Preprints

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

Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease P.S. Winter, M.L. Ramseier, A.W. Navia, S. Saksena, H. Strouf, N. Senhaji, A. DenAdel, M. Mirza, H.H. An, L. Bilal, P. Dennis, C.S. Leahy, K. Shigemori, J. Galvez-Reyes, Y. Zhang, F. Powers, N. Mulugeta, A.J. Gupta, N. Calistri, A.V. Scoyk, K. Jones, H. Liu, K.E. Stevenson, S. Ren, M.R. Luskin, C.P. Couturier, A.P. Amini, S. Raghavan, R.J. Kimmerling, M.M. Stevens, L. Crawford, D.M. Weinstock, S.R. Manalis, A.K. Shalek, M.A. Murakami (Under review)

Journal Articles

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

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

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

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer (2021) S. Raghavan, P.S. Winter, A.W. Navia, H.L. Williams, A. DenAdel, R.L. Kalekar, J. Galvez-Reyes, K.E. Lowder, J. Galvez-Reyes, R.L. Kalekar, N. Mulugeta, K.S. Kapner, M.S. Raghavan, A.A. Borah, N. Liu, S.A. Väyrynen, A. Dias Costa, R.W.S. Ng, J. Wang, E.K. Hill, D.Y. Ragon, L.K. Brais, A.M. Jaeger, L.F. Spurr, Y.Y. Li, A.D. Cherniack, M.A. Booker, E.F. Cohen, M.Y. Tolstorukov, I. Wakiro, A. Rotem, B.E. Johnson, J.M. McFarland, E.T. Sicinska, T.E. Jacks, R.J. Sullivan, T.E. Clancy, K. Perez, D.A. Rubinson, K. Ng, J.M. Cleary, L. Crawford, S.R. Manalis, J.A. Nowak, B.R. Wolpin, W.C. Hahn, A.J. Aguirre, and A.K. Shalek. Cell.