Song Li

The broad ecological range of Salmonella enterica serotype Typhimurium is associated with genomic diversification

This study analyzes 595 Salmonella Typhimurium genomes to show that food animal isolates have more open pangenomes and antimicrobial resistance genes, with swine isolates showing the most diversity and plasmid prevalence.

A chromosome-scale reference genome and single-nucleus root atlas reveal the cellular and molecular basis of coastal adaptation in sand bean (Strophostyles helvola)

The paper generates a chromosome-scale genome and single-nucleus transcriptomic atlas of sand bean roots to study coastal adaptation, finding that salt tolerance in Beach ecotypes relies on pre-existing, spatially organized stress-response programs.

Single nucleus transcriptome analysis of Arabidopsis thaliana roots infected with Phytophthora. capsici

The paper uses snRNA-seq to analyze Arabidopsis root cell responses to P. capsici infection, identifying transcriptional changes and hormone-related pathways in different cell types.

Integrative analysis of papain-like cysteine proteases and cystatins reveals stress-dependent regulatory modules in Arabidopsis thaliana

The paper integrates expression and inhibition data to identify stress-dependent PLCP-cystatin regulatory modules in Arabidopsis thaliana.

Harnessing DNA Foundation Models for Cross-Species Transcription Factor Binding Site Prediction in Plant Genomes

This study evaluates DNA foundation models for predicting TFBSs in plants, finding HyenaDNA outperforms other methods in accuracy and efficiency.

PLM-OMG: Protein Language Model-Based Ortholog Detection for Cross-Species Cell Type Mapping

PLM-OMG uses protein language models to detect orthogroups and map cell types across plant species, showing better accuracy than traditional methods.

scCoBench: Benchmarking single cell RNA-seq co-expression using promoter-reporter lines

scCoBench benchmarks co-expression methods in scRNA-seq using promoter-reporter lines, showing imputation improves correlation and biological relevance.

Cross-species single-cell annotation with orthologous marker gene groups

The paper develops a method to annotate cell types across species using orthologous marker gene groups, identifying conserved cell-type markers in 15 plant species.

Long-read sequencing reveals novel structural variation markers for key agronomic and quality traits of soybean

The paper uses long-read sequencing to identify structural variations in soybean genomes linked to agronomic and quality traits.

Identification of new marker genes from plant single-cell RNA-seq data using interpretable machine learning methods

The paper introduces SPmarker, an interpretable machine learning pipeline to identify new cell-type marker genes in Arabidopsis root single-cell RNA-seq data, finding hundreds of novel markers and expanding trichoblast markers across species.

Identifying gene regulatory networks of senescence in postharvest broccoli (Brassica oleracea)

The paper identifies gene regulatory networks involved in senescence of postharvest broccoli florets using RNA-sequencing to inform breeding and logistics improvements.

DeepTE: a computational method for de novo classification of transposons with convolu-tional neural network

DeepTE classifies transposable elements using convolutional neural networks, outperforming existing tools in benchmark tests.

Comparing Time Series Transcriptome Data Between Plants Using A Network Module Finding Algorithm

The paper describes a protocol to compare time series transcriptome data between plants using a network module finding algorithm to identify conserved developmental stages.

Prediction of condition-specific regulatory maps in Arabidopsis using integrated genomic data

This study develops ConSReg to predict condition-specific gene regulatory networks in Arabidopsis using genomic data, showing improved performance with ATAC-seq and identifying key regulators in root cell types.