Blog Archive

Check out all blog posts in my blog archive. Click on a headline to read the teaser.

3D Chromatin Architecture Remodeling during Human Cardiomyocyte Differentiation Reveals A Novel Role of HERV-H In Demarcating Chromatin Domains
Simultaneous profiling of DNA methylation and chromatin architecture in mixed populations and in single cells
Mooncake Festival › 2018 Mooncake Festival
MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Data/download › ENCODE3 mouse histone and ATAC-seq paper supplementary data files
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers
Identification of H3K4me1-associated proteins at mammalian enhancers
The Three-Dimensional Organization of Mammalian Genomes
Systematic mapping of chromatin state landscapes during mouse development
A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells
Farewell › Juntao's farewell lunch
Congratulations › Sebastian won the first place in poster presentation in Ludwig San Diego Retreat
Hooray! Read More ›

Welcome › Dr. Ramya Raviram joined our lab as a new postdoc.
Welcome! Read More ›

Congratulations › Yarui's CREST-seq paper accepted at Nature Methods
CRISPR screening Read More ›

A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis.
Human centromeric CENP-A chromatin is a homotypic octameric nucleosome at all cell cycle points.
Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity.
Improved regulatory element prediction based on tissue-specific local epigenomic signatures.
Neoadjuvant Therapy in Microsatellite Stable Colorectal Carcinoma Induces Concomitant Loss of MSH6 and Ki67 Expression.
Diagnosing colorectal medullary carcinoma: interobserver variability and clinicopathological implications.
Genome-wide mapping and analysis of chromosome architecture.
Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq.
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.
Programmed Death-Ligand 1 Expression Is Common in Gastric Cancer Associated With Epstein-Barr Virus or Microsatellite Instability.
Genome-wide compendium and functional assessment of in vivo heart enhancers.
Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition.
Chromatin Domains: The Unit of Chromosome Organization.
A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening.
Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation.
Identification of global regulators of T-helper cell lineage specification.
Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq.
EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling.
Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions.
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.
Human body epigenome maps reveal noncanonical DNA methylation variation.
MPE-seq a new method for the genome-wide analysis of chromatin structure.
An alternative pluripotent state confers interspecies chimaeric competency.
A CRISPR Connection between Chromatin Topology and Genetic Disorders.
Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates.
Integrative analysis of haplotype-resolved epigenomes across human tissues.
Integrative analysis of 111 reference human epigenomes.
Chromatin architecture reorganization during stem cell differentiation.
Transcriptional Enhancers: Bridging the Genome and Phenome.
DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.
A comparative encyclopedia of DNA elements in the mouse genome.
Topologically associating domains are stable units of replication-timing regulation.
5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation.
The highly-cited Electrocardiogram-related articles in science citation index expanded: characteristics and hotspots.
[Grain filling dynamics and germination characteristics of Bupleurum chinense seeds].
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.
Distinct and predictive histone lysine acetylation patterns at promoters enhancers and gene bodies.
The 3D genome in transcriptional regulation and pluripotency.
Clinical observation on removal of small foreign bodies touching the optic nerve in the deep orbital region: a case series.
Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis.
Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1.
[Clinical observation on removal of small foreign bodies touching the optic nerve in the deep orbital region].
Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark.
Defining functional DNA elements in the human genome.
Genetics: Closing the distance on obesity culprits.
Neuromuscular and vascular hamartoma: is it a true hamartoma?
Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells.
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells.
N6-methyladenosine-dependent regulation of messenger RNA stability.
Inhibition of retinopathy of prematurity in rat by intravitreal injection of sorafenib.
CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells.
STAR: an integrated solution to management and visualization of sequencing data.
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.
A high-resolution map of the three-dimensional chromatin interactome in human cells.
MACC1 is related to colorectal cancer initiation and early-stage invasive growth.
Fine tuning of craniofacial morphology by distant-acting enhancers.
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues.
Mapping human epigenomes.
Developmental biology. Enhancing pluripotency and lineage specification.
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization.
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis.
Genome organization and long-range regulation of gene expression by enhancers.
Epigenomic analysis of multilineage differentiation of human embryonic stem cells.
Histone acetyltransferase cofactor Trrap maintains self-renewal and restricts differentiation of embryonic stem cells.
Diagnostic value of HMGAs p53 and beta-catenin in discriminating adenocarcinoma from adenoma or reactive atypia in ampulla and common bile duct biopsies.
Comparative annotation of functional regions in the human genome using epigenomic data.
Comparative study of modified and conventional secondary hydroxyapatite orbital implantations.
Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing.
RFECS: a random-forest based algorithm for enhancer identification from chromatin state.
Posterior chamber phakic intraocular lens implantation for high myopia.
Bayesian inference of spatial organizations of chromosomes.
Effects of aminoguanidine on retinal apoptosis in mice with oxygen-induced retinopathy.
Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine.
HiCNorm: removing biases in Hi-C data via Poisson regression.
