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
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CRISPR/Cas9 cleavage efficiency regression through boosting algorithms and Markov sequence profiling.
TL;DR: A two-step averaging method for the regression of cleavage efficiencies of a set of sgRNAs by averaging the predicted efficiency scores of a boosting algorithm and those by a support vector machine (SVM) and it is proposed to use profiled Markov properties as novel features to capture the global characteristics of sGRNAs.
Journal ArticleDOI
Mechanisms of Long Non-Coding RNAs in the Assembly and Plasticity of Neural Circuitry.
TL;DR: This review summarized latest advances concerning roles and mechanisms of lncRNAs in assembly, maintenance and plasticity of neural circuitry, as well as lnc RNAs' implications in neurological disorders.
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IL-6 augments IL-4-induced polarization of primary human macrophages through synergy of STAT3, STAT6 and BATF transcription factors.
Sahil Gupta,Arpit Jain,Shahzad N. Syed,Ryan G. Snodgrass,Beatrice Pflüger-Müller,Matthias S. Leisegang,Andreas Weigert,Ralf P. Brandes,Ingo Ebersberger,Bernhard Brüne,Dmitry Namgaladze +10 more
TL;DR: It is suggested that IL-4 and IL-6 cooperate to alter the human macrophage transcriptome, endowing hMDMs with pro-tumorigenic properties.
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High-Throughput Silencing Using the CRISPR-Cas9 System: A Review of the Benefits and Challenges.
TL;DR: It is envisaged that complementarities between CRISPR, siRNA, and shRNA will ensure that all three technologies remain critical to the success of future functional genomics projects.
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An inducible CRISPR-ON system for controllable gene activation in human pluripotent stem cells.
TL;DR: A CRISPR-ON system to efficiently upregulate endogenous genes in hPSCs and shows that the dCas9-VPR level could be precisely and reversibly controlled by the addition and withdrawal of Dox, and an elevated NANOG level promoted naïve pluripotent gene expression, enhanced cell survival and clonogenicity.
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.