Yanni Sun

Syed Muhammad Umer Abdullah

Bioinform., December, 2023

HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses.

[BibT_eX]

[DOI]

Runzhou Yu

Briefings Bioinform., September, 2023

HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer.

[BibT_eX]

[DOI]

Bioinform., May, 2023

VirBot: an RNA viral contig detector for metagenomic data.

[BibT_eX]

[DOI]

Bioinform., March, 2023

AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data.

[BibT_eX]

[DOI]

Runzhou Yu

Dehan Cai

Bioinform., January, 2023

PhaTYP: predicting the lifestyle for bacteriophages using BERT.

[BibT_eX]

[DOI]

Xubo Tang

Briefings Bioinform., January, 2023

Virus classification for viral genomic fragments using PhaGCN2.

[BibT_eX]

[DOI]

Briefings Bioinform., January, 2023

PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer.

[BibT_eX]

[DOI]

Bioinform., 2023

Research on the Method Matching of Manufacturing Service Resources in a Cloud Manufacturing Environment.

[BibT_eX]

[DOI]

Baohua Yu

Proceedings of the 9th International Conference on Computing and Artificial Intelligence, 2023

2022

HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization.

[BibT_eX]

[DOI]

Dehan Cai

Bioinform., December, 2022

Reconstructing viral haplotypes using long reads.

[BibT_eX]

[DOI]

Dehan Cai

Bioinform., 2022

RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data.

[BibT_eX]

[DOI]

Xubo Tang

Briefings Bioinform., 2022

Accurate identification of bacteriophages from metagenomic data using Transformer.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

CHERRY: a Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

2021

Detecting the hosts of bacteriophages using GCN-based semi-supervised learning.

[BibT_eX]

[DOI]

CoRR, 2021

Bacteriophage classification for assembled contigs using graph convolutional network.

[BibT_eX]

[DOI]

Jingzhe Jiang

Bioinform., 2021

2020

ProDOMA: improve PROtein DOMAin classification for third-generation sequencing reads using deep learning.

[BibT_eX]

[DOI]

Du Nan

CoRR, 2020

The Lung Cancer Associated MicroRNAs and Single Nucleotides Polymorphisms: a Mendelian Randomization Analysis.

[BibT_eX]

[DOI]

Proceedings of the 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society, 2020

2019

Improving the sensitivity of long read overlap detection using grouped short k-mer matches.

[BibT_eX]

[DOI]

Nan Du

BMC Genom., 2019

GPRED-GC: a Gene PREDiction model accounting for 5 <sup>′</sup>- 3<sup>′</sup> GC gradient.

[BibT_eX]

[DOI]

Kevin L. Childs

BMC Bioinform., 2019

Fast and accurate microRNA search using CNN.

[BibT_eX]

[DOI]

Xubo Tang

BMC Bioinform., 2019

A binning tool to reconstruct viral haplotypes from assembled contigs.

[BibT_eX]

[DOI]

BMC Bioinform., 2019

TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data.

[BibT_eX]

[DOI]

Jiating Huang

BMC Bioinform., 2019

2018

De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding.

[BibT_eX]

[DOI]

Yingchao Zhao

Bioinform., 2018

2017

Cap-seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse.

[BibT_eX]

[DOI]

Dongxiao Zhu

Quant. Biol., 2017

A sensitive short read homology search tool for paired-end read sequencing data.

[BibT_eX]

[DOI]

BMC Bioinform., 2017

2016

Application and Realization of Improved Apriori Algorism in Hadoop Simulation Platform for Mass Data Process.

[BibT_eX]

[DOI]

Xinhua Chen

Int. J. Online Eng., 2016

Computer Network Simulation Modeling Based on Object Oriented Petri Net.

[BibT_eX]

[DOI]

Xinhua Chen

Int. J. Online Eng., 2016

Assemble CRISPRs from metagenomic sequencing data.

[BibT_eX]

[DOI]

Bioinform., 2016

Improve homology search sensitivity of PacBio data by correcting frameshifts.

[BibT_eX]

[DOI]

Nan Du

Bioinform., 2016

2015

Reconstructing 16S rRNA genes in metagenomic data.

[BibT_eX]

[DOI]

Bioinform., 2015

LncRNA-ID: Long non-coding RNA IDentification using balanced random forests.

[BibT_eX]

[DOI]

Bioinform., 2015

2014

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data.

[BibT_eX]

[DOI]

James R. Cole

PLoS Comput. Biol., 2014

Ribosomal Database Project: data and tools for high throughput rRNA analysis.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2014

miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data.

[BibT_eX]

[DOI]

Bioinform., 2014

2013

Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-Dimensional Chain Algorithm.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Efficient known ncRNA search including pseudoknots.

[BibT_eX]

[DOI]

Cheng Yuan

BMC Bioinform., 2013

Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads.

[BibT_eX]

[DOI]

James R. Cole

Bioinform., 2013

glu-RNA: aliGn highLy strUctured ncRNAs using only sequence similarity.

[BibT_eX]

[DOI]

Proceedings of the ACM Conference on Bioinformatics, 2013

ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding tools.

[BibT_eX]

[DOI]

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

Designing Filters for Fast-Known NcRNA Identification.

[BibT_eX]

[DOI]

Cheng Yuan

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

MetaDomain: A Profile HMM-Based Protein Domain Classification Tool for Short Sequences.

[BibT_eX]

[DOI]

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

PseudoDomain: identification of processed pseudogenes based on protein domain classification.

[BibT_eX]

[DOI]

Proceedings of the ACM International Conference on Bioinformatics, 2012

2011

Ncrna Consensus Secondary Structure Derivation Using Grammar Strings.

[BibT_eX]

[DOI]

Seyedeh Shohreh Takyar

J. Bioinform. Comput. Biol., 2011

HMM-FRAME: accurate protein domain classification for metagenomic sequences in the presence of frameshift errors.

[BibT_eX]

[DOI]

BMC Bioinform., 2011

NcRNA homology search using Hamming distance seeds.

[BibT_eX]

[DOI]

Proceedings of the ACM International Conference on Bioinformatics, 2011

2010

BLAST Tree: Fast Filtering for Genomic Sequence Classification.

[BibT_eX]

[DOI]

Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010

2009

Designing Patterns and Profiles for Faster HMM Search.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

2007

Designing patterns for profile HMM search.

[BibT_eX]

[DOI]

Bioinform., 2007

2006

Choosing the best heuristic for seeded alignment of DNA sequences.

[BibT_eX]

[DOI]

BMC Bioinform., 2006

2005

Designing seeds for similarity search in genomic DNA.

[BibT_eX]

[DOI]

Uri Keich

J. Comput. Syst. Sci., 2005

Designing Multiple Simultaneous Seeds for DNA Similarity Search.

[BibT_eX]

[DOI]