Publications

An up-to-date list of my publications is also available via my Google Scholar profile.

1. [preprint] (2026) Sweeney, MD. and Kang, HM. (2026) "Practical utility of sequence-to-omics models for improving the reproducibility of genetic fine-mapping". biorXiv, 2026.02.04.70379.
2. [preprint] (2025) Ciotlos, DL., Hanks, SC., Varshney, A., Erdos, MR., Manickam, N., Stringham, HM., Orchard, P., Hill-Burns, EM., Narisu, N., Bonnycastle, LL., Sweeney, MD., Saramies, J., Laakso, M., Tuomilehto, J., Lakka, TA., Mohlke, KL., Boehnke, M., Collins, FS., Koistinen, HA., Parker, SCJ., Scott, LJ. "Inverse directions of association of higher physical activity and higher insulin resistance with human skeletal muscle cell type abundance and fiber-type-level gene expression". biorXiv, 2025.10.27.683567.
3. [preprint] (2025) Johnson, KA., Jones, F.K., Ghadiali, R.S., Lee, G., Torre-Healy, LA., Sweeney, MD., Moffitt, RA., Mamchaoui, K., Ricci, E., Young, I., Pisconti, A. "Enhancement of Prednisolone efficacy and safety in Duchenne muscular dystrophy via neutrophil elastase inhibition". biorXiv, 2025.02.26.640472.
4. [link] (2025) Hanks, SC., Mauger, AS., Varshney, A., Ciotlos, DL., Manickam, N., Narisu, N., Shumway, AJ., Orchard, P., Erdos, MR., Sweeney, MD., Okamoto, J., Jackson, AU., Stringham, HM., Bonnycastle, LL., Zhou, X., Lakka, TA., Mohlke, KL., Tuomilehto, J., Laakso, M., Boehnke, M., Sethupathy, P., Collins, FS., Koistinen, HA., Parker, SCJ., Scott, LJ. "Extensive differential gene expression and regulation by sex in human skeletal muscle". Cell Genomics, 5, 100915.
5. [link] (2023) Sweeney, MD., Torre-Healy, LA., Ma, VL., Hall, MA., Chrastecka, L., Yurovsky, A., Moffitt, RA. "FaStaNMF: a fast and stable non-negative matrix factorization for gene expression". IEEE/ACM Transactions on Computational Biology and Bioinformatics, 21, 1633-1644.