R. You

发表

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

NetGO: improving large-scale protein function prediction with massive network information

Fengzhu Sun, Hiroshi Mamitsuka, Xiaodi Huang, 2019, Nucleic acids research.

GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank

Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu, 2017, bioRxiv.

MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities

Fengzhu Sun, Shanfeng Zhu, R. You, 2021, bioRxiv.

Critical Assessment of Metagenome Interpretation: the second round of challenges

K. Reinert, E. Eskin, F. Beghini, 2021, Nature Methods.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction

Hiroshi Mamitsuka, Ronghui You, Shuwei Yao, 2021, Bioinform..

NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information

Xiaodi Huang, Shanfeng Zhu, Y. Xiong, 2021, Nucleic Acids Res..

NetGO: improving large-scale protein function prediction with massive network information

Hiroshi Mamitsuka, Shanfeng Zhu, Yi Xiong, 2018, bioRxiv.

GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank

Yi Xiong, Hiroshi Mamitsuka, Shanfeng Zhu, 2017, bioRxiv.

DeepText2Go: Improving large-scale protein function prediction with deep semantic text representation

Shanfeng Zhu, Ronghui You, Shanfeng Zhu, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

DeepText2GO: Improving large-scale protein function prediction with deep semantic text representation.

Xiaodi Huang, Shanfeng Zhu, Ronghui You, 2018, Methods.

DeepDock: Enhancing Ligand-protein Interaction Prediction by a Combination of Ligand and Structure Information

Xiaodi Huang, Tao Huang, Ronghui You, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network

Fengzhu Sun, X. Zhou, Shanfeng Zhu, 2021, NAR genomics and bioinformatics.

FullMeSH: improving large-scale MeSH indexing with full text

Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, 2019, Bioinform..

DeepMeSH: deep semantic representation for improving large-scale MeSH indexing

ChengXiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu, 2016, Bioinform..

AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification

Hiroshi Mamitsuka, Shanfeng Zhu, R. You, 2018, NeurIPS.

BERTMeSH: Deep Contextual Representation Learning for Large-scale High-performance MeSH Indexing with Full Text.

Hiroshi Mamitsuka, Shanfeng Zhu, Yuxuan Liu, 2020, Bioinformatics.

BERTMeSH: Deep Contextual Representation Learning for Large-scale High-performance MeSH Indexing with Full Text

Yuxuan Liu, Hiroshi Mamitsuka, Shanfeng Zhu, 2020, bioRxiv.

Cache-oblivious wavefront: improving parallelism of recursive dynamic programming algorithms without losing cache-efficiency

Haibin Kan, Yuan Tang, Ronghui You, 2015, PPoPP.

AttentionXML: Extreme Multi-Label Text Classification with Multi-Label Attention Based Recurrent Neural Networks pdf

Hiroshi Mamitsuka, Shanfeng Zhu, Ronghui You, 2018, ArXiv.

Improving Parallelism of Recursive Stencil Computations without Sacrificing Cache Performance

Haibin Kan, Ronghui You, Pramod Ganapathi, 2014 .

Protein language model powers accurate and fast sequence search for remote homology

Shanfeng Zhu, Y. Xiong, R. You, 2023, bioRxiv.

NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations

Shanfeng Zhu, Y. Xiong, R. You, 2022, bioRxiv.

PLMSearch: Protein language model powers accurate and fast sequence search for remote homology

R. You, Ziye Wang, Hong Wei, 2024, Nature communications.

Protein language model powers accurate and fast sequence search for remote homology

Shanfeng Zhu, Y. Xiong, R. You, 2024, bioRxiv.

DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction

Hiroshi Mamitsuka, Shanfeng Zhu, R. You, 2021, bioRxiv.