01

About Me

I am a senior in bioinformatics at the School of Life Sciences, Peking University, pursuing a double degree in economics at the National School of Development.

My research focuses on spatial multi-omics, machine learning for biology, and scientific agents. In Hu Zeng's lab at Peking University, I work on imaging-based spatial transcriptomics and translatomics, from image processing to downstream analysis. In Xiaojie Qiu's lab at Stanford, I contributed to Bio-Babel and am training a model for joint molecular and cellular inference from spatial transcriptomics images.

I am also developing iST Agent for reliable execution of imaging-based spatial transcriptomics workflows. Since October 2026, I have been a remote research intern at Canchen Technology, mentored by Lei Li, with a focus on agentic world models for virtual tissue.

Outside research, I enjoy playing volleyball.

02

Research Interests

  • Spatial Multi-omics spatial transcriptomics and translatomics, multimodal analysis, and spatial oncology
  • Scientific Agents agentic workflows for scientific software, complex analyses, and biological discovery
  • AI for Biology foundation models, perturbation prediction, and agentic biological world models
  • Bioinformatics Software reliable tools, interoperable packages, and reproducible workflows

03

Research Experience

  • Peking University

    Zeng Lab

    Undergraduate Researcher · July 2024–Present

    Building and optimizing the STATES upstream pipeline, analyzing spatial transcription and translation in glioblastoma, and developing iST Agent for workflow execution.

  • Stanford University

    Qiu Lab

    Undergraduate Researcher · June 2026–Present

    On-site summer research in June–August 2026, followed by remote research. Contributed to Bio-Babel and am developing and training a model for joint decoding, segmentation, and molecule-to-cell assignment.

  • Canchen Technology

    Mentor: Lei Li

    Research Intern · Remote · October 2026–Present

    Research focus: agentic world models for virtual tissue.

04

Publications

  1. Preprint · bioRxiv 2026

    Bio-Babel: autonomous cross-language reconstruction of agent-ready computational biology ecosystems

    Nianping Liu, Xuanzhi Chen, Miao Cui, Xiaoying Liao, Xiaoke Song, Sairam Pantham, Weize Xu, and Xiaojie Qiu.

    doi:10.64898/2026.08.30.743167

05

Selected Work

GitHub profile
  1. In progress

    Spatial Multi-omics Analysis of GBM with STATES

    STATES jointly profiles spatial transcriptomes and translatomes. I benchmarked cell-segmentation methods, integrated 3D Cellpose nuclear segmentation into ClusterMap, and improved image stitching. The proportion of seams misaligned by more than 3 pixels fell from 14.2% to 0.3%; multi-nucleus segments fell from 28.8% to 13–14% against the same nuclear reference. My downstream work examines malignant-cell identities, subtypes, and spatial variation in translation efficiency in glioblastoma.

    Spatial multi-omics · Spatial oncology · GBM

  2. Preprint · bioRxiv 2026

    Bio-Babel

    Bio-Babel reconstructs computational biology software across languages for use by scientific agents. I built an annotation agent that generates machine-readable usage contracts for reconstructed packages, extended coding-agent compatibility, and developed tooling for agent-driven Python-to-C++ reconstruction. In the pancreatic differentiation case study, I prepared and annotated the data, reviewed analyses executed by Bio-Babel's agents, and completed genotype-aware screening and biological interpretation of reduced maturation signatures under SWI/SNF loss. Code: pancreas case study, UMI-tools-cpp.

    Scientific agents · Software translation · Research software

  3. Qiu Lab · In progress

    End-to-End Spatial Transcriptomics Modeling

    I am developing and training a model on public MERFISH data that couples molecular localization and barcode decoding with cell segmentation and molecule-to-cell assignment. It combines RNA fluorescence and cellular morphology, learning cross-round correspondences without a separate image-warping stage. The project tests whether sharing evidence across these interdependent tasks can reduce errors introduced by sequential processing.

    Deep learning · iST · Multimodal learning · Bioimage analysis

  4. Peking University · Undergraduate thesis

    iST Agent

    Inspired by Bio-Babel, I built an agent for reliable execution of heterogeneous imaging-based spatial transcriptomics workflows. It separates usage contracts derived from source code from memory of runtime failures and fixes. I generated contracts for seven pipelines and reproduced one pipeline's decoding byte for byte. In one comparison, preflight checks caught a multi-sample configuration defect with memory but missed it without memory.

    Scientific agents · iST · Bioimage processing · Workflow orchestration

06

Presentations & Honors

  1. Invited oral presentation · October 2026

    Bio-Babel

    Annual Symposium of the Peking University Undergraduate Honors Program in Biology.

  2. Honors and Awards

    Academic Excellence Award, Peking University · 2026
    Peking University Scholarship · 2025
    Peking University Freshmen Scholarship · 2023
    Gold Medal, China National Biology Olympiad Final · 2022

07

Contact

I am always happy to connect—whether you would like to discuss research, share an idea, collaborate, or simply say hello.