Systems Biology in Immunology: A Computational Modeling Perspective

The T Cell Receptor's  -Chain Connecting Peptide Motif Promotes Close Approximation of the CD8 Coreceptor Allowing Efficient Signal Initiation

(2014) M. Mallaun et al.   JOURNAL OF IMMUNOLOGY

Pathogenic Effector T Cell Enrichment Overcomes Regulatory T Cell Control and Generates Autoimmune Gastritis

(2014) J. P. Monteiro et al.   JOURNAL OF IMMUNOLOGY

Rule-based spatial modeling with diffusing, geometrically constrained molecules

(2010) Gerd Gruenert et al.   BMC BIOINFORMATICS

web cellHTS2: A web-application for the analysis of high-throughput screening data

(2010) Oliver Pelz et al.   BMC BIOINFORMATICS

Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

(2010) Dominic P Tolle et al.   BMC Systems Biology

Genome-wide Analysis of the Host Intracellular Network that Regulates Survival of Mycobacterium tuberculosis

(2010) Dhiraj Kumar et al.   CELL

Cellular Networks Involved in the Influenza Virus Life Cycle

(2010) Tokiko Watanabe et al.   Cell Host & Microbe

Quantifying EGFR Alterations in the Lung Cancer Genome with Nanofluidic Digital PCR Arrays

(2010) J. Wang et al.   CLINICAL CHEMISTRY

Challenges in Mass Spectrometry Based Targeted Metabolomics

(2010) T. Koal et al.   CURRENT MOLECULAR MEDICINE

Quantitative Proteomics Reveals Subset-Specific Viral Recognition in Dendritic Cells

(2010) Christian A. Luber et al.   IMMUNITY

The Membrane Skeleton Controls Diffusion Dynamics and Signaling through the B Cell Receptor

(2010) Bebhinn Treanor et al.   IMMUNITY

Immunological synapse: a multi-protein signalling cellular apparatus for controlling gene expression

(2010) Kartika Padhan et al.   IMMUNOLOGY

Dynamic Regulation of CD45 Lateral Mobility by the Spectrin-Ankyrin Cytoskeleton of T Cells

(2010) Christopher W. Cairo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

IL-10 Inhibits miR-155 Induction by Toll-like Receptors

(2010) Claire E. McCoy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantitative Phosphoproteomic Analysis of T Cell Receptor Signaling in Diabetes Prone and Resistant Mice

(2010) Leo K. Iwai et al.   JOURNAL OF PROTEOME RESEARCH

Systematic analysis of the IgG antibody immune response against varicella zoster virus (VZV) using a self-assembled protein microarray

(2010) Alessandro Ceroni et al.   Molecular BioSystems

Differential expression of pathogen-recognition molecules between dendritic cell subsets revealed by plasma membrane proteomic analysis

(2010) Elodie Segura et al.   MOLECULAR IMMUNOLOGY

Clustering phenotype populations by genome-wide RNAi and multiparametric imaging

(2010) Florian Fuchs et al.   Molecular Systems Biology

Systems survey of endocytosis by multiparametric image analysis

(2010) Claudio Collinet et al.   NATURE

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

(2010) Beate Neumann et al.   NATURE

Chronic active B-cell-receptor signalling in diffuse large B-cell lymphoma

(2010) R. Eric Davis et al.   NATURE

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

(2010) Alexander Karlas et al.   NATURE

Single-cell NF-κB dynamics reveal digital activation and analogue information processing

(2010) Savaş Tay et al.   NATURE

Fast, single-molecule localization that achieves theoretically minimum uncertainty

(2010) Carlas S Smith et al.   NATURE METHODS

A photoactivatable marker protein for pulse-chase imaging with superresolution

(2010) Jochen Fuchs et al.   NATURE METHODS

The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

(2010) Matthew D. Dyer et al.   PLoS One

Competing feedback loops shape IL-2 signaling between helper and regulatory T lymphocytes in cellular microenvironments

(2010) D. Busse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins

(2010) J. R. A. Hutchins et al.   SCIENCE

Detailed Simulations of Cell Biology with Smoldyn 2.1

(2010) Steven S. Andrews et al.   PLoS Computational Biology

Identification of Host-Dependent Survival Factors for Intracellular Mycobacterium tuberculosis through an siRNA Screen

(2010) Shilpi Jayaswal et al.   PLoS Pathogens

Stoichiometry Determination of the MP1−p14 Complex Using a Novel and Cost-Efficient Method To Produce an Equimolar Mixture of Standard Peptides

(2009) Johann Holzmann et al.   ANALYTICAL CHEMISTRY

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

GetBonNie for building, analyzing and sharing rule-based models

(2009) B. Hu et al.   BIOINFORMATICS

RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens

(2009) N. Rieber et al.   BIOINFORMATICS

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells

(2009) Jayajit Das et al.   CELL

Phosphorylation-Driven Assembly of the RIP1-RIP3 Complex Regulates Programmed Necrosis and Virus-Induced Inflammation

