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Curriculum Vitae of Puwen Tan

![Puwen Tan](./Puwen Tan.png)

Puwen Tan

Ph.D. in bioinformatics, Southern Medical University, Guangzhou, Guangdong, China, 510515

Email: [email protected]

Tel: (+86) 182 4606 0545 (Wechat ID)

1. Summary:

Puwen Tan is a highly motivated bioinformatician with a strong interest in developing methods to uncover the cell identity and characterize the cell state transition from multiple perspectives. He is proficient in a variety of skills including single-cell RNA-seq analysis, data visualization, and R package development. For the past 5 years, he mainly focused on exploring the cellular heterogeneity of hematopoietic stem cells (2017 Nat Commun, 2018 Autophagy, 2021 Cell Stem Cell, and 2022 Sci Adv) using bioinformatic methods. Most recently, he is looking for a postdoctoral position in computational biology which focuses on developing single-cell multi-omics analysis methods.

2. Education:

2019 - 2022, Ph.D. in bioinformatics, Southern Medical University, China

2016 - 2019, Master of Biomedical Engineering (bioinformatics), Harbin Medical University, China

2011 - 2016, Bachelor of Biotechnology (biomedical software engineering), Harbin Medical University, China

3. Skills:

  1. Strong programming skills in using R language for statistical analysis, visualization, and software development.
  2. Proficient in high-throughput sequencing data (including bulk & single-cell RNA-seq, ChIP-seq, CLIP-seq, and single-cell Nanopore-seq) analysis.
  3. Extensive collaboration experiences with biologists.
  4. Fluent in English writing and speaking.

4. Academic experience:

Here list of the main studies for the last 5 years:

I. A computational framework for transcription factor activity analysis (submitted to Nature Cell Biology).

This research developed an integrated computational framework for gene regulatory network inference and transcription factor activity estimation from single-cell RNA sequencing data. In brief, we utilized an entropy-based algorithm to infer the weighted regulatory relationship between regulators and targets by decomposing the unique information from multivariate information. This framework Embed several functions such as transcriptional factor activity quantification, dimensionality reduction, cell-type-specific regulon analysis, pathway enrichment analysis, and visualization. This work aims to establish a comprehensive single-cell analysis framework for transcription factors just like other commonly used single-cell pipelines such as Seurat.

* First author, mainly responsible for study design, software development, bioinformatics analysis, visualization and manuscript writing. Softwares from this project were deposited in GitHub: https://github.com/hmutpw/scATFR and https://github.com/hmutpw/PUIC.

II. Constructing the RNA subcellular localization landscape of embryonic stem cells (2023 Stem Cell Reports).

This research comprehensively characterized the subcellular localization pattern of RNA molecules in embryonic stem cells. We identified several genes that showed distinct localization patterns among five different subcellular locations. Meanwhile, we explored the subcellular localization pattern of alternative splicing events between cytoplasm and nucleus and predicted several RNA binding proteins that potentially regulate the nuclear export.

* Co-first author, mainly responsible for bioinformatics analysis, visualization, and manuscript writing.

III. Single-cell sequencing reveals the critical role of alternative splicing in hematopoietic stem cell formation (2022 Sci Adv)

This research constructed an isoform-based transcriptional atlas of the murine endothelial-to-hematopoietic stem cell using single-cell full-length RNA sequencing data. In brief, we comprehensively described the isoform diversity and alternative splicing landscape during hematopoietic stem cell formation. Then, we also identified hundreds of stage-specific isoforms that potentially affect the hematopoietic stem cell formation and validated their expression using single-cell Nanopore sequencing of full-length transcripts. Subsequently, in vitro knockdown experiments showed that knockdown of some hemogenic-specific isoforms indeed affects the generation of HSCs. Next, motif enrichment combined with knockout experiments confirmed that the RNA-binding protein (RBP), Srsf2, could affect the specialization of endothelial cells into hematopoietic stem cells by regulating the AS of key transcription factors such as Runx1 and Myb.

SA Abstract

* Co-first author, mainly responsible for study design, bioinformatics analysis, visualization, and manuscript writing. The code was deposited in GitHub:https://github.com/hmutpw/scAS/.

IV. hnRNPLL controls pluripotency exit of embryonic stem cells by modulating alternative splicing of Tbx3 and Bptf (2021 EMBO J)

This research revealed that RNA binding protein hnRNPLL regulates the embryonic stem cell exit from pluripotency by modulating the alternative splicing of some key transcription factors that maintain the pluripotency.

EMBOJ Abstract

* Co-first author, mainly responsible for bioinformatics analysis, and visualization.

V. Depicting the dynamic activity of autophagy at the transcriptome level during the human stem cell differentiation (2018 & 2019, Autophagy)

This research investigated the dynamic patterns of autophagy-related genes during human fetal digestive tract development using single-cell RNA sequencing data. Meanwhile, we also identified several autophagy-related genes that potentially regulate monocytic-granulocytic differentiation.

