All Stories

  1. Unified feature association networks through integration of transcriptomic and proteomic data

    Article • PLoS Computational Biology, September 2019, PLOS

    Dr Jason E McDermott

  2. The landscape of viral proteomics and its potential to impact human health

    Article • Expert Review of Proteomics, May 2016, Taylor & Francis

    Dr Jason E McDermott

  3. ChIP-Seq Analysis of the σE Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response

    Article • PLoS ONE, September 2015, PLOS

    Dr Jason E McDermott

  4. Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics

    Article • Journal of Proteome Research, May 2015, American Chemical Society (ACS)

    Dr Jason E McDermott

  5. Global Analysis of Salmonella Alternative Sigma Factor E on Protein Translation

    Article • Journal of Proteome Research, April 2015, American Chemical Society (ACS)

    Dr Jason E McDermott

  6. Prediction of multi-drug resistance transporters using a novel sequence analysis method

    Article • F1000Research, March 2015, Faculty of 1000, Ltd.

    Steve Lindemann, Dr Jason E McDermott

  7. Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σE-regulated SPI-2 gene expression

    Article • Frontiers in Microbiology, February 2015, Frontiers

    Dr Jason E McDermott

  8. Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

    Article • Molecular & Cellular Proteomics, November 2014, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr Jason E McDermott

  9. CpG Preconditioning Regulates Mirna Expression That Modulates Genomic Reprogramming Associated with Neuroprotection against Ischemic Injury

    Article • Journal of Cerebral Blood Flow & Metabolism, November 2014, SAGE Publications

    Dr Jason E McDermott

  10. Promises and challenges in analysis of biological big data

    Article • January 2014, ACM (Association for Computing Machinery)

    Dr Jason E McDermott

  11. Trelliscope: A system for detailed visualization in the deep analysis of large complex data

    Article • October 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Jason E McDermott

  12. Genus-optimized strategy for the identification of chlamydial type III secretion substrates

    Article • Pathogens and Disease, August 2013, Oxford University Press (OUP)

    Dr Jason E McDermott

  13. Reproducibility: Two more red flags for suspect work

    Article • Nature, July 2013, Nature

    Dr Jason E McDermott

  14. Sequential projection pursuit principal component analysis – dealing with missing data associated with new -omics technologies

    Article • BioTechniques, March 2013, Informa UK (Informa Life Sciences)

    Dr Jason E McDermott

  15. A multi-omic systems approach to elucidating Yersinia virulence mechanisms

    Article • Molecular BioSystems, January 2013, Royal Society of Chemistry

    Dr Jason E McDermott

  16. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes

    Article • Molecular BioSystems, January 2013, Royal Society of Chemistry

    Dr Jason E McDermott

  17. Modeling Emergence in Neuroprotective Regulatory Networks

    Article • January 2013, Springer Science + Business Media

    Dr Jason E McDermott

  18. Interdisciplinary dialogue for education, collaboration, and innovation: Intelligent Biology and Medicine in and beyond 2013

    Article • BMC Genomics, January 2013, Springer Science + Business Media

    Dr Jason E McDermott

  19. A Semiautomated Framework for Integrating Expert Knowledge into Disease Marker Identification

    Article • Disease Markers, January 2013, Hindawi Publishing Corporation

    Dr Jason E McDermott

  20. A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments

    Article • PROTEOMICS, November 2012, Wiley

    Dr Jason E McDermott

  21. Modeling Dynamic Regulatory Processes in Stroke

    Article • PLoS Computational Biology, October 2012, PLOS

    Dr Jason E McDermott

  22. Challenges in biomarker discovery: combining expert insights with statistical analysis of complex omics data

    Article • Expert Opinion on Medical Diagnostics, August 2012, Informa Healthcare

    Dr Jason E McDermott

  23. Suppressed Expression of T-Box Transcription Factors Is Involved in Senescence in Chronic Obstructive Pulmonary Disease

    Article • PLoS Computational Biology, July 2012, PLOS

    Dr Jason E McDermott

  24. Identification and Validation of Ifit1 as an Important Innate Immune Bottleneck

    Article • PLoS ONE, June 2012, PLOS

    Dr Jason E McDermott

  25. Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis

    Article • BMC Systems Biology, January 2012, Springer Science + Business Media

    Dr Jason E McDermott

  26. Studying Salmonellae and Yersiniae Host–Pathogen Interactions Using Integrated ‘Omics and Modeling

    Article • January 2012, Springer Science + Business Media

    Dr Jason E McDermott

  27. MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH

    Article • December 2011, World Scientific Pub Co Pte Lt

    Dr Jason E McDermott

  28. Controlling the Response: Predictive Modeling of a Highly Central, Pathogen-Targeted Core Response Module in Macrophage Activation

    Article • PLoS ONE, February 2011, PLOS

    Dr Jason E McDermott

  29. A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142

    Article • Molecular BioSystems, January 2011, Royal Society of Chemistry

    Professor Louis A Sherman, Dr Jason E McDermott

  30. Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems

    Article • BMC Systems Biology, January 2011, Springer Science + Business Media

    Dr Jason E McDermott

  31. Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts

    Article • International Journal of Computational Biology and Drug Design, January 2011, Inderscience Publishers

