Yu Li

Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 29

Top Topics

Antibiotic Resistance Genes

Top Venues

Bioinformatics (Oxford, England)

Nature computational science

Nature communications

Communications biology

This page only lists publications with an associated author ORCID identifier.

Publications

Han Huang, Ziqian Lin, Dongchen He, Liang Hong, Yu Li
RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Siyuan Chen, Jiuming Wang, Inkyung Jung, Zhaowen Qiu, Xin Gao, Yu Li
A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data. Genome research (2024)
Yimin Fan, Yaxuan Li, Yunhua Zhong, Liang Hong, Lei Li, Yu Li
Learning meaningful representation of single-neuron morphology via large-scale pre-training. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Han Huang, Ziqian Lin, Dongchen He, Liang Hong, Yu Li
RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Liang Hong, Zhihang Hu, Siqi Sun, Xiangru Tang, Jiuming Wang, Qingxiong Tan, Liangzhen Zheng, Sheng Wang, Sheng Xu, Irwin King, Mark Gerstein, Yu Li
Fast, sensitive detection of protein homologs using deep dense retrieval. Nature biotechnology (2024)
Han Huang, Ziqian Lin, Dongchen He, Liang Hong, Yu Li
RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Junkang Wei, Jin Xiao, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles. Database : the journal of biological databases and curation 2024 (2024)
Yimin Fan, Yaxuan Li, Yunhua Zhong, Liang Hong, Lei Li, Yu Li
Learning meaningful representation of single-neuron morphology via large-scale pre-training. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Yunxiang Li, Yumeng Wei, Sheng Xu, Qingxiong Tan, Licheng Zong, Jiuming Wang, Yixuan Wang, Jiayang Chen, Liang Hong, Yu Li
AcrNET: predicting anti-CRISPR with deep learning. Bioinformatics (Oxford, England) 39 (5) (2023)
Junbo Shen, Qinze Yu, Shenyang Chen, Qingxiong Tan, Jingchen Li, Yu Li
Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model. Nature computational science 4 (1) (2023)
Junbo Shen, Qinze Yu, Shenyang Chen, Qingxiong Tan, Jingchen Li, Yu Li
Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model. Nature computational science (2023)
Junbo Shen, Qinze Yu, Shenyang Chen, Qingxiong Tan, Jingchen Li, Yu Li
Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model. Nature computational science 4 (1) (2023)
Yuqi Cheng, Xingyu Fan, Jianing Zhang, Yu Li
A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data. Communications biology 6 (1) (2023)
Junbo Shen, Qinze Yu, Shenyang Chen, Qingxiong Tan, Jingchen Li, Yu Li
Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model. Nature computational science 4 (1) (2023)
Yunxiang Li, Yumeng Wei, Sheng Xu, Qingxiong Tan, Licheng Zong, Jiuming Wang, Yixuan Wang, Jiayang Chen, Liang Hong, Yu Li
AcrNET: predicting anti-CRISPR with deep learning. Bioinformatics (Oxford, England) 39 (5) (2023)
Yuqi Cheng, Xingyu Fan, Jianing Zhang, Yu Li
A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data. Communications biology 6 (1) (2023)
Yuqi Cheng, Xingyu Fan, Jianing Zhang, Yu Li
A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data. Communications biology 6 (1) (2023)
Junbo Shen, Qinze Yu, Shenyang Chen, Qingxiong Tan, Jingchen Li, Yu Li
Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model. Nature computational science (2023)
Yunxiang Li, Yumeng Wei, Sheng Xu, Qingxiong Tan, Licheng Zong, Jiuming Wang, Yixuan Wang, Jiayang Chen, Liang Hong, Yu Li
AcrNET: predicting anti-CRISPR with deep learning. Bioinformatics (Oxford, England) 39 (5) (2023)
Wenkai Han, Yuqi Cheng, Jiayang Chen, Huawen Zhong, Zhihang Hu, Siyuan Chen, Licheng Zong, Liang Hong, Ting-Fung Chan, Irwin King, Xin Gao, Yu Li
Self-supervised contrastive learning for integrative single cell RNA-seq data analysis. Briefings in bioinformatics 23 (5) (2022)
Yanshuo Chen, Yixuan Wang, Yuelong Chen, Yuqi Cheng, Yumeng Wei, Yunxiang Li, Jiuming Wang, Yingying Wei, Ting-Fung Chan, Yu Li
Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis. Nature communications 13 (1) (2022)
Yu Li, Siyuan Chen, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Kevin Y Yip, Xin Gao
Deep learning identifies and quantifies recombination hotspot determinants. Bioinformatics (Oxford, England) 38 (10) (2022)
Kanix Wang, Robert Stevens, Halima Alachram, Yu Li, Larisa N Soldatova, Ross King, Sophia Ananiadou, Annika M Schoene, Maolin Li, Fenia Christopoulou, José Luis Ambite, Joel Matthew, Sahil Garg, Ulf Hermjakob, Daniel Marcu, Emily Sheng, Tim Beißbarth, Edgar Wingender, Aram Galstyan, Xin Gao, Brendan Chambers, Weidi Pan, Bohdan B Khomtchouk, James A Evans, Andrey Rzhetsky
NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding. NPJ systems biology and applications 7 (1) (2021)
Ramzan Umarov, Yu Li, Takahiro Arakawa, Satoshi Takizawa, Xin Gao, Erik Arner
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation. PLoS computational biology 17 (9) (2021)
Ramzan Umarov, Yu Li, Erik Arner
DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment. PLoS computational biology 17 (10) (2021)
Jordy Homing Lam, Yu Li, Lizhe Zhu, Ramzan Umarov, Hanlun Jiang, Amélie Héliou, Fu Kit Sheong, Tianyun Liu, Yongkang Long, Yunfei Li, Liang Fang, Russ B Altman, Wei Chen, Xuhui Huang, Xin Gao
A deep learning framework to predict binding preference of RNA constituents on protein surface. Nature communications 10 (1) (2019)
Gengjie Jia, Yu Li, Hanxin Zhang, Ishanu Chattopadhyay, Anders Boeck Jensen, David R Blair, Lea K Davis, Peter Nick Robinson, Torsten Dahlén, Søren Brunak, Mikael Benson, Gustaf Edgren, Nancy J Cox, Xin Gao, Andrey Rzhetsky
Estimating heritability and genetic correlations from large health datasets in the absence of genetic data. Nature communications 10 (1) (2019)
Jinping Lei, Gang Sheng, Peter Pak-Hang Cheung, Shenglong Wang, Yu Li, Xin Gao, Yingkai Zhang, Yanli Wang, Xuhui Huang
Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proceedings of the National Academy of Sciences of the United States of America 116 (3) (2018)
Vasiliki Kordopati, Adil Salhi, Rozaimi B Mahamad Razali, Aleksandar Radovanovic, Faroug Tifratene, Mahmut Uludag, Yu Li, Ameerah Bokhari, Ahdab AlSaieedi, Arwa Bin Raies, Christophe Van Neste, Magbubah Essack, Vladimir B Bajic
DES-Mutation: System for Exploring Links of Mutations and Diseases. Scientific reports 8 (1) (2018)