Professional Summary

Ph.D. in Bioinformatics from Peking University with 20+ years of experience spanning software engineering, AI/ML platform building, computational infrastructure, and life sciences research. Previously worked at two precision medicine diagnostic companies, contributing to cancer genomic testing and infectious disease detection product development, as well as related research projects. Founded Beijing BioinfoBoost Technology Co., Ltd. as an OPC (One-Person Company) in 2023, applying AI and bioinformatics to the biomedical field. During this entrepreneurial journey, explored the development of LLM-based applications in scenarios such as genetic mutation pathogenicity interpretation. Adept at bridging the gap between data engineering, AI/ML, and biological research.

Core Competencies

  • AI/ML Platform Engineering: LLM API integration (OpenAI, DeepSeek), Prompt Engineering, RAG pipeline building, Agent workflow orchestration, model inference optimization & deployment
  • Software Engineering & Infrastructure: Full-stack software development (Python, TypeScript, C/C++), Linux system programming, HPC environment management, Docker/K8s orchestration, data pipeline design (ETL/ELT), cloud services (Alibaba Cloud, AWS)
  • Drug Discovery & Genomics: Multi-omics integration, biomarker discovery, cancer genomics, immunology & digital pathology, genetic variant interpretation
  • Platform & Team Leadership: Built platforms from scratch as an OPC (CEO/Founder), led 20+ person research teams in prior roles, cross-team collaboration, matrix management

Professional Experience

Oct 2023 - Present

  • Beijing BioinfoBoost Technology Co., Ltd., Founder & CEO
  • Founded and has been operating the company as an OPC (One-Person Company), taking direct responsibility for technical direction, project execution, and business operations. This experience provided hands-on practice in prioritization and end-to-end problem solving across technology and business.
  • Configured and managed cloud-based compute resources, including GPU or DCU instances from cloud providers, to support AI-related experimentation and development.
  • Explored the application of LLMs in the biomedical domain, particularly in genetic mutation pathogenicity interpretation – including retrieval-augmented generation (RAG) pipelines, prompt engineering, and prototype development for variant analysis workflows.
  • Undertook software system development, multi-omics bioinformatics data analysis, and machine learning modeling projects for research institutes and biomedical companies.

Mar 2020 - Sep 2023

  • Simcere Diagnostics Co., Ltd., Senior Bioinformatics Scientist
  • Led a 20+ person research team collaborating with top-tier hospitals on cancer genomics, immunotherapy response prediction, infectious disease testing, and digital pathology.
  • Developed and optimized multi-omics data integration and biomarker discovery pipelines (genomics, transcriptomics, metabolomics, epigenomics) – building the computational infrastructure that enabled large-scale collaborative research.
  • Built AI-assisted models for immunotherapy response prediction, contributing to 4 filed patents and multiple peer-reviewed publications.
  • Managed cross-functional stakeholder relationships across clinical, scientific, and engineering teams, translating between domain-specific requirements and technical solutions.

Sep 2015 - Feb 2020

  • Genecast Biotechnology Co., Ltd., Bioinformatics R&D Manager
  • Built the bioinformatics and IT team from scratch, establishing the technical infrastructure, computational environment, and R&D pipelines for clinical cancer genomic testing product development.
  • Led end-to-end product R&D, including algorithm development for low-frequency somatic mutation detection and gene fusion detection.
  • Designed and set up the backend software and hardware systems to support production-level bioinformatics analysis and data management.

Earlier Career

  • NetPower Information Technology Co., Ltd. (2010), Software Architect – Linux kernel firewall engine design
  • BITC Technology Co., Ltd. (2006-2009), Software Engineer – Built EMR (Electronic Medical Record) system from scratch
  • Motic Industrial Group Co., Ltd. (2005-2006), Software Engineer – Medical microscopy automation software
  • Shine Technology Co., Ltd. (2003-2005), Software Engineer – Video-on-demand and online gaming systems

Education

  • 2010 - 2017: Peking University, Beijing, China – Ph.D. in Bioinformatics, School of Life Sciences
  • 1999 - 2003: Xiamen University, Xiamen, China – B.S. in Biological Sciences, School of Life Sciences