    Dr Jason E McDermott

  32. Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella

    Article • Frontiers in Microbiology, January 2011, Frontiers

    Dr Jason E McDermott

  33. Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella

    Article • BMC Systems Biology, January 2011, Springer Science + Business Media

    Dr Jason E McDermott

  34. Evolutionary Transients in the Rice Transcriptome

    Article • Genomics Proteomics & Bioinformatics, December 2010, Elsevier

    Dr Jason E McDermott

  35. DEFINING THE PLAYERS IN HIGHER-ORDER NETWORKS: PREDICTIVE MODELING FOR REVERSE ENGINEERING FUNCTIONAL INFLUENCE NETWORKS

    Article • November 2010, World Scientific Pub Co Pte Lt

    Dr Jason E McDermott

  36. Temporal Proteome and Lipidome Profiles Reveal Hepatitis C Virus-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics

    Article • PLoS Pathogens, January 2010, PLOS

    Dr Jason E McDermott

  37. A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins

    Article • Molecular BioSystems, January 2010, Royal Society of Chemistry

    Dr Jason E McDermott

  38. Learning biological networks via bootstrapping with optimized go-based gene similarity

    Article • January 2010, ACM (Association for Computing Machinery)

    Dr Jason E McDermott

  39. Separating the Drivers from the Driven: Integrative Network and Pathway Approaches Aid Identification of Disease Biomarkers from High-Throughput Data

    Article • Disease Markers, January 2010, Hindawi Publishing Corporation

    Dr Jason E McDermott

  40. An integrated approach to predictive genomic analytics

    Article • January 2010, ACM (Association for Computing Machinery)

    Dr Jason E McDermott

  41. Proteome of Salmonella Enterica Serotype Typhimurium Grown in a Low Mg2+/pH Medium

    Article • Journal of Proteomics & Bioinformatics, September 2009, OMICS Publishing Group

    Dr Jason E McDermott

  42. TRANSCRIPTIONAL ANALYSIS OF THE UNICELLULAR, DIAZOTROPHIC CYANOBACTERIUMCYANOTHECESP. ATCC 51142 GROWN UNDER SHORT DAY/NIGHT CYCLES

    Article • Journal of Phycology, June 2009, Wiley

    Professor Louis A Sherman, Dr Jason E McDermott

  43. Accurate Prediction of Secreted Substrates and Identification of a Conserved Putative Secretion Signal for Type III Secretion Systems

    Article • PLoS Pathogens, April 2009, PLOS

    Dr Jason E McDermott

  44. A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium

    Article • Annals of the New York Academy of Sciences, March 2009, Wiley

    Dr Jason E McDermott

  45. Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium

    Article • PLoS Pathogens, February 2009, PLOS

    Dr Jason E McDermott

  46. Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium

    Article • Journal of Computational Biology, February 2009, Mary Ann Liebert Inc

    Dr Jason E McDermott

  47. Computational Systems Biology

    Article • January 2009

    Dr Jason E McDermott, Dr Jens Allmer

  48. Prediction and Integration of Regulatory and Protein–Protein Interactions

    Article • January 2009, Springer Science + Business Media

    Dr Jason E McDermott

  49. Inferring Molecular Interactions Pathways from eQTL Data

    Article • January 2009, Springer Science + Business Media

    Dr Jason E McDermott

  50. The Bioverse API and Web Application

    Article • January 2009, Springer Science + Business Media

    Dr Jason E McDermott

  51. Using the gene ontology to enrich biological pathways

    Article • International Journal of Computational Biology and Drug Design, January 2009, Inderscience Publishers

    Dr Jason E McDermott

  52. An analysis pipeline for the inference of protein-protein interaction networks

    Article • International Journal of Data Mining and Bioinformatics, January 2009, Inderscience Publishers

    Dr Jason E McDermott

  53. A BAYESIAN INTEGRATION MODEL OF HIGH-THROUGHPUT PROTEOMICS AND METABOLOMICS DATA FOR IMPROVED EARLY DETECTION OF MICROBIAL INFECTIONS

    Article • November 2008, World Scientific Pub Co Pte Lt

    Dr Jason E McDermott

  54. Proteomics Analysis of the Causative Agent of Typhoid Fever

    Article • Journal of Proteome Research, February 2008, American Chemical Society (ACS)

    Dr Jason E McDermott

  55. SEBINI-CABIN: An Analysis Pipeline for Biological Network Inference, with a Case Study in Protein-Protein Interaction Network Reconstruction

    Article • December 2007, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Jason E McDermott

  56. Enhanced functional information from predicted protein networks

    Article • Trends in Biotechnology, February 2004, Elsevier

    Dr Jason E McDermott

  57. Retrovirus Capsid Protein Assembly Arrangements

    Article • Journal of Molecular Biology, January 2003, Elsevier

    Dr Jason E McDermott

  58. EMXtalOrg: an EM tilt data organization and processing system

    Article • Ultramicroscopy, October 2002, Elsevier

    Dr Jason E McDermott

  59. Hexagonal Organization of Moloney Murine Leukemia Virus Capsid Proteins

    Article • Virology, June 2002, Elsevier

    Dr Jason E McDermott

  60. Analysis of rous sarcoma virus capsid protein variants assembled on lipid monolayers

    Article • Journal of Molecular Biology, February 2002, Elsevier

    Dr Jason E McDermott

  61. Three-dimensional organization of retroviral capsid proteins on a lipid monolayer

    Article • Journal of Molecular Biology, September 2000, Elsevier

    Dr Jason E McDermott

  62. Crosslink Analysis of N-Terminal, C-Terminal, and N/B Determining Regions of the Moloney Murine Leukemia Virus Capsid Protein

    Article • Virology, March 2000, Elsevier

    Dr Jason E McDermott