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Matrix Factorization Methods Applied in Microarray Data Analysis
(Inderscience, 2010)
Numerous methods have been applied to microarray data to group genes into clusters that show similar expression patterns. These methods assign each gene to a single group, which does not reflect the widely held view among ...
Hybrid modeling of cell signaling and transcriptional reprogramming and its application in C. elegans development
(Frontiers Media, 2011)
Modeling of signal driven transcriptional reprogramming is critical for understanding of organism development, human disease, and cell biology. Many current modeling techniques discount key features of the biological ...
Global Reactivation of Epigenetically Silenced Genes in Prostate Cancer
(American Association for Cancer Research, 2010)
Transcriptional silencing associated with aberrant promoter hypermethylation is a common mechanism of inactivation of tumor suppressor genes in cancer cells. To globally profile the genes silenced by hypermethylation in ...
CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network
(Impact Journals, 2016)
Patients with oncogene driven tumors are treated with targeted therapeutics including EGFR inhibitors. Genomic data from The Cancer Genome Atlas (TCGA) demonstrates molecular alterations to EGFR, MAPK, and PI3K pathways ...
Sneak peek: Raptors search for prey using stochastic head turns
(Central Ornithology Publication Office, 2017)
The strategies by which foraging predators decide when to redirect their gaze influence both prey detection rates and the prey's ability to detect and avoid predators. We applied statistical analyses that have been used ...
Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery
(Institute of Electrical and Electronics Engineers, 2013)
Pathway deregulation has been identified as a key driver of carcinogenesis, with proteins in signaling pathways serving as primary targets for drug development. Deregulation can be driven by a number of molecular events, ...
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data
(Oxford University Press, 2010)
Coordinated Gene Activity in Pattern Sets (CoGAPS) provides an integrated package for isolating gene expression driven by a biological process, enhancing inference of biological processes from transcriptomic data. CoGAPS ...
MAGEB2 is Activated by Promoter Demethylation in Head and Neck Squamous Cell Carcinoma
(Public Library of Science, 2012)
Purpose
Although promoter hypermethylation has been an accepted means of tumor suppressor gene inactivation, activation of otherwise normally repressed proto-oncogenes by promoter demethylation has been infrequently ...
Pharmacogenomics of multiple sclerosis: Association of immune response gene polymorphisms with copaxone treatment efficacy
(Springer Verlag, 2011)
A complex association analysis of copaxone (glatiramer acetate) immunotherapy efficacy with allelic polymorphism of the number of immune response genes, including the genes for interferon β (IFNB1), transforming growth ...
AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses
(F1000Research, 2015)
Automated Genomics Analysis (AGA) is an interactive program to analyze high-throughput genomic data sets on a variety of platforms. An easy to use, point and click, guided pipeline is implemented to combine, define, and ...