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

JUMP TO:

Current Schedule
About GE Journal Club
Contact
Suggested Papers

GE Header
Meetings are Mondays, 12:30 PM – 1:30 PM in NRB 354 unless otherwise noted
Pizza and soda generously provided by the HMS Dept. of Genetics

Advances in genome editing occur at a blazing speed, and reading the high volume of papers is too difficult for one person. To address this, we run a Gene Editing Journal Club. By presenting papers in a group setting, we stay up to date on recent technologies, stimulate critical discussion, and establish new contacts for collaboration. We are always looking for new members in the Longwood Medical and Boston area. Everyone is welcome to attend, from postdocs and PIs to students and techs, with any level of experience.

GE Journal Club Flier

CURRENT SCHEDULE

DATE PRESENTERS PAPERS
10/28/2019 1) Baolong Xia
2) Ben Ewen-Campen
1) Anzalone et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019 Oct 21. 
2) Ihry et al. p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nat Med. 2018 Jul;24(7):939-946. 
11/04/2019 1) Jonathan Zirin
2) Stephanie Mohr
1) TBD
2) TBD
11/11/2019 NO MEETING (Holiday) – – – – – – – –
11/18/2019 1) Shannon Knight
2) Josh Li
1) TBD
2) TBD
11/25/2019 NO MEETING – – – – – – – –
12/02/2019 1) Ankita Singh
2) Zhenfei Xie
1) TBD
2) TBD
12/09/2019 1) Charlotte Bellamy
2) Kyle McCracken
1) MacLeod et al. Genome-Wide CRISPR-Cas9 Screens Expose Genetic Vulnerabilities and Mechanisms of Temozolomide Sensitivity in Glioblastoma Stem Cells. Cell Rep. 2019 Apr 16;27(3):971-986.e9
2) TBD
12/16/2019 1) Jinyu Wang
2) Enzo Mameli
1) Wang et al. CRISPR-mediated live imaging of genome editing and transcription. Science. 2019 Sep 5. pii: eaax7852.
2) TBD
12/23/2019 NO MEETING (Holiday) – – – – – – – –
12/30/2019 NO MEETING (Holiday) – – – – – – – –
01/06/2020 NO MEETING  – – – – – – – –

PAST MEETINGS

DATE PRESENTERS PAPERS
10/21/2019 1) Pedro Saavedra
2) Amit Choudhary
1) Hanlon et al. High levels of AAV vector integration into CRISPR-induced DNA breaks. Nat Commun. 2019 Sep 30;10(1):4439.
2) Maji et al.
A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9. Cell. 2019 May 2;177(4):1067-1079.e19.
10/14/2019 NO MEETING (Holiday) – – – – – – – –
10/07/2019 1) Hassan Bukhari
2) Tracy Zhang
1) Jayavaradhan et al. CRISPR-Cas9 fusion to dominant-negative 53BP1 enhances HDR and inhibits NHEJ specifically at Cas9 target sites. Nat Commun. 2019 Jun 28;10(1):2866.
2) Kemaladewi et al.
A mutation-independent approach for muscular dystrophy via upregulation of a modifier gene. Nature. 2019 Aug;572(7767):125-130.
09/30/2019 1) Ram Viswanatha
2) Cole Peters
1) Pickar-Oliver et al. Targeted transcriptional modulation with type I CRISPR–Cas systems in human cells. Nat Biotechnol. 2019 Sept 23.
2) Villiger et al. 
Treatment of a metabolic liver disease by in vivo genome base editing in adult mice. Nat Med. 2018 Oct;24(10):1519-1525.
09/23/2019 1) Afroditi Petsakou
2) Jun Xu
1) Xu et al. CRISPR-Edited Stem Cells in a Patient with HIV and Acute Lymphocytic Leukemia. N Engl J Med. 2019 Sep 11.
2) Xu et al.
Mass spider silk production through targeted gene replacement in Bombyx mori. Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):8757-8762.
09/16/2019 Justin Bosch
Sarah Bowling
1) Strecker et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science. 2019 Jun 6. pii: eaax9181.
2) Dong et al.
Genome-Wide Off-Target Analysis in CRISPR-Cas9 Modified Mice and Their Offspring. G3 (Bethesda). 2019 Sep 6. pii: g3.400503.2019
09/09/2019 Navdar Sever
Ah-Ram Kim
1) Quadros et al. Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins. Genome Biol. 2017 May 17;18(1):92. 
2) Wang et al. 
Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly. Science. 2019 Aug 30;365(6456):922-926.

