Now showing items 1-10 of 13
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 ...
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 ...
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 ...
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 ...
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 ...
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF
(Oxford University Press, 2017)
Non-negative Matrix Factorization (NMF) algorithms associate gene expression with biological processes (e.g. time-course dynamics or disease subtypes). Compared with univariate associations, the relative weights of NMF ...
Identifying context-specific transcription factor targets from prior knowledge and gene expression data
(Institute of Electrical and Electronics Engineers, 2013)
Numerous methodologies, assays, and databases presently provide candidate targets of transcription factors (TFs). However, TFs rarely regulate their targets universally. The context of activation of a TF can change the ...
[Complex analysis of genetic predisposition to ischemic stroke in Russians]
(Springer Verlag, 2009)
Carriage frequencies of alleles and genotypes of 10 functionally important single nucleotide polymorphisms that are located in genes FGA, FGB, APOE, LPL, ACE and CMA1 were analyzed in the ischemic stroke (IS) patients of ...
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer
(Oxford University Press, 2018)
Motivation Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in ...
OnionTree XML: A Format to Exchange Gene-Related Probabilities
(Taylor & Francis, 2011)