Y. S. Song

CherryML provides a scalable method for maximum likelihood estimation of phylogenetic models, achieving significant speedup in parameter estimation for molecular evolution.

The paper assesses the transferability of geometric patterns from protein self-contacts to protein-ligand contacts and shows some contact types are highly transferable, with data released for further research.

The paper examines IFN-I autoantibodies in critical COVID-19 patients through longitudinal single-cell analysis, revealing suppressed ISG-I responses in myeloid cells.

The paper derives an analytic expression for waiting distances in ancestral recombination graphs and identifies biases in existing tree inference methods.

The paper identifies microbial features predictive of necrotizing enterocolitis (NEC) in premature infants using metagenomic analysis and machine learning.

The paper infers population-specific recombination maps across 26 human populations, revealing demographic and genetic factors influencing recombination rates.

The paper compares ribosome exit tunnel structures across bacteria, archaea, and eukarya to understand geometric and sequence conservation patterns and their implications for translation dynamics.

The paper introduces a method to efficiently compute the expected sample frequency spectrum for complex demographic histories described by general directed acyclic graphs, and applies it to estimate a basal Eurasian admixture event in humans.

The paper uses genomic profiling of tumor spheroids from malignant ascites to evaluate tumor evolution in an ovarian cancer patient, finding genetic differences between primary tumor and spheroids.

This paper analyzes the geometry of the sample frequency spectrum and shows that demographic inference methods suffer from inherent pathologies due to the non-convex and open structure of the SFS space.

This study introduces a model-based method to detect Neanderthal introgression in modern humans and finds weak selection against Neanderthal ancestry, possibly due to higher genetic load in Neanderthals.

The paper compares time-resolved proteomics and ribosome profiling to study translation dynamics under stress in multiple myeloma cells treated with bortezomib.

The paper introduces diCal2, a statistical method to infer complex population histories from whole-genome sequences, finding that Australian and Papuan populations diverged from East Asians and Europeans around 100,000 years ago with ongoing gene flow.