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Achievement: Pull Sharkx3Achievement: Pair Extraordinairex3Achievement: Starstruckx3Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor

Achievements

Achievement: Pull Sharkx3Achievement: Pair Extraordinairex3Achievement: Starstruckx3Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor

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Starlitnightly/README.md

Zehua Zeng

AI x Bioinformatics Researcher building open-source tools for multi-omics, single-cell, spatial biology, and reproducible computational workflows.

Email Google Scholar X GitHub followers

Python R Jupyter Scanpy Single-cell Spatial biology Multi-omics Cancer research Open source maintainer

About Me

  • I work at the intersection of AI, bioinformatics, and translational medicine.
  • My core interests are multi-omics integration, single-cell analysis, spatial biology, and cancer-related applications.
  • I build research software, tutorials, and reproducible analysis pipelines for real scientific workflows.
  • I am currently working across 112 Lab, Qiu Lab, University of Science and Technology Beijing, and the Department of Genetics at Stanford University.
  • I am open to collaboration on computational biology methods, open-source infrastructure, and research-driven product building.

Current focus

  • Single-cell and spatial omics tooling
  • Multi-omics integration workflows
  • Reproducible computational biology
  • Open-source platforms for research labs

Selected venues

  • Nature Communications
  • Bioinformatics Advances
  • Scientific Reports
  • Frontiers journals

GitHub Dashboard

GitHub stats GitHub streak

Top languages Productive time

GitHub trophies

Flagship Projects

Project Area Snapshot Links
OmicVerse Single-cell, spatial, multi-omics A Python ecosystem for modern omics analysis and reproducible workflows. Paper · Stars
dynamo-release RNA velocity, vector fields A framework for transcriptomic dynamics, vector field reconstruction, and cell fate modeling in single-cell and multi-omics data. Stars
PantheonOS Agent systems, data science An evolvable distributed agent framework and harness for data science workflows. Stars
epione Single-cell epigenomics A Python framework for single-cell epigenomic analysis and generative modeling. Stars
scltnn Trajectory inference Toolkit for lineage and trajectory-related single-cell analysis. Paper · Stars
omicclaw OmicVerse agent workspace A gateway-first OmicVerse workspace for web UI, channels, notebooks, and agent workflows. Stars

Tutorials and Community Resources

Repository Type Description Links
bioinformatic_tutorial Tutorial Practical tutorials for common bioinformatics workflows. Stars
single_cell_tutorial Tutorial Notes and walkthroughs for single-cell analysis workflows. Stars
USTB-resource Resource hub Curated study and engineering resources from my learning journey. Stars

Reproducibility and Analysis Repositories

These repositories package methods, notebooks, and code behind published work.

Repository Topic Publication Links
omicverse-reproducibility OmicVerse reproducibility Nature Communications Paper · Stars
Analysis_AD Alzheimer's disease Computational and Structural Biotechnology Journal Paper · Stars
Liver_clock Liver aging clock Computational and Structural Biotechnology Journal Paper · Stars
Analysis_Nodal Developmental biology Frontiers in Cell and Developmental Biology Paper · Stars
Analysis_sisheng Pharmacology analysis Current Pharmaceutical Design Paper · Stars
Analysis_JHQG_COVID COVID immunology Frontiers in Immunology Paper · Stars
Analysis_microbiome_msc Microbiome analysis Brain, Behavior, and Immunity Paper · Stars

Research and Tooling Stack

Workflow Single-cell analysis Spatial omics Multi-omics method Cancer biology Translational medicine Reproducibility Maintainer

Activity

Collaboration

If you are building open-source infrastructure for computational biology, single-cell analysis, multi-omics workflows, or research software with real scientific use cases, feel free to reach out.

Support

If you would like to support the development of my open-source work, you can sponsor it via Afdian.

Pinned Loading

  1. omicverse/omicverse omicverse/omicverse Public

    A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

    Python 959 121

  2. aristoteleo/dynamo-release aristoteleo/dynamo-release Public

    Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

    Python 490 62

  3. aristoteleo/PantheonOS aristoteleo/PantheonOS Public

    A general, evolvable, and distributed agent framework & harness for data science.

    Python 406 55