Publications

Huijse, L.^*, Adams, S.M.^*, Burton, J.N.^*, David, J.K.^*, Julian, R.S.^*, Meshulam-Simon, G.^*, Mickalide, H.^*, Tafesse, B.D.^*, Calonga-Solís V., Wolf, I.R., Morrison, A.J., Augusto, D.G., Endlich, S^*. (2023) A pan-MHC reference graph with 246 fully contiguous phased sequences. biorxiv doi:10.1101/2023.09.01.555813. *authors contributed equally

David, J.K.^*, Maden, S.K.^*, Wood, M.A., Thompson, R.F., Nellore, A. (2022) Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads. Genome Biology. 23, 240. *co-first authors

Nguyen, A., David, J.K., Maden S.K., Wood M.A., Weeder, B.R., Nellore, A., Thompson, R.F. (2020). Human leukocyte antigen susceptibility map for SARS-CoV-2. Journal of Virology. JVI.00510-20.

Wood, M.A., Weeder, B.R., David, J.K., Nellore, A., Thompson, R.F. (2020). Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival. Genome Medicine, 12, 33.

David, J.K., Maden, S.K., Weeder, B.R., Thompson, R.F., Nellore, A. (2020). Putatively cancer-specific exon–exon junctions are shared across patients and present in developmental and other non-cancer cells. NAR Cancer, 2, zcaa001.

David, J.K., Wyatt, R.E. (2009). Computation of barrier transmission probabilities from two-dimensional real-valued approximate quantum trajectories. Chemical Physics Letters, 481, 234-239.

David, J.K., Wyatt, R.E. (2008). Barrier scattering with complex-valued quantum trajectories: Taxonomy and analysis of isochrones. Journal of Chemical Physics, 128, 094102.

Manuscripts in Preparation
David, J.K., Prelot, L., Kahles, A., Ratsch, G., Thompson, R.F., Nellore, A. Comprehensive analysis of methods for detection and validation of aberrant splicing-derived cancer-specific neoepitopes.

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