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Biorxiv : the Preprint Server for Biology|December 3, 2025
The Rayleigh Quotient and Contrastive Principal Component Analysis IMaria Carilli, Kayla Jackson, Lior PachterBiorxiv : the Preprint Server for Biology|April 17, 2026
The Rayleigh Quotient and Contrastive Principal Component Analysis IIKayla Jackson, Maria Carilli, Lior PachterBiophysical Journal|May 8, 2024
Spectral neural approximations for models of transcriptional dynamicsGennady Gorin, Maria Carilli, Tara Chari, et al.Biorxiv : the Preprint Server for Biology|January 30, 2023
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing dataMaria Carilli, Gennady Gorin, Yongin Choi, et al.Nature Methods|July 25, 2024
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing dataMaria Carilli, Gennady Gorin, Yongin Choi, et al.Biorxiv : the Preprint Server for Biology|November 24, 2025
Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing dataGennady Gorin, Tara Chari, Maria Carilli, et al.Nature Methods|November 7, 2025
Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing dataGennady Gorin, Tara Chari, Maria Carilli, et al.Biorxiv : the Preprint Server for Biology|January 3, 2024
Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expressionLaura Luebbert, Delaney K Sullivan, Maria Carilli, et al.Nature Biotechnology|April 22, 2025
Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changesLaura Luebbert, Delaney K Sullivan, Maria Carilli, et al.Biorxiv : the Preprint Server for Biology|April 10, 2026
Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variationRyan Weber, Maria Carilli, Elisabeth Rebboah, et al.Pageof 2