Languages: Python, R, bash/shell Genomics: WES, WGS, bulk RNA-seq, scRNA-seq, NanoString, ATAC-seq, TCR-seq, lipidomics, cfDNA, mutation analysis, TMB, neoantigen analysis, pseudotime Spatialomics: 10x Visium, Visium HD, Xenium, Nanostring DSP/GeoMx, CosMx Digital Pathology: QuPath, napari, PathML, HoVerNet, H&E, IHC, WSI, TMA, multiplex IF, tile classification, deep feature clustering, TCGA, wsireg ML / Deep Learning: PyTorch, scikit-learn, GNN, CNN, fastai, HuggingFace, foundation models (Virchow2, LLaVa-Med) Bioinformatics: Seurat, scanpy, survminer, DESeq2, Limma, lme4, EdgeR, nf-core, samtools, CellRanger, SpaceRanger, GSEA, msigdb, TCGA, vegan, IPA, TCGAbiolinks Infrastructure: Nextflow, Singularity, SLURM/HPC, GPU (A100)
UPMC Hillman Cancer Center Bioinformatics Core | Pittsburgh, PA | 2021–Present
Lead computational biology for translational oncology programs, managing high-throughput pipelines across spatial omics and digital pathology. Direct and mentor a team of 5 bioinformaticians supporting multi-institutional immunotherapy studies.
-
Translational Multi-Omics & Biomarker Discovery: Integrate single-cell, spatial, and multiplex imaging datasets to define spatial immune phenotypes predictive of immunotherapy response across tumor types. Identified and validated biomarkers in TCGA survival analyses and downstream studies (Cancer Cell 2025, Cancer Discovery 2025, JCO 2025).
-
Machine Learning for Digital Pathology: Developed MuCTaL, a deployable multi-cancer tumor localization framework for whole-slide imaging, validated with pathologists and released via HuggingFace (Isett et al., arXiv 2026). Designed GNN-based models using foundation model (Virchow2) features to predict progression-free survival.
-
Spatial & Clinical Imaging Analytics: Built end-to-end pipelines for multiplex IF and H&E analysis, including tissue compartmentalization, cell segmentation, and statistical modeling of tumor–immune spatial interactions associated with clinical outcomes.
Carnegie Mellon University | Pittsburgh, PA | 2018–2021
Advisor: Dr. Aryn Gittis
- Awarded NIH F32 Postdoctoral Fellowship (NINDS).
- Developed analysis pipelines for large-scale in vivo electrophysiology (spike sorting, state-transition detection) and behavioral data (unsupervised ML clustering of open-field behavior EthoVision, DeepLabCut ) to interrogate underlying brain circuitry of Parkinson's Disease with DREADDs, light-activated proteins, and transgenic mouse lines.
- Published in Neuron (2023); contributed to Science (2021).
University of California, Berkeley | Berkeley, CA | 2010–2017
Advisor: Dr. Dan Feldman
- NSF Graduate Research Fellow; Outstanding GSI Award.
- Developed closed-loop behavioral conditioning robotics platform, novel signal processing (awake behaving current source density) and statistical analysis pipelines for high-density neural recordings of primary somatosensory cortex in mouse model system.
- Published in Neuron (2018) and Current Biology (2020)
Ph.D., Neuroscience — University of California, Berkeley | 2010–2017
B.S., Biological Sciences (Highest Distinction in Research) — Cornell University | 2005–2009
Isett B, Dadey R, Li A, Augustin RC, Smith K, Singhi AD, Gu Q, Bao R. A Lightweight Multi-Cancer Tumor Localization Framework for Deployable Digital Pathology. arXiv, 2026. doi.org/10.48550/arXiv.2603.08844
Doerfler R, Chen J, Kim C, …, Isett B, …, Bao R. Integrating AI-Driven Digital Pathology and Genomics to Establish Patient-Derived Organoids as a Novel Alternative Model for Drug Response in Head and Neck Cancer. bioRxiv, 2025. doi.org/10.1101/2025.06.24.660824
Nguyen MK, …, Isett B, …, Bao R. Clinical and translational study of ivosidenib plus nivolumab in advanced solid tumors harboring IDH1 mutations. The Oncologist, 2025. doi.org/10.1093/oncolo/oyaf362
Dadey RE, Li R, …, Isett B, …, Bao R. Multiomics identifies tumor-intrinsic SREBP1 driving immune exclusion in hepatocellular carcinoma. Journal for ImmunoTherapy of Cancer, 2025. doi.org/10.1136/jitc-2025-011537
Zandberg DP, Vujanovic L, …, Isett B, …, Bao R. Randomized Phase II Study of Concurrent Versus Sequential Pembrolizumab in Combination With Chemoradiation in Locally Advanced Head and Neck Cancer. Journal of Clinical Oncology, 2025.
Li H, Zandberg DP, …, Isett BR, …, Ferris RL. Distinct CD8+ T cell dynamics associate with response to neoadjuvant cancer immunotherapies. Cancer Cell, 2025.
Garcia GL, …, Isett BR, …, Coffman LG. Aged and BRCA mutated stromal cells drive epithelial cell transformation. Cancer Discovery, 2025.
Ritchlin CT, …, Isett B, et al. Psoriatic Arthritis Subtypes Are Phenocopied in Humanized Mice. JCI Insight, 2024. doi.org/10.1172/jci.insight.178213
Augustin RC, …, Isett B, …, Bao R. Identification of tumor-intrinsic drivers of immune exclusion in acral melanoma. J Immunother Cancer, 2023. doi.org/10.1136/jitc-2023-007567
Tran LM, …, Isett B, …, Thomson AW. Donor-derived regulatory dendritic cell infusion modulates effector CD8+ T cell and NK cell responses after liver transplantation. Science Translational Medicine, 2023.
Spix T, …, Isett BR, …, Gittis AH. Population-specific neuromodulation prolongs therapeutic benefits of deep brain stimulation. Science, 2021.
Isett BR*, Nguyen KP*, …, Gittis AH. The indirect pathway of the basal ganglia promotes transient punishment, but not motor suppression. Neuron, 2023.
Isett BR, Feldman DE. Cortical coding of whisking phase during surface whisking. Current Biology, 2020.
Isett BR*, Willard AM*, Whalen TC, Mastro JK, Ki CS, Mao X, Gittis AH. State transitions in the substantia nigra reticulata predict the onset of motor deficits in models of progressive dopamine depletion in mice. eLife, 2019.
Isett BR, Feasel SH, Lane MA, Feldman DE. Slip-based coding of texture and local shape in mouse S1. Neuron, 2018.
*Co-first authors
| Year | Award |
|---|---|
| 2019 | NIH F32 Postdoctoral Fellowship (NINDS), CMU |
| 2013 | Outstanding GSI Award, Neurobiology Laboratory, UCB |
| 2012 | NSF Graduate Research Fellowship |
| 2009 | Highest Honors for Honors Thesis, Cornell University |
| 2008 | Howard Hughes Summer Scholarship, Cornell University |