7 papers
Structure-guided taxonomic placement of divergent RNA viruses with ViraClass
Sheng Xu, Wenxuan Huang, Shutong Yue +8
Metatranscriptomic sequencing has expanded our knowledge of the RNA virosphere far more rapidly than novel viruses can be taxonomically classified. Taxonomic assignment above the f…
ViraHinter: a dual-modal artificial intelligence framework for predicting virus-host interactions
Weiqiang Bai, Fei Wang, Jialin Wang +10
Protein-protein interactions (PPIs) between a virus and its host govern infection, replication, and pathogenesis. While high-throughput mapping has identified thousands of virus-ho…
Fitness aligned structural modeling enables scalable virtual screening with AuroBind
Zhongyue Zhang, Jiahua Rao, Jie Zhong +22
Most human proteins remain undrugged, over 96% of human proteins remain unexploited by approved therapeutics. While structure-based virtual screening promises to expand the druggab…
Revisiting Convolution Architecture in the Realm of DNA Foundation Models
Yu Bo, Weian Mao, Yanjun Shao +6
In recent years, a variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there…
Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA
Lifeng Qiao, Peng Ye, Yuchen Ren +5
Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed f…
COMET: Benchmark for Comprehensive Biological Multi-omics Evaluation Tasks and Language Models
Yuchen Ren, Wenwei Han, Qianyuan Zhang +13
As key elements within the central dogma, DNA, RNA, and proteins play crucial roles in maintaining life by guaranteeing accurate genetic expression and implementation. Although res…