(2009) YoungSik Cho et al.   CELL

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

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Gene Expression Signatures Diagnose Influenza and Other Symptomatic Respiratory Viral Infections in Humans

(2009) Aimee K. Zaas et al.   Cell Host & Microbe

A Functional Genomic Screen Identifies Cellular Cofactors of Hepatitis C Virus Replication

(2009) Andrew W. Tai et al.   Cell Host & Microbe

Characterization of human epigenomes

(2009) Zhibin Wang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Network design principles from the sea urchin embryo

(2009) Eric H Davidson   CURRENT OPINION IN GENETICS & DEVELOPMENT

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Shine a light: Imaging the immune system

(2009) Milka Sarris et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

A Recurrent Network Involving the Transcription Factors PU.1 and Gfi1 Orchestrates Innate and Adaptive Immune Cell Fates

(2009) Chauncey J. Spooner et al.   IMMUNITY

Modelling naive T-cell homeostasis: consequences of heritable cellular lifespan during ageing

(2009) Mark R Dowling et al.   IMMUNOLOGY AND CELL BIOLOGY

Genome-Wide Study of Pseudomonas aeruginosa Outer Membrane Protein Immunogenicity Using Self-Assembling Protein Microarrays

(2009) W. R. Montor et al.   INFECTION AND IMMUNITY

Towards estimating the true duration of dendritic cell interactions with T cells

(2009) Joost B. Beltman et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Synergy between Individual TNF-Dependent Functions Determines Granuloma Performance for Controlling Mycobacterium tuberculosis Infection

(2009) J. C. J. Ray et al.   JOURNAL OF IMMUNOLOGY

Casein kinase 1α governs antigen-receptor-induced NF-κB activation and human lymphoma cell survival

(2009) Nicolas Bidère et al.   NATURE

Human host factors required for influenza virus replication

(2009) Renate König et al.   NATURE

Absolute abundance for the masses

(2009) Christine Vogel et al.   NATURE BIOTECHNOLOGY

Navigating the network: signaling cross-talk in hematopoietic cells

(2009) Iain D C Fraser et al.   NATURE IMMUNOLOGY

An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome

(2009) Tilmann Bürckstümmer et al.   NATURE IMMUNOLOGY

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

(2009) Paola Picotti et al.   NATURE METHODS

Statistical methods for analysis of high-throughput RNA interference screens

(2009) Amanda Birmingham et al.   NATURE METHODS

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

Supraresolution Imaging in Brain Slices using Stimulated-Emission Depletion Two-Photon Laser Scanning Microscopy

(2009) Jun B. Ding et al.   NEURON

Enhanced Monocyte Response and Decreased Central Memory T Cells in Children with Invasive Staphylococcus aureus Infections

(2009) Monica I. Ardura et al.   PLoS One

A Systems Immunology Approach to the Host-Tumor Interaction: Large-Scale Patterns of Natural Autoantibodies Distinguish Healthy and Tumor-Bearing Mice

(2009) Yifat Merbl et al.   PLoS One

A Novel Method for Detection of Phosphorylation in Single Cells by Surface Enhanced Raman Scattering (SERS) using Composite Organic-Inorganic Nanoparticles (COINs)

(2009) Catherine M. Shachaf et al.   PLoS One

Stage Dependent Aberrant Regulation of Cytokine-STAT Signaling in Murine Systemic Lupus Erythematosus

(2009) Matthew B. Hale et al.   PLoS One

Multiparameter Phospho-Flow Analysis of Lymphocytes in Early Rheumatoid Arthritis: Implications for Diagnosis and Monitoring Drug Therapy

(2009) Carole L. Galligan et al.   PLoS One

Internal coarse-graining of molecular systems

(2009) J. Feret et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional response in the peripheral blood of patients infected with Salmonella enterica serovar Typhi

(2009) Lucinda J. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Complexity of Cell Signaling and the Need for a New Mechanics

(2009) W. S. Hlavacek et al.   Science Signaling

Multiscale modeling for biologists

(2009) Martin Meier-Schellersheim et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen

(2009) Omer Dushek et al.   PLoS Computational Biology

Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies

(2009) Frederic D. Bushman et al.   PLoS Pathogens

Evolutionarily Conserved Herpesviral Protein Interaction Networks

(2009) Even Fossum et al.   PLoS Pathogens

Choreography of Cell Motility and Interaction Dynamics Imaged by Two-Photon Microscopy in Lymphoid Organs

(2008) Michael D. Cahalan et al.   Annual Review of Immunology

Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication

(2008) Renate König et al.   CELL

SILAC Mouse for Quantitative Proteomics Uncovers Kindlin-3 as an Essential Factor for Red Blood Cell Function

(2008) Marcus Krüger et al.   CELL

Genome-Scale RNAi Screen for Host Factors Required for HIV Replication

(2008) Honglin Zhou et al.   Cell Host & Microbe

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Mass spectrometry for proteomics

(2008) Xuemei Han et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Genomic RNAi screening in Drosophila S2 cells: what have we learned about host–pathogen interactions?

