Reprogramming of macrophages employing gene regulatory and metabolic network models

Deoxyribonucleotide Triphosphate Metabolism in Cancer and Metabolic Disease

(2018) Raquel Buj et al.   Frontiers in Endocrinology

Involvement of JNK signaling in IL4-induced M2 macrophage polarization

(2017) Jin Hao et al.   EXPERIMENTAL CELL RESEARCH

Anti-inflammatory effect of IL-10 mediated by metabolic reprogramming of macrophages

(2017) W. K. Eddie Ip et al.   SCIENCE

Reprogramming of Tumor-Associated Macrophages with Anticancer Therapies: Radiotherapy versus Chemo- and Immunotherapies

(2017) Géraldine Genard et al.   Frontiers in Immunology

Bacterial Sepsis Increases Survival in Metastatic Melanoma: Chlamydophila Pneumoniae Induces Macrophage Polarization and Tumor Regression

(2016) Krisztina Buzás et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Broad defects in the energy metabolism of leukocytes underlie immunoparalysis in sepsis

(2016) Shih-Chin Cheng et al.   NATURE IMMUNOLOGY

Mixed Integer Linear Programming based machine learning approach identifiesregulatorsof telomerase in yeast

(2016) Alexandra M. Poos et al.   NUCLEIC ACIDS RESEARCH

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Causes of upregulation of glycolysis in lymphocytes upon stimulation. A comparison with other cell types

(2015) Heiko Stark et al.   BIOCHIMIE

Sequential delivery of immunomodulatory cytokines to facilitate the M1-to-M2 transition of macrophages and enhance vascularization of bone scaffolds

(2015) Kara L. Spiller et al.   BIOMATERIALS

Pyruvate Kinase M2 Regulates Hif-1α Activity and IL-1β Induction and Is a Critical Determinant of the Warburg Effect in LPS-Activated Macrophages

(2015) Eva M. Palsson-McDermott et al.   Cell Metabolism

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

(2015) Abhishek K. Jha et al.   IMMUNITY

Immunometabolism governs dendritic cell and macrophage function

(2015) Luke A.J. O’Neill et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Understanding the Mysterious M2 Macrophage through Activation Markers and Effector Mechanisms

(2015) Tamás Rőszer   MEDIATORS OF INFLAMMATION

Immunosuppressive mechanisms in glioblastoma: Fig. 1.

(2015) Edjah K. Nduom et al.   NEURO-ONCOLOGY

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Infection with Mycobacterium tuberculosis induces the Warburg effect in mouse lungs

(2015) Lanbo Shi et al.   Scientific Reports

Estimating the activity of transcription factors by the effect on their target genes

(2014) Theresa Schacht et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Direct role of nucleotide metabolism in C-MYC-dependent proliferation of melanoma cells

(2014) Sudha Mannava et al.   CELL CYCLE

Regulation of Inflammatory Phenotype in Macrophages by a Diabetes-Induced Long Noncoding RNA

(2014) M. A. Reddy et al.   DIABETES

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Macrophage polarization and function with emphasis on the evolving roles of coordinated regulation of cellular signaling pathways

(2013) Dexi Zhou et al.   CELLULAR SIGNALLING

Anthracyclines Induce DNA Damage Response-Mediated Protection against Severe Sepsis

(2013) Nuno Figueiredo et al.   IMMUNITY

Immunosuppression in sepsis: a novel understanding of the disorder and a new therapeutic approach

(2013) Richard S Hotchkiss et al.   LANCET INFECTIOUS DISEASES

Metabolism of inflammation limited by AMPK and pseudo-starvation

(2013) Luke A. J. O'Neill et al.   NATURE

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Beyond Stem Cells: Self-Renewal of Differentiated Macrophages

(2013) M. H. Sieweke et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

(2012) Aarash Bordbar et al.   Molecular Systems Biology

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A Minimal Connected Network of Transcription Factors Regulated in Human Tumors and Its Application to the Quest for Universal Cancer Biomarkers

(2012) Ahmed Essaghir et al.   PLoS One

Role of c-MYC in alternative activation of human macrophages and tumor-associated macrophage biology

(2011) O. M. Pello et al.   BLOOD

Local Macrophage Proliferation, Rather than Recruitment from the Blood, Is a Signature of TH2 Inflammation

(2011) S. J. Jenkins et al.   SCIENCE

Novel Regulators of the Systemic Response to Lipopolysaccharide

(2010) Ivana V. Yang et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Mechanisms of Action and Clinical Application of Macrolides as Immunomodulatory Medications

(2010) S. Kanoh et al.   CLINICAL MICROBIOLOGY REVIEWS

Transcription Factor E2F1 Suppresses Dendritic Cell Maturation

(2010) F. Fang et al.   JOURNAL OF IMMUNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

(2010) Ahmed Essaghir et al.   NUCLEIC ACIDS RESEARCH

Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica

(2009) L. Shi et al.   INFECTION AND IMMUNITY

Escherichia coli and TNF-α Modulate Macrophage Phagocytosis of Candida glabrata

(2008) Donavon J. Hess et al.   JOURNAL OF SURGICAL RESEARCH

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Global Regulation of Nucleotide Biosynthetic Genes by c-Myc

(2008) Yen-Chun Liu et al.   PLoS One

Context-Specific Metabolic Networks Are Consistent with Experiments

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