed Repair by Cas9:Donor Co-localization in Mammalian Cells. bioRxiv [Internet]. Aug. 6, 2018. 

08/20/2018

Afroditi Petsakou
Ben Ewen-Campen

1) Kundert K, et al. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. bioRxiv [Internet]. May 15, 2018.
2) Chaverra-Rodriguez D, et al. 
Targeted delivery of CRISPR-Cas9 ribonucleoprotein into arthropod ovaries for heritable germline gene editing. Nat Commun. 2018 Aug 1;9(1):3008. 

08/06/2018 Justin Bosch 1) Kosicki M, et al. Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nat Biotechnol. 2018;36 (8) :765-771.

ABOUT GE JOURNAL CLUB


Who are we?
Researchers at HMS (Post-docs, grad students, technicians, PIs, etc).

What do we talk about?
Genome engineering/gene editing – novel methods, technical issues (e.g. off-target analysis), ethical concerns, etc.

Why are we doing this?
To stay up to date on recent techniques, stimulate critical discussions, establish contacts for collaboration

When/where?
12:30 PM – 1:30 PM Mondays, Room 354 New Research Building (see schedule) 

What’s the format?
Presenters choose what they present. 2x presentations per meeting (30min each). Usually, this is a single recent paper in the field, presented as a PowerPoint to show the figure panels. Presenters can present any topic/format they wish, such as multiple papers, reviews, general discussion, chalk talk, etc.

Do I have to read the paper?
No, but it’s recommended.

Will I have to present?
We hope you will! But this is not strictly required.

I’m scheduled to present, what do I do?
Find a paper/topic you are excited about! The topic can be related to your expertise, or not. We provide a list of suggested papers (below) but feel free to consider alternatives. *Send your paper/topic selection to the organizer by the Friday before your presentation.* When you present, 1) introduce yourself, 2) explain why you selected the paper/topic, and 3) give background on the topic. Feel free to cut out panels or entire figures if it improves the presentation. Keep your presentation aimed at a general audience - most people do not read the paper and some will not be familiar with your topic.

CONTACT

Questions? Want to join the mailing list? Want to present? Have paper suggestions? – Contact Justin Bosch (jabosch@hms.harvard.edu) (Perrimon Lab)

HMS Email Accounts: Click here to subscribe yourself to the mailing list.

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SUGGESTED PAPERS (reverse chronological order)


Port et al. A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila. bioRxiv May 13, 2019.

Kundert et al. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 2019 May 9;10(1):2127.

Garcia-Tunon et al. Splice donor site sgRNAs enhance CRISPR/Cas9-mediated knockout efficiency. PLoS One. 2019 May 9;14(5):e0216674.

Meltzer et al. Tissue-specific (ts)CRISPR as an efficient strategy for in vivo screening in Drosophila. Nat Commun. 2019 May 8;10(1):2113.

Rees et al. Analysis and minimization of cellular RNA editing by DNA adenine base editors. Sci Adv, 5:5, eaax5717. 08 May 2019.

Oesinghaus et al. Switching the activity of Cas12a using guide RNA strand displacement circuits. Nat Commun. 2019 May 7;10(1):2092.

Shariati et al. Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9Mol Cell. 2019 May 2;74(3):622-633.e4.

Maji et al. A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9. Cell. 2019 May 2;177(4):1067-1079.e19.

Manna et al. Fast and cloning-free CRISPR/Cas9-mediated genomic editing in mammalian cells. bioRxiv. Apr. 23, 2019.

Ferdosi et al. Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes. Nat Commun. 2019 Apr 23;10(1):1842.

Jeong et al. Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives. Genome Res. 2019 Apr 23. pii: gr.245571.118.

Mimitou et al. Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. Nat Methods. 2019 Apr 22.

He et al. Boosting activity of high-fidelity CRISPR/Cas9 variants using a tRNAGln-processing system in human cells. J Biol Chem. 2019 Apr 22. pii: jbc.RA119.007791.

Zuo et al. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science. 2019 Apr 19;364(6437):289-292.

Jin et al. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science. 2019 Apr 19;364(6437):292-295.

Weinert et al. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. Science. 2019 Apr 19;364(6437):286-289.

Kockak et al. Increasing the specificity of CRISPR systems with engineered RNA secondary structures. Nat Biotechnol. 2019 Apr 15.

Zhang et al. Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design. PNAS 2019 Apr 15.

Gamboa et al. Heat-triggered remote control of CRISPR-dCas9 for tunable transcriptional modulation. bioRxiv. Apr. 12, 2019

Xu et al. Gene activation by a CRISPR-assisted trans enhancer. Elife. 2019 Apr 11;8. pii: e45973.

Behan et al. Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature. 2019 Apr 10.

