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List of works by Jason McDermott

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

scientific article

A comprehensive collection of systems biology data characterizing the host response to viral infection.

scientific article

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

scientific article published on 23 June 2011

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

scientific article

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

scientific article published on 29 September 2010

A network inference workflow applied to virulence-related processes in Salmonella typhimurium

scientific article published in March 2009

A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses

scientific article

A semiautomated framework for integrating expert knowledge into disease marker identification

scientific article published on 10 October 2013

A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm

scientific article

A three-way comparative genomic analysis of Mannheimia haemolytica isolates

scientific article

Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems

scientific article

An Integrative Analysis of Tumor Proteomic and Phosphoproteomic Profiles to Examine the Relationships Between Kinase Activity and Phosphorylation

scientific article published on 21 June 2019

An adaptive coarse graining method for signal transduction in three dimensions

scientific article published on January 2012

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

scientific article published in January 2009

An enhanced Java graph applet interface for visualizing interactomes

scientific article published on 21 December 2004

An integrated approach to predictive genomic analytics

scientific article published in 2010

Analysis of Rous sarcoma virus capsid protein variants assembled on lipid monolayers

scientific article published in February 2002

Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σ(E)-regulated SPI-2 gene expression

scientific article

Assembly of retrovirus capsid-nucleocapsid proteins in the presence of membranes or RNA.

scientific article

BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes

scientific article

Bayesian proteoform modeling improves protein quantification of global proteomic measurements.

scientific article

Biocellion: accelerating computer simulation of multicellular biological system models

scientific article

Bioverse: Functional, structural and contextual annotation of proteins and proteomes

scientific article

Bottlenecks and hubs in inferred networks are important for virulence in Salmonella typhimurium

scientific article published in February 2009

Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies As Revealed by Single-Cell RNA-Seq.

scientific article published on 27 October 2016

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

scientific article published on 21 September 2015

Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data.

scientific article

Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors

scientific article published in Nature Communications

Computational Systems Biology

Computational prediction of type III and IV secreted effectors in gram-negative bacteria

scientific article

Computational representation of biological systems.

scientific article

Conditional infectivity of a human immunodeficiency virus matrix domain deletion mutant ⬇️

scientific article published on December 1, 1993

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

scientific article published on 12 July 2016

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

scientific article

Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation

scientific article

Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium

scientific article

CpG preconditioning regulates miRNA expression that modulates genomic reprogramming associated with neuroprotection against ischemic injury.

scientific article published on 12 November 2014

Crosslink analysis of N-terminal, C-terminal, and N/B determining regions of the Moloney murine leukemia virus capsid protein

scientific article published in March 2000

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

scientific article published in November 2010

Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants

scientific article

Drawing connections

scientific article published in June 2017

EMXtalOrg: an EM tilt data organization and processing system

scientific article

Enhanced functional information from predicted protein networks

scientific article published on 01 February 2004

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

scientific article published on 17 February 2011

Evolutionary transients in the rice transcriptome

scientific article published on December 2010

Functional annotation from predicted protein interaction networks

scientific article

Genome Sequences of Mannheimia haemolytica Serotype A2: Ovine and Bovine Isolates.

scientific article

Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates

scientific article

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

scientific article published on 14 August 2013

Global analysis of Salmonella alternative sigma factor E on protein translation.

scientific article published on 27 February 2015

Hexagonal organization of Moloney murine leukemia virus capsid proteins

scientific article published in June 2002

INTEGRATOR: interactive graphical search of large protein interactomes over the Web.

scientific article

Identification and validation of Ifit1 as an important innate immune bottleneck

scientific article

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome

scientific article published on 17 October 2017

Improving network inference algorithms using resampling methods

scientific article published on 12 October 2018

Inferring molecular interactions pathways from eQTL data

scientific article

Integrative genomics and computational systems medicine

scientific article

Interdisciplinary dialogue for education, collaboration, and innovation: intelligent Biology and Medicine in and beyond 2013

scientific article

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

scientific article published in 2010

Let the Data Do the Talking: Hypothesis Discovery from Large-Scale Data Sets in Real Time

Modeling dynamic regulatory processes in stroke

scientific article

Moisture modulates soil reservoirs of active DNA and RNA viruses

scientific article published on 26 August 2021

Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002.

scientific article published on 27 August 2016

Night shift schedule causes circadian dysregulation of DNA repair genes and elevated DNA damage in humans

scientific article published on 14 March 2021

Organization of HIV-1 capsid proteins on a lipid monolayer

scientific article published on 01 March 1998

Origin and evolution of new exons in rodents

scientific article

Phosphoproteome Analysis Reveals Estrogen-ER Pathway as a Modulator of mTOR Activity Via DEPTOR

scientific article published on 12 June 2019

Prediction and integration of regulatory and protein-protein interactions

scientific article

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

scientific article published on 9 March 2015

Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

scientific article

Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation

scientific article

Proteome of Salmonella Enterica Serotype Typhimurium Grown in a Low Mg/pH Medium

scientific article published on January 2009

Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica

scientific article published on 15 June 2009

Proteomics analysis of the causative agent of typhoid fever

scientific article published on January 2008

RNA type III secretion signals that require Hfq

scientific article published on 8 February 2013

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

scientific article published on 14 December 2015

Retrovirus capsid protein assembly arrangements

scientific article

Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics

scientific article published on 22 April 2015

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

scientific article published on 5 April 2013

Separating the drivers from the driven: Integrative network and pathway approaches aid identification of disease biomarkers from high-throughput data

scientific article

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

scientific article

Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

scientific article published in 2023

Structural analysis of membrane-bound retrovirus capsid proteins

scientific article

Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase

scientific article published in 2022

Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling

scientific article published on January 2013

Suppressed expression of T-box transcription factors is involved in senescence in chronic obstructive pulmonary disease

scientific article

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

scientific article

Systems virology identifies a mitochondrial fatty acid oxidation enzyme, dodecenoyl coenzyme A delta isomerase, required for hepatitis C virus replication and likely pathogenesis

scientific article

TRANSCRIPTIONAL ANALYSIS OF THE UNICELLULAR, DIAZOTROPHIC CYANOBACTERIUM CYANOTHECE SP. ATCC 51142 GROWN UNDER SHORT DAY/NIGHT CYCLES(1).

scientific article published on 18 May 2009

Technologies and approaches to elucidate and model the virulence program of salmonella

scientific article

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

scientific article (publication date: 2010)

Ten Simple Rules to becoming a principal investigator

scientific article published on 20 February 2020

Ten simple rules for drawing scientific comics

scientific article published on 4 January 2018

The Bioverse API and web application.

scientific article

The Genomes of Oryza sativa: a history of duplications

scientific article

The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections

scientific article published on 20 September 2019

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus

scientific article

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

scientific article published on 30 April 2016

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

scientific article published on 01 September 2000

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

scientific article

Unified feature association networks through integration of transcriptomic and proteomic data

scientific article published on 17 September 2019

Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth

scientific article published on 26 July 2016

Using the gene ontology to enrich biological pathways.

scientific article published on 10 December 2009

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