Ideker Lab - UC San Diego
  • Upload

  • Log in

  • Sign up

Search on MyScienceWork
News Publications Members

Publication search

Sort by
  • Relevance
  • Published Date

Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping.

Begley, Tj Rosenbach, As Trey Ideker Samson, Ld

Published in Molecular Cell

DNA repair and checkpoint pathways protect against carcinogen-induced toxicity. Here, we describe additional, equally protective pathways discovered by interrogating 4,733 yeast proteins for their ability to diminish toxicity induced by four known carcinogens. A computational mapping strategy for global phenotypic data was developed to build a syst...

The cancer cell map initiative: defining the hallmark networks of cancer.

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...

Hierarchical modularity and the evolution of genetic interactomes across species.

Ryan, Cj Roguev, A Patrick, K Xu, J Jahari, H Tong, Z Beltrao, P Shales, M Qu, H Collins, Sr ...

Published in Molecular Cell

To date, cross-species comparisons of genetic interactomes have been restricted to small or functionally related gene sets, limiting our ability to infer evolutionary trends. To facilitate a more comprehensive analysis, we constructed a genome-scale epistasis map (E-MAP) for the fission yeast Schizosaccharomyces pombe, providing phenotypic signatur...

A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export...

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,...

Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling.

Hustedt, N Seeber, A Sack, R Tsai-Pflugfelder, M Bhullar, B Vlaming, H Van Leeuwen, F Guénolé, A Van Attikum, H Srivas, R ...

Published in Molecular Cell

Mec1-Ddc2 (ATR-ATRIP) controls the DNA damage checkpoint and shows differential cell-cycle regulation in yeast. To find regulators of Mec1-Ddc2, we exploited a mec1 mutant that retains catalytic activity in G2 and recruitment to stalled replication forks, but which is compromised for the intra-S phase checkpoint. Two screens, one for spontaneous su...

Dissection of DNA damage responses using multiconditional genetic interaction maps.

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...

Genome-wide methylation profiles reveal quantitative views of human aging rates.

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...

Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy.

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...

Powered by Polaris
  • About the Lab
  • Our Research
  • FAQ