Chow et al. In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens. Nat Methods. 2019 Apr 8.

Gisler et al. Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency. Nat Commun. 2019 Apr 8;10(1):1598.

Dolan et al. Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Mol Cell. 2019 Apr 5. pii: S1097-2765(19)30217-5.

Dong et al. An anti-CRISPR protein disables type V Cas12a by acetylation. Nat Struct Mol Biol. 2019 Apr;26(4):308-314.

Knott et al. Broad-spectrum enzymatic inhibition of CRISPR-Cas12a. Nat Struct Mol Biol. 2019 Apr;26(4):315-321

Rose et al. Suppression of unwanted CRISPR/Cas9 editing by co-administration of catalytically inactivating truncated guide RNAs. bioRxiv. Apr. 3, 2019.

Almendros et al. Cas4-Cas1 fusions drive efficient PAM selection and control CRISPR adaptation. Nucleic Acids Res. 2019 Apr 2.

Knapp et al. Decoupling tRNA promoter and processing activities enables specific Pol-II Cas9 guide RNA expression. Nat Commun. 2019 Apr 2;10(1):1490.

Noble et al. Daisy-chain gene drives for the alteration of local populations. PNAS. 2019 Apr 2.

Harrison. Berkeley strikes back in CRISPR patent tussle. Nat Biotechnol. 2019 Apr;37(4):338-339.

Champer et al. CRISPR Gene Drive Efficiency and Resistance Rate Is Highly Heritable with No Common Genetic Loci of Large Effect. Genetics. 2019 Mar 27. pii: genetics.302037.2019

Yin et al. Optimizing genome editing strategy by primer-extension-mediated sequencing. Cell Discov. 2019 Mar 26;5:18.

Slaymaker et al. High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage. Cell Rep. 2019 Mar 26;26(13):3741-3751.e5.

Toda et al. An efficient DNA- and selectable-marker-free genome-editing system using zygotes in rice. Nat Plants. 2019 Mar 25.

Liu et al. Enhanced Cas12a editing in mammalian cells and zebrafish. Nucleic Acids Res. 2019 Mar 20. pii: gkz184.

Sun et al. Development of drug-inducible CRISPR-Cas9 systems for large-scale functional screening. BMC Genomics. 2019 Mar 19;20(1):225.

Li et al. Precise gene replacement in rice by RNA transcript-templated homologous recombination. Nat Biotechnol. 2019 Mar 18.

Hwang et al. Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements. Nat Commun. 2019 Mar 15;10(1):1234.

Bhattacharya et al. A simple genotyping method to detect small CRISPR-Cas9 induced indels by agarose gel electrophoresis. Sci Rep. 2019 Mar 14;9(1):4437.

Kelliher et al. One-step genome editing of elite crop germplasm during haploid induction. Nat Biotechnol. 2019 Mar;37(3):287-292.

Labun et al. Accurate analysis of genuine CRISPR editing events with ampliCan. Genome Res. 2019 Mar 8. pii: gr.244293.118.

Cullot et al. CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations. Nat Commun. 2019 Mar 8;10(1):1136.

Wegner et al. Circular synthesized CRISPR/Cas gRNAs for functional interrogations in the coding and noncoding genome. Elife. 2019 Mar 6;8. pii: e42549.

Zhang et al. A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae. Nat Commun. 2019 Mar 5;10(1):1053.

Zhu et al. Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type IIC Anti-CRISPR Proteins. Mol Cell. 2019 Mar 5. pii: S1097-2765(19)30058-9.

Kim et al. Genome-wide target specificity of CRISPR RNA-guided adenine base editors. Nat Biotechnol. 2019 Mar 4. 

Fu et al. Target-dependent nickase activities of the CRISPR-Cas nucleases Cpf1 and Cas9. Nat Microbiol. 2019 Mar 4. 

Tsui et al. Systematic identification of regulators of antibody-drug conjugate toxicity using CRISPR-Cas9 screens. bioRxiv. Mar. 3, 2019.

Zuo et al. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science. 2019 Feb 28. pii: eaav9973.

Jin et al. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science. 2019 Feb 28. pii: eaaw7166.

O’Brien et al. Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning. Sci Rep. 2019 Feb 26;9(1):2788.

Newton et al. DNA stretching induces Cas9 off-target activity. Nat Struct Mol Biol. 2019 Feb 25.

Edracki et al. A Compact, High-Accuracy Cas9 with a Dinucleotide PAM for In Vivo Genome Editing. Mol Cell. 2019 Feb 21;73(4):714-726.e4.

Wright et al. A Functional Mini-Integrase in a Two-Protein-type V-C CRISPR System. Mol Cell. 2019 Feb 21;73(4):727-737.e3.  

