Modeling Genome-Wide Dynamic Regulatory Network in Mouse Lungs with Influenza Infection Using High-Dimensional Ordinary Differential Equations

Pathways of Antigen Processing

(2013) Janice S. Blum et al.   Annual Review of Immunology

More powerful significant testing for time course gene expression data using functional principal component analysis approaches

(2013) Shuang Wu et al.   BMC BIOINFORMATICS

The Actin and Tetraspanin Networks Organize Receptor Nanoclusters to Regulate B Cell Receptor-Mediated Signaling

(2013) Pieta K. Mattila et al.   IMMUNITY

The Transcription Factor STAT-1 Couples Macrophage Synthesis of 25-Hydroxycholesterol to the Interferon Antiviral Response

(2012) Mathieu Blanc et al.   IMMUNITY

Aiolos promotes TH17 differentiation by directly silencing Il2 expression

(2012) Francisco J Quintana et al.   NATURE IMMUNOLOGY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

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

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Global Transcriptome Analysis in Influenza-Infected Mouse Lungs Reveals the Kinetics of Innate and Adaptive Host Immune Responses

(2012) Claudia Pommerenke et al.   PLoS One

High-Dimensional ODEs Coupled With Mixed-Effects Modeling Techniques for Dynamic Gene Regulatory Network Identification

(2011) Tao Lu et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Shared and Distinct Functions of the Transcription Factors IRF4 and IRF8 in Myeloid Cell Development

(2011) Michio Yamamoto et al.   PLoS One

On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics

(2011) Hongyu Miao et al.   SIAM REVIEW

Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection

(2011) Yongsheng Huang et al.   PLoS Genetics

Sieve estimation of constant and time-varying coefficients in nonlinear ordinary differential equation models by considering both numerical error and measurement error

(2010) Hongqi Xue et al.   ANNALS OF STATISTICS

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Bcl3 prevents acute inflammatory lung injury in mice by restraining emergency granulopoiesis

(2010) Daniel Kreisel et al.   JOURNAL OF CLINICAL INVESTIGATION

Role of CD27/CD70 pathway of activation in immunity and tolerance

(2010) Julie Denoeud et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

Critical role of IRF-5 in regulation of B-cell differentiation

(2010) C. Lien et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of Adaptive Immunity by the Innate Immune System

(2010) A. Iwasaki et al.   SCIENCE

Recursive regularization for inferring gene networks from time-course gene expression profiles

(2009) Teppei Shimamura et al.   BMC Systems Biology

Innate instruction of adaptive immunity revisited: the inflammasome

(2009) Stephanie C. Eisenbarth et al.   EMBO Molecular Medicine

Parameter Estimation for Differential Equation Models Using a Framework of Measurement Error in Regression Models

(2009) Hua Liang et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Smoothly Clipped Absolute Deviation on High Dimensions

(2009) Yongdai Kim et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

The IRF Family Transcription Factors in Immunity and Oncogenesis

(2008) Tomohiko Tamura et al.   Annual Review of Immunology

Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models

(2008) Osamu Hirose et al.   BIOINFORMATICS

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

FADD and the NF-κB family member Bcl-3 regulate complementary pathways to control T-cell survival and proliferation

(2008) Svetla Rangelova et al.   IMMUNOLOGY

Boolean network models of cellular regulation: prospects and limitations

(2008) S. Bornholdt   Journal of the Royal Society Interface