Z
Zhen Ye
Researcher at Ludwig Institute for Cancer Research
Publications - 42
Citations - 22999
Zhen Ye is an academic researcher from Ludwig Institute for Cancer Research. The author has contributed to research in topics: Chromatin & Gene. The author has an hindex of 33, co-authored 40 publications receiving 19687 citations. Previous affiliations of Zhen Ye include University of California, San Diego.
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Journal ArticleDOI
Human DNA methylomes at base resolution show widespread epigenomic differences
Ryan Lister,Mattia Pelizzola,Robert H. Dowen,R. David Hawkins,Gary C. Hon,Julian Tonti-Filippini,Joseph R. Nery,Leonard Lee,Zhen Ye,Que Minh Ngo,Lee Edsall,Jessica Antosiewicz-Bourget,Jessica Antosiewicz-Bourget,Ron Stewart,Ron Stewart,Victor Ruotti,Victor Ruotti,A. Harvey Millar,James A. Thomson,Bing Ren,Bing Ren,Joseph R. Ecker +21 more
TL;DR: The first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors were presented in this article.
Journal ArticleDOI
Histone modifications at human enhancers reflect global cell-type-specific gene expression
Nathaniel D. Heintzman,Gary C. Hon,R. David Hawkins,Pouya Kheradpour,Alexander Stark,Alexander Stark,Lindsey F. Harp,Zhen Ye,Leonard K. Lee,Rhona K. Stuart,Christina W. Ching,Keith A. Ching,Jessica Antosiewicz-Bourget,Hui Liu,Xinmin Zhang,Roland D. Green,Victor V. Lobanenkov,Ron Stewart,James A. Thomson,James A. Thomson,Gregory E. Crawford,Manolis Kellis,Manolis Kellis,Bing Ren +23 more
TL;DR: The results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression.
Journal Article
Histone Modifications at Human Enhancers Reflect Global Cell-Type-Specific Gene Expression
Nathaniel D. Heintzman,Gary C. Hon,R. David Hawkins,Pouya Kheradpour,Alexander Stark,Lindsey F. Harp,Zhen Ye,Leonard K. Lee,Rhona K. Stuart,Christina W. Ching,Keith A. Ching,Jessica Antosiewicz-Bourget,Hui Liu,Xinmin Zhang,Roland D. Green,Victor V. Lobanenkov,Ron Stewart,James A. Thomson,Gregory E. Crawford,Manolis Kellis,Bing Ren +20 more
TL;DR: In this article, a chromatin-immunoprecipitation-based microarray method (ChIP-chip) was used to locate promoters, enhancers and insulators in the human genome and investigate their roles in cell-type specific gene expression.
Journal ArticleDOI
Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification
Minjia Tan,Hao Luo,Sangkyu Lee,Fulai Jin,Jeong Soo Yang,Emilie Montellier,Thierry Buchou,Zhongyi Cheng,Sophie Rousseaux,Nisha Rajagopal,Zhike Lu,Zhen Ye,Qin Zhu,Joanna Wysocka,Yang Ye,Saadi Khochbin,Bing Ren,Yingming Zhao +17 more
TL;DR: The identification of 67 previously undescribed histone modifications is reported, increasing the current number of known histone marks by about 70%, and lysine crotonylation (Kcr) is investigated, confirming that it represents an evolutionarily-conserved histone posttranslational modification.
Journal ArticleDOI
Chromatin architecture reorganization during stem cell differentiation
Jesse R. Dixon,Inkyung Jung,Siddarth Selvaraj,Yin Shen,Jessica Antosiewicz-Bourget,Ah Young Lee,Zhen Ye,Audrey Kim,Nisha Rajagopal,Wei Xie,Yarui Diao,Jing Liang,Huimin Zhao,Victor V. Lobanenkov,Joseph R. Ecker,James A. Thomson,Bing Ren +16 more
TL;DR: Mapping genome-wide chromatin interactions in human embryonic stem cells and four human ES-cell-derived lineages reveals extensive chromatin reorganization during lineage specification, providing a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.