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

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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
02/03/2020 NO MEETING – – – – – – – –
02/10/2020 1) Patrick Griffin
2) Jinyu Wang 		1) TBD
2) TBD
02/17/2020 NO MEETING (Holiday) – – – – – – – –
02/24/2020 NO MEETING (Dept. Retreat) – – – – – – – –
03/02/2020 1) Claire Hu
2) Gabriel Birchak 		1) TBD
2) TBD
03/09/2020 1) Navdar Sever
2) Justin Bosch 		1) TBD
2) TBD
03/16/2020 1) Sarah Bowling
2) Jun Xu 		1) TBD
​​​​​​​2) TBD
03/23/2020 1) TBD
​​​​​​​2) TBD 		1) TBD
​​​​​​​2) TBD
03/30/2020 1) Afroditi Petsakou
2) Cole Peters 		1) TBD
​​​​​​​2) TBD
04/06/2020 1) Ram Viswanatha
2) Hassan Bukhari 		1) TBD
​​​​​​​2) TBD
04/13/2020 1) Tracy Zhang
2) Pedro Saavedra 		1) TBD
​​​​​​​2) TBD
04/20/2020 1) TBD
​​​​​​​2) TBD 		1) TBD
​​​​​​​2) TBD
04/27/2020 1) Baolong Xia
2) Ben Ewen-Campen 		1) TBD
​​​​​​​2) TBD
05/04/2020 1) Jonathan Zirin
2) Stephanie Mohr 		1) TBD
​​​​​​​2) TBD
05/11/2020 1) Shannon Knight
2) Enzo Mameli 		1) TBD
​​​​​​​2) TBD
05/18/2020 1) TBD
​​​​​​​2) TBD 		1) TBD
​​​​​​​2) TBD
05/25/2020 NO MEETING (Holiday) – – – – – – – –

PAST MEETINGS

DATE PRESENTERS PAPERS
01/27/2020

1) Erik Aznauryan

2) Ah-Ram Kim

1) Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs.
https://www.nature.com/articles/s41587-019-0387-5
2) A tunable orthogonal coiled-coil interaction toolbox for engineering mammalian cells.
https://www.nature.com/articles/s41589-019-0443-y
1/13/2020 1) Giulia Ceglie
2) Sara Nunes

1) Highly efficient editing of the β-globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease. Nucleic Acids Res. Sep. 2019
https://academic.oup.com/nar/article/47/15/7955/5506860

2) De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat Commun. Oct 2019
https://www.nature.com/articles/s41467-019-12489-8

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) Abudayyeh et al. A cytosine deaminase for programmable single-base RNA editing. Science. 2019 Jul 26;365(6451):382-386
12/02/2019 1) Ankita Singh
2) Zhenfei Xie 		1) Loveless et al. DNA writing at a single genomic site enables lineage tracing and analog recording in mammalian cells. bioRxiv. Sept. 29, 2019.
2) Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems
https://www.sciencedirect.com/science/article/pii/S1097276519308020?via%...
11/25/2019 NO MEETING – – – – – – – –
11/18/2019 1) Shannon Knight
2) Enzo Mameli 		1) 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.
2) Freije et al. Programmable Inhibition and Detection of RNA Viruses Using Cas13. Mol Cell. 2019 Oct 2. pii: S1097-2765(19)30698-7
11/11/2019 NO MEETING (Holiday) – – – – – – – –
11/04/2019 1) Jonathan Zirin
2) Stephanie Mohr 		1) Lin et al. Microhomology based CRISPR tagging tools for protein tracking, purification, and depletion. J Biol Chem. 2019 May 28.
2) Smits et al. Biological Plasticity Rescues Target Activity in CRISPR Knockouts. Nat Methods. 2019 Oct 28.
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. 
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.

