Cai Li

The paper develops a variational framework for modeling population genetic dynamics, incorporating mutation, recombination, and selection, and validates it against simulations.

The paper identifies APOBEC3-associated hypermutability in spliceosomal snRNA genes across species, showing lineage-specific activity rather than R-loop formation alone.

The paper identifies high mutation rates in histone genes due to AID/APOBEC enzymes and introduces HistMTR to predict pathogenicity, showing histone mutations contribute to diseases.

This study reconstructs a time-calibrated hummingbird phylogeny, finding stepwise diversification in the Andes rather than a monophyletic Andean clade.

The paper measures de novo mutation rates in amphioxus, finding a mutation rate comparable to vertebrates and attributing high heterozygosity to large population size.

MuRaL-indel predicts germline INDEL mutation rates using deep learning, achieving high accuracy and broad applicability across species and genomic scales.

This paper develops a bioinformatic pipeline to detect meiotic recombination events in the highly heterozygous amphioxus genome using short-read sequencing of a two-generation pedigree.

MuRaL, a two-module neural network using only DNA sequence, estimates nucleotide-level germline substitution rates, outperforming k-mer and feature-based human models at fine regional scales.

The paper investigates how nucleosome positioning stability influences germline mutation rates using de novo mutation data and high-resolution nucleosome maps.

The paper presents a draft genome assembly of the alkali bee and identifies genes under selection and population genetic patterns.

The paper analyzes 200,000 human TSSs to understand how new TSSs originate and evolve, finding that repetitive sequences and regulatory modules influence their emergence and modification over time.

The paper reports the nuclear and mitochondrial genome sequences of the orchid bee Euglossa dilemma, providing a high-quality assembly and gene set, and highlighting gene synteny conservation with honey bees.