Progressive degeneration of human neural stem cells caused by pathogenic LRRK2.
The absence of PspA or presence of antibody to PspA facilitates the complement-dependent phagocytosis of pneumococci in vitro.
Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells.
Combined gene expression and DNA occupancy profiling identifies potential therapeutic targets of t(8;21) AML.
An encyclopedia of mouse DNA elements (Mouse ENCODE).
A map of the cis-regulatory sequences in the mouse genome.
CBX3 regulates efficient RNA processing genome-wide.
Magnetic resonance tumor targeting imaging using gadolinium labeled human telomerase reverse transcriptase antisense probes.
[Near-infrared spectroscopy analysis of adenosine and water in fermentation cordyceps powder and wavelength assignment].
Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.
Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome.
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.
Transcriptional regulation by Pol II(G) involving mediator and competitive interactions of Gdown1 and TFIIF with Pol II.
Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.
Enhancers: multi-dimensional signal integrators.
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency.
Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual.
SERPINB13 is a novel RUNX1 target gene.
Mapping higher order structure of chromatin domains.
Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells.
Insulin-like growth factor binding protein-3 interacts with the thyroid hormone receptor alpha1 and modulates transcription of thyroid hormone responsive gene.
PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers.
A cis-regulatory map of the Drosophila genome.
Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A.
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.
9p21 DNA variants associated with coronary artery disease impair interferon-gamma signalling response.
Effects of minocycline on expression of bcl-2 bax in early retinal neuropathy of diabetes in rats.
An assessment of histone-modification antibody quality.
Identification of functional elements and regulatory circuits by Drosophila modENCODE.
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
The NIH Roadmap Epigenomics Mapping Consortium.
p16(INK4a) -mediated suppression of telomerase in normal and malignant human breast cells.
ChIP-Seq identification of weakly conserved heart enhancers.
Next-generation genomics: an integrative approach.
Transcription: Enhancers make non-coding RNA.
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.
Genome-wide prediction of transcription factor binding sites using an integrated model.
Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing.
Finding distal regulatory elements in the human genome.
Human DNA methylomes at base resolution show widespread epigenomic differences.
Discovery and annotation of functional chromatin signatures in the human genome.
Predictive chromatin signatures in the mammalian genome.
Histone modifications at human enhancers reflect global cell-type-specific gene expression.
ChIP-seq accurately predicts tissue-specific activity of enhancers.
An integrated approach to identifying cis-regulatory modules in the human genome.
Prediction of regulatory elements in mammalian genomes using chromatin signatures.
HPLC method for the determination of bezafibrate in human plasma and application to a pharmacokinetic study of bezafibrate dispersible tablet.
ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.
Role of the histone H3 lysine 4 methyltransferase SET7/9 in the regulation of
Genome-wide mapping of allele-specific protein-DNA interactions in human cells.
Vaccine-induced human antibodies to PspA augment complement C3 deposition on Streptococcus pneumoniae.
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
Unraveling epigenetic regulation in embryonic stem cells.
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs.
Identification of the transcriptional targets of FOXP2 a gene linked to speech and language in developing human brain.
ChIP-chip: data model and analysis.
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.
ChIP-chip for genome-wide analysis of protein binding in mammalian cells.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.
Liquid chromatography-mass spectrometry method for the determination of venlafaxine in human plasma and application to a pharmacokinetic study.
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
A new single-well potential stochastic resonance algorithm to detect the weak signal.
Mnt-deficient mammary glands exhibit impaired involution and tumors with characteristics of myc overexpression.
The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding.
Genome-wide location analysis: insights on transcriptional regulation.
Positive inter-regulation between beta-catenin/T cell factor-4 signaling and endothelin-1 signaling potentiates proliferation and survival of prostate cancer cells.
Genome-wide analysis of protein-DNA interactions.
An all-round view of eukaryotic transcription.
A high-resolution map of active promoters in the human genome.
Direct isolation and identification of promoters in the human genome.
beta-Catenin activates the growth factor endothelin-1 in colon cancer cells.
The virulence function of Streptococcus pneumoniae surface protein A involves inhibition of complement activation and impairment of complement receptor-mediated protection.
[Effects of aspirin on lowering plasma level of lysophosphatidic acid in cerebral ischemic patients].
[The change of renin endothelin and prostaglandin in blood during long time left ventricular assist].
Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors.
Effects of PspA and antibodies to PspA on activation and deposition of complement on the pneumococcal surface.
[Continuous veno-venous hemofiltration in treatment of acute severe hyponatremia: a report of 6 cases].
Relative roles of genetic background and variation in PspA in the ability of antibodies to PspA to protect against capsular type 3 and 4 strains of Streptococcus pneumoniae.
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells.
[In vivo and in vitro evaluation of inflow cannula of left ventricular assist].
Both family 1 and family 2 PspA proteins can inhibit complement deposition and confer virulence to a capsular serotype 3 strain of Streptococcus pneumoniae.
Transcriptional regulatory networks in Saccharomyces cerevisiae.
Preliminary in vivo study of an intra-aortic impeller pump driven by an extracorporeal whirling magnet.
E2F integrates cell cycle progression with DNA repair replication and G(2)/M checkpoints.