Our Team

Fan Zhang, PhD

Assistant Professor and Principal Investigator (PI)

‍Google Scholar | ORCID | Linkedin | Twitter | Bluesky

Fan’s research, spanning computational AI method development and translational immunology, is supported by multiple NIH and foundation grants as PI, including an NIH NIAMS R01, NIH AMP-AIM Team Science Leadership Scholars Program, NIH Office of Women’s Health, NIH Office of Data Science Strategy, NIAID P01 (Project Lead), Arthritis Foundation, Arthritis National Research Foundation, and PhRMA.

Fan completed her Postdoc research with Prof. Soumya Raychaudhuri at Harvard Medical School, Brigham and Women’s Hospital, and Broad Institute of Harvard/MIT (2017 - 2021), where she developed computational approaches to integrate single-cell multi-omics data to study autoimmune diseases through the NIH-funded Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) network.

Fan earned her Ph.D. (2013-2017) from Worcester Polytechnic Institute, Massachusetts. She developed novel statistical machine learning methods in the fields of variational Bayesian inference and mixed-membership matrix factorization with Prof. Patrick Flaherty (UMass Amherst Dept. of Mathematics & Statistics) for large genomic data.

Team Members

  • Lauren Vanderlinden, PhD

    Postdoc Fellow
    Github | Linkedin | ORCID
    Lauren earned her PhD in Epidemiology and a Master in Biostatistics from CU. She is interested in connecting genetics with single-cell phenotypes.

  • Shunsuke Uchiyama, MD/PhD

    Postdoc Fellow
    ORCID

    As a computational biologist and rheumatologist, Shunsuke’s work focuses on modeling proteomics and integration with genomics for disease progression.

  • Jade Young

    PhD Student

    CPBS PhD Program
    ORCID | LinkedIn

    Jade is interested in leveraging large omics to develop AI and foundation models for identifying targets in precision medicine.

  • Nanxi Guo

    PhD Student
    Biostatistics and Informatics
    ORCID | LinkedIn
    Nanxi focuses on developing statistical machine learning models for single-cell spatial transcriptomics to uncover disease-associated spatial niches.

  • Samantha Reynoso

    PhD Student
    CPBS PhD Program
    ORCID | LinkedIn

    Sam is interested in developing new machine learning tools for spatial transcriptomics using spatial information.

  • Breanna Remigio

    PhD student
    CPBS PhD program
    LinkedIn

    Breanna’s research focuses on developing tensor decomposition methods for single-cell spatial omics.

  • Christian Anderson

    PhD Student
    CPBS PhD program
    LinkedIn

    Christian is interested in developing computational approaches for trajectory inference for omics data.

  • Revanth Krishna, MS

    Software Engineer

    LinkedIn | Github | ORCID

    Master in Data Science. Co-supervised with Chuangqi Wang’s lab. Revanth builds user-friendly software tools for single-cell omics.

  • Juan Vargas, MPH

    Bioinformatician

    Github

    Juan focuses on developing computational pipelines and software to analyze and interpret complex datasets.

Alumni

  • Jun Inamo, MD/PhD

    Postdoc Fellow
    Twitter | ORCID | Google Scholar
    Jun’s research focuses on integrating single-cell data to identify predictive markers for autoimmune disease progression.

  • Courtney Schiebout, PhD

    Bioinformatician

    Courtney graduated from Dartmouth College in the Quantitative Biomedical Sciences.

  • Helen Wolde, BS

    Computational Bioscience (CPBS) Summer student (2022)

    Biostatistics MS program (2023-2025)

  • Yonatan Wolde, BS

    Computational Bioscience (CPBS) Summer student (2022)

    Biostatistics MS program (2023-2025)

  • Kewalin Samart

    PhD Rotating Student 2023
    Computational Bioscience (CPBS) PhD Program
    CU School of Medicine

  • Hope Townsend

    PhD Rotating Student 2023

    Interdisciplinary Quantitative Biology Program CU Boulder

  • Douglas Fritz

    MSTP Rotating Student 2022

    Interested in ML for complex immunology system. He is now in NIH Oxford-Cambridge Scholars Program.

  • Hannah Wang

    Research Intern (2022)
    Hannah was a talented local Colorado high school student. Now she is an undergraduate student at MIT.

  • Jessica Lee

    PhD Rotating Student 2024
    Immunology PhD Program
    CU School of Medicine

  • Grace Akatsu

    MSTP Rotating Student 2023

    CU School of Medicine

  • Nicholas Cordaro

    MSTP Rotating Student 2023

    CU School of Medicine

Collaborators

  • Dr. A. Helena Jonsson: University of Colorado Anschutz Medical Campus

  • Dr. Kevin Deane: University of Colorado Anschutz Medical Campus

  • Dr. Michael Holers: University of Colorado Anschutz Medical Campus

  • Dr. Kristi Kuhn: University of Colorado Anschutz Medical Campus

  • Dr. Laura Donlin: Hospital for Special Surgery (HSS) and Weill Cornell Medicine

  • Dr. Deepak Rao: Brigham and Women’s Hospital and Harvard Medical School

  • Dr. Michael Brenner: Brigham and Women’s Hospital and Harvard Medical School

  • Dr. Edy Kim: Brigham and Women’s Hospital and Harvard Medical School