07/01/2019-
09/02/2019

No Meetings – – – – – – – –
06/24/2019 Claire Hu
Ricky Brathwaite
1a) Dandage et al. beditor: A Computational Workflow for Designing Libraries of Guide RNAs for CRISPR-Mediated Base Editing. Genetics. 2019 Jun;212(2):377-385. 
1b) Erard et al.
A CRISPR Resource for Individual, Combinatorial, or Multiplexed Gene Knockout. Mol Cell. 2017 Sep 21;67(6):1080.
2) 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.
06/17/2019 NO MEETING – – – – – – – –
06/10/2019 Josh Li 
Zhenfei Xie
1) 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.
2) Li, et al. 
CRISPR–Cas9-mediated base-editing screening in mice identifies DND1 amino acids that are critical for primordial germ cell development. Nat Cell Biol. 2018 Nov;20(11):1315-1325.
06/04/2019 Stephanie Mohr
Shannon Knight
1) Port et al. A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila. bioRxiv May 13, 2019.
2) 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
05/27/2019 NO MEETING – – – – – – – –
05/20/2019 NO MEETING – – – – – – – –
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.

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

SUGGESTED PAPERS (reverse chronological order)

Feldman et al. Optical Pooled Screens in Human Cells. Cell. 2019 Oct 17;179(3):787-799.e17.

Wang et al. Multiplexed activation of endogenous genes by CRISPRa elicits potent antitumor immunity. Nat Immunol. 2019 Oct 14.

Watters et al. Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes. bioRxiv. Oct. 9, 2019.

Reis et al. Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays. Nat Biotechnol. 2019 Oct 7.

Young et al. Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull. Nat Biotechnol. 2019 Oct 7.

He et al. De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat Commun. 2019 Oct 4;10(1):4541.

Hamilton et al. Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing. Nat Commun. 2019 Oct 4;10(1):4544.

Freije et al. Programmable Inhibition and Detection of RNA Viruses Using Cas13. Mol Cell. 2019 Oct 2. pii: S1097-2765(19)30698-7.

Karageorgi et al. Genome editing retraces the evolution of toxin resistance in the monarch butterfly. Nature. 2019 Oct 2.

Acharya et al. Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing. PNAS. 2019 Sep 30. pii: 201818461.

Tan et al. Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity. PNAS. 2019 Sep 30. pii: 201906843.

Loveless et al. DNA writing at a single genomic site enables lineage tracing and analog recording in mammalian cells. bioRxiv. Sept. 29, 2019.

Kim et al. Adenine base editors catalyze cytosine conversions in human cells. Nat Biotechnol. 2019 Sep 23.

Taghbalout et al. Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways. Nat Commun. 2019 Sep 20;10(1):4296.

Molina et al. Structure of Csx1-cOA4 complex reveals the basis of RNA decay in Type III-B CRISPR-Cas. Nat Commun. 2019 Sep 20;10(1):4302.

Macias et al. Cas9-mediated gene-editing in the malaria mosquito Anopheles stephensi by ReMOT Control. bioRxiv. Sept. 19, 2019.

Bhoobalan-Chitty et al. Inhibition of Type III CRISPR-Cas Immunity by an Archaeal Virus-Encoded Anti-CRISPR Protein. Cell. 2019 Sep 19. pii: S0092-8674(19)31009-8.

