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Yanni Sun
Person information
- affiliation: City University of Hong Kong, Department of Electrical Engineering
- affiliation (former): Michigan State University, East Lansing, MI, USA
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2020 – today
- 2024
- [j46]Runzhou Yu
, Ziyi Huang, Theo Y. C. Lam
Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review. Briefings Bioinform. 25(4) (2024) - [i6]Xiangyu Dong, Xingyi Zhang, Yanni Sun, Lei Chen, Mingxuan Yuan, Sibo Wang:
SmoothGNN: Smoothing-based GNN for Unsupervised Node Anomaly Detection. CoRR abs/2405.17525 (2024) - [i5]Jiaojiao Guan, Yongxin Ji, Cheng Peng, Wei Zou, Xubo Tang, Jiayu Shang, Yanni Sun:
PhaGO: Protein function annotation for bacteriophages by integrating the genomic context. CoRR abs/2408.06402 (2024) - 2023
- [j45]Jingzhe Jiang
Virus classification for viral genomic fragments using PhaGCN2. Briefings Bioinform. 24(1) (2023) - [j44]Jiayu Shang
PhaTYP: predicting the lifestyle for bacteriophages using BERT. Briefings Bioinform. 24(1) (2023) - [j43]Runzhou Yu
HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses. Briefings Bioinform. 24(5) (2023) - [j42]Jiaojiao Guan, Cheng Peng, Jiayu Shang, Xubo Tang, Yanni Sun:
PhaGenus: genus-level classification of bacteriophages using a Transformer model. Briefings Bioinform. 24(6) (2023) - [j41]Runzhou Yu
AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data. Bioinform. 39(1) (2023) - [j40]Guowei Chen
VirBot: an RNA viral contig detector for metagenomic data. Bioinform. 39(3) (2023) - [j39]Yongxin Ji
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer. Bioinform. 39(5) (2023) - [j38]Herui Liao
GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data. Bioinform. 39(12) (2023) - [j37]Jiayu Shang
PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer. Bioinform. 39(Supplement-1): 30-39 (2023) - [c10]Yanni Sun
Research on the Method Matching of Manufacturing Service Resources in a Cloud Manufacturing Environment. ICCAI 2023: 398-407 - 2022
- [j36]Xubo Tang
RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data. Briefings Bioinform. 23(2) (2022) - [j35]Jiayu Shang
Accurate identification of bacteriophages from metagenomic data using Transformer. Briefings Bioinform. 23(4) (2022) - [j34]Jiayu Shang
CHERRY: a Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model. Briefings Bioinform. 23(5) (2022) - [j33]Dehan Cai
Reconstructing viral haplotypes using long reads. Bioinform. 38(8): 2127-2134 (2022) - [j32]Dehan Cai
HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization. Bioinform. 38(24): 5360-5367 (2022) - [i4]Jiayu Shang, Yanni Sun:
CHERRY: a Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model. CoRR abs/2201.01018 (2022) - 2021
- [j31]Jiayu Shang
Bacteriophage classification for assembled contigs using graph convolutional network. Bioinform. 37(Supplement): 25-33 (2021) - [i3]Jiayu Shang, Jingzhe Jiang, Yanni Sun:
Bacteriophage classification for assembled contigs using Graph Convolutional Network. CoRR abs/2102.03746 (2021) - [i2]Jiayu Shang, Yanni Sun:
Detecting the hosts of bacteriophages using GCN-based semi-supervised learning. CoRR abs/2105.13570 (2021) - 2020
- [c9]Ruixuan Huang
The Lung Cancer Associated MicroRNAs and Single Nucleotides Polymorphisms: a Mendelian Randomization Analysis. EMBC 2020: 2346-2352 - [i1]Nan Du, Jiayu Shang, Yanni Sun:
ProDOMA: improve PROtein DOMAin classification for third-generation sequencing reads using deep learning. CoRR abs/2009.12591 (2020)
2010 – 2019
- 2019
- [j30]Jiao Chen, Jiating Huang
TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data. BMC Bioinform. 20(1): 305:1-305:14 (2019) - [j29]Jiao Chen, Jiayu Shang
A binning tool to reconstruct viral haplotypes from assembled contigs. BMC Bioinform. 20(1): 544:1-544:13 (2019) - [j28]Prapaporn Techa-angkoon, Kevin L. Childs
GPRED-GC: a Gene PREDiction model accounting for 5 ′- 3′ GC gradient. BMC Bioinform. 20-S(15): 482 (2019) - [j27]Xubo Tang
Fast and accurate microRNA search using CNN. BMC Bioinform. 20-S(23): 646 (2019) - [j26]Nan Du
Improving the sensitivity of long read overlap detection using grouped short k-mer matches. BMC Genom. 20(S2) (2019) - 2018
- [j25]Jiao Chen, Yingchao Zhao
De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding. Bioinform. 34(17): 2927-2935 (2018) - 2017
- [j24]Prapaporn Techa-angkoon, Yanni Sun
