Chuang Ma

deepTFBS improves TFBS prediction within and across species using deep multi-task and transfer learning, outperforming existing methods in Arabidopsis and wheat.

This study identifies ECT1 as an m6A reader protein that promotes seed germination in Arabidopsis through a DAG2-ECT1-PHYB regulatory cascade involving transcriptional and post-transcriptional control.

easyMF is a web platform that uses matrix factorization to analyze large-scale transcriptome data, enabling biological discovery through metagene-based analysis.

DeepGS predicts phenotypes from genotypes using deep learning, achieving higher accuracy than conventional methods and RR-BLUP across multiple traits.

PEA is an R toolkit for plant epitranscriptome analysis, offering CMR calling, prediction, and annotation with high accuracy for m6A modifications in Arabidopsis thaliana.