X. ZENG

Xin ZENG, Ph.D. Computational Postdoctoral Fellow (May 2024 - Present) Siepel Lab Simons Center for Quantitative Biology Cold Spring Harbor Laboratory [ORCID], [X], [Bluesky], [LinkedIn]

Summary

• Computational biologist studying the interplay between genome organization, epigenomic regulation, and transcription dynamics.

• Developing machine learning and probabilistic methods to model RNA polymerase dynamics from nascent RNA sequencing data. [Github]

• Integrating genomics, epigenomics, and 3D genomics features with transcription dynamics to study gene regulation at high temporal and spatial resolution.

Education

• Ph.D., University of Tokyo, Oct. 2018 - Mar. 2024

  • Supervisor: Prof. Kenta NAKAI

  • Department of Computational Biology and Medical Sciences

• B.S., China Agricultural University, Sep. 2014 - Jul. 2018

  • Advisor: Prof. Ziding ZHANG

  • College of Biological Science

Research Experience

• Postdoc, Cold Spring Harbor Laboratory (Advisor: Adam Siepel), May 2024 – Present

• Visiting Scholar, SciLifeLab (Host: Stefania Giacomello), Oct 2022

• Research Intern, ENS de Lyon (Supervisor: Yad Ghavi-Helm), Sep 2019 – Dec 2019

Award and Fellowship

• SPRING-GX fellowship, University of Tokyo (Grant Number: JPMJSP2108), Sep. 2021 - Mar. 2024

• DSTEP program, University of Tokyo, Apr. 2021 - Mar. 2024

Oral Presentation

• Comparative Gene Regulatory Network Analysis in Vertebrate Retinal Cell by Single-cell RNA-seq Data
  X. Zeng, F. Gyoja, T. G. Kusakabe, K. Nakai.
  Informatics In Biology, Medicine and Pharmacology (IIBMP 2023) 07-09 September 2023, Kashiwa, Japan

• Computational Inference of Gene Regulatory Network in the ascidian brain by single cell RNA-seq data
  X. Zeng, F. Gyoja, T. Kusakabe, K. Nakai.
  The 11th International Tunicate Meeting 11-15 July 2022, Kobe, Japan

• Characterizing promoter and enhancer sequences by a deep learning method
  X. Zeng, SJ. Park, and K. Nakai.
  The 19th International Conference on Bioinformatics 25-29 November 2020, World Wide Web

Selected Publication

• Ful list@[Google Scholar]
  

• A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation
  X. Zeng, G. Barshad, R. Hassett, E.J. Rice, C.G. Danko, A. Siepel and Y. Zhao
  bioRxiv (2026)

• Spatial transcriptomics of Ciona adult brains reveals functional zonalization and insights into neural gland function
  X. Zeng, F. Gyoja, A. Maruo, N. Okawa, K. Mizutani, Y. Suzuki, K. Nakai and T.G. Kusakabe
  iScience 29(9), 117346 (2026)

• Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks
  X. Zeng, S. Liu, B. Liu, W. Zhang, W. Xu, F. Toriumi and K. Nakai
  BMC Bioinformatics 26, 134 (2025)

• Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina
  X. Zeng, F. Gyoja, Y. Cui, M. Loza, T. G Kusakabe, K. Nakai.
  NAR Genomics and Bioinformatics 6(4), lqae149 (2024)

• Characterizing promoter and enhancer sequences by a deep learning method
  X. Zeng, SJ. Park, and K. Nakai.
  Fronters in Genetics 12, 681259 (2021)

Apart From Research

• Proficient in Japaneses (JLPT N2 level)

• Recreational Badminton Player 🏸 (Weekly 1-2 sessions)

• Experienced Mountaineer 🥾⛰️ (Climbed 16 of 100 Famous Japanese Mountains)

• Passionate Photographer 📸 (Specialized in landscape and astro-photography)

• Stargazer (Love navigating the sky by eyes 👀 and telescopes 🔭 without GOTO system ❌🧭)

Contact

2117, Koch Building
One Bungtown Road
Cold Spring Harbor,
NY, US, 11724
Email: zengATcshl.edu