T M Murali

Summary

Affiliation: Virginia Polytechnic Institute and State University
Country: USA

Publications

  1. pmc Summarizing cellular responses as biological process networks
    Christopher D Lasher
    Genetics, Bioinformatics, and Computational Biology Ph D Program, Virginia Tech, Blacksburg, VA 24061 USA
    BMC Syst Biol 7:68. 2013
  2. pmc XcisClique: analysis of regulatory bicliques
    Amrita Pati
    Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    BMC Bioinformatics 7:218. 2006
  3. pmc Network-based prediction and analysis of HIV dependency factors
    T M Murali
    Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
    PLoS Comput Biol 7:e1002164. 2011
  4. doi request reprint Network legos: building blocks of cellular wiring diagrams
    T M Murali
    Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
    J Comput Biol 15:829-44. 2008
  5. pmc Reconciling differential gene expression data with molecular interaction networks
    Christopher L Poirel
    Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
    Bioinformatics 29:622-9. 2013
  6. pmc Supervised learning and prediction of physical interactions between human and HIV proteins
    Matthew D Dyer
    Virginia Bioinformatics Institute, Virginia Tech, 1 Washington St, Blacksburg, VA 24061, USA
    Infect Genet Evol 11:917-23. 2011
  7. pmc PIG--the pathogen interaction gateway
    Tim Driscoll
    Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    Nucleic Acids Res 37:D647-50. 2009
  8. pmc The landscape of human proteins interacting with viruses and other pathogens
    Matthew D Dyer
    Genetics, Bioinformatics, and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
    PLoS Pathog 4:e32. 2008
  9. pmc The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis
    Matthew D Dyer
    Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
    PLoS ONE 5:e12089. 2010
  10. pmc Sensitive detection of pathway perturbations in cancers
    Corban G Rivera
    Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
    BMC Bioinformatics 13:S9. 2012