Autophagy Abstract

* First author, mainly responsible for bioinformatics analysis, visualization, and manuscript writing.

VI. Construction of the RNA subcellular localization resources. (2017 & 2021, Nucleic Acids Res)

These studies constructed and updated the RNA subcellular localization database for the transcriptome level.

NAR Abstract

* Co-first author, mainly responsible for data collecting and visualization.

5. Research Interests:

Single-cell multi-omics

Machine learning

Software development

Hematopoietic stem cell

6. Full list of Publications:

( †: equally contribution; *: corresponding author )

2024

  1. Fanqi Zhou†, Puwen Tan†, Siqi Liu, Le Chang, Jiabin Yang, Mengyao Sun, Yuehong Guo, Yanmin Si, Dong Wang*, Jia Yu*, Yanni Ma*. Subcellular RNA distribution and its change during human embryonic stem cell differentiation. Stem Cell Reports. 2024 Jan 9;19(1):126-140.Full-text.

2023

  1. Tianyuan Liu†, Bohao Zou†, Manman He†, Yongfei Hu, Yiying Dou, Tianyu Cui, Puwen Tan, Shaobin Li, Shuan Rao, Yan Huang, Sixi Liu*, Kaican Cai*, Dong Wang*. LncReader: identification of dual functional long noncoding RNAs using a multi-head self-attention mechanism. Brief Bioinform. 2023 Jan 19;24(1):bbac579.Full-text.

2022

  1. Fang Wang†, Puwen Tan†, Pengcheng Zhang†, Yue Ren†, Jie Zhou, Yunqiao Li, Siyuan Hou, Shuaili Li, Linlin Zhang, Yanni Ma, Chaojie Wang, Wanbo Tang, Xiaoshuang Wang, Yue Huo, Yongfei Hu, Tianyu Cui, Chao Niu, Dong Wang*, Bing Liu*, Yu Lan*, Jia Yu*. Single-cell architecture and functional requirement of alternative splicing during hematopoietic stem cell formation. Sci Adv. 2022 Jan 7;8(1):eabg5369. Full-text

2021

  1. Juanjuan Kang, Qiang Tang, Jun He, Le Li, Nianling Yang, Shuiyan Yu, Mengyao Wang, Yuchen Zhang, Jiahao Lin, Tianyu Cui, Yongfei Hu, Puwen Tan, Jun Cheng, Hailong Zheng, Dong Wang*, Xi Su*, Wei Chen*, Yan Huang*. RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. Nucleic Acids Res. 2021 Oct 30;gkab997. Full-text
  2. Tianyu Cui†, Yiying Dou†, Puwen Tan†, Zhen Ni, Tianyuan Liu, DuoLin Wang, Yan Huang, Kaican Cai, Xiaoyang Zhao, Dong Xu*, Hao Lin*, Dong Wang*. RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. Nucleic Acids Res. 2021 Sep 22;gkab825. Full-text
  3. Yang Zhang*, Tianyuan Liu, Xuesong Hu, Mei Wang, Jing Wang, Bohao Zou, Puwen Tan, Tianyu Cui, Yiying Dou, Lin Ning, Yan Huang, Shuan Rao, Dong Wang*, Xiaoyang Zhao*. CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication. Nucleic Acids Res. 2021 Sep 7;49(15):8520-8534. Full-text
  4. Jingyuan Tong, Ting Sun, Shihui Ma, Yanhong Zhao, Mankai Ju, Yuchen Gao, Ping Zhu, Puwen Tan, Rongfeng Fu, Anqi Zhang, Ding Wang, Di Wang, Zhijian Xiao, Jiaxi Zhou, Renchi Yang, Stephen J Loughran, Juan Li, Anthony R Green, Emery H Bresnick, Dong Wang*, Tao Cheng*, Lei Zhang*, Lihong Shi*. Hematopoietic stem cell heterogeneity is linked to the initiation and therapeutic response of myeloproliferative neoplasms. Cell Stem Cell. 2021 Mar 4;28(3):502-513.e6. Full-text
  5. Xue Wang†, Changyun Ping†, Puwen Tan†, Chenguang Sun, Guang Liu, Tao Liu, Shuchun Yang, Yanmin Si, Lijun Zhao, Yongfei Hu, Yuyan Jia, Xiaoshuang Wang, Meili Zhang, Fang Wang, Dong Wang*, Jia Yu*, Yanni Ma*, Yue Huang*. hnRNPLL controls pluripotency exit of embryonic stem cells by modulating alternative splicing of Tbx3 and Bptf. EMBO J. 2021 Feb 15;40(4):e104729. Full-text

