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Samuel Presman

Leanne Mahraj

RIPTiDe integrates transcriptomic data with a model to reveal metabolic differences between wildtype and mutated KRAS samples.

Mariah Snelson

Data collection techniques and image analysis for the study of glioblastoma multiforme and pancreatic ductal adenocarcinoma progression.

Joseph Guillen

Seth Boehringer

Bryan Rangel Valle

Riko Mukoyama

Iylan Howson

Olga Buhlak

A project under the SASCO umbrella focusing on studying the effect, and ultimately mechanism by which mitochondrial morphology and topology influences the distribution of proteins within the cell. My role in the project is to work with mitochondrial immunofluorescence data in order to develop a meaningful way to quantitatively describe mitochondrial morphology and topology, ultimately aiming to develop a set of features that can serve as a mitochondrial “fingerprint” for cell lines with distinct mitochondrial networks.

George Marshall

Treating glioblastoma cells with Prozac and chloroquine, then measuring effect on cell count.

Rose Olumuyide

My project will investigate how CCNF regulates FOXM1 activation throughout the cell cycle by combining protein measurements with transcriptional snapshots and computational modeling. First, I’ll synchronize cells at key cycle phases and directly quantify Foxm1 and Cyclin F protein levels at each stage. Next, I’ll use RNA-seq data from those synchronized cultures—and from breast cancer samples—to infer stage-specific FOXM1 transcriptional activity. Finally, I’ll map those activity profiles onto a model to reveal how CCNF-driven timing shapes FOXM1 dynamics and downstream regulatory programs. 2026 update: Rose is a Barry Goldwater Scholar in addition to previous honors of Ronald E McNair Scholar, John P & Anne Welsh McNulty Scholar, and NIH STEP UP Scholar.

Calum Dudgeon

Annabelle Cao

Annabelle, a senior at Albemarle County High School, worked with the SASCO data manager, Andrea Denton, on A Bibliometric Analysis of Citation Practices Among Basic Clinical Faculty in SASCO.  Annabelle will be attending Columbia University as an Egleston Scholar fall 2026.

Devora Slodowitz

Optimizing the Single-Cell Segmentation and Quality Control Pipeline for Highly Multiplexed Premalignant Breast Tissue – Iterative indirect immunofluorescence imaging (4i) is a multiplexed imaging method that enables single-cell spatial quantification of proteins across whole-tissue sections.  However, downstream analysis of 4i images is limited by inaccurate single-cell segmentation and imaging artifacts. A major challenge is whole-cell segmentation of dense cellular clusters. Using a 30-plex antibody panel applied to 14 archival premalignant breast specimens, we developed a streamlined image-processing pipeline for segmentation, feature extraction, and quality control. Starting with the nuclear (Hoechst) channel, we trained a deep-learning CellPose model that accurately segmented all cell types within the premalignant breast microenvironment. The custom-trained model significantly improved segmentation accuracy, capturing 97.8% of ground truth mask area compared to 85.5% for the CellPose base model. We then dilated the nuclear masks up to 7.5 µm to provide approximate whole-cell and cytoplasmic masks. To determine the optimal mask type for each protein marker, we generated log-transformed intensity histograms across candidate mask types, selecting for the mask type that maximized separation between positive and negative cell populations. Last, we used CyLinter to exclude imaging artifacts and tissue defects prior to downstream spatial analysis.  Overall, the newly streamlined image processing pipeline improves the accuracy of single-cell protein measurements from high-content images and ensures reliable spatial profiling of cell states within the premalignant breast microenvironment.

Alison Griffin

Automated micronucleus and nuclear condensation quantification for FOXM1 induced chromosomal instability – FOXM1 is a transcription factor that regulates different mitotic signaling proteins. Overexpression of FOXM1 is associated with cancer aggressiveness and aneuploidy in breast cancer, and recent work has suggested an important role for its condensation state in the nucleus. Breast epithelial cells were engineered with an inducible active ΔN-FOXM1 with or without S376 mutations that alter condensation. The objective is to quantify the effects on chromosomal instability by micronuclei formation and nuclear condensation. Cells were arrested in G2 and then released for 12 hours to evaluate micronuclei formation during the first cell cycle. The FOXM1 expression and nuclear condensation were evaluated by immunofluorescence in the ΔN-FOXM1, FOXM1S376A, and FOXM1S376E cells previously arrested in the G1/S and G2 phases. We found that FOXM1S376A cells have increased nuclear condensation compared with FOXM1S376E cells, where FOXM1 expression is diffusely localized in the nucleus. We are developing automated segmentation pipelines to distinguish micronuclei in hundreds to thousands of high-magnification images with the goal of defining the early impact on chromosome missegregation.

Riddhi Mishra

SHP2 base editing to prospectively identify mechanisms of resistance to RTK inhibitors –

Mutations in the phosphatase SHP2, encoded by PTPN11, cause developmental disorders, are common in hematologic malignancies, and drive resistance to kinase inhibitors in solid cancers. SHP2 mutations of unknown biochemical function arise frequently in genetic profiling of tumors, and there is an urgent need to prospectively identify those that cause resistance to targeted therapies. We used a base editing approach to systematically identify PTPN11 mutations that promote resistance to the EGFR inhibitor osimertinib in PC9 cells, a common model of EGFR oncogene addiction in non-small cell lung cancer. An sgRNA library targeting PTPN11 was designed to screen the effects of loss- and gain-of-function mutations in base editor-transduced PC9 cells treated with osimertinib. The five sgRNAs producing the greatest depletion and enrichment of PC9s, along with the five sgRNAs predicted to make the most clinically prevalent and base editor-accessible naturally occurring alleles, were prioritized for evaluation by cloning single sgRNAs. In base editor-expressing cells, the abundance of guide-transduced (GFP+) PC9 cells was tracked over time with or without osimertinib selection to confirm phenotypes inferred from the library screen. PTPN11 sequencing confirmed base edits and demonstrated the ability of the experimental pipeline to map mutations of unknown consequence to EGFR inhibitor resistance.

Sarah Groves

Sarah Groves developed the first of three videos designed to introduce clinicians to systems concepts and approaches.

Watch the Video here.

• Multiple meetings with Todd Stukenberg to brainstorm and outline first video
• Met with BJ Purrow (MD/PhD Project 3) to discuss challenges/goals of working with MDs
• Established collaborations with Cimona Hinton to provide feedback for each of the stages of the video

Rusty Hawes

Rusty Hawes will develop the second of three videos designed to introduce clinicians to systems concepts and approaches.

Cimona Hinton

Our first scholar-in-residence collaborator, Cimona Hinton, PhD is featured in this UVa School of Medicine article.

Nakea Pennant

Lecia Robinson, PhD

Lecia Robinson PhD, our second scholar-in-residence collaborator, worked in the Kashatus Project 2 Lab.

Christopher Bolden, PhD