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SUGGESTED PAPERS (reverse chronological order)

 

High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells.
https://www.nature.com/articles/s41551-019-0505-1

Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses.
https://www.nature.com/articles/s41551-019-0501-5

A transcomplementing gene drive provides a flexible platform for laboratory investigation and potential field deployment.
https://www.nature.com/articles/s41467-019-13977-7

CRISPR/Cas9-mediated precise genome modification by a long ssDNA template in zebrafish.
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6493-4

Single-cell analysis of a mutant library generated using CRISPR-guided deaminase
https://www.biorxiv.org/content/10.1101/610725v2

Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency.
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioi...

High-throughput screens of PAM-flexible Cas9 variants for gene knock-out and transcriptional modulation
https://www.biorxiv.org/content/10.1101/2020.01.22.916064v1

Production of genetically engineered mice with higher efficiency, lower mosaicism, and multiplexing capability using maternally expressed Cas9.
https://www.nature.com/articles/s41598-020-57996-7

scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1928-4

Single AAV-mediated mutation replacement genome editing in limited number of photoreceptors restores vision in mice.
https://www.nature.com/articles/s41467-019-14181-3

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing.
https://www.nature.com/articles/s41467-020-14362-5

 

 

Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform.
https://www.nature.com/articles/s41467-019-14012-5

Reactivation of γ-globin expression through Cas9 or base editor to treat β-hemoglobinopathies.
https://www.nature.com/articles/s41422-019-0267-z

RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons.
https://www.nature.com/articles/s41588-019-0555-z

A tunable orthogonal coiled-coil interaction toolbox for engineering mammalian cells.
https://www.nature.com/articles/s41589-019-0443-y

Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs.
https://www.nature.com/articles/s41587-019-0387-5

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors.
https://www.nature.com/articles/s41587-019-0393-7

CRISPR-Cas13d induces efficient mRNA knock-down in animal embryos
https://www.biorxiv.org/content/10.1101/2020.01.13.904763v1

 

Herpesviral lytic gene functions render the viral genome susceptible to novel editing by CRISPR/Cas9.
https://elifesciences.org/articles/51662

CRISPR-Cas3 induces broad and unidirectional genome editing in human cells.
https://www.nature.com/articles/s41467-019-13226-x

Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency.
https://www.nature.com/articles/s41587-019-0325-6

A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases.
https://www.nature.com/articles/s41586-019-1786-y

Synthetic chimeric nucleases function for efficient genome editing.
https://www.nature.com/articles/s41467-019-13500-y

Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing.
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz1136/565...

Expanding the editable genome and CRISPR-Cas9 versatility using DNA cutting-free gene targeting based on in trans paired nicking.
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz1121/565...

Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9
https://genome.cshlp.org/content/early/2019/12/12/gr.248559.119.abstract

A bacterial gene-drive system efficiently edits and inactivates a high copy number antibiotic resistance locus
https://www.nature.com/articles/s41467-019-13649-6

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells
https://www.nature.com/articles/s41592-019-0392-0

Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq
https://www.biorxiv.org/content/10.1101/503367v1

Structural basis of DNA targeting by a transposon-encoded CRISPR–Cas system
https://www.nature.com/articles/s41586-019-1849-0

Multi-functional genome-wide CRISPR system for high throughput genotype-phenotype mapping.
https://www.nature.com/articles/s41467-019-13621-4

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets.
https://www.nature.com/articles/s41467-019-13805-y

Cas12a mediates efficient and precise endogenous gene tagging via MITI: microhomology-dependent targeted integrations.
https://link.springer.com/article/10.1007/s00018-019-03396-8

Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing.
https://www.nature.com/articles/s41467-019-11454-9

A transient reporter for editing enrichment (TREE) in human cells.
https://academic.oup.com/nar/article/47/19/e120/5552066

Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor.
https://www.nature.com/articles/s41587-019-0331-8

Expanding C-T base editing toolkit with diversified cytidine deaminases.
https://www.nature.com/articles/s41467-019-11562-6

Conditional control of RNA-guided nucleic acid cleavage and gene editing.
https://www.nature.com/articles/s41467-019-13765-3

Assessment of a Split Homing Based Gene Drive for Efficient Knockout of Multiple Genes.
https://www.g3journal.org/content/early/2019/12/27/g3.119.400985

An efficient gene knock-in strategy using 5'-modified double-stranded DNA donors with short homology arms
https://www.nature.com/articles/s41589-019-0432-1

 

Song et al. AcrIIA5 Inhibits a Broad Range of Cas9 Orthologs by Preventing DNA Target Cleavage. Cell Rep. 2019 Nov 26;29(9):2579-2589.e4.

