Literature DB >> 32284587

Design and analysis of CRISPR-Cas experiments.

Ruth E Hanna1, John G Doench2.   

Abstract

A large and ever-expanding set of CRISPR-Cas systems now enables the rapid and flexible manipulation of genomes in both targeted and large-scale experiments. Numerous software tools and analytical methods have been developed for the design and analysis of CRISPR-Cas experiments, including resources to design optimal guide RNAs for various modes of manipulation and to analyze the results of such experiments. A major recent focus has been the development of comprehensive tools for use on data from large-scale CRISPR-based genetic screens. As this field continues to progress, a clear ongoing challenge is not only to innovate, but to actively maintain and improve existing tools so that researchers across disciplines can rely on a stable set of excellent computational resources for CRISPR-Cas experiments.

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Year:  2020        PMID: 32284587     DOI: 10.1038/s41587-020-0490-7

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


  103 in total

1.  Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria.

Authors:  Giedrius Gasiunas; Rodolphe Barrangou; Philippe Horvath; Virginijus Siksnys
Journal:  Proc Natl Acad Sci U S A       Date:  2012-09-04       Impact factor: 11.205

2.  Cardiologists send up a trial balloon in new efforts to relieve heart failure.

Authors:  M F Goldsmith
Journal:  JAMA       Date:  1987-01-16       Impact factor: 56.272

3.  Enhanced CRISPR/Cas9-mediated precise genome editing by improved design and delivery of gRNA, Cas9 nuclease, and donor DNA.

Authors:  Xiquan Liang; Jason Potter; Shantanu Kumar; Namritha Ravinder; Jonathan D Chesnut
Journal:  J Biotechnol       Date:  2016-11-11       Impact factor: 3.307

4.  Serum and cell-mediated viral-specific delayed cutaneous basophil reactions during cytomegalovirus infection of guinea pigs.

Authors:  B P Griffith; P W Askenase; G D Hsiung
Journal:  Cell Immunol       Date:  1982-05-01       Impact factor: 4.868

5.  Optimization of scarless human stem cell genome editing.

Authors:  Luhan Yang; Marc Guell; Susan Byrne; Joyce L Yang; Alejandro De Los Angeles; Prashant Mali; John Aach; Caroline Kim-Kiselak; Adrian W Briggs; Xavier Rios; Po-Yi Huang; George Daley; George Church
Journal:  Nucleic Acids Res       Date:  2013-07-31       Impact factor: 16.971

6.  Targeted genomic rearrangements using CRISPR/Cas technology.

Authors:  Peter S Choi; Matthew Meyerson
Journal:  Nat Commun       Date:  2014-04-24       Impact factor: 14.919

7.  Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage.

Authors:  Nicole M Gaudelli; Alexis C Komor; Holly A Rees; Michael S Packer; Ahmed H Badran; David I Bryson; David R Liu
Journal:  Nature       Date:  2017-10-25       Impact factor: 49.962

8.  Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage.

Authors:  Alexis C Komor; Yongjoo B Kim; Michael S Packer; John A Zuris; David R Liu
Journal:  Nature       Date:  2016-04-20       Impact factor: 49.962

9.  Search-and-replace genome editing without double-strand breaks or donor DNA.

Authors:  Andrew V Anzalone; Peyton B Randolph; Jessie R Davis; Alexander A Sousa; Luke W Koblan; Jonathan M Levy; Peter J Chen; Christopher Wilson; Gregory A Newby; Aditya Raguram; David R Liu
Journal:  Nature       Date:  2019-10-21       Impact factor: 69.504

10.  Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.

Authors:  Luke A Gilbert; Max A Horlbeck; Britt Adamson; Jacqueline E Villalta; Yuwen Chen; Evan H Whitehead; Carla Guimaraes; Barbara Panning; Hidde L Ploegh; Michael C Bassik; Lei S Qi; Martin Kampmann; Jonathan S Weissman
Journal:  Cell       Date:  2014-10-09       Impact factor: 41.582

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  31 in total

Review 1.  Technologies and Computational Analysis Strategies for CRISPR Applications.

Authors:  Kendell Clement; Jonathan Y Hsu; Matthew C Canver; J Keith Joung; Luca Pinello
Journal:  Mol Cell       Date:  2020-07-02       Impact factor: 17.970

Review 2.  High-throughput methods for genome editing: the more the better.

Authors:  Yong Huang; Meiqi Shang; Tingting Liu; Kejian Wang
Journal:  Plant Physiol       Date:  2022-03-28       Impact factor: 8.340

Review 3.  A new era in functional genomics screens.

Authors:  Laralynne Przybyla; Luke A Gilbert
Journal:  Nat Rev Genet       Date:  2021-09-20       Impact factor: 53.242

Review 4.  Tutorial: design and execution of CRISPR in vivo screens.

Authors:  Christian J Braun; Andrés Carbonell Adames; Dieter Saur; Roland Rad
Journal:  Nat Protoc       Date:  2022-07-15       Impact factor: 17.021

5.  Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.

Authors:  James K Nuñez; Jin Chen; Greg C Pommier; J Zachery Cogan; Joseph M Replogle; Carmen Adriaens; Gokul N Ramadoss; Quanming Shi; King L Hung; Avi J Samelson; Angela N Pogson; James Y S Kim; Amanda Chung; Manuel D Leonetti; Howard Y Chang; Martin Kampmann; Bradley E Bernstein; Volker Hovestadt; Luke A Gilbert; Jonathan S Weissman
Journal:  Cell       Date:  2021-04-09       Impact factor: 41.582

Review 6.  The role of epigenetic mechanisms in the regulation of gene expression in the cyclical endometrium.

Authors:  Alejandra Monserrat Retis-Resendiz; Ixchel Nayeli González-García; Moisés León-Juárez; Ignacio Camacho-Arroyo; Marco Cerbón; Edgar Ricardo Vázquez-Martínez
Journal:  Clin Epigenetics       Date:  2021-05-25       Impact factor: 6.551

Review 7.  Current Applications and Future Perspectives of CRISPR-Cas9 for the Treatment of Lung Cancer.

Authors:  Markeshaw Tiruneh G/Medhin; Endeshaw Chekol Abebe; Tekeba Sisay; Nega Berhane; Tesfahun Bekele; Tadesse Asmamaw Dejenie
Journal:  Biologics       Date:  2021-05-31

8.  Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9.

Authors:  Sahil Sharma; Gaurav Dugar; Chunlei Jiao; Natalia L Peeck; Thorsten Bischler; Franziska Wimmer; Yanying Yu; Lars Barquist; Christoph Schoen; Oliver Kurzai; Cynthia M Sharma; Chase L Beisel
Journal:  Science       Date:  2021-04-27       Impact factor: 47.728

Review 9.  COVID-19 one year later: a retrospect of CRISPR-Cas system in combating COVID-19.

Authors:  Yan Zhan; Xiang-Ping Li; Ji-Ye Yin
Journal:  Int J Biol Sci       Date:  2021-05-13       Impact factor: 6.580

Review 10.  Genome engineering and disease modeling via programmable nucleases for insulin gene therapy; promises of CRISPR/Cas9 technology.

Authors:  Yunus E Eksi; Ahter D Sanlioglu; Bahar Akkaya; Bilge Esin Ozturk; Salih Sanlioglu
Journal:  World J Stem Cells       Date:  2021-06-26       Impact factor: 5.326

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