Publications

Publications List

  1. A. DenAdel, M. Hughes, A. Thoutam, A. Gupta, A.W. Navia, N. Fusi, S. Raghavan, P.S. Winter, A.P. Amini, L. Crawford. (2026) Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance. Nature Methods.

  2. M. DenAdel, C. Hamilton, A. Frankel, A. DenAdel, M. Dahlman. (2026) Genomic insights into endometriosis, adenomyosis, and uterine fibroids for the clinician. Current Opinion in Obstetrics and Gynecology.

  3. A. DenAdel, M.L. Ramseier, A.W. Navia, A.K. Shalek, S. Raghavan, P.S. Winter, A.P. Amini, L. Crawford. (2025) Artificial variables help to avoid over-clustering in single-cell RNA-sequencing. American Journal of Human Genetics.

  4. J. Stamp, A. DenAdel, D. Weinreich, L. Crawford. (2023) Leveraging the genetic correlation between traits improves the detection of epistasis in genome-wide association studies. G3: Genes, Genomes, Genetics.

  5. A. Conard*, A. DenAdel*, and L. Crawford. (2023) A spectrum of explainable and interpretable machine learning approaches for genomic studies. WIREs Computational Statistics.

  6. S. Raghavan, P.S. Winter, A.W. Navia, H.L. Williams, A. DenAdel, …, L. Crawford, S.R. Manalis, J.A. Nowak, B.R. Wolpin, W.C. Hahn, A.J. Aguirre, and A.K. Shalek. (2021) Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer. Cell.

Preprints and Under Review

  1. P.S. Winter, M.L. Ramseier, A.W. Navia, S. Saksena, H. Strouf, N. Senhaji, A. DenAdel, …, L. Crawford, D.M. Weinstock, S.R. Manalis, A.K. Shalek, M.A. Murakami. (2024) Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease. (under review at Cell)

  2. M. DenAdel, A. DenAdel, S. Rachid Zaim, K. Fox, M. Dahlman, M. Loring. (2026) Reoperation rates following surgical management of endometriosis: a single center retrospective cohort study. (under review at the Journal of Minimally Invasive Gynecology)