2020

  1. Yunqing Lin, Tianyuan Liu, Tianyu Cui, Zhao Wang, Yuncong Zhang, Puwen Tan, Yan Huang, Jia Yu, Dong Wang*. RNAInter in 2020: RNA interactome repository with increased coverage and annotation. Nucleic Acids Res. 2020 Jan 8;48(D1):D189-D197. Full-text

2019

  1. Puwen Tan†, Yue Ren†, Yuncong Zhang†, Yunqing Lin, Tianyu Cui, Yan Huang, Yang Zhang, Lin Ning, Jia Yu, Shuai Gao, Dong Wang, He Huang*. Dissecting dynamic expression of autophagy-related genes during human fetal digestive tract development via single-cell RNA sequencing. Autophagy. 2019 Nov;15(11):2019-2021. Full-text

2018

  1. Yan Huang†, Puwen Tan†, Xiaoshuang Wang, Ying Yi, Yongfei Hu*, Dong Wang*, Fang Wang*. Transcriptomic insights into temporal expression pattern of autophagy genes during monocytic and granulocytic differentiation. Autophagy. 2018;14(3):558-559. Full-text
  2. Tianyu Cui, Lin Zhang, Yan Huang, Ying Yi, Puwen Tan, Yue Zhao, Yongfei Hu, Liyan Xu, Enmin Li, Dong Wang. MNDR v2. 0: an updated resource of ncRNA–disease associations in mammals. Nucleic Acids Res. 2018 Jan 4;46(D1):D371-D374. Full-text

2017

  1. Hongmei Zhao, Xiaoshuang Wang, Ping Yi, Yanmin Si, Puwen Tan, Jinrong He, Shan Yu, Yue Ren, Yanni Ma, Junwu Zhang, Dong Wang*, Fang Wang*, Jia Yu*. KSRP specifies monocytic and granulocytic differentiation through regulating miR-129 biogenesis and RUNX1 expression. Nat Commun. 2017 Nov 10;8(1):1428. Full-text
  2. Ying Yi, Yue Zhao, Chunhua Li, Lin Zhang, Huiying Huang, Yana Li, Lanlan Liu, Ping Hou, Tianyu Cui, Puwen Tan, Yongfei Hu, Ting Zhang, Yan Huang, Xiaobo Li*, Jia Yu*, Dong Wang*. RAID v2.0: an updated resource of RNA-associated interactions across organisms. Nucleic Acids Res. 2017 Jan 4;45(D1):D115-D118. Full-text
  3. Ting Zhang†, Puwen Tan†, Liqiang Wang†, Nana Jin†, Yana Li, Lin Zhang, Huan Yang, Zhenyu Hu, Lining Zhang, Chunyu Hu, Chunhua Li, Kun Qian, Changjian Zhang, Yan Huang, Kongning Li*, Hao Lin*, Dong Wang*. RNALocate: a resource for RNA subcellular localizations. Nucleic Acids Res. 2017 Jan 4;45(D1):D135-D138. Full-text

Before 2016

  1. Deng Wu, Yan Huang, Juanjuan Kang, Kongning Li, Xiaoman Bi, Ting Zhang, Nana Jin, Yongfei Hu, Puwen Tan, Lu Zhang, Ying Yi, Wenjun Shen, Jian Huang, Xiaobo Li, Xia Li, Jianzhen Xu, Dong Wang. ncRDeathDB: A comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system. Autophagy. 2015;11(10):1917-26. Full-text
  2. Liqiang Wang, Kun Qian, Yan Huang, Nana Jin, Hongyan Lai, Ting Zhang, Chunhua Li, Chunrui Zhang, Xiaoman Bi, Deng Wu, Changliang Wang, Hao Wu, Puwen Tan, Jianping Lu, Liqun Chen, Kongning Li, Xia Li, Dong Wang. SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology. Sci Rep. 2015 Jan 28;5:8090. Full-text
  3. Xiaomeng Zhang, Deng Wu, Liqun Chen, Xiang Li, Jinxurong Yang, Dandan Fan, Tingting Dong, Mingyue Liu, Puwen Tan, Jintian Xu, Ying Yi, Yuting Wang, Hua Zou, Yongfei Hu, Kaili Fan, Juanjuan Kang, Yan Huang, Zhengqiang Miao, Miaoman Bi, Nana Jin, Kongning Li, Xia Li, Jianzhen Xu, Dong Wang. RAID: a comprehensive resource for human RNA-associated (RNA–RNA/RNA–protein) interaction. RNA. 2014 Jul;20(7):989-93. Full-text

7. Other materials:

GitHub: https://github.com/hmutpw

ResearchGate: https://www.researchgate.net/profile/Puwen-Tan

Google Scholar: Puwen Tan

Academic transcripts: English version 中文成绩单