Research

My research interests are centered around developing computational methods for analyzing genomics data.

This list of papers is out of date. For an up to date list, please visit my google scholar.

Papers

R. Kunes*, T. Walle*, T. Nawy, D. Pe’er. Supervised discovery of interpretable gene programs from single-cell data. 2023. (link)
J. Remsik, X. Tong, R. Kunes … D. Pe’er, A. Boire. Leptomeningeal anti-tumor immunity follows unique signaling principles. (link)
R. Kunes, Mingzhang Yin, Max Land, D. Pe’er, S.Tavaré. Gradient Estimation for Binary Latent Variables via Gradient Variance Clipping. 2023. AAAI Conference on Artificial Intelligence Oral Presentation.(link)
S. Mani, D. Haviv, R. Kunes, D. Pe’er. SPOT: Spatial Optimal Transport for Analyzing Cellular Microenvironments. ICML Workshop in Computational Biology 2023 (link)
T. Walle … R. Kunes … Cytokine release syndrome-like serum responses after Covid-19 vaccination are frequent but clinically inapparent in patients under immune checkpoint therapy. Nature Cancer 2022 (link)
Y. Xiao … R. Kunes … Cross-platform analysis reveals cellular and molecular landscape of glioblastoma invasion. Neuro-oncology. 2022 (link)
R. Kunes, S. He, Y. Xiao, S. Tavare, D. Knowles. (2020) Supervised Tumor Cell Subtype Identification via SCAN. ICML Workshop in Computational Biology 2020.(link)
R. Kunes*, J. Ren*, F. Doshi Velez. (2020) Prediction Focused Topic Models via Vocab Filtering. In AISTATS ‘20 (link)
R. Kunes*, J. Ren*, F. Doshi Velez. (2019) Prediction Focused Topic Models for Electronic Health Records. Neural Information Processing Sytems Workshop in Machine Learning for Healthcare ‘19 (link)

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing. Cell. 2019. (link)