Search Results - "IDEKER, Trey"

A census of pathway maps in cancer systems biology by Kuenzi, Brent M., Ideker, Trey

“…A key goal of cancer systems biology is to use big data to elucidate the molecular networks by which cancer develops. However, to date there has been no…”
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Protein networks in disease by Ideker, Trey, Sharan, Roded

“…During a decade of proof-of-principle analysis in model organisms, protein networks have been used to further the study of molecular evolution, to gain insight…”
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Network propagation: a universal amplifier of genetic associations by Cowen, Lenore, Ideker, Trey, Raphael, Benjamin J., Sharan, Roded

“…Key Points Network propagation transforms a short list of candidate genes into a genome-wide profile of gene scores that are based on proximity to candidates…”
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Differential network biology by Ideker, Trey, Krogan, Nevan J

“…Protein and genetic interaction maps can reveal the overall physical and functional landscape of a biological system. To date, these interaction maps have…”
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DNA Methylation Clocks in Aging: Categories, Causes, and Consequences by Field, Adam E., Robertson, Neil A., Wang, Tina, Havas, Aaron, Ideker, Trey, Adams, Peter D.

“…Age-associated changes to the mammalian DNA methylome are well documented and thought to promote diseases of aging, such as cancer. Recent studies have…”
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Network-based stratification of tumor mutations by Hofree, Matan, Shen, John P, Carter, Hannah, Gross, Andrew, Ideker, Trey

“…This paper reports a strategy for combining somatic mutation profiles of human tumors with gene networks to stratify tumors into biologically and clinically…”
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Using deep learning to model the hierarchical structure and function of a cell by Ma, Jianzhu, Yu, Michael Ku, Fong, Samson, Ono, Keiichiro, Sage, Eric, Demchak, Barry, Sharan, Roded, Ideker, Trey

“…Embedding a deep-learning model in the known structure of cellular systems yields DCell, a ‘visible’ neural network that can be used to mechanistically…”
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Integrative approaches for finding modular structure in biological networks by Mitra, Koyel, Carvunis, Anne-Ruxandra, Ramesh, Sanath Kumar, Ideker, Trey

“…Key Points Bioinformatics approaches for integrating molecular networks across various types of interaction data, omics profiles, conditions or species have…”
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The great hairball gambit by Flint, Jonathan, Ideker, Trey

“…[...]protein interaction networks are central to cell and tissue biology, otherwise there’d be no organization of proteins into large multimeric complexes, or…”
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Network approaches and applications in biology by Ideker, Trey, Nussinov, Ruth

“…About the Authors: Trey Ideker * E-mail: tideker@ucsd.edu (TI); NussinoR@mail.nih.gov (RN) Affiliation: Department of Medicine, University of California San…”
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Cytoscape 2.8: new features for data integration and network visualization by SMOOT, Michael E, ONO, Keiichiro, RUSCHEINSKI, Johannes, WANG, Peng-Liang, IDEKER, Trey

“…Cytoscape is a popular bioinformatics package for biological network visualization and data integration. Version 2.8 introduces two powerful new…”
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Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls by Shen, John Paul, Ideker, Trey

“…Synthetic lethal interactions, in which the simultaneous loss of function of two genes produces a lethal phenotype, are being explored as a means to…”
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Author Correction: A census of pathway maps in cancer systems biology by Kuenzi, Brent M., Ideker, Trey

“…A correction to this paper has been published: https://doi.org/10.1038/s41568-020-00331-7…”
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MHC-I Genotype Restricts the Oncogenic Mutational Landscape by Marty, Rachel, Kaabinejadian, Saghar, Rossell, David, Slifker, Michael J., van de Haar, Joris, Engin, Hatice Billur, de Prisco, Nicola, Ideker, Trey, Hildebrand, William H., Font-Burgada, Joan, Carter, Hannah

“…MHC-I molecules expose the intracellular protein content on the cell surface, allowing T cells to detect foreign or mutated peptides. The combination of six…”
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DNA methylation aging clocks: challenges and recommendations by Bell, Christopher G, Lowe, Robert, Adams, Peter D, Baccarelli, Andrea A, Beck, Stephan, Bell, Jordana T, Christensen, Brock C, Gladyshev, Vadim N, Heijmans, Bastiaan T, Horvath, Steve, Ideker, Trey, Issa, Jean-Pierre J, Kelsey, Karl T, Marioni, Riccardo E, Reik, Wolf, Relton, Caroline L, Schalkwyk, Leonard C, Teschendorff, Andrew E, Wagner, Wolfgang, Zhang, Kang, Rakyan, Vardhman K

“…Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular…”
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NDEx 2.0: A Clearinghouse for Research on Cancer Pathways by Pratt, Dexter, Chen, Jing, Pillich, Rudolf, Rynkov, Vladimir, Gary, Aaron, Demchak, Barry, Ideker, Trey

“…We present NDEx 2.0, the latest release of the Network Data Exchange (NDEx) online data commons (www.ndexbio.org) and the ways in which it can be used to (i)…”
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Protein networks as logic functions in development and cancer by Dutkowski, Janusz, Ideker, Trey

“…Many biological and clinical outcomes are based not on single proteins, but on modules of proteins embedded in protein networks. A fundamental question is how…”
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Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power by Ideker, Trey, Dutkowski, Janusz, Hood, Leroy

“…A major difficulty in the analysis of complex biological systems is dealing with the low signal-to-noise inherent to nearly all large biological datasets. We…”
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Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates by Hannum, Gregory, Guinney, Justin, Zhao, Ling, Zhang, Li, Hughes, Guy, Sadda, SriniVas, Klotzle, Brandy, Bibikova, Marina, Fan, Jian-Bing, Gao, Yuan, Deconde, Rob, Chen, Menzies, Rajapakse, Indika, Friend, Stephen, Ideker, Trey, Zhang, Kang

“…The ability to measure human aging from molecular profiles has practical implications in many fields, including disease prevention and treatment, forensics,…”
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De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences by Vakirlis, Nikolaos, Acar, Omer, Hsu, Brian, Castilho Coelho, Nelson, Van Oss, S. Branden, Wacholder, Aaron, Medetgul-Ernar, Kate, Bowman, Ray W., Hines, Cameron P., Iannotta, John, Parikh, Saurin Bipin, McLysaght, Aoife, Camacho, Carlos J., O’Donnell, Allyson F., Ideker, Trey, Carvunis, Anne-Ruxandra

“…Recent evidence demonstrates that novel protein-coding genes can arise de novo from non-genic loci. This evolutionary innovation is thought to be facilitated…”
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