A sensitive short read homology search tool for paired-end read sequencing data. BMC Bioinform. 18(S-12): 77-89 (2017) - [j23]Jiao Chen, Dongxiao Zhu, Yanni Sun
Cap-seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse. Quant. Biol. 5(4): 352-367 (2017) - 2016
- [j22]Jikai Lei, Yanni Sun
Assemble CRISPRs from metagenomic sequencing data. Bioinform. 32(17): 520-528 (2016) - [j21]Nan Du
Improve homology search sensitivity of PacBio data by correcting frameshifts. Bioinform. 32(17): 529-537 (2016) - [j20]Yanni Sun, Xinhua Chen:
Application and Realization of Improved Apriori Algorism in Hadoop Simulation Platform for Mass Data Process. Int. J. Online Eng. 12(2): 16-19 (2016) - [j19]Xinhua Chen, Yanni Sun:
Computer Network Simulation Modeling Based on Object Oriented Petri Net. Int. J. Online Eng. 12(2): 25-28 (2016) - 2015
- [j18]Cheng Yuan, Jikai Lei, James R. Cole, Yanni Sun
Reconstructing 16S rRNA genes in metagenomic data. Bioinform. 31(12): 35-43 (2015) - [j17]Rujira Achawanantakun, Jiao Chen, Yanni Sun
LncRNA-ID: Long non-coding RNA IDentification using balanced random forests. Bioinform. 31(24): 3897-3905 (2015) - 2014
- [j16]Jikai Lei
miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data. Bioinform. 30(19): 2837-2839 (2014) - [j15]James R. Cole, Qiong Wang, Jordan A. Fish, Benli Chai, Donna M. McGarrell, Yanni Sun
Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42(Database-Issue): 633-642 (2014) - [j14]Yuan Zhang, Yanni Sun
A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data. PLoS Comput. Biol. 10(8) (2014) - 2013
- [j13]Yuan Zhang, Yanni Sun
A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads. Bioinform. 29(17): 2103-2111 (2013) - [j12]Rujira Achawanantakun, Yanni Sun
Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM. BMC Bioinform. 14(S-2): S1 (2013) - [j11]Cheng Yuan, Yanni Sun
Efficient known ncRNA search including pseudoknots. BMC Bioinform. 14(S-2): S25 (2013) - [j10]Jikai Lei
Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-Dimensional Chain Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. 10(2): 274-285 (2013) - [c8]Prapaporn Techa-angkoon, Yanni Sun
glu-RNA: aliGn highLy strUctured ncRNAs using only sequence similarity. BCB 2013: 508 - [c7]Jikai Lei
ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding tools. BCB 2013: 535 - 2012
- [j9]Yanni Sun
Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy. BMC Bioinform. 13(S-3): S12 (2012) - [j8]Yanni Sun
Designing Filters for Fast-Known NcRNA Identification. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 774-787 (2012) - [c6]Yuan Zhang, Yanni Sun
PseudoDomain: identification of processed pseudogenes based on protein domain classification. BCB 2012: 178-185 - [c5]Yuan Zhang, Yanni Sun:
MetaDomain: A Profile HMM-Based Protein Domain Classification Tool for Short Sequences. Pacific Symposium on Biocomputing 2012: 271-282 - 2011
- [j7]Yuan Zhang, Yanni Sun
HMM-FRAME: accurate protein domain classification for metagenomic sequences in the presence of frameshift errors. BMC Bioinform. 12: 198 (2011) - [j6]Rujira Achawanantakun, Yanni Sun
Ncrna Consensus Secondary Structure Derivation Using Grammar Strings. J. Bioinform. Comput. Biol. 9(2): 317-337 (2011) - [c4]Osama Aljawad, Yanni Sun
NcRNA homology search using Hamming distance seeds. BCB 2011: 209-217 - 2010
- [c3]Stuart King, Yanni Sun
BLAST Tree: Fast Filtering for Genomic Sequence Classification. BIBE 2010: 58-65
2000 – 2009
- 2009
- [j5]Yanni Sun
Designing Patterns and Profiles for Faster HMM Search. IEEE ACM Trans. Comput. Biol. Bioinform. 6(2): 232-243 (2009) - 2007
- [j4]Yanni Sun
Designing patterns for profile HMM search. Bioinform. 23(2): 42-43 (2007) - 2006
- [j3]Yanni Sun
Choosing the best heuristic for seeded alignment of DNA sequences. BMC Bioinform. 7: 133 (2006) - 2005
- [j2]Yanni Sun
Designing Multiple Simultaneous Seeds for DNA Similarity Search. J. Comput. Biol. 12(6): 847-861 (2005) - [j1]Jeremy Buhler, Uri Keich
Designing seeds for similarity search in genomic DNA. J. Comput. Syst. Sci. 70(3): 342-363 (2005) - 2004
- [c2]Yanni Sun
Designing multiple simultaneous seeds for DNA similarity search. RECOMB 2004: 76-84 - 2003
- [c1]Jeremy Buhler
Designing seeds for similarity search in genomic DNA. RECOMB 2003: 67-75
Coauthor Index
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last updated on 2024-11-26 20:43 CET by the dblp team
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