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Achievement: Pair Extraordinairex4Achievement: Pull Sharkx3Achievement: Starstruckx3Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor

Achievements

Achievement: Pair Extraordinairex4Achievement: Pull Sharkx3Achievement: 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.

EmailGoogle ScholarXGitHub followers

PythonRJupyterScanpySingle-cellSpatial biologyMulti-omicsCancer researchOpen 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 statsGitHub streak

Top languagesProductive time

GitHub trophies

Flagship Projects

ProjectAreaSnapshotLinks
OmicVerseSingle-cell, spatial, multi-omicsA Python ecosystem for modern omics analysis and reproducible workflows.Paper · Stars
dynamo-releaseRNA velocity, vector fieldsA framework for transcriptomic dynamics, vector field reconstruction, and cell fate modeling in single-cell and multi-omics data.Stars
PantheonOSAgent systems, data scienceAn evolvable distributed agent framework and harness for data science workflows.Stars
epioneSingle-cell epigenomicsA Python framework for single-cell epigenomic analysis and generative modeling.Stars
scltnnTrajectory inferenceToolkit for lineage and trajectory-related single-cell analysis.Paper · Stars
omicclawOmicVerse agent workspaceA gateway-first OmicVerse workspace for web UI, channels, notebooks, and agent workflows.Stars

Tutorials and Community Resources

RepositoryTypeDescriptionLinks
bioinformatic_tutorialTutorialPractical tutorials for common bioinformatics workflows.Stars
single_cell_tutorialTutorialNotes and walkthroughs for single-cell analysis workflows.Stars
USTB-resourceResource hubCurated study and engineering resources from my learning journey.Stars

Reproducibility and Analysis Repositories

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

RepositoryTopicPublicationLinks
omicverse-reproducibilityOmicVerse reproducibilityNature CommunicationsPaper · Stars
Analysis_ADAlzheimer's diseaseComputational and Structural Biotechnology JournalPaper · Stars
Liver_clockLiver aging clockComputational and Structural Biotechnology JournalPaper · Stars
Analysis_NodalDevelopmental biologyFrontiers in Cell and Developmental BiologyPaper · Stars
Analysis_sishengPharmacology analysisCurrent Pharmaceutical DesignPaper · Stars
Analysis_JHQG_COVIDCOVID immunologyFrontiers in ImmunologyPaper · Stars
Analysis_microbiome_mscMicrobiome analysisBrain, Behavior, and ImmunityPaper · Stars

Research and Tooling Stack

WorkflowSingle-cell analysisSpatial omicsMulti-omics methodCancer biologyTranslational medicineReproducibilityMaintainer

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/omicverseomicverse/omicversePublic

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

    Python 1.2k 147

  2. aristoteleo/dynamo-releasearistoteleo/dynamo-releasePublic

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

    Python 509 60

  3. aristoteleo/PantheonOSaristoteleo/PantheonOSPublic

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

    Python 482 65