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The cancer cell map initiative: defining the hallmark networks of cancer. PDF available through Get Fulltext Research

Krogan, Nevan J Lippman, Scott Agard, David A Ashworth, Alan Ideker, Trey

Published in Molecular cell

Progress in DNA sequencing has revealed the startling complexity of cancer genomes, which typically carry thousands of somatic mutations. However, it remains unclear which are the key driver mutations or dependencies in a given cancer and how these influence pathogenesis and response to therapy. Although tumors of similar types and clinical outcome...

A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export... PDF available through Get Fulltext Research

Gm, Wilmes M, Bergkessel S, Bandyopadhyay M, Shales H, Braberg G, Cagney Sr, Collins Gb, Whitworth Tl, Kress Js, Weissman ...

Published in Molecular Cell

We used a quantitative, high-density genetic interaction map, or E-MAP (Epistatic MiniArray Profile), to interrogate the relationships within and between RNA-processing pathways. Due to their complexity and the essential roles of many of the components, these pathways have been difficult to functionally dissect. Here, we report the results for 107,...

Dissection of DNA damage responses using multiconditional genetic interaction maps. PDF available through Get Fulltext Research

Guénolé, Aude Srivas, Rohith Vreeken, Kees Wang, Ze Zhong Wang, Shuyi Krogan, Nevan J Ideker, Trey van Attikum, Haico

Published in Molecular cell

To protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among these pathways, we systematically mapped changes in the cell's genetic network across a panel of different DNA-damaging agents, resulting in ~1,800,000 diffe...

Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy. PDF available through Get Fulltext Research

Wilkinson, Deepti S Jariwala, Jinel S Anderson, Ericka Mitra, Koyel Meisenhelder, Jill Chang, Jessica T Ideker, Trey Hunter, Tony Nizet, Victor Dillin, Andrew ...

Published in Molecular cell

The protein LC3 is indispensible for the cellular recycling process of autophagy and plays critical roles during cargo recruitment, autophagosome biogenesis, and completion. Here, we report that LC3 is phosphorylated at threonine 50 (Thr(50)) by the mammalian Sterile-20 kinases STK3 and STK4. Loss of phosphorylation at this site blocks autophagy by...

Genome-wide methylation profiles reveal quantitative views of human aging rates. PDF available through Get Fulltext Research

Hannum, Gregory Guinney, Justin Zhao, Ling Zhang, Li Hughes, Guy Sadda, SriniVas Klotzle, Brandy Bibikova, Marina Fan, Jian-Bing Gao, Yuan ...

Published in Molecular cell

The ability to measure human aging from molecular profiles has practical implications in many fields, including disease prevention and treatment, forensics, and extension of life. Although chronological age has been linked to changes in DNA methylation, the methylome has not yet been used to measure and compare human aging rates. Here, we build a q...

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