PSAF
Plant Small RNA Analysis Framework
A computational framework for plant small RNA analysis, hierarchical annotation, multi-mapping assignment, and mutant-informed miRNA identification.
small RNAmiRNARNA-seqmachine learning
About
Computational frameworks for RNA regulation.
My work connects sequencing evidence, genetic mutants, machine learning, and biological model evaluation to make RNA regulation easier to inspect, annotate, and reason about across species and omics layers.
2019-2026
Ph.D. Researcher, Fudan University
Developed small RNA analysis frameworks, miRNA classifiers, mutant-informed annotation strategies, and RNA-end modification analysis workflows.
Now
Foundation models for biology
Exploring RNA language models, multimodal biological representation learning, and benchmarks across DNA, RNA, protein, and omics data.
Featured work
Selected research projects
BEACON
RNA Foundation Model Benchmark
Benchmark tasks and unified evaluation pipelines for RNA language models across downstream biological prediction settings.
RNA modelsbenchmarkingdeep learning
COMET
Cross-Omics Foundation Model Benchmark
A multi-omics benchmark spanning DNA, RNA, and protein tasks, focused on representation learning and cross-omics transfer.
multi-omicsfoundation modelsrepresentation learning
miRNA Annotation
High-confidence plant miRNA classification
Mutant-informed scoring and classifier design for re-annotating plant miRNAs and evaluating prediction tools.
plant biologyannotationclassification
GitHub
Open research code and tools
TRMRNAseqToolsIntegrated plant small RNA-seq analysis pipelinerenlab_tailing_trimming_parallelParallel workflow for miRNA 3-prime tailing and trimming analysisPBOX-manuscriptAnalysis code for the published PBOX-sRNA-seq studyrenlab_rnaseq_pipelineRestartable bulk RNA-seq workflow from QC to differential analysisrenlab_WGBS_analysisOne-command WGBS processing, methylation analysis, and reportingsRNA_Track_ViewerInteractive visualization tools for small RNA sequencing tracks
Technical stack
Built across genomics, ML, and reproducible workflows.
PythonRBashSQLPyTorchHugging FaceTransformersscikit-learnBioconductorNextflowSnakemakeSAMtoolsDockerGitHub Actions