Wang et al. Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning. Nat Commun. 2019 Sep 19;10(1):4284.

Songailiene et al. Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length. Cell Rep. 2019 Sep 17;28(12):3157-3166.e4.

Whinn et al. Nuclease dead Cas9 is a programmable roadblock for DNA replication. Sci Rep. 2019 Sep 16;9(1):13292.

Lin et al. Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials. Sci Transl Med. 2019 Sep 11;11(509). pii: eaaw8412.

Forsberg et al. Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome. Elife. 2019 Sep 10;8. pii: e46540.

Chen et al. A biodegradable nanocapsule delivers a Cas9 ribonucleoprotein complex for in vivo genome editing. Nat Nanotechnol. 2019 Sep 9.

Tycko et al. Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. Nat Commun. 2019 Sep 6;10(1):4063.

Tuladhar et al. CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation. Nat Commun. 2019 Sep 6;10(1):4056.

Gomez-Ospina et al. Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I. Nat Commun. 2019 Sep 6;10(1):4045.

Grunewald et al. CRISPR DNA base editors with reduced RNA off-target and self-editing activities. Nat Biotechnol. 2019 Sep;37(9):1041-1048.

Campa et al. Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts. Nat Methods. 2019 Sep;16(9):887-893.

Nihongaki et al. A split CRISPR-Cpf1 platform for inducible genome editing and gene activation. Nat Chem Biol. 2019 Sep;15(9):882-888.

Liu et al. Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates. Nat Chem Biol. 2019 Sep;15(9):865-871.

Kweon et al. A CRISPR-based base-editing screen for the functional assessment of BRCA1 variants. Oncogene. 2019 Aug 29.

Fleiss et al. Reshuffling yeast chromosomes with CRISPR/Cas9. PLoS Genet. 2019 Aug 29;15(8):e1008332.

Sanson et al. Optimization of AsCas12a for combinatorial genetic screens in human cells. bioRxiv. Aug. 28, 2019.

Rasys et al. CRISPR-Cas9 Gene Editing in Lizards through Microinjection of Unfertilized Oocytes. Cell Rep. 2019 Aug 27;28(9):2288-2292.e3.

Liu et al. Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria. Nat Commun. 2019 Aug 26;10(1):3693.

Gurumurthy et al. Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation. Genome Biol. 2019 Aug 26;20(1):171.

English et al. Programmable CRISPR-responsive smart materials. Science. 2019 Aug 23;365(6455):780-785.

Norman et al. Exploring genetic interaction manifolds constructed from rich single-cell phenotypes. Science. 2019 Aug 23;365(6455):786-793.

Dong et al. Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells. Cell. 2019 Aug 22;178(5):1189-1204.e23.

Yosef et al. A genetic system for biasing the sex ratio in mice. EMBO Rep. 2019 Aug;20(8):e48269.

Choi et al. Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9. Nat Methods. 2019 Aug;16(8):722-730.

Keough et al. AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design. Genome Biol. 2019 Aug 15;20(1):167.

Brown et al. CRISPR screens are feasible in TP53 wildtype cells. Mol Syst Biol. 2019 Aug;15(8):e8679.

Josipovic et al. Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system. Nucleic Acids Res. 2019 Aug 14. pii: gkz709.

Bhatt et al. Targeted DNA transposition in vitro using a dCas9-transposase fusion protein. bioRxiv. April 12, 2019.

Lim et al. A conjugation platform for CRISPR-Cas9 allows efficient β-cell engineering. bioRxiv. August 12, 2019.

Lee et al. Cytosine but not adenine base editor generates mutations in mice. bioRxiv. August 12, 2019.

Knott et al. Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a. Elife. 2019 Aug 9;8. pii: e49110.

Ratner et al. Catalytically Active Cas9 Mediates Transcriptional Interference to Facilitate Bacterial Virulence. Mol Cell. 2019 Aug 8;75(3):498-510.e5.

