Y. S. Song

CherryML: Scalable Maximum Likelihood Estimation of Phylogenetic Models

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

Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions

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.

Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19

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 distribution of waiting distances in ancestral recombination graphs and its applications

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

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors

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

Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

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

Differences in the path to exit the ribosome across the three domains of life

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.

Efficiently inferring the demographic history of many populations with allele count data

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.

Evaluating Tumor Evolution via Genomic Profiling of Individual Tumor Spheroids in a Malignant Ascites from a Patient with Ovarian Cancer Using a Laser-aided Cell Isolation Technique

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.

Geometry of the sample frequency spectrum and the perils of demographic inference

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.

Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans

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.

Time-resolved proteomics vs. ribosome profiling reveals translation dynamics under stress

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

Inference of complex population histories using whole-genome sequences from multiple populations

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.