Yanni Sun

73 papers A* 1B 2C 1Misc 1Journal 62Unranked 6
YearRankTypeTitle / Venue / Authors
2025 J jnl
From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction.
Briefings Bioinform.
Jiayu Shang, Cheng Peng, Jiaojiao Guan, Dehan Cai, Donglin Wang, Yanni Sun
2025 J jnl
GOPhage: protein function annotation for bacteriophages by integrating the genomic context.
Briefings Bioinform.
Jiaojiao Guan, Yongxin Ji, Cheng Peng, Wei Zou, Xubo Tang, Jiayu Shang, Yanni Sun
2025 J jnl
GiantHunter: accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search.
Bioinform.
Fuchuan Qu, Cheng Peng, Jiaojiao Guan, Donglin Wang, Yanni Sun, Jiayu Shang
2025 J jnl
MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction.
Bioinform.
Wei Zou, Yongxin Ji, Jiaojiao Guan, Yanni Sun
2025 J jnl
Reinforcement learning-guided sample selection for improved identification of phage receptor binding proteins.
Briefings Bioinform.
Xiling Luo, Le Ou-Yang, Yang Shen, Yanni Sun, Jiayu Shang
2025 J jnl
SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples.
Briefings Bioinform.
Xue Liu, Jianbin Kong, Yongtao Shan, Ziyue Yang, Jiafan Miao, Yuanfei Pan, Tianyang Luo, Zhiyuan Shi, Yingmei Wang, Qinyu Gou, Chunhui Yang, Hanzong Li, Chunmei Li, Shaochuan Li, Xu Zhang, Yanni Sun, Edward C. Holmes, Deyin Guo, Mang Shi
2025 A* conf
SmoothGNN: Smoothing-aware GNN for Unsupervised Node Anomaly Detection.
WWW
Xiangyu Dong, Xingyi Zhang, Yanni Sun, Lei Chen, Mingxuan Yuan, Sibo Wang
2024 J jnl
Accurate and efficient protein embedding using multi-teacher distillation learning.
Bioinform.
Jiayu Shang, Cheng Peng, Yongxin Ji, Jiaojiao Guan, Dehan Cai, Xubo Tang, Yanni Sun
2024 J jnl
PhaGO: Protein function annotation for bacteriophages by integrating the genomic context.
CoRR
Jiaojiao Guan, Yongxin Ji, Cheng Peng, Wei Zou, Xubo Tang, Jiayu Shang, Yanni Sun
2024 J jnl
SmoothGNN: Smoothing-based GNN for Unsupervised Node Anomaly Detection.
CoRR
Xiangyu Dong, Xingyi Zhang, Yanni Sun, Lei Chen, Mingxuan Yuan, Sibo Wang
2024 J jnl
Towards more accurate microbial source tracking via non-negative matrix factorization (NMF).
Bioinform.
Ziyi Huang, Dehan Cai, Yanni Sun
2024 J jnl
Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review.
Briefings Bioinform.
Runzhou Yu, Ziyi Huang, Theo Y. C. Lam, Yanni Sun
2024 J jnl
VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation.
Bioinform.
Yilin Zhu, Guowei Chen, Yanni Sun
2024 J jnl
ViraLM: empowering virus discovery through the genome foundation model.
Bioinform.
Cheng Peng, Jiayu Shang, Jiaojiao Guan, Donglin Wang, Yanni Sun
2023 J jnl
AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data.
Bioinform.
Runzhou Yu, Dehan Cai, Yanni Sun
2023 J jnl
GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data.
Bioinform.
Herui Liao, Jiayu Shang, Yanni Sun
2023 J jnl
HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses.
Briefings Bioinform.
Runzhou Yu, Syed Muhammad Umer Abdullah, Yanni Sun
2023 J jnl
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer.
Bioinform.
Yongxin Ji, Jiayu Shang, Xubo Tang, Yanni Sun
2023 J jnl
PhaGenus: genus-level classification of bacteriophages using a Transformer model.
Briefings Bioinform.
Jiaojiao Guan, Cheng Peng, Jiayu Shang, Xubo Tang, Yanni Sun
2023 J jnl
PhaTYP: predicting the lifestyle for bacteriophages using BERT.
Briefings Bioinform.
Jiayu Shang, Xubo Tang, Yanni Sun
2023 J jnl
PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer.
