Research

Data integration

  • Baharav, T.Z.\(^*\), Nicol, P.B.\(^*\), Irizarry, R.A., and Ma, R. (2025). Stacked SVD or SVD Stacked? A Random Matrix Theory perspective on data integration. [Paper]

Statistical methods for single-cell and spatial sequencing data

  • Nicol,P.B., Ma, R., Xu, R.J., Moffitt, J.R., and Irizarry, R.A. (2025). Identifying spatially variable genes by projecting to morphologically relevant curves. [Paper][Software]

  • Nicol, P.B. and Miller, J.W. (2025). Model-based dimensionality reduction for single-cell RNA-seq using generalized bilinear models. Biostatistics. [Paper][Software]

  • Nicol, P.B., Paulson, D., Qian, G., Liu, X.S., Irizarry, R.A., and Sahu, A.D. (2024). Robust identification of perturbed cell types in single-cell RNA-seq data. Nature Communications. [Paper][Software]

Cancer evolution

  • McDonald, T.O., Cheng, Y., Graser, C., Nicol, P.B., Temko, D., and Michor, F. Computational approaches to modelling and optimizing cancer treatment. (2023). Nature Reviews Bioengineering. [Paper]

  • Nicol, P.B., Barabási, D.L., Coombes, K.R. and Asiaee, A. (2022). SITH: an R package for visualizing and analyzing a spatial model of intratumor heterogeneity. Computational and Systems Oncology. [Paper][Software]

  • Nicol,P.B., Coombes, K.R., Deaver, C., Chkrebtii, O.A., Paul, S., Toland, A.E., and Asiaee, A. (2021). Oncogenetic network estimation with disjunctive Bayesian networks. Computational and Systems Oncology. [Paper][Software]

  • Nicol, P.B. (2021). Modeling cancer evolution as an interacting particle system. Bachelor’s thesis, Harvard College. [Paper]

  • Nicol, P.B. (2020). Detecting subclones from spatially resolved RNA-seq data. In proceedings for International Symposium on Mathematical and Computational Oncology (ISMCO’20). [Paper]

Computational biology

  • Xu, R.J., Cadinu, P., Nicol, P.B., Herrmann, U.S., Lee, T., Geitslinger, L., Irizarry, R.A., and Moffitt, J.R. (2025). An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut. [Paper]

  • Sahu, A., Wang, X., Munson, P., Klomp, J., Wang, X., Gu, S., Qian, G., Nicol, P.B., Zeng, Z., Wang, C., Tokheim, C., Zhang, W., Fu, J., Wang, J., Nair, N.U., Rens, J., Bourajjaj, M., Jansen, B., Leenders, I., Lemmers, J., Musters, M., Zanten, S., Zelst, L., Worthington, J., Brown, M., Liu, J.S., Juric, D., Meyer, C.A., Oubrie, A., Liu, X.S., Fisher, D.E., and Flaherty, K.T. (2023). Discovery of targets for immune-metabolic antitumor drugs identifies Estrogen-related Receptor Alpha. Cancer Discovery. [Paper]