Systems virology: host-directed approaches to viral pathogenesis and drug targeting

Multiscale Analysis of Biological Systems

(2013) Annick Lesne   ACTA BIOTHEORETICA

Next-Generation Sequencing of Small RNAs from HIV-Infected Cells Identifies Phased microRNA Expression Patterns and Candidate Novel microRNAs Differentially Expressed upon Infection

(2013) S. T. Chang et al.   mBio

Epigenetic mechanisms as targets and companions of viral assaults

(2012) Ingemar Ernberg et al.   Annals of the New York Academy of Sciences

A network perspective on metabolic inconsistency

(2012) Nikolaus Sonnenschein et al.   BMC Systems Biology

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

In-silico drug screening and potential target identification for hepatocellular carcinoma using Support Vector Machines based on drug screening result

(2012) Wu-Lung R. Yang et al.   GENE

The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population

(2012)   GENETICS

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

(2012) Deborah L. Diamond et al.   HEPATOLOGY

Early transcriptional programming links progression to hepatitis C virus-induced severe liver disease in transplant patients

(2012) Angela L. Rasmussen et al.   HEPATOLOGY

Herpes Simplex Virus 1 Infection Activates Poly(ADP-Ribose) Polymerase and Triggers the Degradation of Poly(ADP-Ribose) Glycohydrolase

(2012) S. L. Grady et al.   JOURNAL OF VIROLOGY

Increased Viral Loads and Exacerbated Innate Host Responses in Aged Macaques Infected with the 2009 Pandemic H1N1 Influenza A Virus

(2012) L. Josset et al.   JOURNAL OF VIROLOGY

Into the Eye of the Cytokine Storm

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

Viruses and Interactomes in Translation

(2012) Laurène Meyniel-Schicklin et al.   MOLECULAR & CELLULAR PROTEOMICS

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins

(2012) Orit Rozenblatt-Rosen et al.   NATURE

Suppression of the antiviral response by an influenza histone mimic

(2012) Ivan Marazzi et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Protein–RNA interactions: new genomic technologies and perspectives

(2012) Julian König et al.   NATURE REVIEWS GENETICS

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

Genomic modulators of the immune response

(2012) Julian C. Knight   TRENDS IN GENETICS

Virus–host interactomes — antiviral drug discovery

(2012) Yue Ma-Lauer et al.   Current Opinion in Virology

Cell-based genomic screening: elucidating virus–host interactions

(2012) Debasis Panda et al.   Current Opinion in Virology

Expression Quantitative Trait Loci for Extreme Host Response to Influenza A in Pre-Collaborative Cross Mice

(2012) Daniel Bottomly et al.   G3-Genes Genomes Genetics

Multi-Scale In Vivo Systems Analysis Reveals the Influence of Immune Cells on TNF-α-Induced Apoptosis in the Intestinal Epithelium

(2012) Ken S. Lau et al.   PLOS BIOLOGY

HCMV Targets the Metabolic Stress Response through Activation of AMPK Whose Activity Is Important for Viral Replication

(2012) Jessica McArdle et al.   PLoS Pathogens

The Viral and Cellular MicroRNA Targetome in Lymphoblastoid Cell Lines

(2012) Rebecca L. Skalsky et al.   PLoS Pathogens

Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition

(2011) C. Becavin et al.   BIOINFORMATICS

A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections

(2011) Stewart T Chang et al.   BMC Systems Biology

Systems Biology: Evolving into the Mainstream

(2011) Colin Macilwain   CELL

The pathogenesis of influenza virus infections: the contributions of virus and host factors

(2011) Satoshi Fukuyama et al.   CURRENT OPINION IN IMMUNOLOGY

The multiple dimensions of Integrative Biology

(2011)   Integrative Biology

Systems Virology Identifies a Mitochondrial Fatty Acid Oxidation Enzyme, Dodecenoyl Coenzyme A Delta Isomerase, Required for Hepatitis C Virus Replication and Likely Pathogenesis

(2011) A. L. Rasmussen et al.   JOURNAL OF VIROLOGY

Human Cytomegalovirus Induces the Activity and Expression of Acetyl-Coenzyme A Carboxylase, a Fatty Acid Biosynthetic Enzyme Whose Inhibition Attenuates Viral Replication

(2011) C. M. Spencer et al.   JOURNAL OF VIROLOGY

Uncovering the global host cell requirements for influenza virus replication via RNAi screening

(2011) Silke Stertz et al.   MICROBES AND INFECTION

Systems biology of vaccination for seasonal influenza in humans

(2011) Helder I Nakaya et al.   NATURE IMMUNOLOGY

Predictive, personalized, preventive, participatory (P4) cancer medicine

(2011) Leroy Hood et al.   Nature Reviews Clinical Oncology

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Vaccinomics and a New Paradigm for the Development of Preventive Vaccines Against Viral Infections

