Now showing items 1-20 of 68

    • Activation of the NOTCH Pathway in Head and Neck Cancer 

      Ochs, Michael F.; Gaykalova, Daria A.; Sun, Wenyue; Mambo, Elizabeth; Arnaoutakis, Demetri; Liu, Yan; Loyo, Myriam; Agrawal, Nishant; Howard, Jason D.; Li, Ryan; Ahn, Sun Mi; Fertig, Elana J.; Sidransky, David; Houghton, Jeffery; Buddavarapu, Kalyan; Sanford, Tiffany; Choudhary, Ashish; Darden, Will; Adai, Alex; Latham, Gary; Bishop, Justin A.; Sharma, Rajni; Westra, William H.; Hennessey, Patrick T.; Chung, Christine H.; Califano, Joseph A. (American Association for Cancer Research, 2014)
      NOTCH1 mutations have been reported to occur in 10% to 15% of head and neck squamous cell carcinomas (HNSCC). To determine the significance of these mutations, we embarked upon a comprehensive study of NOTCH signaling in ...
    • AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses 

      Ochs, Michael F.; Considine, Michael; Parker, Hilary; Wei, Yingying; Xia, Xaio; Cope, Leslie; Fertig, Elana J. (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 ...
    • Application of Bayesian Decomposition for analysing microarray data 

      Moloshok, Thomas D.; Klevecz, R.R.; Grant, Jeffrey D.; Manion, Frank J.; Speier, William; Ochs, Michael F. (Oxford University Press, 2002)
      Motivation: Microarray and gene chip technology provide high throughput tools for measuring gene expression levels in a variety of circumstances, including cellular response to drug treatment, cellular growth and development, ...
    • An argument for mechanism-based statistical inference in cancer 

      Ochs, Michael F.; German, Donald; Price, Nathan D.; Tomasetti, Cristian; Younes, Laurent (Springer Verlag, 2015)
      Cancer is perhaps the prototypical systems disease, and as such has been the focus of extensive study in quantitative systems biology. However, translating these programs into personalized clinical care remains elusive and ...
    • ASAP: automated sequence annotation pipeline fo rw eb-based updating of sequence information with a local dynamic database 

      Ochs, Michael F.; Kossenkov, Andrew; Manion, Frank J.; Korotkov, Eugene; Moloshok, Thomas D. (Oxford University Press, 2003)
      The automated sequence annotation pipeline (ASAP) is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible ...
    • Bayesian decomposition analysis of bacterial phylogenomic profiles 

      Ochs, Michael F.; Bidaut, Ghislain; Suhre, Karsten; Claverie, Jean-Michel (Adis, 2005)
      BACKGROUND: The past two decades have seen the appearance of new infectious diseases and the reemergence of old diseases previously thought to be under control. At the same time, the effectiveness of the existing ...
    • BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster 

      Ochs, Michael F.; Grant, Jeffrey D.; Dunbrack, R.L.; Manion, Frank J. (Oxford University Press, 2002)
      BeoBLAST is an integrated software package that handles user requests and distributes BLAST and PSI-BLAST searches to nodes of a Beowulf cluster, thus providing a simple way to implement a scalable BLAST system on top of ...
    • Biomedical informatics in cancer research 

      Ochs, Michael F.; Casagrande, John T.; Davuluri, Ramana V. (Springer, 2010)
    • ClutrFree: cluster tree visualization and interpretation 

      Ochs, Michael F.; Bidaut, Ghislain (Oxford University Press, 2004)
      ClutrFree facilitates the visualization and interpretation of clusters or patterns computed from microarray data through a graphical user interface that displays patterns, membership information of the genes and annotation ...
    • 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 ...
    • Comparison of simian immunodeficiency virus isolates 

      Ochs, Michael F.; Kestler, Henry W. III; Li, Yen; Naidu, Yathirajulu M.; Butler, Carole V.; Jaenel, Gerlinde; King, Norval W.; Daniel, Muthiah D.; Desrosiers, Ronald C. (Nature Publishing Group, 1988)
      Information on the extent of genetic variability among non-human primate lentiviruses related to human immunodeficiency virus (HIV) is sorely lacking. Here we describe the isolation of two molecular clones from the simian ...
    • 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 ...
    • A Comprehensive Statistical Model for Cell Signaling 

      Ochs, Michael F.; Yörük, Erdem; German, Donald; Younes, Laurent (Institute of Electrical and Electronics Engineers, 2011)
      Protein signaling networks play a central role in transcriptional regulation and the etiology of many diseases. Statistical methods, particularly Bayesian networks, have been widely used to model cell signaling, mostly for ...
    • Coordinated Activation of Candidate Proto-Oncogenes and Cancer Testes Antigens via Promoter Demethylation in Head and Neck Cancer and Lung Cancer 

      Ochs, Michael F.; Smith, Ian M.; Glazer, Chad A.; Mithani, Suhail; Sun, Wenyue; Bhan, Sheetal; Vostrov, Alexander; Abdullaev, Ziedulla; Lobanenkov, Victor; Gray, Andrew; Liu, Chunyan; Chang, Steven S.; Ostrow, Kimberly L.; Westra, William H.; Begum, Shahnaz; Dhara, Mousumi; Califano, Joseph A. (Public Library of Science, 2009)
      Background Epigenetic alterations have been implicated in the pathogenesis of solid tumors, however, proto-oncogenes activated by promoter demethylation have been sporadically reported. We used an integrative method to ...
    • Coordinated Gene Activity of Pattern Sets (CoGAPS) 

      Taylor, Matt; Hauser, Paloma; Ochs, Michael F. (2015)
      Cancer, one of the leading causes of death, is a group of complex genetic diseases that result from changes to genes which cause abnormal cell growth. CoGAPS, an R package that utilizes a Bayesian Markov Chain Monte Carlo ...
    • Data Standards for Flow Cytometry 

      Ochs, Michael F.; Spidlen, Josef; Gentleman, Robert C.; Haaland, Perry D.; Langille, Morgan; Le Meur, Nolwenn; Schmitt, Charles; Smith, Clayton A.; Treister, Adam S.; Brinkman, Ryan R. (Mary Ann Liebert, 2006)
      Flow cytometry (FCM) is an analytical tool widely used for cancer and HIV/AIDS research, and treatment, stem cell manipulation and detecting microorganisms in environmental samples. Current data standards do not capture ...
    • Detection of Treatment-Induced Changes in Signaling Pathways in Gastrointestinal Stromal Tumors Using Transcriptomic Data 

      Ochs, Michael F.; Rink, Lori; Tarn, Chi; Mburu, Sarah; Taguchi, Takahiro; Eisenberg, Burton; Godwin, Andrew K. (American Association for Cancer Research, 2009)
      Cell signaling plays a central role in the etiology of cancer. Numerous therapeutics in use or under development target signaling proteins; however, off-target effects often limit assignment of positive clinical response ...
    • Determination of strongly overlapping signaling activity from microarray data 

      Ochs, Michael F.; Bidaut, Ghislain; Suhre, Karsten; Claverie, Jean-Michel (BioMed Central, 2006)
      Background As numerous diseases involve errors in signal transduction, modern therapeutics often target proteins involved in cellular signaling. Interpretation of the activity of signaling pathways during disease development ...