Now showing items 1-13 of 13

    • CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network 

      Ochs, Michael F.; Fertig, Elana J.; Ozawa, Hiroyuki; Thakar, Manjusha; Howard, Jason D.; Kagohara, Luciane T.; Krigsfeld, Gabriel; Ranaweera, Ruchira S.; Hughes, Robert M.; Perez, Jimena; Jonaes, Siân; Favorov, Alexander V.; Carey, Jacob L.; Stein-O'Brien, Genevieve L.; Gaykalova, Daria A.; Chung, Christine H. (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 ...
    • CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data 

      Fertig, Elana J.; Ding, Jie; Favorov, Alexander V.; Parmigiani, Giovanni; Ochs, Michael F. (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 ...
    • Complex analysis of association of inflammation gene polymorphisms with myocardial infarction 

      Ochs, Michael F.; Sudomoina, Marina A.; Sukhinina, T.S.; Barsova, R.M.; Favorov, Alexander V.; Sakhnovich, R.M.; Titov, B.V.; Matveeva, N.A.; Rybalkin, I.N.; Vlasik, T.N.; Ruda, M. Ya; Favorova, Olʹga Olegovna (Springer Verlag, 2010)
      Frequencies of the carriership of alleles and genotypes of functionally important polymorphous loci of some inflammation genes (proinflammatory cytokine genes IL-6, LTA, and TNF; anti-inflammatory cytokine gene TGFB1; and ...
    • [Complex analysis of genetic predisposition to ischemic stroke in Russians] 

      Ochs, Michael F.; Parfenov, M.G.; Titov, B.V.; Sudomoina, Marina A.; Martynov, M.Yu.; Favorov, Alexander V.; Gusev, E.I.; Favorova, Olʹga Olegovna (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 ...
    • Genetic polymorphisms, their allele combinations and IFN-β treatment response in Irish multiple sclerosis patients 

      Ochs, Michael F.; O'Doherty, Catherine; Favorov, Alexander V.; Heggarty, Shirley; Graham, Colin; Favorova, Olʹga Olegovna; Hawkins, Stanley; Hutchinson, Michael; O'Rourke, Killian; Vandenbroeck, Koen (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 ...
    • Hybrid modeling of cell signaling and transcriptional reprogramming and its application in C. elegans development 

      Ochs, Michael F.; Danilova, Ludmila V.; Favorov, Alexander V.; Fertig, Elana J. (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 ...
    • Identifying context-specific transcription factor targets from prior knowledge and gene expression data 

      Fertig, Elana J.; Favorov, Alexander V.; Ochs, Michael F. (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 ...
    • A Markov Chain Monte Carlo Technique for Identification of Combinations of Allelic Variants Underlying Complex Diseases in Humans 

      Ochs, Michael F.; Favorov, Alexander V.; Andreewski, Timofey V.; Sudomoina, Marina A.; Favorova, Olʹga Olegovna; Parmigiani, Giovanni (Genetics Society of America, 2005)
      In recent years, the number of studies focusing on the genetic basis of common disorders with a complex mode of inheritance, in which multiple genes of small effect are involved, has been steadily increasing. An improved ...
    • OnionTree XML: A Format to Exchange Gene-Related Probabilities 

      Ochs, Michael F.; Parmigiani, Giovanni; Speier, William; Lvov, Dmitrijs; Favorov, Alexander V. (Taylor & Francis, 2011)
    • PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF 

      Ochs, Michael F.; Stein-O'Brien, Genevieve L.; Carey, Jacob L.; Lee, Wai Shing; Considine, Michael; Favorov, Alexander V.; Flam, Emily; Guo, Theresa; Li, Sijia; Marchionni, Luigi; Sherman, Thomas; Sivy, Shawn; Gaykalova, Daria A.; McKay, Ronald D.; Colantuoni, Carlo; Fertig, Elana J. (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 ...
    • Pharmacogenomics of multiple sclerosis: Association of immune response gene polymorphisms with copaxone treatment efficacy 

      Ochs, Michael F.; Tsareva, E.Yu.; Kulakova, O.G.; Makarycheva, O.Yu.; Boyko, A.N.; Shchur, S.G.; Lashch, N.Yu.; Popova, N.F.; Gusev, E.I.; Bashinskaya, V.V.; Lvov, D.V.; Favorov, Alexander V.; Favorova, Olʹga Olegovna (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 ...
    • Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer 

      Ochs, Michael F.; Bahman, Asfari; Guo, Theresa; Considine, Michael; Florea, Liliana; Kagohara, Luciane T.; Stein-O'Brien, Genevieve L.; Kelley, Dylan; Flam, Emily; Zambo, Kristina; Ha, Patrick K.; German, Donald; Califano, Joseph A.; Gaykalova, Daria A.; Favorov, Alexander V.; Fertig, Elana J. (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 ...
    • Three allele combinations associated with Multiple Sclerosis 

      Ochs, Michael F.; Favorova, Olʹga Olegovna; Favorov, Alexander V.; Boiko, Alexey N.; Andreewski, Timofey V.; Sudomoina, Marina A.; Alekseenkov, Alexey D.; Kulakova, O.G.; Gusev, E.I.; Parmigiani, Giovanni (BioMed Central, 2006)
      Background Multiple sclerosis (MS) is an immune-mediated disease of polygenic etiology. Dissection of its genetic background is a complex problem, because of the combinatorial possibilities of gene-gene interactions. As ...