Ideker Lab - UC San Diego
  • Upload

  • Log in

  • Sign up

Search on MyScienceWork
1 News 161 Publications 32 Members

Parenchymal Volumetric Assessment as a Predictive Tool to Determine Renal Function Benefit of Nephron-Sparing Surgery Co...

Liss, Michael A DeConde, Robert Caovan, Dominique Hofler, Joseph Gabe, Michael Palazzi, Kerrin L Patel, Nishant D Lee, Hak J Ideker, Trey Van Poppel, Hendrik ...

Published in Journal of endourology

To develop a preoperative prediction model using a computer-assisted volumetric assessment of potential spared parenchyma to estimate the probability of chronic kidney disease (CKD, estimated glomerular filtration rate [eGFR]

Transcriptional repression of IFNβ1 by ATF2 confers melanoma resistance to therapy

Lau, E Sedy, J Sander, C Shaw, M A Feng, Y Scortegagna, M Claps, G Robinson, S Cheng, P Srivas, R ...

Published in Oncogene

The resistance of melanoma to current treatment modalities represents a major obstacle for durable therapeutic response, and thus the elucidation of mechanisms of resistance is urgently needed. The crucial functions of activating transcription factor-2 (ATF2) in the development and therapeutic resistance of melanoma have been previously reported, a...

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...

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...

Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer... PDF available through Get Fulltext Research

Gross, Andrew M Kreisberg, Jason F Ideker, Trey

Published in PloS one

To identify the transcriptional regulatory changes that are most widespread in solid tumors, we performed a pan-cancer analysis using over 600 pairs of tumors and adjacent normal tissues profiled in The Cancer Genome Atlas (TCGA). Frequency of upregulation was calculated across mRNA expression levels, microRNA expression levels and CpG methylation ...

Mitochondria, energetics, epigenetics, and cellular responses to stress.

Shaughnessy, Daniel T McAllister, Kimberly Worth, Leroy Haugen, Astrid C Meyer, Joel N Domann, Frederick E Van Houten, Bennett Mostoslavsky, Raul Bultman, Scott J Baccarelli, Andrea A ...

Published in Environmental health perspectives

Understanding mitochondria-cell signaling will provide insight into individual responses to environmental hazards, improving prediction of hazard and susceptibility to environmental stressors.

Inferring gene ontologies from pairwise similarity data.

Kramer, Michael Dutkowski, Janusz Yu, Michael Bafna, Vineet Ideker, Trey

Published in Bioinformatics (Oxford, England)

While the manually curated Gene Ontology (GO) is widely used, inferring a GO directly from -omics data is a compelling new problem. Recognizing that ontologies are a directed acyclic graph (DAG) of terms and hierarchical relations, algorithms are needed that: analyze a full matrix of gene-gene pairwise similarities from -omics data; infer true hier...

Siri of the cell: what biology could learn from the iPhone. PDF available through Get Fulltext Research

Carvunis, Anne-Ruxandra Ideker, Trey

Published in Cell

Modern genomics is very efficient at mapping genes and gene networks, but how to transform these maps into predictive models of the cell remains unclear. Recent progress in computer science, embodied by intelligent agents such as Siri, inspires an approach for moving from networks to multiscale models able to predict a range of cellular phenotypes ...

Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders.

Novarino, Gaia Fenstermaker, Ali G Zaki, Maha S Hofree, Matan Silhavy, Jennifer L Heiberg, Andrew D Abdellateef, Mostafa Rosti, Basak Scott, Eric Mansour, Lobna ...

Published in Science (New York, N.Y.)

Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in co...

Porting and using PanGIA for Cytoscape 3: challenges and solutions. PDF available through Get Fulltext Research

Welker, David Demchak, Barry

Published in F1000Research

Much of the biologically significant functionality in Cytoscape is contained within third-party add-ons, called plugins in Cytoscape 2 and apps in Cytoscape 3. In the transition from Cytoscape 2 to Cystoscape 3, some of the underlying assumptions upon which plugins relied changed, requiring a significant porting effort for plugins to work as Cytosc...

  • ← Previous
  • 1 (current)
  • 2
  • 3
  • 4
  • 5
  • …
  • 15
  • Next →
Powered by Polaris
  • About the Lab
  • Our Research
  • FAQ