Kim et al. CRISPR DNA elements controlling site-specific spacer integration and proper repeat length by a Type II CRISPR-Cas system. Nucleic Acids Res. 2019 Aug 8. pii: gkz677.

Sakata et al. A single CRISPR base editor to induce simultaneous C-to-T and A-to-G mutations. bioRxiv. August 8, 2019.

Riesenberg et al. Simultaneous precise editing of multiple genes in human cells. Nucleic Acids Res. 2019 Aug 8. pii: gkz669. d

Martens et al. Visualisation of dCas9 target search in vivo using an open-microscopy framework. Nat Commun. 2019 Aug 7;10(1):3552.

Tian et al. CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons. Neuron. 2019 Aug 5. pii: S0896-6273(19)30640-3.

Liu et al. Establishment of knockout adult sea urchins by using a CRISPR-Cas9 system.  Dev Growth Differ. 2019 Aug;61(6):378-388.

Miller et al. Enhancing gene editing specificity by attenuating DNA cleavage kinetics. Nat Biotechnol. 2019 Aug;37(8):945-952.

Garcia-Marques. Unlimited Genetic Switches for Cell-Type-Specific Manipulation. Neuron. 2019 Jul 31. pii: S0896-6273(19)30603-8.

Nambiar et al. Stimulation of CRISPR-mediated homology-directed repair by an engineered RAD18 variant. Nat Commun. 2019 Jul 30;10(1):3395.

Zuo et al. Structural and functional insights into the bona fide catalytic state of Streptococcus pyogenes Cas9 HNH nuclease domain. Elife. 2019 Jul 30;8. pii: e46500.

Leenay et al. Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells. Nat Biotechnol. 2019 Jul 29.

Jost et al. Titrating gene expression with series of systematically compromised CRISPR guide RNAs. bioRxiv. July 28, 2019.

Abudayyeh et al. A cytosine deaminase for programmable single-base RNA editing. Science. 2019 Jul 26;365(6451):382-386.

Smits et al. Biological Plasticity Rescues Target Activity in CRISPR Knockouts. bioRxiv. July 26, 2019.

Gyorgy et al. Allele-specific gene editing prevents deafness in a model of dominant progressive hearing loss. Nat Med. 2019 Jul;25(7):1123-1130.

Wang et al. The histone chaperone FACT induces Cas9 multi-turnover behavior and modifies genome manipulation in human cells. bioRxiv. July 23, 2019.

Andreazza et al. Mitochondrially-targeted APOBEC1 is a potent mtDNA mutator affecting mitochondrial function and organismal fitness in Drosophila. Nat Commun. 2019 Jul 23;10(1):3280.

Thuronyi et al. Continuous evolution of base editors with expanded target compatibility and improved activity. Nat Biotechnol. 2019 Jul 22.

Liu et al. Pooled library screening with multiplexed Cpf1 library. Nat Commun. 2019 Jul 17;10(1):3144.

Qu et al. Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs. Nat Biotechnol. 2019 Jul 15.

Jones et al. Massively parallel kinetic profiling of natural and engineered CRISPR nucleases. bioRxiv. July 9, 2019.

Liao et al. Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis. Nat Commun. 2019 Jul 3;10(1):2948.

Kim et al. An anionic human protein mediates cationic liposome delivery of genome editing proteins into mammalian cells. Nat Commun. 2019 Jul 2;10(1):2905.

Hew et al. RNA-guided piggyBac transposition in human cells. Synth Biol (Oxf). 2019;4(1):ysz018. Epub 2019 Jul 2.

Thavalingam et al. Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2. Nat Commun. 2019 Jun 26;10(1):2806.

Chen et al. CRISPR-READI: Efficient Generation of Knockin Mice by CRISPR RNP Electroporation and AAV Donor Infection. Cell Rep. 2019 Jun 25;27(13):3780-3789.e4.

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.

Lopez Del Amo et al. Small-molecule control of super-Mendelian inheritance in gene drives. bioRxiv. June 14, 2019.

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.

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/Cas9Mol 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.