GE Journal Club (genome engineering/gene editing) at Harvard Medical School

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.

–  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  –  – 

SUGGESTED PAPERS (reverse chronological order)

DeWeirdt et al. Genetic screens in isogenic mammalian cell lines without single cell cloning. bioRxiv. June 23, 2019.

Roberts et al. Cas9+ conditionally-immortalized macrophages as a tool for bacterial pathogenesis and beyond. Elife. 2019 Jun 17;8. pii: e45957.

Brunner et al. CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms. Life Sci Alliance. 2019 Jun 13;2(3). pii: e201800267.

Klompe et al. Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration. Nature. 2019 Jun 12.

Phillip et al. Mos1 Element-Mediated CRISPR Integration of Transgenes in Caenorhabditis elegans. G3 (Bethesda). 2019 Jun 11.

Zhou et al. Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis. Nature. 2019 Jun 10.

Strecker et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science. 2019 Jun 6. pii: eaax9181.

Zhan et al. Multiplexed promoterless gene expression with CRISPReader. Genome Biol. 2019 Jun 3;20(1):113.

Park et al. Highly efficient editing of the β-globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease. Nucleic Acids Res. 2019 May 31.

Garcia-Marques et al. CLADES: a programmable sequence of reporters for lineage analysis. bioRxiv. May 30, 2019.

Lin et al. Microhomology based CRISPR tagging tools for protein tracking, purification, and depletion. J Biol Chem. 2019 May 28.

Shahbazi et al. Targeted homology-directed repair in blood stem and progenitor cells with CRISPR nanoformulations. Nat Mater. 2019 May 27.

Wesley et al. Expanding The CRISPR Toolbox With Mad7 In Zebrafish And Human Cells. bioRxiv. May 25, 2019.

Wierson et al. GeneWeld: a method for efficient targeted integration directed by short homology. bioRxiv. May 25, 2019.

Owens et al. Microhomologies are prevalent at Cas9-induced larger deletions. Nucleic Acids Res. 2019 May 25.

Mann et al. The Gene Sculpt Suite: a set of tools for genome editing. Nucleic Acids Res. 2019 May 25.

Li et al. Development of a Confinable Gene-Drive System in the Human Disease Vector, Aedes aegypti. bioRxiv. May 24, 2019.

Duan et al. Model-based understanding of single-cell CRISPR screening. Nat Commun. 2019 May 20;10(1):2233.

Huang et al. Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Nat Biotechnol. 2019 May 20.

Rees et al. Development of hRad51-Cas9 nickase fusions that mediate HDR without double-stranded breaks. Nat Commun. 2019 May 17;10(1):2212.

Loveless, et al. Ordered insertional mutagenesis at a single genomic site enables lineage tracing and analog recording in mammalian cells. bioRxiv. May 16, 2019.

Chan, et al. Molecular recording of mammalian embryogenesis. Nature. 2019 May 13.

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.

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/Cas9. Mol Cell. 2019 May 2;74(3):622-633.e4.

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.

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.

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. 

Cyranoski, et al. Genome-edited baby claim provokes international outcry. Nature. 2018 Nov;563(7733):607-608.

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.

Yuan et al. Genetic Modulation of RNA Splicing with a CRISPR-Guided Cytidine Deaminase. Mol Cell. 2018 Sep 21. pii: S1097-2765(18)30741-X.

Oberhofer et al. Behavior of homing endonuclease gene drives targeting genes required for viability or female fertility with multiplexed guide RNAs. PNAS. 2018 Sep 17.

Wang et al. An Efficient Genome Editing Strategy To Generate Putative Null Mutants in Caenorhabditis elegans Using CRISPR/Cas9. G3. 2018 Sep 17.

Serebrenik et al. Scalable tagging of endogenous genes by homology-independent intron targeting. bioRxiv. Sept. 10, 2018.

Yarrington et al. Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo. PNAS. 2018 Sep 10. 

Champer et al. Molecular safeguarding of CRISPR gene drive experiments. bioRxiv. Sept 8, 2018.

Bin Moon et al. Highly efficient genome editing by CRISPR-Cpf1 using CRISPR RNA with a uridinylate-rich 3'-overhang. Nat Comm. 2018 Sep 7;9(1):3651. 

Marino et al. Discovery of widespread Type I and Type V CRISPR-Cas inhibitors. Science. 2018 Sep 6. 

Watters et al. Systematic discovery of natural CRISPR-Cas12a inhibitors. Science. 2018 Sep 6. 

Sinha et al. A systematic genome-wide mapping of the oncogenic risks associated with CRISPR-Cas9 editing. bioRxiv. Sept. 3, 2018.

Lee et al. Unexpected CRISPR on-target effects. Nat Biotech. 2018 Sep;36(8):703-704. 

Kalhor et al. Developmental barcoding of whole mouse via homing CRISPR. Science. 2018 Aug 31;361(6405).

Gutierrez-Triana et al. Efficient single-copy HDR by 5' modified long dsDNA donors. Elife. 2018 Aug 29;7.

