While transcriptomic profiling has become routine, identifying the TFs underlying these expression patterns remains a major challenge, particularly for crops and non-model species lacking efficient transformation systems. To connect expression correlations with candidate regulatory mechanisms, we developed PURE (Plant...
Chuan-Shun Li, Le-Yi Yang, Kan-De Lin et al.· Plant Communications· 0 citations
Synonymous codon choices shape mRNA stability, translation, and folding, and codon language models (cLMs) are increasingly reported to read this biology from sequence. However, when a true signal is thin relative to a confounding one, standard evaluation protocols can manufacture the reported gain rather than measure i...
ProRB is introduced, a unified sequence-based framework that jointly estimates protein–RNA binding affinity, predicts binding interfaces in proteins and RNAs, and generates protein-binding RNA sequences from protein sequences that provides a scalable unified model for decoding the protein–RNA interaction and engineerin...
An RNA design approach, AlignIF, that leverages multiple structure alignment with cross-graph modeling and carefully hand-designed features to capture evolutionarily conserved structural patterns at the structural level, facilitating RNA sequence design outperforms existing state-of-the-art methods in test sets.
Sheng-Fan Wang, Jun Wang, Xiao-Jian Liu et al.· Nature Computational Science· 2 citations· ⚡1
This work proposes a multimodal framework for learning subcellularly resolved cell embeddings by jointly leveraging RNA expression profiles, protein sequence representations, and protein structural information, and is the first framework that produces subcellularly resolved cell embeddings by jointly incorporating tran...
Zhen Zhou, Jia-Chen Li, Yuan Liu et al.· 0 citations
This benchmark establishes a standardized framework for evaluating protein similarity search methods, providing a practical resource for method selection and a foundation for the development of next-generation approaches capable of addressing diverse homology search challenges.
Yuan Liu, Ying-Quan Zhou, Yan Huang et al.· Genome Biology· 1 citation
IgGM2 follows a structure-to-design strategy: it first learns how immune receptors are positioned around fixed target structures, and then transfers this target-conditioned structural prior to CDR design, allowing frame-work geometry to adapt to designed CDRs without separate inverse folding or external sidechain packi...
Jian Ma, Fandi Wu, Lin Yao et al.· bioRxiv· 0 citations
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