Blog Archive

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

Kubo_molecularcell_2024
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Congratulations! › Naoki Kubo's KMT2C/D and KMT2B (MLL3/4 and MLL2) paper is published in Molecular Cell!
H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation Read More ›

Kubo_molecularcell_2024
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Congratulations! › Naoki Kubo's KMT2C/D and KMT2B (MLL3/4 and MLL2) paper is published in Molecular Cell!
H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation Read More ›

Zhang_nmethods_2024
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Congratulations! › Kai Zhang's paper on a fast, scalable and versatile tool for analysis of single-cell omics data is published in Nature Methods!
A fast, scalable and versatile tool for analysis of single-cell omics data Read More ›

Zu_nature_2023
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Congratulations! › Songpeng Zu, Yang Eric Li and Kangli Wang's single-cell anlaysis of chromatin accessibility in the adult mouse brain paper is published in Nature!
Single-cell analysis of chromatin accessibility in the adult mouse brain Read More ›

Zemke_nature_2023
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Congratulations! › Nathan Zemke's and Ethan Armand's paper on comparative analysis of gene regulatory programs in mammalian primary motor cortex is published in Nature!
Conserved and divergent gene regulatory programs of the mammalian neocortex Read More ›

Yang_science_2023 Paper
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Congratulations! › Yang's human brain snATAC-seq paper is published in Science!
Human Brain Cell Atlas Offers Unprecedented Look at Neuropsychiatric Disorders Read More ›

Yang_nsmb_2023
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Congratulations! › Yang Xie & Chenxu Zhu's Droplet Paired-Tag paper is published in NSMB!
A fast, convenient and robust method in joint profiling of single-cell transcriptome and histone modification landscape Read More ›

A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH
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Congratulations! › Blair's spatial genome alignment (SGA) paper is published in Nature Biotechnology!
In spatial genomics, instead of ACGT genes are spatial positions (x, y, z). An ortholog of sequence aligners, SGA aligns these (x, y, z)'s to a reference polymer model of DNA, to see if they 'fit'. Read More ›

Single-cell Epigenome Analysis Reveals Age-associated Decay of Heterochromatin Domains in Excitatory Neurons in the Mouse Brain
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Congratulations › Yanxiao and Luisa's mouse single-cell aging paper published on Cell Research today!
Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain Read More ›

A single-cell atlas of chromatin accessibility in the human genome
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Congratulations › Kai and Jake's human single-cell chromatin accessibility paper published on Cell today!
A single-cell atlas of chromatin accessibility in the human genome Read More ›

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum
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Congratulations › Yang & Sebastian's single cell mouse brain paper published on Nature today!
An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum. Read More ›

SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data.
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Congratulations › Miao's SnapHiC paper published on Nature Methods today!
SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data Read More ›

CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains
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Congratulations › Hui's CTCF paper published on Nature Genetics today!
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains Read More ›

Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association
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Congratulations › Jake's single-cell heart paper published on Science Advances today!
Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association Read More ›

MLL3/MLL4 Histone Methyltranferase Activity Dependent Chromatin Organization at Enhancers during Embryonic Stem Cell Differentiation
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Comprehensive analysis of single cell ATAC-seq data with SnapATAC
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Congratulations › Rongxin's SnapATAC paper published on Nature Communications today!
Comprehensive analysis of single cell ATAC-seq data with SnapATAC Read More ›

Joint profiling of histone modifications and transcriptome in single cells from mouse brain
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Congratulations › Chenxu's paired-tag paper published on Nature Methods today!
Joint profiling of histone modifications and transcriptome in single cells from mouse brain Read More ›

Discovery and Functional Characterization of Pro-growth Enhancers in Human Cancer Cells
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Systematic analysis of binding of transcription factors to noncoding variants
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Congratulations › Jian and Yunjiang's SNP-SELEX paper published on Nature.
Systematic analysis of binding of transcription factors to noncoding variants Read More ›

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation
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Congratulations › Naoki's paper published on Nature Structural and Molecular Biology.
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation Read More ›

An atlas of dynamic chromatin landscapes in mouse fetal development
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Common DNA sequence variation influences 3-dimensional conformation of the human genome.
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Congratulations › David's and Yunjiang's LCL paper published on Genome Biology
Common DNA sequence variation influences 3-dimensional conformation of the human genome. Read More ›

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
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Congratulations › Chenxu's Paired-seq paper published on Nature Structural & Molecular Biology
Simultaneous profiling of transcriptome and chromatin accessility in single cells. Read More ›

A compendium of promoter-centered long-range chromatin interactions in the human genome
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Congratulations › Inkyung, Anthony and Yarui's Promoter capture Hi-C paper published on Nature Genetics
Promoter capture Hi-C of 27 human cell/tissue types. Read More ›

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells
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Congratulations › Yanxiao & Sebastian's HERV-H TAD paper published on Nature Genetics
HERV-H retrotranspons form TAD boundaries in primate pluripotent stem cells Read More ›

Joint profiling of DNA methylation and chromatin architecture in single cells
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Congratulations › Jason's single-cell Methyl-HiC paper published on Nature Methods
Hi-C & methylation in one assay and in single cells Read More ›

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
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Data/download › 3D QTL paper supplementary data files
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Mooncake Festival › 2018 Mooncake Festival
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Data/download › ENCODE3 mouse histone and ATAC-seq paper supplementary data files
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Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
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Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers
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Identification of H3K4me1-associated proteins at mammalian enhancers
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The Three-Dimensional Organization of Mammalian Genomes
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A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells
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Farewell › Juntao's farewell lunch
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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.
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Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq.
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A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.
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Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition.
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Chromatin Domains: The Unit of Chromosome Organization.
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A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening.
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Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq.
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EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling.
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Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions.
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MPE-seq a new method for the genome-wide analysis of chromatin structure.
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A CRISPR Connection between Chromatin Topology and Genetic Disorders.
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Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates.
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Integrative analysis of haplotype-resolved epigenomes across human tissues.
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Integrative analysis of 111 reference human epigenomes.
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Chromatin architecture reorganization during stem cell differentiation.
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Transcriptional Enhancers: Bridging the Genome and Phenome.
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A comparative encyclopedia of DNA elements in the mouse genome.
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5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation.
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Distinct and predictive histone lysine acetylation patterns at promoters enhancers and gene bodies.
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The 3D genome in transcriptional regulation and pluripotency.
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Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1.
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Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells.
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CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells.
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Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.
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A high-resolution map of the three-dimensional chromatin interactome in human cells.
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Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues.
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Mapping human epigenomes.
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Developmental biology. Enhancing pluripotency and lineage specification.
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Genome organization and long-range regulation of gene expression by enhancers.
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Epigenomic analysis of multilineage differentiation of human embryonic stem cells.
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RFECS: a random-forest based algorithm for enhancer identification from chromatin state.
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A map of the cis-regulatory sequences in the mouse genome.
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CBX3 regulates efficient RNA processing genome-wide.
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Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.
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Topological domains in mammalian genomes identified by analysis of chromatin interactions.
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Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome.
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Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.
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Enhancers: multi-dimensional signal integrators.
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Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency.
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Mapping higher order structure of chromatin domains.
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PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers.
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Next-generation genomics: an integrative approach.
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Transcription: Enhancers make non-coding RNA.
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Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.
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Finding distal regulatory elements in the human genome.
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Discovery and annotation of functional chromatin signatures in the human genome.
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Predictive chromatin signatures in the mammalian genome.
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Histone modifications at human enhancers reflect global cell-type-specific gene expression.
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An integrated approach to identifying cis-regulatory modules in the human genome.
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ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.
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Genome-wide mapping of allele-specific protein-DNA interactions in human cells.
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Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs.
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
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Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.
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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
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The gateway to transcription: identifying characterizing and understanding promoters in the eukaryotic genome
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The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding.
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Genome-wide location analysis: insights on transcriptional regulation.
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Genome-wide analysis of protein-DNA interactions.
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An all-round view of eukaryotic transcription.
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A high-resolution map of active promoters in the human genome.
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Direct isolation and identification of promoters in the human genome.
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beta-Catenin activates the growth factor endothelin-1 in colon cancer cells.
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The ENCODE (ENCyclopedia Of DNA Elements) Project
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Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors.
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A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells.
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E2F integrates cell cycle progression with DNA repair replication and G(2)/M checkpoints.
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Remodeling of Yeast Genome Expression in Response to Environmental Changes
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Genome-wide location and function of DNA binding proteins
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PRDI-BF1/Blimp-1 repression is mediated by corepressors of the Groucho family of proteins
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Regulation of Drosophila Adh promoter switching by an initiator-targeted repression mechanism.
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