Open Access
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
Silvana Konermann,Mark D. Brigham,Alexandro E. Trevino,Julia Joung,Clea Barcena,Patrick D. Hsu,Naomi Habib,Jonathan S. Gootenberg,Hiroshi Nishimasu,Osamu Nureki,Feng Zhang,Omar O. Abudayyeh +11 more
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The article was published on 2016-05-22 and is currently open access. It has received 1792 citations till now. The article focuses on the topics: CRISPR.read more
Citations
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APOBEC: From mutator to editor
TL;DR: The physiological functions and structural characteristics of APOBEC family members and their roles as endogenous mutators that contribute to hypermutations during carcinogenesis are reviewed.
Journal ArticleDOI
Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development.
TL;DR: The current state of knowledge on cis-regulatory regions is summarized and novel technologies such as massively-parallel reporter assay systems, CRISPR-Cas9-based screens and computational approaches that help to further elucidate the emerging role of the non-coding genome in disease are discussed.
Journal ArticleDOI
MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer.
Marcel A. Dammert,Johannes Brägelmann,Rachelle R. Olsen,Stefanie Böhm,Niloufar Monhasery,Christopher P. Whitney,Milind D. Chalishazar,Hannah L. Tumbrink,Matthew R. Guthrie,Sebastian Klein,Abbie S. Ireland,Jeremy Ryan,Anna Schmitt,Annika Marx,Luka Ozretić,Roberta Castiglione,Carina Lorenz,Ron D. Jachimowicz,Elmar Wolf,Roman K. Thomas,John T. Poirier,Reinhard Büttner,Triparna Sen,Lauren Averett Byers,H. Christian Reinhardt,Anthony Letai,Trudy G. Oliver,Martin L. Sos +27 more
TL;DR: The authors show that MYC, but not MYCN or MYCL, represses BCL2, resulting in cells that are uniquely sensitive to apoptosis, and find that CHK1 and AURKA inhibitors may be useful for treating these cancers.
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Genomes by design
TL;DR: In this Review, techniques and applications in genome engineering are explored, outlining key advances and defining challenges.
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Designed nucleases for targeted genome editing
TL;DR: The repair mechanism and outcomes of DSBs are reviewed and the three types of designed nucleases are discussed with the hope that such understanding will facilitate applications to genome editing.
References
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Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Bo Li,Colin N. Dewey +1 more
TL;DR: It is shown that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads, and estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired- end reads, depending on the number of possible splice forms for each gene.
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A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Martin Jinek,Krzysztof Chylinski,Krzysztof Chylinski,Ines Fonfara,Michael H. Hauer,Jennifer A. Doudna,Emmanuelle Charpentier +6 more
TL;DR: This study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Jordi Barretina,Giordano Caponigro,Nicolas Stransky,Kavitha Venkatesan,Adam A. Margolin,Adam A. Margolin,Sungjoon Kim,Christine D. Wilson,Joseph Lehar,Gregory V. Kryukov,Dmitriy Sonkin,Anupama Reddy,Manway Liu,Lauren Murray,Michael F. Berger,Michael F. Berger,John Monahan,Paula Morais,Jodi Meltzer,Adam Korejwa,Judit Jané-Valbuena,Judit Jané-Valbuena,Felipa A. Mapa,Joseph Thibault,Eva Bric-Furlong,Pichai Raman,Aaron Shipway,Ingo H. Engels,Jill Cheng,Guoying K. Yu,Jianjun Yu,Peter Aspesi,Melanie de Silva,Kalpana Jagtap,Michael D. Jones,Li Wang,Charlie Hatton,Emanuele Palescandolo,Supriya Gupta,Scott Mahan,Carrie Sougnez,Robert C. Onofrio,Ted Liefeld,Laura E. MacConaill,Wendy Winckler,Michael R. Reich,Nanxin Li,Jill P. Mesirov,Stacey Gabriel,Gad Getz,Kristin G. Ardlie,Vivien W. Chan,Vic E. Myer,Barbara L. Weber,Jeffrey A. Porter,Markus Warmuth,Peter Finan,Jennifer L. Harris,Matthew Meyerson,Matthew Meyerson,Todd R. Golub,Michael Morrissey,William R. Sellers,Robert Schlegel,Levi A. Garraway,Levi A. Garraway +65 more
TL;DR: The results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents and the generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of ‘personalized’ therapeutic regimens.
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Molecular signatures database (MSigDB) 3.0
Arthur Liberzon,Aravind Subramanian,Reid M. Pinchback,Helga Thorvaldsdottir,Pablo Tamayo,Jill P. Mesirov +5 more
TL;DR: A new version of the database, MSigDB 3.0, is reported, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site.