Metabolic modeling of single Th17 cells reveals regulators of autoimmunity

Immunometabolism: From basic mechanisms to translation

(2020) Liza Makowski et al.   IMMUNOLOGICAL REVIEWS

Determinants of Tissue-Specific Metabolic Adaptation of T Cells

(2020) Siva Karthik Varanasi et al.   Cell Metabolism

Modification of Proteins by Metabolites in Immunity

(2020) C. Diskin et al.   IMMUNITY

Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis

(2020) Saige L. Pompura et al.   JOURNAL OF CLINICAL INVESTIGATION

Immunometabolism in the Tumor Microenvironment

(2020) Dominic G. Roy et al.   Annual Review of Cancer Biology-Series

Continuum of Gene-Expression Profiles Provides Spatial Division of Labor within a Differentiated Cell Type

(2019) Miri Adler et al.   Cell Systems

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

(2019) Chiara Damiani et al.   PLoS Computational Biology

Biphasic Dynamics of Macrophage Immunometabolism during Mycobacterium tuberculosis Infection

(2019) Lanbo Shi et al.   mBio

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation

(2019) Ricardo J. Miragaia et al.   IMMUNITY

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq

(2019) Michael B. Cole et al.   Cell Systems

Revealing dynamics of gene expression variability in cell state space

(2019) Dominic Grün   NATURE METHODS

Functional interpretation of single cell similarity maps

(2019) David DeTomaso et al.   Nature Communications

Lactate Buildup at the Site of Chronic Inflammation Promotes Disease by Inducing CD4+ T Cell Metabolic Rewiring

(2019) Valentina Pucino et al.   Cell Metabolism

Unraveling the Complex Interplay Between T Cell Metabolism and Function

(2018) Ramon I. Klein Geltink et al.   Annual Review of Immunology

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Etomoxir Inhibits Macrophage Polarization by Disrupting CoA Homeostasis

(2018) Ajit S. Divakaruni et al.   Cell Metabolism

Etomoxir Actions on Regulatory and Memory T Cells Are Independent of Cpt1a-Mediated Fatty Acid Oxidation

(2018) Brenda Raud et al.   Cell Metabolism

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

SAVER: gene expression recovery for single-cell RNA sequencing

(2018) Mo Huang et al.   NATURE METHODS

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

(2018) Eugen Bauer et al.   mSystems

Distinct Regulation of Th17 and Th1 Cell Differentiation by Glutaminase-Dependent Metabolism

(2018) Marc O. Johnson et al.   CELL

Metabolism as a guiding force for immunity

(2018) Jonathan Jung et al.   NATURE CELL BIOLOGY

Foundations of Immunometabolism and Implications for Metabolic Health and Disease

(2017) Gökhan S. Hotamisligil   IMMUNITY

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Succinate Dehydrogenase Supports Metabolic Repurposing of Mitochondria to Drive Inflammatory Macrophages

(2016) Evanna L. Mills et al.   CELL

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

(2016) Meromit Singer et al.   CELL

Interferon-Induced Spermidine-Spermine Acetyltransferase and Polyamine Depletion Restrict Zika and Chikungunya Viruses

(2016) Bryan C. Mounce et al.   Cell Host & Microbe

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity

(2015) Chao Wang et al.   CELL

Network Integration of Parallel Metabolic and Transcriptional Data Reveals Metabolic Modules that Regulate Macrophage Polarization

(2015) Abhishek K. Jha et al.   IMMUNITY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

ORegAnno 3.0: a community-driven resource for curated regulatory annotation

(2015) Robert Lesurf et al.   NUCLEIC ACIDS RESEARCH

The histone H3 lysine-27 demethylase Jmjd3 plays a critical role in specific regulation of Th17 cell differentiation

(2015) Zhi Liu et al.   Journal of Molecular Cell Biology

The Treg/Th17 Axis: A Dynamic Balance Regulated by the Gut Microbiome

(2015) Sara Omenetti et al.   Frontiers in Immunology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Small-Molecule RORγt Antagonists Inhibit T Helper 17 Cell Transcriptional Network by Divergent Mechanisms

(2014) Sheng Xiao et al.   IMMUNITY

Unexpected Targets and Triggers of Autoimmunity

(2014) Youjin Lee et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Metabolic programming and PDHK1 control CD4+ T cell subsets and inflammation