Vicente et al. A CyclinB2-Cas9 fusion promotes the homology-directed repair of double-strand breaks. bioRxiv. Feb. 20, 2019.

Schmidt et al. Nucleic Acid Cleavage with a Hyperthermophilic Cas9 from an Unculturable Ignavibacterium. bioRxiv. Feb. 20, 2019.

Michaels et al. Precise tuning of gene expression levels in mammalian cells. Nat Commun. 2019 Feb 18;10(1):818.

Prowse et al. A Y-chromosome shredding gene drive for controlling pest vertebrate populations. Elife. 2019 Feb 15;8. pii: e41873.

Oberhofer et al. Cleave and Rescue, a novel selfish genetic element and general strategy for gene drive. PNAS. 2019 Feb 13. pii: 201816928.

Papikian et al. Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems. Nat Commun. 2019 Feb 13;10(1):729.

Back et al. Neuron-Specific Genome Modification in the Adult Rat Brain Using CRISPR-Cas9 Transgenic Rats. Neuron. 2019 Feb 8. pii: S0896-6273(19)30062-5

Teng et al. Enhanced mammalian genome editing by new Cas12a orthologs with optimized crRNA scaffolds. Genome Biol. 2019 Feb 5;20(1):15.

Goncalves et al. Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects. Genome Biol. 2019 Feb 5;20(1):27.  

Liu et al. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature. 2019 Feb 4.

Ma et al. Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information. Nat Comm. 2019 Feb 4;10(1):560.

Graf et al. sgRNA Sequence Motifs Blocking Efficient CRISPR/Cas9-Mediated Gene Editing. Cell Rep. 2019 Jan 29;26(5):1098-1103.e3.

Merkle et al. Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides. Nat Biotech. 2019 Jan 28.

Charlesworth el al. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat Med. 2019 Jan 28.

Anderson et al. Targeted Cleavage and Polyadenylation of RNA by CRISPR-Cas13. bioRxiv. Jan. 26, 2019.

Fulco et al. Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations. bioRxiv. Jan. 26, 2019.

Fortin et al. Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens. Genome Biol. 2019 Jan 25;20(1):21.

Tan et al. Engineering of high-precision base editors for site-specific single nucleotide replacement. Nat Comm. 2019 Jan 25;10(1):439.

Zhu et al. Guide RNAs with embedded barcodes boost CRISPR-pooled screens. Genome Biol. 2019 Jan 24;20(1):20.

Strecker et al. Engineering of CRISPR-Cas12b for human genome editing. Nat Commun. 2019 Jan 22;10(1):212. 

Guo et al. Structural insights into a high fidelity variant of SpCas9. Cell Res. 2019 Jan 21. 

Tycko et al. Identification and mitigation of pervasive off-target activity in CRISPR-Cas9 screens for essential non-coding elements. bioRxiv . Jan. 18, 2019.

Nobles et al. iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity. Genome Biol. 2019 Jan 17;20(1):14.

Nakamura et al. Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nat Comm. 2019 Jan 14;10(1):194.

Rubin et al. Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks. Cell. 2019 Jan 10;176(1-2):361-376.e17.

Gasperini et al. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell. 2019 Jan 10;176(1-2):377-390.e19.

Kandul et al. Transforming insect population control with precision guided sterile males with demonstration in flies. Nat Comm. 2019 Jan 8;10(1):84.

Goudarzi et al. Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility. Elife. 2019 Jan 8;8. pii: e40815.

Yan et al. Functionally diverse type V CRISPR-Cas systems. Science. 2019 Jan 4;363(6422):88-91.

Gilles et al. Clonal analysis by tunable CRISPR-mediated excision. Develop. 2019 Jan 4;146(1).

Mangeot et al. Genome editing in primary cells and in vivo using viral-derived Nanoblades loaded with Cas9-sgRNA ribonucleoproteins. Nat Comm. 2019 Jan 3;10(1):45.

Breinig et al. Multiplexed orthogonal genome editing and transcriptional activation by Cas12a. Nat Methods. 2019 Jan;16(1):51-54.

Laughery et al. R-loop formation by dCas9 is mutagenic in Saccharomyces cerevisiae. Nucleic Acids Res. 2018 Dec 21.

Reploge et al. Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq. bioRxiv. Dec. 21, 2018.

Globyte. CRISPR/Cas9 searches for a protospacer adjacent motif by lateral diffusion. EMBO J. 2018 Dec 20. pii: e99466.

Jiang et al. Temperature-Responsive Competitive Inhibition of CRISPR-Cas9. Mol Cell. 2018 Dec 19. pii: S1097-2765(18)30986-9.