Bioinform.
Jiayu Shang, Cheng Peng, Xubo Tang, Yanni Sun
2023 — conf
Research on the Method Matching of Manufacturing Service Resources in a Cloud Manufacturing Environment.
ICCAI
Yanni Sun, Baohua Yu
2023 J jnl
VirBot: an RNA viral contig detector for metagenomic data.
Bioinform.
Guowei Chen, Xubo Tang, Mang Shi, Yanni Sun
2023 J jnl
Virus classification for viral genomic fragments using PhaGCN2.
Briefings Bioinform.
Jingzhe Jiang, Wen-Guang Yuan, Jiayu Shang, Ying-Hui Shi, Li-Ling Yang, Min Liu, Peng Zhu, Tao Jin, Yanni Sun, Li-Hong Yuan
2022 J jnl
Accurate identification of bacteriophages from metagenomic data using Transformer.
Briefings Bioinform.
Jiayu Shang, Xubo Tang, Ruocheng Guo, Yanni Sun
2022 J jnl
CHERRY: a Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model.
Briefings Bioinform.
Jiayu Shang, Yanni Sun
2022 J jnl
CHERRY: a Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model.
CoRR
Jiayu Shang, Yanni Sun
2022 J jnl
HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization.
Bioinform.
Dehan Cai, Jiayu Shang, Yanni Sun
2022 J jnl
RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data.
Briefings Bioinform.
Xubo Tang, Jiayu Shang, Yanni Sun
2022 J jnl
Reconstructing viral haplotypes using long reads.
Bioinform.
Dehan Cai, Yanni Sun
2021 J jnl
Bacteriophage classification for assembled contigs using Graph Convolutional Network.
CoRR
Jiayu Shang, Jingzhe Jiang, Yanni Sun
2021 J jnl
Bacteriophage classification for assembled contigs using graph convolutional network.
Bioinform.
Jiayu Shang, Jingzhe Jiang, Yanni Sun
2021 J jnl
Detecting the hosts of bacteriophages using GCN-based semi-supervised learning.
CoRR
Jiayu Shang, Yanni Sun
2020 J jnl
ProDOMA: improve PROtein DOMAin classification for third-generation sequencing reads using deep learning.
CoRR
Nan Du, Jiayu Shang, Yanni Sun
2020 — conf
The Lung Cancer Associated MicroRNAs and Single Nucleotides Polymorphisms: a Mendelian Randomization Analysis.
EMBC
Ruixuan Huang, William C. Cho, Yanni Sun, Kei Hang Katie Chan
2019 J jnl
A binning tool to reconstruct viral haplotypes from assembled contigs.
BMC Bioinform.
Jiao Chen, Jiayu Shang, Jianrong Wang, Yanni Sun
2019 J jnl
Fast and accurate microRNA search using CNN.
BMC Bioinform.
Xubo Tang, Yanni Sun
2019 J jnl
GPRED-GC: a Gene PREDiction model accounting for 5
BMC Bioinform.
Prapaporn Techa-angkoon, Kevin L. Childs, Yanni Sun
2019 J jnl
Improving the sensitivity of long read overlap detection using grouped short k-mer matches.
BMC Genom.
Nan Du, Jiao Chen, Yanni Sun
2019 J jnl
TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data.
BMC Bioinform.
Jiao Chen, Jiating Huang, Yanni Sun
2018 J jnl
De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding.
Bioinform.
Jiao Chen, Yingchao Zhao, Yanni Sun
2017 J jnl
A sensitive short read homology search tool for paired-end read sequencing data.
BMC Bioinform.
Prapaporn Techa-angkoon, Yanni Sun, Jikai Lei
2017 J jnl
Cap-seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse.
Quant. Biol.
Jiao Chen, Dongxiao Zhu, Yanni Sun
2016 J jnl
Application and Realization of Improved Apriori Algorism in Hadoop Simulation Platform for Mass Data Process.
Int. J. Online Eng.
Yanni Sun, Xinhua Chen
2016 J jnl
Assemble CRISPRs from metagenomic sequencing data.
Bioinform.
Jikai Lei, Yanni Sun
2016 J jnl
Computer Network Simulation Modeling Based on Object Oriented Petri Net.
Int. J. Online Eng.