(2014) Valerie A. Gerriets et al.   JOURNAL OF CLINICAL INVESTIGATION

Oral-resident natural Th17 cells and γδ T cells control opportunisticCandida albicansinfections

(2014) Heather R. Conti et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Focused specificity of intestinal TH17 cells towards commensal bacterial antigens

(2014) Yi Yang et al.   NATURE

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

De novo fatty acid synthesis controls the fate between regulatory T and T helper 17 cells

(2014) Luciana Berod et al.   NATURE MEDICINE

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Critical role of histone demethylase Jmjd3 in the regulation of CD4+ T-cell differentiation

(2014) Qingtian Li et al.   Nature Communications

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Metabolic control of the Treg/Th17 axis

(2013) Joseph Barbi et al.   IMMUNOLOGICAL REVIEWS

Dynamic regulatory network controlling TH17 cell differentiation

(2013) Nir Yosef et al.   NATURE

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Succinate: a metabolic signal in inflammation

(2013) Evanna Mills et al.   TRENDS IN CELL BIOLOGY

Increased Polyamines Alter Chromatin and Stabilize Autoantigens in Autoimmune Diseases

(2013) Wesley H. Brooks   Frontiers in Immunology

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

Pathogen-induced human TH17 cells produce IFN-γ or IL-10 and are regulated by IL-1β

(2012) Christina E. Zielinski et al.   NATURE

Induction and molecular signature of pathogenic TH17 cells

(2012) Youjin Lee et al.   NATURE IMMUNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Increased recycling of polyamines is associated with global DNA hypomethylation in rheumatoid arthritis synovial fibroblasts

(2011) Emmanuel Karouzakis et al.   ARTHRITIS AND RHEUMATISM

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

IL-17 signaling in host defense against Candida albicans

(2011) Sarah L. Gaffen et al.   IMMUNOLOGIC RESEARCH

HIF1α–dependent glycolytic pathway orchestrates a metabolic checkpoint for the differentiation of TH17 and Tregcells

(2011) Lewis Z. Shi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Cutting Edge: Distinct Glycolytic and Lipid Oxidative Metabolic Programs Are Essential for Effector and Regulatory CD4+ T Cell Subsets

(2011) R. D. Michalek et al.   JOURNAL OF IMMUNOLOGY

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Generation of pathogenic TH17 cells in the absence of TGF-β signalling

(2010) Kamran Ghoreschi et al.   NATURE

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Th17 cytokines in mucosal immunity and inflammation

(2010) Lokesh Guglani et al.   Current Opinion in HIV and AIDS

IL-17 and Th17 Cells

(2009) Thomas Korn et al.   Annual Review of Immunology

Critical Regulation of Early Th17 Cell Differentiation by Interleukin-1 Signaling

(2009) Yeonseok Chung et al.   IMMUNITY

Th1, Th17, and Th9 Effector Cells Induce Experimental Autoimmune Encephalomyelitis with Different Pathological Phenotypes

(2009) A. Jager et al.   JOURNAL OF IMMUNOLOGY

Cutting Edge: IL-23 Receptor GFP Reporter Mice Reveal Distinct Populations of IL-17-Producing Cells

(2009) Amit Awasthi et al.   JOURNAL OF IMMUNOLOGY

The interleukin 23 receptor is essential for the terminal differentiation of interleukin 17–producing effector T helper cells in vivo

(2009) Mandy J McGeachy et al.   NATURE IMMUNOLOGY

The Treg/Th17 Cell Balance: A New Paradigm for Autoimmunity

(2009) Eli M Eisenstein et al.   PEDIATRIC RESEARCH

Halofuginone Inhibits TH17 Cell Differentiation by Activating the Amino Acid Starvation Response

(2009) M. S. Sundrud et al.   SCIENCE

Spermidine/spermine-N1-acetyltransferase: a key metabolic regulator

(2008) Anthony E. Pegg   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

Th17 Cell Differentiation: The Long and Winding Road

(2008) Mandy J. McGeachy et al.   IMMUNITY

The Biological Functions of T Helper 17 Cell Effector Cytokines in Inflammation

(2008) Wenjun Ouyang et al.   IMMUNITY

Induction and effector functions of TH17 cells

(2008) Estelle Bettelli et al.   NATURE

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY