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Transcription factor-driven coordination of cell cycle exit and lineage-specification in vivo during granulocytic differentiation

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Immunoglobulin superfamily 9 (IGSF9) is trans-activated by p53, inhibits breast cancer metastasis via FAK

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Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

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H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions

(2021) Yichao Cai et al.   Nature Communications

A model of active transcription hubs that unifies the roles of active promoters and enhancers

(2021) Iris Zhu et al.   NUCLEIC ACIDS RESEARCH

3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia

(2021) Lu Yang et al.   Nature Communications

Computational characterization of domain‐segregated 3D chromatin structure and segmented DNA methylation status in carcinogenesis

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Noncoding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability

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A Guide to Conquer the Biological Network Era Using Graph Theory

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Social Network Analysis Based Localization Technique with Clustered Closeness Centrality for 3D Wireless Sensor Networks

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Coupling chromatin structure and dynamics by live super-resolution imaging

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Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

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Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

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Targeting Chromatin Remodeling for Cancer Therapy

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Key role for CTCF in establishing chromatin structure in human embryos

(2019) Xuepeng Chen et al.   NATURE

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

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Dissecting super-enhancer hierarchy based on chromatin interactions

(2018) Jialiang Huang et al.   Nature Communications

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Understanding Tissue-Specific Gene Regulation

(2017) Abhijeet Rajendra Sonawane et al.   Cell Reports

Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies

(2017) Guangdun Peng et al.   National Science Review

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(2017) Maryam Zamani et al.   Scientific Reports

Dynamic enhancer–promoter interactions for transcriptional bursting

(2016) Ross Cloney   NATURE REVIEWS GENETICS

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

Understanding Spatial Genome Organization: Methods and Insights

(2016) Vijay Ramani et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

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(2015) Jesse R. Dixon et al.   NATURE

Disrupted Functional Brain Connectivity and Its Association to Structural Connectivity in Amnestic Mild Cognitive Impairment and Alzheimer’s Disease

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The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Analysis of Average Shortest-Path Length of Scale-Free Network

(2013) Guoyong Mao et al.   Journal of Applied Mathematics

The UCSC genome browser and associated tools

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Insulators, long-range interactions, and genome function

(2012) Jingping Yang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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(2012) Enys Mones et al.   PLoS One

Control Centrality and Hierarchical Structure in Complex Networks

(2012) Yang-Yu Liu et al.   PLoS One

Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks

(2012) Kuljeet Singh Sandhu et al.   Cell Reports

Embryonic stem cell-specific signatures in cancer: insights into genomic regulatory networks and implications for medicine

(2011) Jonghwan Kim et al.   Genome Medicine

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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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Model-based Analysis of ChIP-Seq (MACS)

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