Xinhua Chen, Yanni Sun
2016 J jnl
Improve homology search sensitivity of PacBio data by correcting frameshifts.
Bioinform.
Nan Du, Yanni Sun
2015 J jnl
LncRNA-ID: Long non-coding RNA IDentification using balanced random forests.
Bioinform.
Rujira Achawanantakun, Jiao Chen, Yanni Sun, Yuan Zhang
2015 J jnl
Reconstructing 16S rRNA genes in metagenomic data.
Bioinform.
Cheng Yuan, Jikai Lei, James R. Cole, Yanni Sun
2014 J jnl
A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data.
PLoS Comput. Biol.
Yuan Zhang, Yanni Sun, James R. Cole
2014 J jnl
Ribosomal Database Project: data and tools for high throughput rRNA analysis.
Nucleic Acids Res.
James R. Cole, Qiong Wang, Jordan A. Fish, Benli Chai, Donna M. McGarrell, Yanni Sun, C. Titus Brown, Andrea Porras-Alfaro, Cheryl R. Kuske, James M. Tiedje
2014 J jnl
miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data.
Bioinform.
Jikai Lei, Yanni Sun
2013 J jnl
A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads.
Bioinform.
Yuan Zhang, Yanni Sun, James R. Cole
2013 J jnl
Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-Dimensional Chain Algorithm.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jikai Lei, Prapaporn Techa-angkoon, Yanni Sun
2013 — conf
ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding tools.
BCB
Jikai Lei, Prapaporn Techa-angkoon, Yanni Sun, Rujira Achawanantakun
2013 J jnl
Efficient known ncRNA search including pseudoknots.
BMC Bioinform.
Cheng Yuan, Yanni Sun
2013 J jnl
Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM.
BMC Bioinform.
Rujira Achawanantakun, Yanni Sun
2013 — conf
glu-RNA: aliGn highLy strUctured ncRNAs using only sequence similarity.
BCB
Prapaporn Techa-angkoon, Yanni Sun
2012 J jnl
Designing Filters for Fast-Known NcRNA Identification.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yanni Sun, Jeremy Buhler, Cheng Yuan
2012 J jnl
Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy.
BMC Bioinform.
Yanni Sun, Osama Aljawad, Jikai Lei, Alex Liu
2012 Misc conf
MetaDomain: A Profile HMM-Based Protein Domain Classification Tool for Short Sequences.
Pacific Symposium on Biocomputing
Yuan Zhang, Yanni Sun
2012 — conf
PseudoDomain: identification of processed pseudogenes based on protein domain classification.
BCB
Yuan Zhang, Yanni Sun
2011 J jnl
HMM-FRAME: accurate protein domain classification for metagenomic sequences in the presence of frameshift errors.
BMC Bioinform.
Yuan Zhang, Yanni Sun
2011 — conf
NcRNA homology search using Hamming distance seeds.
BCB
Osama Aljawad, Yanni Sun, Alex Liu, Jikai Lei
2011 J jnl
Ncrna Consensus Secondary Structure Derivation Using Grammar Strings.
J. Bioinform. Comput. Biol.
Rujira Achawanantakun, Yanni Sun, Seyedeh Shohreh Takyar
2010 C conf
BLAST Tree: Fast Filtering for Genomic Sequence Classification.
BIBE
Stuart King, Yanni Sun, James R. Cole, Sakti Pramanik
2009 J jnl
Designing Patterns and Profiles for Faster HMM Search.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yanni Sun, Jeremy Buhler
2007 J jnl
Designing patterns for profile HMM search.
Bioinform.
Yanni Sun, Jeremy Buhler
2006 J jnl
Choosing the best heuristic for seeded alignment of DNA sequences.
BMC Bioinform.
Yanni Sun, Jeremy Buhler
2005 J jnl
Designing Multiple Simultaneous Seeds for DNA Similarity Search.
J. Comput. Biol.
Yanni Sun, Jeremy Buhler
2005 J jnl
Designing seeds for similarity search in genomic DNA.
J. Comput. Syst. Sci.
Jeremy Buhler, Uri Keich, Yanni Sun
2004 B conf
Designing multiple simultaneous seeds for DNA similarity search.
RECOMB
Yanni Sun, Jeremy Buhler
2003 B conf
Designing seeds for similarity search in genomic DNA.
RECOMB
Jeremy Buhler, Uri Keich, Yanni Sun