Jason E McDermott

Summary

Affiliation: Pacific Northwest National Laboratory
Country: USA

Publications

  1. pmc Technologies and approaches to elucidate and model the virulence program of salmonella
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory Richland, WA, USA
    Front Microbiol 2:121. 2011
  2. pmc Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems
    Ram Samudrala
    Department of Microbiology, University of Washington, Seattle, Washington, United States of America
    PLoS Pathog 5:e1000375. 2009
  3. pmc Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, Washington, USA
    BMC Syst Biol 5:190. 2011
  4. pmc Identification and validation of Ifit1 as an important innate immune bottleneck
    Jason E McDermott
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS ONE 7:e36465. 2012
  5. pmc Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella
    Hyunjin Yoon
    Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon 97239, USA
    BMC Syst Biol 5:100. 2011
  6. pmc A three-way comparative genomic analysis of Mannheimia haemolytica isolates
    Paulraj K Lawrence
    Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164 7040, USA
    BMC Genomics 11:535. 2010
  7. pmc Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation
    Jason E McDermott
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS ONE 6:e14673. 2011
  8. pmc Computational prediction of type III and IV secreted effectors in gram-negative bacteria
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, MSIN J4 33, 902 Battelle Boulevard, P O Box 999, Richland, WA 99352, USA
    Infect Immun 79:23-32. 2011
  9. doi request reprint A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, MSIN J4 33, Richland, WA 99352, USA
    Mol Biosyst 7:2407-18. 2011
  10. pmc Separating the drivers from the driven: Integrative network and pathway approaches aid identification of disease biomarkers from high-throughput data
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Dis Markers 28:253-66. 2010