Li et al. Synthetic Oligonucleotides Inhibit CRISPR-Cpf1-Mediated Genome Editing. Cell Rep. 2018 Dec 18;25(12):3262-3272.e3.

Chakrabarti et al. Target-Specific Precision of CRISPR-Mediated Genome Editing. Mol Cell. 2018 Dec 10. pii: S1097-2765(18)31001-3.

Siu et al. Riboregulated toehold-gated gRNA for programmable CRISPR–Cas9 function. Nat Chem Biol. 2018 Dec 10.

Yan et al. Functionally diverse type V CRISPR-Cas systems. Science. 2018 Dec 6. eaav7271

Amrani et al. NmeCas9 is an intrinsically high-fidelity genome-editing platform. Genome Biol. 2018 Dec 5;19(1):214.

Yang et al. Shortening the Half-Life of Cas9 Maintains Its Gene Editing Ability and Reduces Neuronal Toxicity. Cell Rep. 2018 Dec 04. 25:10, P2653-2659.E3.

Poe et al. Robust CRISPR/Cas9-mediated tissue specific mutagenesis reveals gene redundancy and perdurance in Drosophila. Genetics. 2018 Nov 30.

Ikeda et al. Efficient scarless genome editing in human pluripotent stem cells. Nat Methods. 2018 Nov 30. 

Chen et al. Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-Tag. Nat Comm. 2018 Nov 29;9(1):5065.

Chen et al. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. bioRxiv. Nov. 28, 2018.

Allen et al. Predicting the mutations generated by repair of Cas9-induced double-strand breaks. Nat Biotech. 2018 Nov 27. 

Hoffmann et al. Cell-specific CRISPR/Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins. bioRxiv. Nov. 27, 2018.

Yang et al. Base editing generates substantial off-target single nucleotide variants. bioRxiv. Nov. 27, 2018.

Gao et al. Improvement of the CRISPR-Cpf1 system with ribozyme-processed crRNA. RNA Biol. 2018 Nov 23.

Buchmuller et al. Pooled clone collections by multiplexed CRISPR/Cas12a-assisted gene tagging in yeast. bioRxiv. Nov. 22, 2018.

Bolukbasi et al. Orthogonal Cas9-Cas9 chimeras provide a versatile platform for genome editing. Nat Comm. 2018 Nov 19;9(1):4856. 

Lee et al. Targeting fidelity of adenine and cytosine base editors in mouse embryos. Nat Comm. 2018 Nov 15;9(1):4804.

Burg et al. Conditional mutagenesis by oligonucleotide-mediated integration of loxP sites in zebrafish. PLoS Genet. 2018 Nov 14;14(11):e1007754.

Wienert et al. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. bioRxiv. Nov. 14, 2018.

Zhu et al. Spatial control of in vivo CRISPR–Cas9 genome editing via nanomagnets. Nature Biomed Engineer. 2018 Nov 12.

Kim et al. DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA. Genome Res. 2018 Nov 9. 

Liu et al. Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites. Nat Biotech. 2018 Nov 5. 

Wang et al. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nat Biotech. 2018 Nov;36(10):946-949. 

Ma et al. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat Methods. 2018 Oct 30.

Bubeck et al. Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9. Nat Methods. 2018 Oct 30.

Chatterjee et al. Minimal PAM specificity of a highly similar SpCas9 ortholog. Science Advances  24 Oct 2018: Vol. 4, no. 10, eaau0766.

Liu et al. Intrinsic Nucleotide Preference of Diversifying Base Editors Guides Antibody Ex Vivo Affinity Maturation. Cell Rep. 2018 Oct 23. 25:4, P884-892.E3.

Guo et al. Harnessing accurate non-homologous end joining for efficient precise deletion in CRISPR/Cas9-mediated genome editing. Genome Biol. 2018 Oct 19;19(1):170. 

Wang et al. Cas9-mediated allelic exchange repairs compound heterozygous recessive mutations in mice. Nat Biotech. 2018 Oct;36(9):839-842. 

Koblan et al. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat Biotech. 2018 Oct;36(9):843-846. 

Ting et al. Guide Swap enables genome-scale pooled CRISPR-Cas9 screening in human primary cells. Nat Methods. 2018 Oct 8. 

Wang et al. CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization. Cell. 2018 Oct 8. pii: S0092-8674(18)31185-1. 

Shariati et al. Reversible disruption of specific transcription factor-DNA interactions using CRISPR/Cas9. bioRxiv. Sept. 28, 2018.

Jakimo et al. A Cas9 with Complete PAM Recognition for Adenine Dinucleotides. bioRxiv. Sept. 27, 2018.

Kyrou et al. A CRISPR-Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes. Nat Biotech. 2018 Sep 24.

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