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Article
Open AccessTranscription factor-mediated direct cellular reprogramming yields cell-type specific DNA methylation signature
Direct reprogramming, inducing the conversion of one type of somatic cell into another by the forced expression of defined transcription factors, is a technology with anticipated medical applications. However,...
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Article
Open AccessDNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle
Each tissue has a dominant set of functional proteins required to mediate tissue-specific functions. Epigenetic modifications, transcription, and translational efficiency control tissue-dominant protein produc...
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Article
Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin
The accurate and early diagnosis and classification of cancer origin from either tissue or liquid biopsy is crucial for selecting the appropriate treatment and reducing cancer-related mortality. Here, we estab...
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Article
Reconstitution of the oocyte transcriptional network with transcription factors
During female germline development, oocytes become a highly specialized cell type and form a maternal cytoplasmic store of crucial factors. Oocyte growth is triggered at the transition from primordial to prima...
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Article
Publisher Correction: Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
Open AccessBase-resolution methylomes of gliomas bearing histone H3.3 mutations reveal a G34 mutant-specific signature shared with bone tumors
Two recurrent mutations, K27M and G34R/V, in H3F3A, encoding non-canonical histone H3.3, are reported in pediatric and young adult gliomas, whereas G34W mutation is prevalent in bone tumors. In contrast to K27M m...
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Article
Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity
A contribution of epigenetic modifications to B cell tolerance has been proposed but not directly tested. Here we report that deficiency of ten–eleven translocation (Tet) DNA demethylase family members Tet2 an...
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Article
Open AccessMap** of histone-binding sites in histone replacement-completed spermatozoa
The majority of histones are replaced by protamines during spermatogenesis, but small amounts are retained in mammalian spermatozoa. Since nucleosomes in spermatozoa influence epigenetic inheritance, it is imp...
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Article
Open AccessThe AP-1 transcription factor JunB is required for Th17 cell differentiation
Interleukin (IL)-17-producing T helper (Th17) cells are crucial for host defense against extracellular microbes and pathogenesis of autoimmune diseases. Here we show that the AP-1 transcription factor JunB is ...
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Article
Haptoglobin promoter polymorphism rs5472 as a prognostic biomarker for peptide vaccine efficacy in castration-resistant prostate cancer patients
Personalized peptide vaccination (PPV) is an attractive approach to cancer immunotherapy with strong immune-boosting effects conferring significant clinical benefit. However, as with most therapeutic agents, t...
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Article
Open AccessChangepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape
Base-resolution methylome data generated by whole-genome bisulfite sequencing (WGBS) is often used to segment the genome into domains with distinct methylation levels. However, most segmentation methods includ...
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Article
Open AccessAssociation of haptoglobin genetic polymorphism with overall survival in advanced castration-resistant prostate cancer patients with personalized peptide vaccination
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Article
Open AccessVasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis
Apoptosis is a critical process in endothelial cell (EC) biology and pathology, which has been extensively studied at protein level. Numerous gene expression studies of EC apoptosis have also been performed, h...
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Article
Open AccessComputational gene network analysis reveals TNF-induced angiogenesis
TNF (Tumor Necrosis Factor-α) induces HUVEC (Human Umbilical Vein Endothelial Cells) to proliferate and form new blood vessels. This TNF-induced angiogenesis plays a key role in cancer and rheumatic disease. H...
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Computational Drug Target Pathway Discovery: A Bayesian Network Approach
Genome-wide transcriptome data together with statistical analysis enable us to reverse-engineer gene networks that can be a kind of views useful for understanding dynamic behaviour of biological elements in ce...
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Article
Analysis of PPARα-dependent and PPARα-independent transcript regulation following fenofibrate treatment of human endothelial cells
Fenofibrate is a synthetic ligand for the nuclear receptor peroxisome proliferator-activated receptor (PPAR) alpha and has been widely used in the treatment of metabolic disorders, especially hyperlipemia, due...