Detail Information

Publications28

  1. pmc Technologies and approaches to elucidate and model the virulence program of salmonella
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory Richland, WA, USA
    Front Microbiol 2:121. 2011
    ....
  2. pmc Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems
    Ram Samudrala
    Department of Microbiology, University of Washington, Seattle, Washington, United States of America
    PLoS Pathog 5:e1000375. 2009
    ..This approach provides a new way to identify secreted effectors in a broad range of pathogenic bacteria for further experimental characterization and provides insight into the nature of the type III secretion signal...
  3. pmc Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, Washington, USA
    BMC Syst Biol 5:190. 2011
    ..Each of these systems has been studied extensively in isolation, but little effort has been directed toward systematically characterizing the conservation of host response on a global level beyond known immune signaling cascades...
  4. pmc Identification and validation of Ifit1 as an important innate immune bottleneck
    Jason E McDermott
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS ONE 7:e36465. 2012
    ..Our study demonstrates the utility of network analysis for identification of interesting targets related to innate immune function, and highlights that Ifit1 can exert a positive regulatory effect on downstream genes...
  5. pmc Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella
    Hyunjin Yoon
    Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon 97239, USA
    BMC Syst Biol 5:100. 2011
    ..Genes that are coordinately controlled by the set of regulators required for systemic infection are potentially required for pathogenicity...
  6. pmc A three-way comparative genomic analysis of Mannheimia haemolytica isolates
    Paulraj K Lawrence
    Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164 7040, USA
    BMC Genomics 11:535. 2010
    ..haemolytica at molecular level and assist in devising an effective control strategy...
  7. pmc Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation
    Jason E McDermott
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS ONE 6:e14673. 2011
    ..We speculate that this module may be an early checkpoint for progression to apoptosis and/or inflammation during macrophage activation...
  8. pmc Computational prediction of type III and IV secreted effectors in gram-negative bacteria
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, MSIN J4 33, 902 Battelle Boulevard, P O Box 999, Richland, WA 99352, USA
    Infect Immun 79:23-32. 2011
    ..Computational prediction of secreted effectors from protein sequences represents an important step toward better understanding the interaction between pathogens and hosts...
  9. doi request reprint A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, MSIN J4 33, Richland, WA 99352, USA
    Mol Biosyst 7:2407-18. 2011
    ....
  10. pmc Separating the drivers from the driven: Integrative network and pathway approaches aid identification of disease biomarkers from high-throughput data
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Dis Markers 28:253-66. 2010
    ....
  11. doi request reprint Bottlenecks and hubs in inferred networks are important for virulence in Salmonella typhimurium
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, US Department of Energy, Richland, WA, USA
    J Comput Biol 16:169-80. 2009
    ..Analysis of the differences between the two CLR-derived networks suggests that the bottleneck nodes are either mediators of transitions between system states or sentinels that reflect the dynamics of these transitions...
  12. pmc Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes
    Young Mo Kim
    Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Mol Biosyst 9:1522-34. 2013
    ..For example, cellular concentrations of polyamines were perturbed, as well as the predicted capacity for secretion and uptake...
  13. pmc Modeling dynamic regulatory processes in stroke
    Jason E McDermott
    Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS Comput Biol 8:e1002722. 2012
    ....
  14. pmc A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins
    Garry W Buchko
    Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Mol Biosyst 6:2448-58. 2010
    ..Typhimurium effectors SptP, SopD-2, GtgE, and the Yersinia pestis effector YopH...
  15. pmc A semiautomated framework for integrating expert knowledge into disease marker identification
    Jing Wang
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Dis Markers 35:513-23. 2013
    ..However, a recurring problem in deriving biological information from large data sets is how to best incorporate expert knowledge into the biomarker selection process...
  16. pmc Systems virology identifies a mitochondrial fatty acid oxidation enzyme, dodecenoyl coenzyme A delta isomerase, required for hepatitis C virus replication and likely pathogenesis
    Angela L Rasmussen
    Department of Microbiology, University of Washington School of Medicine, Box 358070, Seattle, WA 98195, USA
    J Virol 85:11646-54. 2011
    ..These findings demonstrate the utility of systems biology approaches to gain novel insight into the biology of HCV infection and identify novel, translationally relevant therapeutic targets...
  17. pmc A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses
    Hugh D Mitchell
    Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS ONE 8:e69374. 2013
    ..Our results demonstrate the utility of integrating diverse 'omic datasets to predict and prioritize regulatory features conserved across multiple pathogen infection models. ..
  18. pmc A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments
    Melissa M Matzke
    Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Proteomics 13:493-503. 2013
    ....
  19. pmc Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis
    Jason E McDermott
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    BMC Syst Biol 6:28. 2012
    ..We present topological analysis of co-abundance networks as an alternative to differential regulation for confident identification of target proteins from two related global proteomics studies of hepatitis C virus (HCV) infection...
  20. doi request reprint Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling
    Charles Ansong
    Biological Separations and Mass Spectroscopy Group, Pacific Northwest National Laboratory, PO Box 999, MSIN K8 98, Richland, WA, 99352, USA
    Curr Top Microbiol Immunol 363:21-41. 2013
    ..We will review the evolving technological approaches toward understanding complex microbial life through multi-omic measurements and integration, while highlighting some of our most recent successes in this area...
  21. pmc Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica
    Liang Shi
    Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Infect Immun 77:3227-33. 2009
    ....
  22. ncbi request reprint Sequential projection pursuit principal component analysis--dealing with missing data associated with new -omics technologies
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA, USA
    Biotechniques 54:165-8. 2013
    ..Our results demonstrate that this approach generates robust and informative low-dimensional data representations compared to commonly used imputation approaches...
  23. doi request reprint Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts
    Ronald C Taylor
    Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Int J Comput Biol Drug Des 4:56-82. 2011
    ..We describe two applications of this approach and discuss its added value in terms of corroboration, annotation and expansion of manually constructed and reversed engineered networks...
  24. ncbi request reprint An analysis pipeline for the inference of protein-protein interaction networks
    Ronald C Taylor
    Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory US Department of Energy, Richland, WA 99352, USA
    Int J Data Min Bioinform 3:409-30. 2009
    ..Also, the pipeline incorporates the Collective Analysis of Biological Interaction Networks (CABIN) software. We have thus created a structured workflow for protein-protein network inference and supplemental analysis...
  25. pmc Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation
    Deborah L Diamond
    Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195 8070, USA
    Hepatology 56:28-38. 2012
    ..Computational modeling approaches further highlight a potentially important link between HCV-associated oxidative stress and epigenetic regulatory mechanisms impacting on liver fibrogenesis...
  26. pmc A multi-omic systems approach to elucidating Yersinia virulence mechanisms
    Charles Ansong
    Biological Sciences Division, Pacific Northwest National Laboratory, P O Box 999, Richland, WA 99352, USA
    Mol Biosyst 9:44-54. 2013
    ..Finally, the omics data was coupled with a computational network analysis, allowing an efficient prediction of novel Yersinia virulence factors based on gene and protein expression patterns...
  27. pmc Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics
    Deborah L Diamond
    Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA
    PLoS Pathog 6:e1000719. 2010
    ....
  28. doi request reprint Proteomics analysis of the causative agent of typhoid fever
    Charles Ansong
    Biological Sciences Division, and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    J Proteome Res 7:546-57. 2008
    ..When our observations are taken together with the current literature, they suggest that this subset of proteins may play a role in S. typhi pathogenesis and human host specificity...