Schaefer et al. PAVOOC: Designing CRISPR sgRNAs using 3D protein structures and functional domain annotation. bioRxiv. Aug. 23, 2018.

Park et al. Extension of the crRNA enhances Cpf1 gene editing in vitro and in vivo. Nat Comm. 2018 Aug 17;9(1):3313.

Gapinske et al. CRISPR-SKIP: programmable gene splicing with single base editors. Genome Biol. 2018 Aug 15;19(1):107. 

Sternberg et al. An efficient genome editing strategy to generate putative null mutants in Caenorhabditis elegans using CRISPR/Cas9. bioRxiv. Aug. 13, 2018.

Chakrabarti et al. Target-specific precision of CRISPR-mediated genome editing. bioRxiv. Aug. 9, 2018.

Su et al. CRISPR/Cas9-based gene targeting using synthetic guide RNAs enables robust cell biological analyses. Mol Biol Cell. 2018 Aug 9:mbcE18040214. 

Kuscu et al. Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells. J Mol Biol. 2018 Aug 9. 

Roche et al. Homology Directed Repair by Cas9:Donor Co-localization in Mammalian Cells. bioRxiv . Aug. 6, 2018.

Lee et al. Directed evolution of CRISPR-Cas9 to increase its specificity. Nat Commun. 2018 Aug 6;9(1):3048. 

Richardson et al. CRISPR-Cas9 genome editing in human cells occurs via the Fanconi anemia pathway. Nat Genet. 2018 Aug;50(8):1132-1139. 

Halperin et al. CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature. 2018 Aug;560(7717):248-252.

Yeo et al. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods. 2018 Aug;15(8):611-616. 

Chaverra-Rodriguez et al. Targeted delivery of CRISPR-Cas9 ribonucleoprotein into arthropod ovaries for heritable germline gene editing. Nat Comm. 2018 Aug 1;9(1):3008. 

Gehrke et al. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotech. 2018 Jul 30. 

Kandul et al. Transforming Insect Population Control with Precision Guided Sterile Males. bioRxiv. July 26, 2018.

Grunwald et al. Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline. bioRxiv. July 7, 2018.

Suzuki et al. Switchable genome editing via genetic code expansion. Sci Rep. 2018 Jul 3;8(1):10051.

Ihry et al. p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nat Med. 2018 Jul;24(7):939-946. 

Mello et al. Robust genome editing with short single-stranded and long, partially single-stranded DNA donors in C. elegans. bioRxiv. June 20, 2018.

Noble et al. Current CRISPR gene drive systems are likely to be highly invasive in wild populations. Elife. 2018 Jun 19;7.

Knapp et al. Decoupling tRNA promoter and processing activities enables specific Pol-II Cas9 guide RNA expression. bioRxiv. June 8, 2018.

Li-Kroeger et al. An expanded toolkit for gene tagging based on MiMIC and scarless CRISPR tagging in Drosophila. bioRxiv. June 2, 2018.

Savic et al. Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. Elife. 2018 May 29;7.

Kurata et al. Highly Multiplexed Genome Engineering Using CRISPR/Cas9 gRNA Arrays. bioRxiv. May 25, 2018.

Kundert et al. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. bioRxiv. May 15, 2018.

Liao et al. One-step assembly of large CRISPR arrays enables multi-functional targeting and reveals constraints on array design. bioRxiv. May 2, 2018.

Chen et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018 Apr 27;360(6387):436-439. 

Tang et al. Rewritable multi-event analog recording in bacterial and mammalian cells. Science. 2018 Apr 13;360(6385). 

Hu et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature. 2018 Apr 5;556(7699):57-63.

Tsui et al. dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. PNAS. 2018 Mar 20;115(12):E2734-E2741

Chen et al. CRISPR-Tag: an Efficient DNA Tagging System in Living Cells. bioRxiv. March 12, 2018.

Kim et al. Deep learning improves prediction of CRISPR-Cpf1 guide RNA activity. Nat Biotech. 2018 Mar;36(3):239-241. 

Casini et al. A highly specific SpCas9 variant is identified by in vivo screening in yeast. Nat Biotech. 2018 Mar;36(3):265-271. 

Zhou et al. In vivo simultaneous transcriptional activation of multiple genes in the brain using CRISPR-dCas9-activator transgenic mice. Nat Neurosci. 2018 Mar;21(3):440-446. 

Poe et al. Highly efficient CRISPR/Cas9-mediated tissue specific mutagenesis in Drosophila. bioRxiv. Feb. 20, 2018.

Strutt et al. RNA-dependent RNA targeting by CRISPR-Cas9. Elife. 2018 Jan 5;7.

Moreno-Mateos et al. CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing. Nat Comm. 2017 Dec 8;8(1):2024.

Gaudelli et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature. 2017 Nov 23;551(7681):464-471. 

Chen et al. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature. 2017 Oct 19;550(7676):407-410. 

Abudayyeh et al. RNA targeting with CRISPR-Cas13. Nature. 2017 Oct 12;550(7675):280-284.