Now showing items 1-20 of 66

    • Ab initio Gene Identification in Metagenomic Sequences 

      Zhu, Wenhan; Lomsadze, Alexandre; Borodovsky, Mark (Georgia Institute of TechnologyOxford University Press, 2010)
      We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered ...
    • Adaptive wavelet estimator for nonparametric density deconvolution 

      Pensky, Marianna; Vidakovic, Brani (Georgia Institute of TechnologyInstitute of Mathematical Statistics, 1999)
      The problem of estimating a density g based on a sample X ₁ X ₂,…,X [subscript n] from p = q ∗ g is considered. Linear and nonlinear wavelet estimators based on Meyer-type wavelets are constructed. The estimators are ...
    • An analog VLSI model of muscular contraction 

      Hudson, Tina A.; Bragg, Julian A.; Hasler, Paul; DeWeerth, Stephen P. (Georgia Institute of TechnologyInstitute of Electrical and Electronics Engineers, 2003-07)
      We have developed analog VLSI circuits to model the behavior demonstrated by biological sarcomeres, the force generating components of muscle tissue. The circuits are based upon the mathematical description of crossbridge ...
    • ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses 

      Stokes, Todd H.; Torrance, J. T.; Li, Henry; Wang, May D. (Georgia Institute of TechnologyBioMed Central, 2008)
      Background. A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only ...
    • An asynchronous architecture for modeling intersegmental neural communication 

      Patel, Girish N.; Reid, Michael S.; Schimmel, David E.; DeWeerth, Stephen P. (Georgia Institute of TechnologyInstitute of Electrical and Electronics Engineers, 2006-02)
      This paper presents an asynchronous VLSI architecture for modeling the oscillatory patterns seen in segmented biological systems. The architecture emulates the intersegmental synaptic connectivity observed in these biological ...
    • Automated smoother for numerical decoupling of dynamic models 

      Vilela, Marco; Borges, Carlos C. H.; Vinga, Susana; Vasconcelos, Ana Tereza R.; Santos, Helena; Voit, Eberhard O.; Almeida, Jonas S. (Georgia Institute of TechnologyBioMed Central, 2007-08)
      Background Structure identification of dynamic models for complex biological systems is the cornerstone of their reverse engineering. Biochemical Systems Theory (BST) offers a particularly convenient solution because its ...
    • Bacillus anthracis genome organization in light of whole transcriptome sequencing 

      Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark (Georgia Institute of TechnologyBioMed Central, 2010)
      Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants ...
    • BAMS Method: Theory and Simulations 

      Vidakovic, Brani; Ruggeri, Fabrizio (Georgia Institute of TechnologyPublished by: Springer on behalf of the Indian Statistical Institute. Article Stable URL: http://www.jstor.org/stable/25053173, 2001-08)
      In this paper we address the problem of model-induced wavelet shrinkage. Assuming the independence model according to which the wavelet coefficients are treated individually, we discuss a level-adaptive Bayesian model in ...
    • caCORRECT2: improving accuracy and reliability of microarray data in the presence of artifacts 

      Moffitt, Richard A.; Yin-Goen, Qiqin; Stokes, Todd H.; Parry, R. M.; Torrance, James H.; Phan, John H.; Young, Andrew N.; Wang, May D. (Georgia Institute of TechnologyBioMed Central, 2011)
      Background. In previous work, we reported the development of caCORRECT, a novel microarray quality control system built to identify and correct spatial artifacts commonly found on Affymetrix arrays. We have made recent ...
    • Canonical modeling: a review of concepts with emphasis on environmental health 

      Voit, Eberhard O. (Georgia Institute of TechnologyNational Institute of Environmental Health Sciences, 2000-10)
      The article reviews concepts of canonical modeling in the context of environmental health. Based on biochemical systems theory, the canonical approach was developed over the past thirty years and applied to complex systems ...
    • Catch bonds govern adhesion through L-selectin at threshold shear 

