Now showing items 21-40 of 250

    • VIRGO: computational prediction of gene functions 

      Massjouni, Naveed; Rivera, Corban G.; Murali, T. M. (2006-07-01)
      Dramatic advances in sequencing technology and sophisticated experimental assays that interrogate the cell, combined with the public availability of the resulting data, herald the era of systems biology. However, the ...
    • Automatic layout and visualization of biclusters 

      Grothaus, Gregory A; Mufti, Adeel; Murali, T. M. (2006-09-04)
      Background Biclustering has emerged as a powerful algorithmic tool for analyzing measurements of gene expression. A number of different methods have emerged for computing biclusters in gene expression data. Many of these ...
    • A computational study of nucleosomal DNA flexibility 

      Ruscio, J. Z.; Onufriev, Alexey V. (CELL PRESS, 2006-12-01)
      Molecular dynamics simulations of the nucleosome core particle and its isolated DNA free in solution are reported. The simulations are based on the implicit solvent methodology and provide insights into the nature of ...
    • Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates 

      Pan, Deng; Zhang, Liqing (2007-08-02)
      Background The rate of gene duplication is an important parameter in the study of evolution, but the influence of gene conversion and technical problems have confounded previous attempts to provide a satisfying estimate. ...
    • Expression Divergence of Tandemly Arrayed Genes in Human and Mouse 

      Shoja, Valia; Murali, T. M.; Zhang, Liqing (Hindawi, 2007-10-30)
      Tandemly arrayed genes (TAGs) account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published ...
    • CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining 

      Pati, Amrita; Jin, Ying; Klage, Karsten; Helm, Richard F.; Heath, Lenwood S.; Ramakrishnan, Naren (Oxford Univ Press, 2008-01-01)
      CMGSDB (Database for Computational Modeling of Gene Silencing) is an integration of heterogeneous data sources about Caenorhabditis elegans with capabilities for compositional data mining (CDM) across diverse domains. ...
    • Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction 

      Yang, Kuan; Zhang, Liqing (2008-03)
      Phylogenetic tree reconstruction requires construction of a multiple sequence alignment (MSA) from sequences. Computationally, it is difficult to achieve an optimal MSA for many sequences. Moreover, even if an optimal MSA ...
    • Overlapping genes in the human and mouse genomes 

      Sanna, Chaitanya R; Li, Wen-Hsiung; Zhang, Liqing (2008-04-14)
      Background Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs ...
    • Cooperative Object Manipulation in Collaborative Virtual Environments 

      Pinho, Marcio S.; Bowman, Doug A.; Dal Sasso Freitas, Carla M. (Springer Nature, 2008-06-20)
      Cooperative manipulation refers to the simultaneous manipulation of a virtual object by multiple users in an immersive virtual environment (VE). In this work, we present techniques for cooperative manipulation based on ...
    • Memory Switches in Chemical Reaction Space 

      Ramakrishnan, Naren; Upinder, S. Bhalla (Public Library of Science, 2008-07-18)
      Just as complex electronic circuits are built from simple Boolean gates, diverse biological functions, including signal transduction, differentiation, and stress response, frequently use biochemical switches as a functional ...
    • Tandemly Arrayed Genes in Vertebrate Genomes 

      Pan, Deng; Zhang, Liqing (Hindawi, 2008-09-21)
      Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available ...
    • Stochastic simulation of enzyme-catalyzed reactions with disparate timescales 

      Barik, D.; Paul, Mark R.; Baumann, W. T.; Cao, Y.; Tyson, John J. (CELL PRESS, 2008-10-01)
      Many physiological characteristics of living cells are regulated by protein interaction networks. Because the total numbers of these protein species can be small, molecular noise can have significant effects on the dynamical ...
    • Electronic Theses and Dissertations: Progress, Issues, and Prospects 

      McMillan, Gail; Fox, Edward A.; Srinivasan, Venkat (Center for Digital Discourse and Culture, Virginia Tech, 2009)
    • PIG-the pathogen interaction gateway 

      Driscoll, Tim; Dyer, Matthew D.; Murali, T. M.; Sobral, Bruno W. (2009-01)
      Protein-protein interactions (PPIs) play a vital role in initiating infection in a number of pathogens. Identifying which interactions allow a pathogen to infect its host can help us to understand methods of pathogenesis ...
    • The Genome Reverse Compiler: an explorative annotation tool 

      Warren, Andrew S.; Setubal, João C. (2009-01-27)
      Background As sequencing costs have decreased, whole genome sequencing has become a viable and integral part of biological laboratory research. However, the tools with which genes can be found and functionally characterized ...
    • Identifying disease associations via genome-wide association studies 

      Huang, Wenhui; Wang, Pengyuan; Liu, Zhen; Zhang, Liqing (2009-01-30)
      Background Genome-wide association studies prove to be a powerful approach to identify the genetic basis of different human diseases. We studied the relationship between seven diseases characterized in a previous genome-wide ...
    • Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology 

      Tseng, Tsai-Tien; Tyler, Brett M.; Setubal, João C. (2009-02-19)
      Protein secretion plays a central role in modulating the interactions of bacteria with their environments. This is particularly the case when symbiotic bacteria (whether pathogenic, commensal or mutualistic) are interacting ...
    • Burst of Young Retrogenes and Independent Retrogene Formation in Mammals 

      Pan, Deng; Zhang, Liqing (PLOS, 2009-03-27)
      Retroposition and retrogenes gain increasing attention as recent studies show that they play an important role in human new gene formation. Here we examined the patterns of retrogene distribution in 8 mammalian genomes ...
    • Sexy gene conversions: locating gene conversions on the X-chromosome 

      Lawson, Mark J.; Zhang, Liqing (2009-08)
      Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X-chromosomes of human (Homo sapiens), chimpanzee (Pan ...
    • Service-based analysis of biological pathways 

      Zheng, George; Bouguettaya, Athman (2009-10-01)
      Background Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at ...