Now showing items 21-40 of 269

    • 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 ...
    • 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, ...
    • A Class of Exponent-Sum Two Equations Over Groups 

      Clifford, Andrew (Cambridge University Press, 2002)
      In this paper, relative pictures are used to analyze a certain family of exponent-sum two equations over groups.
    • Response markers and the molecular mechanisms of action of Gleevec in gastrointestinal stromal tumors 

      Ochs, Michael F.; Frolov, A.; Chahwan, S.; Arnoletti, J.P.; Pan, Z.Z.; Favorova, Olʹga Olegovna; Fletcher, J.; Mehren, Margaret von; Eisenberg, Burton; Godwin, Andrew K. (American Association for Cancer Research, 2003)
      Gastrointestinal stromal tumors (GISTs), defined by the presence of constitutively activated KIT, are the most common gastrointestinal mesenchymal malignancies. This observation has been successfully exploited in clinical ...
    • 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 ...
    • Non-amenable type K equations over groups 

      Clifford, Andrew (Cambridge University Press, 2003)
      We define a class of equations that are not amenable but are type K and are therefore solvable over torsion-free groups. Moreover, we show that these new equations are solvable over all groups.
    • Microarrays in cancer: research and applications 

      Ochs, Michael F.; Godwin, Andrew K. (Future Science, 2003-03)
    • FGDP: functional genomics data pipeline for automated, multiple microarray data analyses 

      Ochs, Michael F.; Grant, Jeffrey D.; Somers, Luke A.; Zhang, Yue; Manion, Frank J.; Bidaut, Ghislain (Oxford University Press, 2004)
      Gene expression microarrays and oligonucleotide GeneChips™ have provided biologists with a means of measuring, in a single experiment, the expression levels of entire genomes under a variety of conditions. As with any ...
    • 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 ...
    • Bayesian decomposition: analyzing microarray data within a biological context 

      Ochs, Michael F.; Moloshok, Thomas D.; Bidaut, Ghislain; Toby, Garabet (Wiley, 2004-05)
      The detection and correct identification of cancer, especially at an early stage, are vitally important for patient survival and quality of life. Since signaling pathways play critical roles in cancer development and ...
    • In vitro RNA random pools are not structurally diverse: A computational analysis 

      Gevertz, Jana L.; Gan, Hin Hark; Schlick, Tamar (RNA Society, 2005)
      In vitro selection of functional RNAs from large random sequence pools has led to the identification of many ligand-binding and catalytic RNAs. However, the structural diversity in random pools is not well understood. Such ...
    • Mathematical Model of Real-Time PCR Kinetics 

      Gevertz, Jana L.; Dunn, Stanley M.; Roth, Charles M. (Wiley Periodicals, Inc, 2005)
      Several real-time PCR (rtPCR) quantification techniques are currently used to determine the expression levels of individual genes from rtPCR data in the form of fluorescence intensities. In most of these quantification ...
    • 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 ...
    • 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 ...
    • A PSL(2,C) Casson Invariant 

      Curtis, Cynthia (American Mathematical Society, 2005)
      We use intersection theory techniques to define an invariant of closed 3-manifolds counting the characters of irreducible representations of the fundamental group in PSL(2,C). We note several properties of the invariant ...
    • LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates 

      Ochs, Michael F.; Wang, Guoli; Kossenkov, Andrew (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 ...
    • Pathway-specific differences between tumor cell lines and normal and tumor tissue cells 

      Ochs, Michael F.; Ertel, Adam; Verghese, Arun; Byers, Stephen W.; Tozeren, Aydin (BioMed Central, 2006)
      Background Cell lines are used in experimental investigation of cancer but their capacity to represent tumor cells has yet to be quantified. The aim of the study was to identify significant alterations in pathway usage ...
    • 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 ...
    • The SL(2,C) Casson invariant for Seifert fibered homology spheres and surgeries on twist knots 

      Curtis, Cynthia; Boden, Hans U. (World Scientific Publishing, 2006)
      We derive a simple closed formula for the SL(2,C) Casson invariant for Seifert fibered homology 3-spheres using the correspondence between SL(2,C) character varieties and moduli spaces of parabolic Higgs bundles of rank ...