Publications

  1. Liu M, Yang M, Zhang B, Xia S, Zhao J, Yan L, Ren Y, Guo H, and Zhao J. PCDH11X mutation as a potential biomarker for immune checkpoint therapies in lung adenocarcinoma. Journal of Molecular Medicine. 2024;102:899-912. doi:10.1007/S00109-024-02450-8.
  2. Xu J, Hu Y, Zhao J, Kong X, Xia S, Dai S, Ding L, Bu T, Cao Y, Liu M, Yan L, Xiao Q, Guo H, Yuan Y, Xu D, Ding K. Single-cell sequencing reveals alterations in the peripheral blood mononuclear cell landscape and monocyte status during colorectal adenocarcinoma formation. Clinical and Translational Medicine. 2024;14;e1609. doi:10.1002/ctm2.1609.
  3. Wu X, Yan H, Qiu M, Qu X, Wang J, Xu S, Zheng Y, Ge M, Yan L, and Liang L. Comprehensive characterization of tumor microenvironment in colorectal cancer via molecular analysis. eLife. 2023;12:e86032. doi:10.7554/eLife.86032.
  4. Shan N, Lu Y, Guo H, Li D, Jiang J, Yan L, Gao J, Ren Y, Zhao X, Hou L. CITEdb: a manually curated database of cell-cell interactions in human. Bioinformatics. 2022;38(22):5144-5148. doi:10.1093/bioinformatics/btac654.
  5. Liu M, Xia S, Zhang X, Zhang B, Yan L, Yang M, Ren Y, Guo H, Zhao J. Development and validation of a blood-based genomic mutation signature to predict the clinical outcomes of atezolizumab therapy in NSCLC. Lung Cancer. 2022;170:148-155. doi:10.1016/j.lungcan.2022.06.016.
  6. Wang S, Yang Y, Li L, Ma P, Jiang Y, Ge M, Yu Y, Huang H, Fang Y, Jiang N, Miao H, Guo H, Yan L, Ren Y, Sun L, Zha Y, Li N. Identification of Tumor Antigens and Immune Subtypes of Malignant Mesothelioma for mRNA Vaccine Development. Vaccines. 2022;10(8):1168. doi:10.3390/vaccines10081168.
  7. Xu B, Lu M, Yan L, Ge M, Ren Y, Wang R, Shu Y, Hou L, Guo H. A Pan-Cancer Analysis of Predictive Methylation Signatures of Response to Cancer Immunotherapy. Frontiers in Immunology. 2021;12. doi:10.3389/fimmu.2021.796647.
  8. Zhao B, Wu Q, Ye AY, Guo J, Zheng X, Yang X, Yan L, Liu Q, Hyde TM, Wei L, Huang AY. Somatic LINE-1 retrotransposition in cortical neurons and non-brain tissues of Rett patients and healthy individuals. PLOS Genetics. 2019;15(4):e1008043. doi:10.1371/journal.pgen.1008043.
  9. Yang CH, Li JR, Wu QX, Yang XX, Huang AY, Zhang J, Ye AY, Dou YM, Yan L, Zhou WZ, Kong L, Wang M, Ai C, Yang DC, Wei LP. AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder. Database, 2018. doi:10.1093/database/bay106.
  10. Dou YM, Yang XX, Li ZY, Wang S, Zhang Z, Ye AY, Yan L, Yang CH, Wu QX, Li JR, Zhao BX, Huang AY, Wei LP. Post-zygotic single-nucleotide mosaicisms contribute to the etiology of autism spectrum disorder and autistic traits and the origin of mutations. Human Mutation, 2017;38:1002-1013. doi:10.1002/humu.23255.
  11. Huang AY, Zhang Z, Ye AY, Dou YM, Yan L, Yang XX, Zhang YH, Wei LP. MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples. Nucleic Acids Research, 2017;45(10):e76-e76. doi:10.1093/nar/gkx024.
  12. Huang AY, Xu XJ, Ye AY, Wu QX, Yan L, Zhao BX, Yang XX, He Y, Wang S, Zhang Z, Gu BW, Zhao HQ, Wang M, Gao H, Gao G, Zhang ZC, Yang XL, Wu XR, Zhang YH, Wei LP. Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals. Cell Research, 2014;24:1311-1327. doi:10.1038/cr.2014.131.

Conference Papers:

  1. Hong YY, …, Yan L, et al. Validation of a comprehensive cancer genomic profiling assay. J Clin Oncol (ASCO 2019).
  2. Sun X, Fan LY, Yan L, et al. Deliver Bioinformatics Services in Public Cloud: Challenges and Research Framework. IEEE ICEBE, 2011.

Patents

  1. Guo H, et al., Yan L, et al. Method for constructing tumor immune checkpoint inhibitor therapy efficacy evaluation model based on DNA methylation profile. CN 112735513 A.
  2. Liu MJ, Guo H, Yan L, et al. Application of PCDH11X mutation in predicting sensitivity to immune checkpoint inhibitor therapy in NSCLC. CN 113355424 B.
  3. Liu MJ, Yan L, et al. Application of PCDHGB1 mutation in predicting sensitivity to immune checkpoint inhibitor therapy in lung adenocarcinoma. CN 113403399 B.
  4. Liu MJ, et al., Yan L, et al. Predicting immunotherapy efficacy in NSCLC based on bGMS. CN 114242157 A.

Open Source Software

Certifications

  • Project Management Professional (PMP), PMI ID: 6935481, 2021
  • International Genetic Counseling Certification (CUHK, Baylor College of Medicine, PUMCH), 2019

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