Collaborators

Detail Information

Publications21

  1. pmc Summarizing cellular responses as biological process networks
    Christopher D Lasher
    Genetics, Bioinformatics, and Computational Biology Ph D Program, Virginia Tech, Blacksburg, VA 24061 USA
    BMC Syst Biol 7:68. 2013
    ..However, even these methods can yield hundreds of enriched functions that may overlap considerably...
  2. pmc XcisClique: analysis of regulatory bicliques
    Amrita Pati
    Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    BMC Bioinformatics 7:218. 2006
    ..Greater statistical significance is associated with a set of genes that shares a common set of regulatory motifs, while simultaneously exhibiting highly correlated gene expression under given experimental conditions...
  3. pmc Network-based prediction and analysis of HIV dependency factors
    T M Murali
    Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
    PLoS Comput Biol 7:e1002164. 2011
    ....
  4. doi request reprint Network legos: building blocks of cellular wiring diagrams
    T M Murali
    Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
    J Comput Biol 15:829-44. 2008
    ..Source code implementing our algorithms is available under version 2 of the GNU General Public License at http://bioinformatics.cs.vt.edu/ murali/software/network-lego...
  5. pmc Reconciling differential gene expression data with molecular interaction networks
    Christopher L Poirel
    Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
    Bioinformatics 29:622-9. 2013
    ..However, these methods may not uncover the spectrum of pathways perturbed in a particular experiment or disease...
  6. pmc Supervised learning and prediction of physical interactions between human and HIV proteins
    Matthew D Dyer
    Virginia Bioinformatics Institute, Virginia Tech, 1 Washington St, Blacksburg, VA 24061, USA
    Infect Genet Evol 11:917-23. 2011
    ..While a number of methods have been proposed for predicting protein-protein interactions (PPIs), they have primarily focused on intra-species protein-protein interactions...
  7. pmc PIG--the pathogen interaction gateway
    Tim Driscoll
    Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    Nucleic Acids Res 37:D647-50. 2009
    ..Additionally, PIG includes a tool for visualizing a single HP-PPI network or two HP-PPI networks. PIG can be accessed at http://pig.vbi.vt.edu...
  8. pmc The landscape of human proteins interacting with viruses and other pathogens
    Matthew D Dyer
    Genetics, Bioinformatics, and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
    PLoS Pathog 4:e32. 2008
    ..Supplementary data accompanying this paper is available at http://staff.vbi.vt.edu/dyermd/publications/dyer2008a.html...
  9. pmc The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis
    Matthew D Dyer
    Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
    PLoS ONE 5:e12089. 2010
    ..However, the interactions between human proteins and proteins in these bacteria remain poorly characterized leading to an incomplete understanding of their pathogenesis and mechanisms of immune evasion...
  10. pmc Sensitive detection of pathway perturbations in cancers
    Corban G Rivera
    Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
    BMC Bioinformatics 13:S9. 2012
    ..Associations detected between diseases and perturbations in well-defined pathways within such interaction networks have the potential to illuminate the molecular mechanisms underlying disease progression and response to treatment...
  11. pmc Discovering networks of perturbed biological processes in hepatocyte cultures
    Christopher D Lasher
    Genetics, Bioinformatics, and Computational Biology PhD Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
    PLoS ONE 6:e15247. 2011
    ..Our approach may provide a new route to explore, analyze, and understand cellular responses to internal and external cues within the context of the intricate networks of molecular interactions that control cellular behavior...
  12. pmc Top-down network analysis to drive bottom-up modeling of physiological processes
    Christopher L Poirel
    Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
    J Comput Biol 20:409-18. 2013
    ..Finally, we highlight how networks computed by LINKER elucidate the role of a protein kinase (Cdc5) in the mitotic exit network of a dynamic model of the cell cycle...
  13. pmc Network-based functional enrichment
    Christopher L Poirel
    Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
    BMC Bioinformatics 12:S14. 2011
    ..e., it treats the network simply as a set of genes. In this paper, we introduce a novel method for functional enrichment that explicitly takes network interactions into account...
  14. pmc A comparative study of genome-wide transcriptional profiles of primary hepatocytes in collagen sandwich and monolayer cultures
    Yeonhee Kim
    Department of Chemical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
    Tissue Eng Part C Methods 16:1449-60. 2010
    ..These results provide a baseline for further explorations into the systems biology of engineered liver mimics...
  15. pmc Designing a multicellular organotypic 3D liver model with a detachable, nanoscale polymeric Space of Disse
    Adam L Larkin
    1 Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia
    Tissue Eng Part C Methods 19:875-84. 2013
    ..These results demonstrate the ability of the tri-cellular 3D cultures to serve as an organotypic hepatic model that elicits proliferation and maintenance of phenotype and in vivo-like cellular ratios. ..
  16. pmc The landscape of host transcriptional response programs commonly perturbed by bacterial pathogens: towards host-oriented broad-spectrum drug targets
    Yared H Kidane
    Genetics, Bioinformatics, and Computational Biology PhD Program, Virginia Tech, Blacksburg, Virginia, United States of America
    PLoS ONE 8:e58553. 2013
    ..e., host-oriented broad-spectrum (HOBS) drug targets. An important first step in the discovery of such drug targets is the identification of host responses that are commonly perturbed by multiple pathogens...
  17. pmc Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions
    Yared H Kidane
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
    BMC Microbiol 13:224. 2013
    ....
  18. pmc Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
    Jory Z Ruscio
    Genetics, Bioinformatics, and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    Proc Natl Acad Sci U S A 105:9204-9. 2008
    ..Localized structural fluctuations are the primary physical origin of the simulated CO migration pathways inside the protein...
  19. pmc VIRGO: computational prediction of gene functions
    Naveed Massjouni
    660 McBryde Hall, Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    Nucleic Acids Res 34:W340-4. 2006
    ..For each prediction, VIRGO also provides an informative 'propagation diagram' that traces the flow of information in the FLN that led to the prediction. VIRGO is available at http://whipple.cs.vt.edu:8080/virgo...
  20. ncbi request reprint Computational prediction of host-pathogen protein-protein interactions
    Matthew D Dyer
    Genetics, Bioinformatics and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    Bioinformatics 23:i159-66. 2007
    ..Developing computational methods that identify which PPIs enable a pathogen to infect a host has great implications in identifying potential targets for therapeutics...
  21. doi request reprint Systems biology characterization of engineered tissues
    Padmavathy Rajagopalan
    Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24060, USA
    Annu Rev Biomed Eng 15:55-70. 2013
    ..In turn, the unique challenges posed by tissue engineering will usher in new experimental techniques and computational advances in systems biology. ..