A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses

Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells

(2013) A. C. Sims et al.   JOURNAL OF VIROLOGY

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

(2012) Jason E McDermott et al.   BMC Systems Biology

Protective effects of long pentraxin PTX3 on lung injury in a severe acute respiratory syndrome model in mice

(2012) Bing Han et al.   LABORATORY INVESTIGATION

Into the Eye of the Cytokine Storm

(2012) J. R. Tisoncik et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Integrated Proteomic, Transcriptomic, and Biological Network Analysis of Breast Carcinoma Reveals Molecular Features of Tumorigenesis and Clinical Relapse

(2012) Marcin Imielinski et al.   MOLECULAR & CELLULAR PROTEOMICS

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Integrating the Alzheimer's Disease Proteome and Transcriptome: A Comprehensive Network Model of a Complex Disease

(2012) Peter Hallock et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Network Analysis of Epidermal Growth Factor Signaling Using Integrated Genomic, Proteomic and Phosphorylation Data

(2012) Katrina M. Waters et al.   PLoS One

A20 (Tnfaip3) Deficiency in Myeloid Cells Protects against Influenza A Virus Infection

(2012) Jonathan Maelfait et al.   PLoS Pathogens

Infection Strategies of Bacterial and Viral Pathogens through Pathogen–Human Protein–Protein Interactions

(2012) Saliha Durmuş Tekir et al.   Frontiers in Microbiology

Improved quality control processing of peptide-centric LC-MS proteomics data

(2011) Melissa M. Matzke et al.   BIOINFORMATICS

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

(2011) Hyunjin Yoon et al.   BMC Systems Biology

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

(2011) Jason E McDermott et al.   BMC Systems Biology

Beta-2 microglobulin as an immunological marker to assess the progression of human immunodeficiency virus infected patients on highly active antiretroviral therapy

(2011) Pachiappan Chitra et al.   CLINICA CHIMICA ACTA

Distinct Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury Pathways in Two Different Nonhuman Primate Species

(2011) S. L. Smits et al.   JOURNAL OF VIROLOGY

Host Regulatory Network Response to Infection with Highly Pathogenic H5N1 Avian Influenza Virus

(2011) C. Li et al.   JOURNAL OF VIROLOGY

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

(2011) Daniel Hurley et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Jason E. McDermott et al.   PLoS One

Integrative Identification of Arabidopsis Mitochondrial Proteome and Its Function Exploitation through Protein Interaction Network

(2011) Jian Cui et al.   PLoS One

Critical role for macrophage migration inhibitory factor (MIF) in Ross River virus-induced arthritis and myositis

(2011) L. J. Herrero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors

(2011) Bobbie-Jo M. Webb-Robertson et al.   PROTEOMICS

Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-Based Proteomics Data

(2010) Bobbie-Jo M. Webb-Robertson et al.   JOURNAL OF PROTEOME RESEARCH

Transcriptomic Analysis Reveals a Mechanism for a Prefibrotic Phenotype in STAT1 Knockout Mice during Severe Acute Respiratory Syndrome Coronavirus Infection

(2010) G. A. Zornetzer et al.   JOURNAL OF VIROLOGY

Culturing the Unculturable: Human Coronavirus HKU1 Infects, Replicates, and Produces Progeny Virions in Human Ciliated Airway Epithelial Cell Cultures

(2010) K. Pyrc et al.   JOURNAL OF VIROLOGY

Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication

(2010) Alexander Karlas et al.   NATURE

Dynamic Innate Immune Responses of Human Bronchial Epithelial Cells to Severe Acute Respiratory Syndrome-Associated Coronavirus Infection

(2010) Tomoki Yoshikawa et al.   PLoS One

Inflammasomes as mediators of immunity against influenza virus

(2010) Iris K. Pang et al.   TRENDS IN IMMUNOLOGY

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

(2010) Deborah L. Diamond et al.   PLoS Pathogens

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

(2009) Navdeep Jaitly et al.   BMC BIOINFORMATICS

Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients

(2009) Christiaan GJ Saris et al.   BMC GENOMICS

A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection

(2009) Sagi D. Shapira et al.   CELL

The IFITM Proteins Mediate Cellular Resistance to Influenza A H1N1 Virus, West Nile Virus, and Dengue Virus

(2009) Abraham L. Brass et al.   CELL

Systems-based candidate genes for human response to influenza infection

(2009) Lyna Zhang et al.   INFECTION GENETICS AND EVOLUTION

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

(2009) Jason E. McDermott et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

ATF3 transcription factor and its emerging roles in immunity and cancer

(2009) Matthew R. Thompson et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Cellular Immune Responses to Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) Infection in Senescent BALB/c Mice: CD4+ T Cells Are Important in Control of SARS-CoV Infection

(2009) J. Chen et al.   JOURNAL OF VIROLOGY

Interplay between influenza A virus and the innate immune signaling

(2009) Christina Ehrhardt et al.   MICROBES AND INFECTION

Human host factors required for influenza virus replication

(2009) Renate König et al.   NATURE

The use of Random Homozygous Gene Perturbation to identify novel host-oriented targets for influenza

(2009) Baoquan Sui et al.   VIROLOGY

DAnTE: a statistical tool for quantitative analysis of -omics data

(2008) A. D. Polpitiya et al.   BIOINFORMATICS

Characterization of the Mouse Pancreatic Islet Proteome and Comparative Analysis with Other Mouse Tissues

(2008) Vladislav A. Petyuk et al.   JOURNAL OF PROTEOME RESEARCH

Systematic Assembly of a Full-Length Infectious Clone of Human Coronavirus NL63

(2008) E. F. Donaldson et al.   JOURNAL OF VIROLOGY

Drosophila RNAi screen identifies host genes important for influenza virus replication

(2008) Linhui Hao et al.   NATURE

Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice

(2008) M. M. Becker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a Novel Transcriptional Repressor (HEPIS) That Interacts with nsp-10 of SARS Coronavirus

(2008) Min Hong et al.   VIRAL IMMUNOLOGY

Fully Automated Four-Column Capillary LC−MS System for Maximizing Throughput in Proteomic Analyses

(2007) Eric A. Livesay et al.   ANALYTICAL CHEMISTRY