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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Designing custom CRISPR libraries for hypothesis-driven drug target discovery
Vaishnavi Srinivasan Iyer,Vaishnavi Srinivasan Iyer,Long Jiang,Yunbing Shen,Sanjay V. Boddul,Sudeepta Kumar Panda,Zsolt Kasza,Bernhard Schmierer,Bernhard Schmierer,Fredrik Wermeling +9 more
TL;DR: A brief background to CRISPR screens is given and the pros and cons of different design approaches are discussed, including unbiased genome-wide screens that target all known genes, as well as hypothesis-driven custom screens in which selected subsets of genes are targeted.
Journal ArticleDOI
Cause-and-Effect relationship between FGFR1 expression and epithelial-mesenchymal transition in EGFR-mutated non-small cell lung cancer cells.
TL;DR: It is found that FGFR1 expression correlates with a ZEB1-associated EMT gene expression profile in NSCLC cells, and an increase in Z EB1 expression is a driver of EMT resulting in concomitant increased FG FR1 expression, whereas an increaseIn FGFR 1 expression is insufficient to drive conComitant EMT.
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Key elements for designing and performing a CRISPR/Cas9-based genetic screen.
TL;DR: These CRISPR/Cas9-based screens are outlined, guidance on the design of effective screens is provided, and the potential future directions of development of this field is discussed.
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Functional Genomics in Pancreatic β Cells: Recent Advances in Gene Deletion and Genome Editing Technologies for Diabetes Research
TL;DR: Some of the disease-associated genes and variants whose roles have been probed up to now are reviewed and a perspective as to how CRISPR/Cas9 technology may find clinical application in patients with diabetes is provided.
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MAUDE: inferring expression changes in sorting-based CRISPR screens
TL;DR: MAUDE (Mean Alterations Using Discrete Expression) is created for quantifying the impact of guide RNAs on a target gene’s expression in a pooled, sorting-based expression screen and outperforms previous approaches.
References
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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.