Pan Li

The contribution of recent and historical demographic histories to genomic diversity and conservation status in plant species

This study assesses conservation status in 101 plant species by analyzing demographic parameters and genomic diversity, finding that census size is the best predictor of extinction risk.

Evidence for plastome loss in the holoparasitic Mystropetalaceae

The paper provides evidence for plastome loss in the holoparasitic family Mystropetalaceae using DNA and RNA sequencing data.

Whole chloroplast genomes reveal a complex genetic legacy of lost lineages, past radiations and secondary contacts in the dominant temperate deciduous tree genus Fagus

The paper uses whole chloroplast genomes to trace the genetic history of Fagus, revealing ancient lineages, past radiations, and genetic admixture events.

Phylogenomics of Aristolochia subg. Siphisia (Aristolochiaceae) reveals widespread incomplete lineage sorting and supports a novel pollinator-filtering hypothesis

This study uses phylogenomic data to resolve Siphisia systematics, revealing incomplete lineage sorting and a novel pollinator-filtering pollination syndrome.

Retrieval Augmented Protein Language Models for Protein Structure Prediction

This paper introduces AIDO.RAGPLM and AIDO.RAGFold, models that improve protein structure prediction by integrating retrieved MSA with language models, achieving faster performance and better accuracy with limited MSA data.

Unveiling allopolyploidization-driven genome duplications through progressive analysis of deep genome skimming data

This study uses deep genome skimming data to analyze whole-genome duplication events in polyploid Prunus species, revealing allopolyploidization as a dominant evolutionary mechanism.

MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training

MSAGPT improves protein structure prediction by generating virtual MSAs through pre-training, enhancing accuracy in low-MSA scenarios.

Brassica napus L. dwarfing gene: Determining candidate intervals of dwarfing genes by BSA and SNP typing

This paper identifies a candidate interval for the dwarfing gene DW871 in Brassica napus using BSA and SNP typing, narrowing it to 15.51-16.60Mb on ChrA10.