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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 ...
LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates
(BioMed Central, 2006)
Background
Non-negative matrix factorisation (NMF), a machine learning algorithm, has been applied to the analysis of microarray data. A key feature of NMF is the ability to identify patterns that together explain the ...
Genetic polymorphisms, their allele combinations and IFN-β treatment response in Irish multiple sclerosis patients
(Future Medicine, 2009)
IFN-β is widely used as first-line immunomodulatory treatment for multiple sclerosis. Response to treatment is variable (30–50% of patients are nonresponders) and requires a long treatment duration for accurate assessment ...
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 ...