X. ZENG

Xin ZENG, Ph.D. Computational Postdoctoral Fellow Siepel Lab Simons Center for Quantitative Biology Cold Spring Harbor Laboratory [Google Scholar], [ORCID], [X], [Bluesky], [LinkedIn]

Summary

• Very motivated in the field of genomics, epigenomics, and transcriptomics.

• Highly knowledgeable in molecular biology and machine learning.

• Strongly experienced in leveraging computational methods for diverse genomics projects.

• Programming languages: Python and R [Github].

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

Internship and Exchange Prgram

• Visiting Scholar under Dr. Stefania GIACOMELLO at SciLifeLab (Sweden), Oct. 12th, 2022 - Oct. 21st, 2022

  • Studied deep learning in spatial transcriptomics for enhanced resolution.

  • Skills Acquired: Deep learning methods for integrating count matrix and image information from spatial transcriptomics.

• Interned under Dr. Yad GHAVI-HELM at ENS Lyon (France), Sep. 2019 - Dec. 2019

  • Studied enhancer-promoter interactions using Drosophila as a model system.

  • Skills Acquired: Familiarity with integrating single-cell RNA-seq and single-cell ATAC-seq data for basic downstream analyses.

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

• SignedS2V: structural embedding method for signed networks
  S. Liu, F. Toriumi, X. Zeng, M. Nishiguchi, K. Nakai.
  The 11th International Conference on Complex Networks and their Applications 08-10 November 2022, Palermo, Italy

• 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

Publication

• 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 (2025)

• STAIG: Spatial Transcriptomics Analysis via Image-Aided Graph Contrastive Learning for Domain Exploration and Alignment-Free Integration
  Y. Yang, Y. Cui, X. Zeng, Y. Zhang, M. Loza, SJ. Park, K. Nakai.
  Nature Communications 16, 1067 (2025)

• Computational analysis of the functional impact of MHC-II-expressing triple-negative breast cancer
  Y. Cui, W. ZHANG, X. Zeng, Y. Yang, SJ. Park and K. Nakai
  Frontiers in Immunology 15, 1497251 (2024)

• 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)

• TF-EPI: an interpretable enhancer-promoter interaction detection method based on Transformer
  B. Liu, W. Zhang, X. Zeng, M. Loza, SJ. Park, K. Nakai.
  Frontiers in Genetics 15, 1444459(2024)

• LONRF2 is a protein quality control ubiquitin ligase whose deficiency causes late-onset neurological deficits
  D. Li, Y. Johmura, S. Morimoto, M. Doi, K. Nakanishi, M. Ozawa, Y. Tsunekawa, A. Inoue-Yamauchi, H. Naruse, T. Matsukawa, Y. Takeshita, N. Suzuki, M. Aoki, A. Nishiyama, X. Zeng, C. Konishi, N. Suzuki, A. Nishiyama, A. S. Harris, M. Morita, K. Yamaguchi, Y. Furukawa, K. Nakai, S. Tsuji, S. Yamazaki, Y. Yamanashi, S. Shimada, T. Okada, H. Okano, T. Toda & M. Nakanishi.
  Nature Aging 3, 1001–1019 (2023)

• SignedS2V: Structural Embedding Method for Signed Networks
  S. Liu, F. Toriumi, X. Zeng, M. Nishiguchi, K. Nakai.
  Complex Networks and Their Applications XI 1, 337-349 (2023)

• iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations
  J. Jin, Y. Yu, R. Wang, X. Zeng, C. Pang, Y. Jiang, Z. Li, Y. Dai, R. Su, Q. Zou, K. Nakai, and L. Wei.
  Genome Biology 23, 219 (2022)

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

Manuscripts in Progress

• DenoiseST: A dual-channel unsupervised deep learning-based denoising method to identify spatial domains and functionally variable genes in spatial transcriptomics
  Y. Cui, R. Wang, X. Zeng, Y. Cui, Z. Zhu, K. Nakai, X. Ye, T. Sakurai, L. Wei

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