Cancellieri et al. CRISPRitz: rapid, high-throughput, and variant-aware in silico off-target site identification for CRISPR genome editing. Bioinformatics. 2019 Nov 25. pii: btz867.

Wells et al. Ranking of non-coding pathogenic variants and putative essential regions of the human genome. Nat Commun. 2019 Nov 20;10(1):5241.

Webber et al. Highly efficient multiplex human T cell engineering without double-strand breaks using Cas9 base editors. Nat Commun. 2019 Nov 19;10(1):5222.

Wierson et al. Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells. CRISPR J. 2019 Nov 19.

Alexander et al. Concurrent genome and epigenome editing by CRISPR-mediated sequence replacement. BMC Biol. 2019 Nov 18;17(1):90.

Askary et al. In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription. Nat Biotechnol. 2019 Nov 18.

Cermon et al. Harnessing type I CRISPR-Cas systems for genome engineering in human cells. Nat Biotechnol. 2019 Nov 18.

Camsund et al. Time-resolved imaging-based CRISPRi screening. Nat Methods. 2019 Nov 18.

Paix et al. Rapid Tagging of Human Proteins with Fluorescent Reporters by Genome Engineering using Double-Stranded DNA Donors. Curr Protoc Mol Biol. 2019 Dec;129(1):e102.

Kulkarni et al. Programmable CRISPR interference for gene silencing using Cas13a in mosquitoes. bioRxiv. Nov. 18, 2019.

Fei et al. Deciphering essential cistromes using genome-wide CRISPR screens. PNAS 2019 Nov 14. pii: 201908155.

Wei et al. CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for over 5,500 Drosophila genes conserved in humans. Genome Res. 2019 Nov 13. pii: gr.250811.119.

Canaj et al. Deep profiling reveals substantial heterogeneity of integration outcomes in CRISPR knock-in experiments. bioRxiv. Nov. 13, 2019.

Minev et al. Rapid in vitro production of single-stranded DNA. Nucleic Acids Res. 2019 Nov 12. pii: gkz998.

Garcia et al. Anti-CRISPR AcrIIA5 Potently Inhibits All Cas9 Homologs Used for Genome Editing. Cell Rep. 2019 Nov 12;29(7):1739-1746.e5.

Chiarella et al. Dose-dependent activation of gene expression is achieved using CRISPR and small molecules that recruit endogenous chromatin machinery. Nat Biotechnol. 2019 Nov 11.

Hoshijima et al. Highly Efficient CRISPR-Cas9-Based Methods for Generating Deletion Mutations and F0 Embryos that Lack Gene Function in Zebrafish. Dev Cell. 2019 Nov 7.

Querques et al. A highly soluble Sleeping Beauty transposase improves control of gene insertion. Nat Biotechnol. 2019 Nov 4.

Kanca et al. An efficient CRISPR-based strategy to insert small and large fragments of DNA using short homology arms. Elife. 2019 Nov 1;8. pii: e51539.

Wainberg et al. A genome-wide almanac of co-essential modules assigns function to uncharacterized genes. bioRxiv. Nov. 1, 2019.

Li et al. One-step efficient generation of dual-function conditional knockout and geno-tagging alleles in zebrafish. Elife. 2019 Oct 30;8. pii: e48081.

Schmidt et al. Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium. PNAS. 2019 Oct 28. pii: 201904273.

Grajcarek et al. Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations. Nat Commun. 2019 Oct 24;10(1):4856.

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