Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens

A Serpin Shapes the Extracellular Environment to Prevent Influenza A Virus Maturation

(2015) Meike Dittmann et al.   CELL

Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation

(2015) Ezekiel J. Maier et al.   GENOME RESEARCH

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

(2015) Bobbie-Jo M. Webb-Robertson et al.   JOURNAL OF PROTEOME RESEARCH

The 1918 Influenza Virus PB2 Protein Enhances Virulence through the Disruption of Inflammatory and Wnt-Mediated Signaling in Mice

(2015) Adriana Forero et al.   JOURNAL OF VIROLOGY

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

The diverse role of RIP kinases in necroptosis and inflammation

(2015) John Silke et al.   NATURE IMMUNOLOGY

Functions of the influenza A virus NS1 protein in antiviral defense

(2015) Robert M Krug   Current Opinion in Virology

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

(2015) Emma Pierson et al.   PLoS Computational Biology

An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation

(2015) Jason E. Shoemaker et al.   PLoS Pathogens

A Functional Role of Fibroblast Growth Factor Receptor 1 (FGFR1) in the Suppression of Influenza A Virus Replication

(2015) Xin Liu et al.   PLoS One

A minimum-labeling approach for reconstructing protein networks across multiple conditions

(2014) Arnon Mazza et al.   Algorithms for Molecular Biology

Influenza Virus-Host Interactome Screen as a Platform for Antiviral Drug Development

(2014) Tokiko Watanabe et al.   Cell Host & Microbe

Linking signaling pathways to transcriptional programs in breast cancer

(2014) Hatice U. Osmanbeyoglu et al.   GENOME RESEARCH

Circadian Clock Proteins and Immunity

(2014) Anne M. Curtis et al.   IMMUNITY

Heat Shock Protein 70 Modulates Influenza A Virus Polymerase Activity

(2014) Rashid Manzoor et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Elucidating Influenza Inhibition Pathways via Network Reconstruction

(2014) Arnon Mazza et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Pathway connectivity and signaling coordination in the yeast stress-activated signaling network

(2014) D. Chasman et al.   Molecular Systems Biology

Unifying immunology with informatics and multiscale biology

(2014) Brian A Kidd et al.   NATURE IMMUNOLOGY

The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease

(2014) Janan T. Eppig et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Alzheimer's Associated β-Amyloid Protein Inhibits Influenza A Virus and Modulates Viral Interactions with Phagocytes

(2014) Mitchell R. White et al.   PLoS One

Influenza Viruses and mRNA Splicing: Doing More with Less

(2014) J. Dubois et al.   mBio

Sirtuins Are Evolutionarily Conserved Viral Restriction Factors

(2014) Emre Koyuncu et al.   mBio

Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches To Control Interferon-Stimulated Gene Responses

(2014) V. D. Menachery et al.   mBio

Influenza A virus protein PB1-F2 translocates into mitochondria via Tom40 channels and impairs innate immunity

(2014) Takuma Yoshizumi et al.   Nature Communications

Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu

(2014) Siddhartha Jain et al.   PLoS Computational Biology

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

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

(2014) Brian D. Aevermann et al.   Scientific Data

Identifying proteins controlling key disease signaling pathways

(2013) Anthony Gitter et al.   BIOINFORMATICS

Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

(2013) Nicolas Tchitchek et al.   BMC Systems Biology

Construction of human activity-based phosphorylation networks

(2013) R. H. Newman et al.   Molecular Systems Biology

HDAC Inhibition Suppresses Primary Immune Responses, Enhances Secondary Immune Responses, and Abrogates Autoimmunity During Tumor Immunotherapy

(2013) Byram W Bridle et al.   MOLECULAR THERAPY

Dynamic regulatory network controlling TH17 cell differentiation

(2013) Nir Yosef et al.   NATURE

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Hugh D. Mitchell et al.   PLoS One

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

(2013) Sushmita Roy et al.   PLoS Computational Biology

The Interactomes of Influenza Virus NS1 and NS2 Proteins Identify New Host Factors and Provide Insights for ADAR1 Playing a Supportive Role in Virus Replication

(2013) Benoît de Chassey et al.   PLoS Pathogens

BOLA1 Is an Aerobic Protein That Prevents Mitochondrial Morphology Changes Induced by Glutathione Depletion

(2012) Peter Willems et al.   ANTIOXIDANTS & REDOX SIGNALING

Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs

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

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

(2012) Anne-Claire Haury et al.   BMC Systems Biology

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

(2012) A. Gitter et al.   GENOME RESEARCH

Computational tools for prioritizing candidate genes: boosting disease gene discovery

(2012) Yves Moreau et al.   NATURE REVIEWS GENETICS

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores

(2012) Martin H. Schaefer et al.   PLoS One

Physical Module Networks: an integrative approach for reconstructing transcription regulation

(2011) N. Novershtern et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

Proteolytic processing of Alzheimer’s β-amyloid precursor protein

(2011) Han Zhang et al.   JOURNAL OF NEUROCHEMISTRY

Regression shrinkage and selection via the lasso: a retrospective

(2011) Robert Tibshirani   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Generation and Comprehensive Analysis of an Influenza Virus Polymerase Cellular Interaction Network

(2011) L. Tafforeau 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

Serpin Induced Antiviral Activity of Prostaglandin Synthetase-2 against HIV-1 Replication

(2011) James B. Whitney et al.   PLoS One

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Emerging Role of ISG15 in Antiviral Immunity

(2010) Brian Skaug et al.   CELL

Systems biology approaches to dissect mammalian innate immunity

(2010) Sagi D Shapira et al.   CURRENT OPINION IN IMMUNOLOGY

Hoxa9 Regulates Flt3 in Lymphohematopoietic Progenitors

(2010) K. Gwin et al.   JOURNAL OF IMMUNOLOGY

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

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

(2010) Alexander Karlas et al.   NATURE

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

EHD proteins: key conductors of endocytic transport

(2010) Naava Naslavsky et al.   TRENDS IN CELL BIOLOGY

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

The Tyrosine Kinase c-Src Enhances RIG-I (Retinoic Acid-inducible Gene I)-elicited Antiviral Signaling

(2009) Ingvild B. Johnsen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Critical Role of IL-1 Receptor-Associated Kinase-M in Regulating Chemokine-Dependent Deleterious Inflammation in Murine Influenza Pneumonia

(2009) M. Seki et al.   JOURNAL OF IMMUNOLOGY

Toward accurate reconstruction of functional protein networks

(2009) Nir Yosef et al.   Molecular Systems Biology

Human host factors required for influenza virus replication

(2009) Renate König et al.   NATURE

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

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

(2009) Baoquan Sui et al.   VIROLOGY

Identification of interleukin-1 and interleukin-6-responsive genes in human monocyte-derived macrophages using microarrays

(2008) Jolanta Jura et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The effects of Ankrd2 alteration indicate its involvement in cell cycle regulation during muscle differentiation

(2008) Camilla Bean et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

CD47 in the Immune Response: Role of Thrombospondin and SIRP-α Reverse Signaling

(2008) Marika Sarfati et al.   CURRENT DRUG TARGETS

Thrombospondin 1 binding to calreticulin-LRP1 signals resistance to anoikis

(2008) Manuel A. Pallero et al.   FASEB JOURNAL

Drosophila RNAi screen identifies host genes important for influenza virus replication

(2008) Linhui Hao et al.   NATURE