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News 2022

2022

October 26-28, 2022
Congratulation

PI Yang CHEN, MD Student.2019 Qiaoyi SHEN, and MD Student.2019 Zhizhuo CHEN formed the first iGEM competition team PUMC to participate in the competition and won the bronze award.

 
September 24, 2022
Activity
The second fitness test ended successfully!
 
September 5, 2022
Publication

CASPIAN: A method to identify chromatin topological associated

CASPIAN requires few parameters to call TADs. This method is realized using the hierarchical density-based clustering method HDBSCAN, where the distance of pairwise bins is calculated based on three distance metrics (Euclidean, Manhattan, and Chebyshev distance metric) to adapt to the characteristics of the Hi-C contact matrix generated from simulation experiments or normalized methods. Our results show that, same as standard methods (e.g., Insulation Score, TopDom), CASPIAN can enrich factors related to promoting the gene expression, such as CTCF, H3K4me1, H3K4me3, RAD21, POLR2A, and SMC3. We also calculated the approximate proportion of various factors anchored at the TAD boundaries to observe the distribution of these factors surrounding the TAD boundaries. In conclusion, CASPIAN is an easy method to explore the relationship between transcription factors and TAD boundaries.

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陈阳、张晓彤合作团队发表时空基因组新工具CASPIAN

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September 1, 2022
New members

Welcome Xueyuan LI, Biao SONG, Yurong YANG, and  Xueli WU  to join our team!

July 2, 2022
Activity
The first fitness test ended successfully!
 
February 22,  2022
 

PI Yang CHEN joins CANCER INNOVATION as an Editorial Board Member (2022-2024).

 
 
February 18, 2022
Congratulation
 空间单细胞核代谢组分析方法—SEAM入选2021年度中国生物信息学十大进展
January 24, 2022
New member

Welcome  Lisha WANG to join our team!

王莉莎-科研项目助力
January 11, 2022
Publication

MyoD is a 3D genome structure organizer for muscle cell identity

Here, we analyzed 3D genome structures in muscle cells from mice lacking the muscle lineage transcription factor (TF), MyoD, versus wild-type mice. We show that MyoD functions as a “genome organizer” that specifies 3D genome architecture unique to muscle cell development, and that H3K27ac is insufficient for the establishment of MyoD-induced chromatin loops in muscle cells. Moreover, we present evidence that other cell lineage-specific TFs might also exert functional roles in orchestrating lineage-specific 3D genome organization during development.

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朱大海/张勇/张奇伟/陈阳合作揭示转录因子MyoD在细胞特异性基因组3D结构构建中的新功能

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