Ziyang Xu

Ziyang Xu, Haitian Zhong, Bingrui He et al.

Phosphorylation is pivotal in numerous fundamental cellular processes and plays a significant role in the onset and progression of various diseases. The accurate identification of these phosphorylation sites is crucial for unraveling the molecular mechanisms within cells and during viral infections, potentially leading to the discovery of novel therapeutic targets. In this study, we develop PTransIPs, a new deep learning framework for the identification of phosphorylation sites. Independent testing results demonstrate that PTransIPs outperforms existing state-of-the-art (SOTA) methods, achieving AUCs of 0.9232 and 0.9660 for the identification of phosphorylated S/T and Y sites, respectively. PTransIPs contributes from three aspects. 1) PTransIPs is the first to apply protein pre-trained language model (PLM) embeddings to this task. It utilizes ProtTrans and EMBER2 to extract sequence and structure embeddings, respectively, as additional inputs into the model, effectively addressing issues of dataset size and overfitting, thus enhancing model performance; 2) PTransIPs is based on Transformer architecture, optimized through the integration of convolutional neural networks and TIM loss function, providing practical insights for model design and training; 3) The encoding of amino acids in PTransIPs enables it to serve as a universal framework for other peptide bioactivity tasks, with its excellent performance shown in extended experiments of this paper. Our code, data and models are publicly available at https://github.com/StatXzy7/PTransIPs.

Haonan He, Yuchen Ren, Yining Tang et al.

Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale instruction-tuning dataset for multi-omics biological sequences, including DNA, RNA, proteins, and multi-molecules. This dataset bridges LLMs and complex biological sequence-related tasks, enhancing their versatility and reasoning while maintaining conversational fluency. We also highlight significant limitations of current state-of-the-art LLMs on multi-omics tasks without specialized training. To overcome this, we propose ChatMultiOmics, a strong baseline with a novel three-stage training pipeline, demonstrating superior biological understanding through Biology-Instructions. Both resources are publicly available, paving the way for better integration of LLMs in multi-omics analysis. The Biology-Instructions is publicly available at: https://github.com/hhnqqq/Biology-Instructions.