Publications

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Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation

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)
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Functional and computational interrogation of the juvenile idiopathic arthritis risk loci identifies candidate causal SNPs and target genes in CD4+ T cells

Published in medRxiv, 2025

Recommended citation: K. Jiang, E. K. Haley, G. Barshad, A. Y. He, A. Rogic, E. Rice, M. Sudman, S. D. Thompson, C. G. Danko, J. Jarvis. Functional and computational interrogation of the juvenile idiopathic arthritis risk loci identifies candidate causal SNPs and target genes in CD4+ T cells. medRxiv. doi:10.64898/2025.12.15.25342296
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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

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, T. Sims, G. A. Daniels, A. Meisel, A. Sezer, M. Gogishvili, T. Melkadze, A. Baramidze, T. Makharadze, A. Y. He, V. Jankovic, G. Geba, A. Pillai, F. Seebach, P. Rietschel, G. Gullo, J. 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. doi:10.1016/j.ctarc.2025.100959.
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Training deep learning models on personalized genomic sequences improves variant effect prediction

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
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Using functional genomic data in monocytes/macrophages and genotyping to nominate disease-driving single nucleotide polymorphisms in juvenile idiopathic arthritis.

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
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Topological descriptions of protein folding

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.
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Bcl-2 overexpression improves survival and efficacy of neural stem cell-mediated enzyme prodrug therapy

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.
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Adam Y. He