Published in BioRxiv, 2026
Recommended citation: A. Y. He and C. G. Danko. pydreg: a fast Python package for identifying active cis-regulatory elements from nascent transcription. BioRxiv. doi:10.64898/2026.09.06.745329
Download Paper
Published in HGG Advances, 2026
Recommended citation: K. Jiang, E. K. Haley, G. Barshad, A. Y. He, A. Rogic, E. Rice, M. Sudman, S. D. Thompson, D. A. Murphy, Y. Fu, L. Ponder, M. D. Munoz, P. Kolachala, S. Prahalad, P. M. Gaffney, C. G. Danko, and J. N. Jarvis. Functional and computational interrogation of juvenile idiopathic arthritis risk loci in CD4+ T cells. HGG Adv. 7(3):100619. doi:10.1016/j.xhgg.2026.100619
Download Paper
Published in Nature Genetics, 2026
Recommended citation: A. Y. He and C. G. Danko. Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation. Nat. Genet. (in press)
Download Paper
Published in Cancer Treatment and Research Communications, 2025
Recommended citation: R. J. Acosta, D. A. G. McIntyre, J. C. Murray, V. Anagnostou, J. R. Brahmer, A. Meisel, A. Sezer, M. Gogishvili, T. Melkadze, A. Baramidze, T. Makharadze, A. Y. He, V. Jankovic, G. P. Geba, A. Pillai, F. Seebach, P. Rietschel, G. Gullo, J.-F. Pouliot, and Y. Kim. Peripheral blood cells as prognostic markers in patients with advanced non-small cell lung cancer treated with cemiplimab as monotherapy or in combination with chemotherapy. Cancer Treat. Res. Commun. 44:100959. doi:10.1016/j.ctarc.2025.100959.
Download Paper
Published in BioRxiv, 2024
Recommended citation: A. Y. He, N. P. Palamuttam, and C. G. Danko. Training deep learning models on personalized genomic sequences improves variant effect prediction. BioRxiv. doi.org/10.1101/2024.10.15.618510
Download Paper
Published in BioRxiv, 2024
Recommended citation: E. K. Haley, G. Barshad, A. Y. He, E. J. Rice, M. Sudman, S. D. Thompson, E. A. Crinzi, K. Jiang, C. G. Danko, and J. N. Jarvis. Using functional genomic data in monocytes/macrophages and genotyping to nominate disease-driving single nucleotide polymorphisms in juvenile idiopathic arthritis. BioRxiv. doi:10.1101/2024.08.19.608312
Download Paper
Published in Proceedings of the National Academy of Sciences of the United States of America, 2019
Recommended citation: E. Flapan, A. Y. He, and H. Wong. Topological descriptions of protein folding. Proc. Natl. Acad. Sci. U.S.A. doi:10.1073/pnas.1808312116.
Download Paper
Published in Stem Cells International, 2018
Recommended citation: R. Mooney, A. A. Majid, D. Mota, S. Aramburo, A. Y. He, J. Covello-Batalla, D. Machado, J. Gonzaga, L. Flores, and K. S. Aboody. Bcl-2 overexpression improves survival and efficacy of neural stem cell-mediated enzyme prodrug therapy. Stem Cells Int. doi:10.1155/2018/7047496.
Download Paper