Literature DB >> 30504875

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data.

Jonathan Y Hsu1,2, Charles P Fulco3,4, Mitchel A Cole5,6,7, Matthew C Canver2,5,6,7, Danilo Pellin8,9, Falak Sher5,6,7, Rick Farouni2,3,10, Kendell Clement2,3,10, Jimmy A Guo2, Luca Biasco8,9, Stuart H Orkin5,6,7,11, Jesse M Engreitz3,12, Eric S Lander3,4,13, J Keith Joung2,10, Daniel E Bauer14,15,16, Luca Pinello17,18,19.   

Abstract

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Year:  2018        PMID： 30504875      PMCID： PMC6620603          DOI： 10.1038/s41592-018-0225-6

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  8 in total

1.  Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9.

Authors:  Gozde Korkmaz; Rui Lopes; Alejandro P Ugalde; Ekaterina Nevedomskaya; Ruiqi Han; Ksenia Myacheva; Wilbert Zwart; Ran Elkon; Reuven Agami
Journal:  Nat Biotechnol       Date:  2016-01-11       Impact factor: 54.908

2.  An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level.

Authors:  Daniel E Bauer; Sophia C Kamran; Samuel Lessard; Jian Xu; Yuko Fujiwara; Carrie Lin; Zhen Shao; Matthew C Canver; Elenoe C Smith; Luca Pinello; Peter J Sabo; Jeff Vierstra; Richard A Voit; Guo-Cheng Yuan; Matthew H Porteus; John A Stamatoyannopoulos; Guillaume Lettre; Stuart H Orkin
Journal:  Science       Date:  2013-10-11       Impact factor: 47.728

3.  High-resolution interrogation of functional elements in the noncoding genome.

Authors:  Neville E Sanjana; Jason Wright; Kaijie Zheng; Ophir Shalem; Pierre Fontanillas; Julia Joung; Christine Cheng; Aviv Regev; Feng Zhang
Journal:  Science       Date:  2016-09-30       Impact factor: 47.728

4.  Systematic mapping of functional enhancer-promoter connections with CRISPR interference.

Authors:  Charles P Fulco; Mathias Munschauer; Rockwell Anyoha; Glen Munson; Sharon R Grossman; Elizabeth M Perez; Michael Kane; Brian Cleary; Eric S Lander; Jesse M Engreitz
Journal:  Science       Date:  2016-09-29       Impact factor: 47.728

5.  Discovery of stimulation-responsive immune enhancers with CRISPR activation.

Authors:  Dimitre R Simeonov; Benjamin G Gowen; Mandy Boontanrart; Theodore L Roth; John D Gagnon; Maxwell R Mumbach; Ansuman T Satpathy; Youjin Lee; Nicolas L Bray; Alice Y Chan; Dmytro S Lituiev; Michelle L Nguyen; Rachel E Gate; Meena Subramaniam; Zhongmei Li; Jonathan M Woo; Therese Mitros; Graham J Ray; Gemma L Curie; Nicki Naddaf; Julia S Chu; Hong Ma; Eric Boyer; Frederic Van Gool; Hailiang Huang; Ruize Liu; Victoria R Tobin; Kathrin Schumann; Mark J Daly; Kyle K Farh; K Mark Ansel; Chun J Ye; William J Greenleaf; Mark S Anderson; Jeffrey A Bluestone; Howard Y Chang; Jacob E Corn; Alexander Marson
Journal:  Nature       Date:  2017-08-30       Impact factor: 49.962

6.  BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis.

Authors:  Matthew C Canver; Elenoe C Smith; Falak Sher; Luca Pinello; Neville E Sanjana; Ophir Shalem; Diane D Chen; Patrick G Schupp; Divya S Vinjamur; Sara P Garcia; Sidinh Luc; Ryo Kurita; Yukio Nakamura; Yuko Fujiwara; Takahiro Maeda; Guo-Cheng Yuan; Feng Zhang; Stuart H Orkin; Daniel E Bauer
Journal:  Nature       Date:  2015-09-16       Impact factor: 49.962

7.  CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

Authors:  Tyler S Klann; Joshua B Black; Malathi Chellappan; Alexias Safi; Lingyun Song; Isaac B Hilton; Gregory E Crawford; Timothy E Reddy; Charles A Gersbach
Journal:  Nat Biotechnol       Date:  2017-04-03       Impact factor: 54.908