(2008) Sara Cherry   CURRENT OPINION IN MICROBIOLOGY

A flow cytometer for the measurement of Raman spectra

(2008) Dakota A. Watson et al.   CYTOMETRY PART A

Virtual Cell modelling and simulation software environment

(2008) I.I. Moraru et al.   IET Systems Biology

The Balance between T Cell Receptor Signaling and Degradation at the Center of the Immunological Synapse Is Determined by Antigen Quality

(2008) Sašo Čemerski et al.   IMMUNITY

Membrane heterogeneities in the formation of B cell receptor–Lyn kinase microclusters and the immune synapse

(2008) Hae Won Sohn et al.   JOURNAL OF CELL BIOLOGY

Deriving a germinal center lymphocyte migration model from two-photon data

(2008) Marc Thilo Figge et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Virion-Wide Protein Interactions of Kaposi's Sarcoma-Associated Herpesvirus

(2008) R. Rozen et al.   JOURNAL OF VIROLOGY

How Antigen Quantity and Quality Determine T-Cell Decisions in Lymphoid Tissue

(2008) H. Zheng et al.   MOLECULAR AND CELLULAR BIOLOGY

Epidermal Growth Factor–induced Enhancement of Glioblastoma Cell Migration in 3D Arises from an Intrinsic Increase in Speed But an Extrinsic Matrix- and Proteolysis-dependent Increase in Persistence

(2008) Hyung-Do Kim et al.   MOLECULAR BIOLOGY OF THE CELL

Quantitative Analysis of Pathways Controlling Extrinsic Apoptosis in Single Cells

(2008) John G. Albeck et al.   MOLECULAR CELL

Hepatitis C virus infection protein network

(2008) B de Chassey et al.   Molecular Systems Biology

IRF4 addiction in multiple myeloma

(2008) Arthur L. Shaffer et al.   NATURE

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

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

(2008) Manoj N. Krishnan et al.   NATURE

Direct multiplexed measurement of gene expression with color-coded probe pairs

(2008) Gary K Geiss et al.   NATURE BIOTECHNOLOGY

MicroRNAs: new regulators of immune cell development and function

(2008) David Baltimore et al.   NATURE IMMUNOLOGY

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY

T cell sensing of antigen dose governs interactive behavior with dendritic cells and sets a threshold for T cell activation

(2008) Sarah E Henrickson et al.   NATURE IMMUNOLOGY

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

(2008) Ina Poser et al.   NATURE METHODS

An in vitro microfluidic approach to generating protein-interaction networks

(2008) Doron Gerber et al.   NATURE METHODS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

Literature-curated protein interaction datasets

(2008) Michael E Cusick et al.   NATURE METHODS

The art and design of genetic screens: RNA interference

(2008) Michael Boutros et al.   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Effects of Intracellular Calcium and Actin Cytoskeleton on TCR Mobility Measured by Fluorescence Recovery

(2008) Omer Dushek et al.   PLoS One

The Landscape of Human Proteins Interacting with Viruses and Other Pathogens

(2008) Matthew D. Dyer et al.   PLoS Pathogens

A gene regulatory network armature for T lymphocyte specification

(2008) C. Georgescu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Compensatory IKK  activation of classical NF- B signaling during IKK  inhibition identified by an RNA interference sensitization screen

(2008) L. T. Lam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating the size of the human interactome

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

An in Vivo Map of the Yeast Protein Interactome

(2008) K. Tarassov et al.   SCIENCE

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

(2008) Abraham L. Brass et al.   SCIENCE

In Vivo Imaging of T Cell Priming

(2008) S. E. Henrickson et al.   Science Signaling

New Regulators of Wnt/ -Catenin Signaling Revealed by Integrative Molecular Screening

(2008) M. B. Major et al.   Science Signaling

Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces

(2008) Rex A. Kerr et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

A permissive geometry model for TCR–CD3 activation

(2008) Susana Minguet et al.   TRENDS IN BIOCHEMICAL SCIENCES

Applications of microarrays in pathogen detection and biodefence

(2008) Mahesh Uttamchandani et al.   TRENDS IN BIOTECHNOLOGY

Identification of structural protein–protein interactions of herpes simplex virus type 1

(2008) Jin H. Lee et al.   VIROLOGY

Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Death

(2008) John G Albeck et al.   PLOS BIOLOGY

The receptor deformation model of TCR triggering

(2007) Zhengyu Ma et al.   FASEB JOURNAL