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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.

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.

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...

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...

Porting and using PanGIA for Cytoscape 3: challenges and solutions.

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...

The Cytoscape app article collection.

Pico, Alexander R Bader, Gary D Demchak, Barry Guitart Pla, Oriol Hull, Timothy Longabaugh, William Lopes, Christian Lotia, Samad Molenaar, Piet Montojo, Jason ...

Published in F1000Research

As a network visualization and analysis platform, Cytoscape relies on apps to provide domain-specific features and functions. There are many resources available to support Cytoscape app development and distribution, including the Cytoscape App Store and an online "cookbook" for app developers. This article collection is another resource to help res...

An integrated map of HIV-human protein complexes that facilitate viral infection.

Emig-Agius, Dorothea Olivieri, Kevin Pache, Lars Shih, Hsin Ling Pustovalova, Olga Bessarabova, Marina Young, John A T Chanda, Sumit K Ideker, Trey

Published in PloS one

Recent proteomic and genetic studies have aimed to identify a complete network of interactions between HIV and human proteins and genes. This HIV-human interaction network provides invaluable information as to how HIV exploits the host machinery and can be used as a starting point for further functional analyses. We integrated this network with com...

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