8.  Functional footprinting of regulatory DNA.

Authors:  Jeff Vierstra; Andreas Reik; Kai-Hsin Chang; Sandra Stehling-Sun; Yuanyue Zhou; Sarah J Hinkley; David E Paschon; Lei Zhang; Nikoletta Psatha; Yuri R Bendana; Colleen M O'Neil; Alexander H Song; Andrea K Mich; Pei-Qi Liu; Gary Lee; Daniel E Bauer; Michael C Holmes; Stuart H Orkin; Thalia Papayannopoulou; George Stamatoyannopoulos; Edward J Rebar; Philip D Gregory; Fyodor D Urnov; John A Stamatoyannopoulos
Journal:  Nat Methods       Date:  2015-08-31       Impact factor: 28.547
  8 in total
  13 in total

1.  Functional Enhancers Shape Extrachromosomal Oncogene Amplifications.

Authors:  Andrew R Morton; Nergiz Dogan-Artun; Zachary J Faber; Graham MacLeod; Cynthia F Bartels; Megan S Piazza; Kevin C Allan; Stephen C Mack; Xiuxing Wang; Ryan C Gimple; Qiulian Wu; Brian P Rubin; Shashirekha Shetty; Stephane Angers; Peter B Dirks; Richard C Sallari; Mathieu Lupien; Jeremy N Rich; Peter C Scacheri
Journal:  Cell       Date:  2019-11-21       Impact factor: 41.582

Review 2.  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

3.  Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease.

Authors:  Johanna Dahlqvist; Charles P Fulco; John P Ray; Thomas Liechti; Carl G de Boer; David J Lieb; Thomas M Eisenhaure; Jesse M Engreitz; Mario Roederer; Nir Hacohen
Journal:  Hum Mol Genet       Date:  2022-06-22       Impact factor: 5.121

Review 4.  Using CRISPR to understand and manipulate gene regulation.

Authors:  Ersin Akinci; Marisa C Hamilton; Benyapa Khowpinitchai; Richard I Sherwood
Journal:  Development       Date:  2021-04-29       Impact factor: 6.868

5.  The human origin recognition complex is essential for pre-RC assembly, mitosis, and maintenance of nuclear structure.

Authors:  Hsiang-Chen Chou; Kuhulika Bhalla; Osama El Demerdesh; Olaf Klingbeil; Kaarina Hanington; Sergey Aganezov; Peter Andrews; Habeeb Alsudani; Kenneth Chang; Christopher R Vakoc; Michael C Schatz; W Richard McCombie; Bruce Stillman
Journal:  Elife       Date:  2021-02-01       Impact factor: 8.140

6.  Functional mapping of androgen receptor enhancer activity.

Authors:  Chia-Chi Flora Huang; Shreyas Lingadahalli; Tunc Morova; Dogancan Ozturan; Eugene Hu; Ivan Pak Lok Yu; Simon Linder; Marlous Hoogstraat; Suzan Stelloo; Funda Sar; Henk van der Poel; Umut Berkay Altintas; Mohammadali Saffarzadeh; Stephane Le Bihan; Brian McConeghy; Bengul Gokbayrak; Felix Y Feng; Martin E Gleave; Andries M Bergman; Colin Collins; Faraz Hach; Wilbert Zwart; Eldon Emberly; Nathan A Lack
Journal:  Genome Biol       Date:  2021-05-11       Impact factor: 13.583

7.  MAUDE: inferring expression changes in sorting-based CRISPR screens.

Authors:  Carl G de Boer; John P Ray; Nir Hacohen; Aviv Regev
Journal:  Genome Biol       Date:  2020-06-03       Impact factor: 13.583

Review 8.  Gaining insight into metabolic diseases from human genetic discoveries.

Authors:  Melina Claussnitzer; Katalin Susztak
Journal:  Trends Genet       Date:  2021-07-24       Impact factor: 11.639

9.  Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features.

Authors:  John P Ray; Carl G de Boer; Charles P Fulco; Caleb A Lareau; Masahiro Kanai; Jacob C Ulirsch; Ryan Tewhey; Leif S Ludwig; Steven K Reilly; Drew T Bergman; Jesse M Engreitz; Robbyn Issner; Hilary K Finucane; Eric S Lander; Aviv Regev; Nir Hacohen
Journal:  Nat Commun       Date:  2020-03-06       Impact factor: 14.919

Review 10.  A benchmark of algorithms for the analysis of pooled CRISPR screens.

Authors:  Sunil Bodapati; Timothy P Daley; Xueqiu Lin; James Zou; Lei S Qi
Journal:  Genome Biol       Date:  2020-03-09       Impact factor: 13.583
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