Sam Wang

About

I am a computational biologist with expertise in AI/Machine Learning and Cancer Genomics. I am passionate about developing novel models for cancer research and have experience in various bioinformatics techniques and programming languages.

Education

Harvard Medical School - S.M. in Biomedical Informatics, GPA: 4.0/4.0 (Aug 2022 – May 2024)

Concentrations: AI/Machine-Learning and Cancer Genomics

University of California – San Diego - B.S. in Bioengineering: Bioinformatics, GPA: 3.84/4.0 (Sep 2018 – June 2022)

Concentrations: Computer Science and Cancer Genomics

Publications

• Xi Wang, Simona Cristea, evoCancerGPT: Generating Cancer Progression Using Single-Cell RNA Sequencing Data in a Zero-Shot Manner, October 2024.
  Submitted to The 29th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2025).
  (Manuscript).
• Marcos Díaz-Gay, Raviteja Vangara, Mark Barnes, Xi Wang, S M Ashiqul Islam, Ian Vermes, Stephen Duke, Nithish Bharadhwaj Narasimman, Ting Yang, Zichen Jiang, Sarah Moody, Sergey Senkin, Paul Brennan, Michael R Stratton, Ludmil B Alexandrov, Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment, Bioinformatics, Volume 39, Issue 12, December 2023.
  (Manuscript).

Presentations

• Xi Wang, Simona Cristea, Generating Cancer Progression and Cell State Dynamics Using Single-Cell RNA Sequencing Data with evoCancerGPT, The 18th Program in Quantitative Genomics (PQG Conference 2024), October 2024 (Poster).
  Stellar Abstract Award.
  (Poster).
• Omar Albastaki, Terry Cho, Qassi Gaba, Sivateja Tangirala, Xi Wang, Machine Learning for Early Detection of Dementia-Related Diagnoses from Routine Blood Lab Test Data, Harvard Medical School Deep Learning for Biomedical Data, May 2023 (Presentation).
  (Poster).
• Xi Wang, Marcos Díaz-Gay, Ludmil Alexandrov, Mutational Signature Assignment Benchmark, The Annual 35th Undergraduate Research Conference at UC San Diego, May 2022 (Presentation).
  (Poster).

Research Experience

Cristea Lab, Hale Family Center for Pancreatic Cancer Research

Role: Computational Biologist (July 2024 – Current)

Developing novel AI/ML transformer decoder-only large foundation language models for inferring and generating cancer evolution at the single-cell level using scRNAseq data under Dr. Simona Cristea, PhD. The work includes data aggregation using publicly available scRNAseq datasets, pseudo cell evolution progression generations from k-nearest neighbors, and constructing custom transformer models for cancer cell evolution prediction.

Wolpin-Nowak Lab, Dana-Farber Cancer Institute

Role: Computational Biologist (July 2024 – Current)

Collaborating with Dr. Brian Wolpin, MD, MPH, Dr. Jonathan Nowak, MD, PhD, and Dr. Andrew Aguirre, MD, PhD, on a project analyzing biomarkers and tumor micro-environments of pancreatic cancer using spatially resolved single-cell RNA sequencing data. This study involves constructing standardized pipelines for cell type annotations and tumor subtyping, and validating results with spatial information.

Liu Lab, Dana-Farber Cancer Institute

Role: Graduate Student Researcher (Nov 2022 – May 2024)

Focused on developing deep neural networks for inferring melanoma tumor ploidy, purity, cancer cell fractions, and heterogeneity from tumor-only targeted panel sequencing data under Dr. David Liu, MD, MPH, MS. Responsibilities included data cleaning, variant allele frequency (VAF) analysis, read depth analysis, and developing statistical models for cancer cell fraction and heterogeneity inferences.

Alexandrov Lab, University of California, San Diego

Role: Undergraduate Bioinformatics Researcher (May 2021 – Aug 2022)

Conducted a comprehensive benchmarking of mutational signature assignment tools under Dr. Ludmil B. Alexandrov, PhD. This involved the installation and execution of over 20 different mutational signature assignment tools, data analysis, benchmarking using synthetic datasets, and upgrading SigProfilerSingleSample, the assignment tool developed by the Alexandrov lab.

Masuda Lab, University of California, San Diego

Role: Staff Research Associate (May 2022 – Aug 2022)

Worked on intervertebral disc restoration using a rabbit model under Dr. Koichi Masuda, MD. Responsibilities included performing pre-operational, surgical, and post-operational procedures, and conducting 2D x-rays and 3D micro-CT post-harvesting analysis.

Cartilage Tissue Engineering Lab, University of California, San Diego

Role: Undergraduate Researcher (Apr 2019 – Aug 2022)

Worked on a senior design project for surgical restoration of the anterior cruciate ligament and knee biomechanics, including improving surgical techniques for ACL reconstruction using rabbit models and quantifying marine animal teeth enamel structure using micro-CT.

Projects

RxPlorer, Harvard University

Pre-trained Large Language Model for biomedical research meta-analysis. Involved fine-tuning Llama2 and creating a web-frontend and backend.

Yogurt World

Designed a website for UCSD’s favorite yogurt place using HTML and Figma, implemented on GitHub.

Zoo Seeker

Android app that uses the Traveling Salesman algorithm to find the shortest path to animal exhibits.

Skills

AI/ML, Programming Languages (R, Python, Java, C, C++), Git, Node.js, React, MySQL, MongoDB, Flask, AWS, Docker, Google Cloud Service, Linux, HTML/CSS, Bioinformatics Techniques.

Contact

Email: xiwang@hms.harvard.edu