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Advances in Neural Information Processing Systems|June 9, 2025
Ultrafast classical phylogenetic method beats large protein language models on variant effect predictionSebastian Prillo, Wilson Wu, Yun S Song
Genome Research|May 14, 2026
Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-JoiningKevin An, Sebastian Prillo, Wilson Wu, et al.
Systematic Biology|August 12, 2025
ConvexML: Fast and accurate branch length estimation under irreversible mutation models, illustrated through applications to CRISPR/Cas9-based lineage tracingSebastian Prillo, Akshay Ravoor, Nir Yosef, et al.
Proceedings of the National Academy of Sciences of the United States of America|May 14, 2025
Exact and efficient phylodynamic simulation from arbitrarily large populationsMichael Celentano, William S DeWitt, Sebastian Prillo, et al.
Biorxiv : the Preprint Server for Biology|December 11, 2023
ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing dataSebastian Prillo, Akshay Ravoor, Nir Yosef, et al.
Arxiv|March 11, 2024
Exact and efficient phylodynamic simulation from arbitrarily large populationsMichael Celentano, William S DeWitt, Sebastian Prillo, et al.
Nature Methods|June 29, 2023
CherryML: scalable maximum likelihood estimation of phylogenetic modelsSebastian Prillo, Yun Deng, Pierre Boyeau, et al.
Biorxiv : the Preprint Server for Biology|February 27, 2026
Deep models of protein evolution in time generate realistic evolutionary trajectories and functional proteinsAntoine Koehl, Sebastian Prillo, Matthew Liu, et al.
Biorxiv : the Preprint Server for Biology|September 26, 2025
Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language modelsChengzhong Ye, Gonzalo Benegas, Carlos Albors, et al.
Biorxiv : the Preprint Server for Biology|July 10, 2026
Can you trust your reconstructed lineage tree? A homoplasy-based approach for irreversible evolutionPini Zilber, Sebastian Prillo, Yaara Neumeier, et al.
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