(2011) Gregory A. Poland et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A Higher-Order Generalized Singular Value Decomposition for Comparison of Global mRNA Expression from Multiple Organisms

(2011) Sri Priya Ponnapalli et al.   PLoS One

Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress

(2011) S. T. H. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In Vivo Systems Analysis Identifies Spatial and Temporal Aspects of the Modulation of TNF- -Induced Apoptosis and Proliferation by MAPKs

(2011) K. S. Lau et al.   Science Signaling

Virus–host interactomes and global models of virus-infected cells

(2011) Caroline C. Friedel et al.   TRENDS IN MICROBIOLOGY

A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm

(2011) A. Aderem et al.   mBio

Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection

(2011) X. Peng et al.   mBio

Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4+ T Cell Line

(2011) S. T. Chang et al.   mBio

Dynamics of innate immunity are key to chronic immune activation in AIDS

(2011) Arndt Benecke et al.   Current Opinion in HIV and AIDS

Host Defense against Viral Infection Involves Interferon Mediated Down-Regulation of Sterol Biosynthesis

(2011) Mathieu Blanc et al.   PLOS BIOLOGY

Divergent Effects of Human Cytomegalovirus and Herpes Simplex Virus-1 on Cellular Metabolism

(2011) Livia Vastag et al.   PLoS Pathogens

The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors

(2011) Susanne Pfefferle et al.   PLoS Pathogens

New dimensionality reduction methods for the representation of high dimensional ‘omics’ data

(2010) Christophe Bécavin et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

What is systems biology?

(2010) Jennifer R Tisoncik et al.   Future Microbiology

Systems Vaccinology

(2010) Bali Pulendran et al.   IMMUNITY

Lethal Dissemination of H5N1 Influenza Virus Is Associated with Dysregulation of Inflammation and Lipoxin Signaling in a Mouse Model of Infection

(2010) C. Cilloniz et al.   JOURNAL OF VIROLOGY

Inhibition of Calmodulin-Dependent Kinase Kinase Blocks Human Cytomegalovirus-Induced Glycolytic Activation and Severely Attenuates Production of Viral Progeny

(2010) J. McArdle et al.   JOURNAL OF VIROLOGY

Network based analysis of hepatitis C virus Core and NS4B protein interactions

(2010) Lokesh P. Tripathi et al.   Molecular BioSystems

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Significance Analysis and Statistical Mechanics: An Application to Clustering

(2010) Marta Łuksza et al.   PHYSICAL REVIEW LETTERS

Gene Expression Signature-Based Screening Identifies New Broadly Effective Influenza A Antivirals

(2010) Laurence Josset et al.   PLoS One

Unique Signatures of Long Noncoding RNA Expression in Response to Virus Infection and Altered Innate Immune Signaling

(2010) X. Peng et al.   mBio

Genome-scale DNA methylation analysis

(2010) Shaun D Fouse et al.   Epigenomics

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

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

MULTI-FACTORIAL ANALYSIS OF CLASS PREDICTION ERROR: ESTIMATING OPTIMAL NUMBER OF BIOMARKERS FOR VARIOUS CLASSIFICATION RULES

(2010) MIZANUR R. KHONDOKER et al.   Journal of Bioinformatics and Computational Biology

MicroRNA detection by microarray

(2009) Wei Li et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

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

The NLRP3 Inflammasome Mediates In Vivo Innate Immunity to Influenza A Virus through Recognition of Viral RNA

(2009) Irving C. Allen et al.   IMMUNITY

The Intracellular Sensor NLRP3 Mediates Key Innate and Healing Responses to Influenza A Virus via the Regulation of Caspase-1

(2009) Paul G. Thomas et al.   IMMUNITY

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

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

Inflammasome recognition of influenza virus is essential for adaptive immune responses

(2009) Takeshi Ichinohe et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Discovery of insect and human dengue virus host factors

(2009) October M. Sessions et al.   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Early and sustained innate immune response defines pathology and death in nonhuman primates infected by highly pathogenic influenza virus

(2009) C. R. Baskin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genome-wide genetic screen for host factors required for hepatitis C virus propagation

(2009) Q. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

(2009) S.-s. C. Huang et al.   Science Signaling

Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes

(2009) Cristian Cillóniz et al.   PLoS Pathogens

Gene regulatory network inference using out of equilibrium statistical mechanics

(2008) Arndt Benecke   HFSP Journal

RNA interference screen for human genes associated with West Nile virus infection

(2008) Manoj N. Krishnan et al.   NATURE

Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy

(2008) Joshua Munger et al.   NATURE BIOTECHNOLOGY

Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans

(2008) Troy D Querec et al.   NATURE IMMUNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Out-of-Equilibrium Dynamics of Gene Expression and the Jarzynski Equality

(2008) Johannes Berg   PHYSICAL REVIEW LETTERS

Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen

(2008) Abraham L. Brass et al.   SCIENCE