THE QUESTION

Cancer is a heterogeneous disease that complicates its study and therefore treatment. Immunotherapy has revolutionized cancer treatment but many patients still are faced with little or no clinical benefit with the same treatment. Recent high-dimensional technologies have allowed us the ability to understand the tumor ecosystem and its impact on treatment response. We are motivated by the question of how the tumor microenvironment changes upon cancer progression, before and after treatment, and if we can predict treatment responses based on blood immune cell signatures.

THE APPROACH

We follow a computational biology approach, using high-dimensional data from multi-omics genome-wide (genomics and epigenomics) and single-cell assays, data mining, and bioinformatics. We develop and employ computational biology methods to mine publicly available data and in-house generated data for the specific questions we ask.
Ultimately, our goal is to understand how tumor immune microenvironment changes toward finding immunotherapeutic biomarkers and targets.

Although our central questions focus on cancer, we are open to the collaborative environment in Madison to explore similar questions in other diseases.

Lab News

  • Aisha joined the lab as a postdoc! Welcome!

    Dr. Aisha Mergaert, a newly graduate from Dr. Miriam Shelef lab at the UW CMP program, joined us since June 01, 2021 to lead our effort in studying myeloid heterogeneity in cancer using high-dimensional flow …

  • Incoming summer students are joining the lab!

    This summer, we will welcome talented students joining the lab. Daniela Mejía, a PhD from BMI BioData Science (BDS), joined us this summer for a rotation project. She will be working on analyzing single-cell RNA-Seq …

  • Our fallopian tube epithelial scRNA-Seq paper is out:

    Single-cell transcriptomics create a cellular atlas for benign fallopian tubes A secretory-intermediate-ciliated path is projected for epithelial differentiation PAX8, SOX17, and RUNX3 potentially drive fallopian epithelial differentiation ‘‘Early secretory’’ epithelial cells are likely precursors for …

  • ACS IRG pilot grant awarded.

    We are awarded a pilot grant from Spring 2021 American Cancer Society Institutional Research Grant Pilot Award competition at University of Wisconsin Carbone Cancer Center (UWCCC). We will study monocyte and neutrophil heterogeneity in Multiple …

  • Graduate student joined the lab!

    Josh Brand joined us from the Cellular & Molecular Pathology program as the first graduate student in the lab. Welcome and looking forward to a fun ride. Parth Khatri joined us as an hourly master …

  • More News