      Yago, Tadayuki; Wu, Jianhua; Wey, C. Diana; Klopocki, Arkadiusz G.; Zhu, Cheng; McEver, Rodger P. (Georgia Institute of TechnologyRockefeller University Press, 2004-09)
      Flow-enhanced cell adhesion is an unexplained phenomenon that might result from a transport-dependent increase in on-rates or a force-dependent decrease in off-rates of adhesive bonds. L-selectin requires a threshold shear ...
    • Challenges for the identification of metabolic pathways from time series data 

      Voit, Eberhard O.; Marino, Simeone; Lall, Raman (Georgia Institute of TechnologyBioinformation Systems e.V., 2004-12-23)
    • Challenges of Complexity and Integration in Quantitative Systems Biotechnology 

      Voit, Eberhard O. (Georgia Institute of TechnologyNational Science Foundation, 2000-09-13)
      It is widely acknowledged that the enormous amount of data produced by the human and other genome projects requires new mathematical and computational strategies of analysis and integration. Classified very broadly, ...
    • The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex 

      Blanc, Guillaume; Duncan, Garry; Agarkova, Irina; Borodovsky, Mark; Gurnon, James; Kuo, Ala; Lindquist, Erika; Lucas, Susan; Pangilinan, Jasmyn; Polle, Juergen; Salamov, Asaf; Terry, Astrid; Yamada, Takashi; Dunigan, David D.; Grigoriev, Igor V.; Claverie, Jean-Michel; Van Etten, James L. (Georgia Institute of TechnologyAmerican Society of Plant Physiologists, 2010-09)
      Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb ...
    • Collective decision making in bacterial viruses 

      Weitz, Joshua S.; Mileyko, Yuriy; Joh, Richard I.; Voit, Eberhard O. (Georgia Institute of TechnologyBiophysical Society, 2008-09)
      For many bacterial viruses, the choice of whether to kill host cells or enter a latent state depends on the multiplicity of coinfection. Here, we present a mathematical theory of how bacterial viruses can make collective ...
    • Computational systems analysis of dopamine metabolism 

      Qi, Zhen; Miller, Gary W.; Voit, Eberhard O. (Georgia Institute of TechnologyPublic Library of Science, 2008-06)
      A prominent feature of Parkinson’s disease (PD) is the loss of dopamine in the striatum, and many therapeutic interventions for the disease are aimed at restoring dopamine signaling. Dopamine signaling includes the synthesis, ...
    • Constructing stochastic models from deterministic process equations by propensity adjustment 

      Wu, Jialiang; Vidakovic, Brani; Voit, Eberhard O. (Georgia Institute of TechnologyBioMed Central, 2011-11)
      BACKGROUND: Gillespie's stochastic simulation algorithm (SSA) for chemical reactions admits three kinds of elementary processes, namely, mass action reactions of 0th, 1st or 2nd order. All other types of reaction processes, ...
    • Controlled delivery of PDGF-BB, and endothelial-derived cardiomyocyte survival factor, for myocardial protection using injectable self-assembling peptide nanofibers 

      Hsieh, Patrick C.H.; Davis, Michael E.; Gannon, Joseph; MacGillivray, Catherine; Lee, Richard T. (Georgia Institute of TechnologyAmerican Society for Clinical Investigation, 2006-01)
      Endothelial cells can protect cardiomyocytes from injury, but the mechanism of this protection is incompletely described. Here we demonstrate that protection of cardiomyocytes by endothelial cells occurs through PDGF-BB ...
    • Coordination of the dynamics of yeast sphingolipid metabolism during the diauxic shift 

      Alvarez-Vasquez, Fernando; Sims, Kellie J.; Voit, Eberhard O.; Hannun, Yusuf A.: (Georgia Institute of TechnologyBioMed Central, 2007-10)
      Background: The diauxic shift in yeast requires cells to coordinate a complicated response that involves numerous genes and metabolic processes. It is unknown whether responses of this type are mediated in vivo through ...
    • Custom design of the cardiac microenvironment with biomaterials 

      Davis, Michael E.; Hsieh, Patrick C.H.; Grodzinsky, Alan J.; Lee, Richard T. (Georgia Institute of TechnologyAmerican Heart Association, 2005-07)
      Many strategies for repairing injured myocardium are under active investigation, with some early encouraging results. These strategies include cell therapies, despite little evidence of long-term survival of exogenous ...