CPPLS-MLP: a method for constructing cell-cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data.

[BibT_eX]

[DOI]

Tianjiao Zhang

Zhenao Wu

Briefings Bioinform., 2024

GAADE: identification spatially variable genes based on adaptive graph attention network.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

HLAIImaster: a deep learning method with adaptive domain knowledge predicts HLA II neoepitope immunogenic responses.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

Meta learning for mutant HLA class I epitope immunogenicity prediction to accelerate cancer clinical immunotherapy.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

Deep learning in template-free <i>de novo</i> biosynthetic pathway design of natural products.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

DeePhafier: a phage lifestyle classifier using a multilayer self-attention neural network combining protein information.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

DrugReSC: targeting disease-critical cell subpopulations with single-cell transcriptomic data for drug repurposing in cancer.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

scLEGA: an attention-based deep clustering method with a tendency for low expression of genes on single-cell RNA-seq data.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

SVDF: enhancing structural variation detect from long-read sequencing via automatic filtering strategies.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

Hierarchical multimodal self-attention-based graph neural network for DTI prediction.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

2023

MDformer: A transformer-based method for predicting miRNA-Disease associations using multi-source feature fusion and maximal meta-path instances encoding.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, December, 2023

MMCL-CDR: enhancing cancer drug response prediction with multi-omics and morphology images contrastive representation learning.

[BibT_eX]

[DOI]

Bioinform., December, 2023

Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling.

[BibT_eX]

[DOI]

Nat. Mac. Intell., October, 2023

DeepICSH: a complex deep learning framework for identifying cell-specific silencers and their strength from the human genome.

[BibT_eX]

[DOI]

Briefings Bioinform., September, 2023

ASAS-EGB: A statistical framework for estimating allele-specific alternative splicing events using transcriptome data.

[BibT_eX]

[DOI]

Lili Dong

Jianan Wang

Guohua Wang

Comput. Biol. Medicine, June, 2023

Identifying cancer driver genes using a two-stage random walk with restart on a gene interaction network.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, May, 2023

miProBERT: identification of microRNA promoters based on the pre-trained model BERT.

[BibT_eX]

[DOI]

Briefings Bioinform., May, 2023

End-to-end interpretable disease-gene association prediction.

[BibT_eX]

[DOI]

Briefings Bioinform., May, 2023

PlantCADB: A Comprehensive Plant Chromatin Accessibility Database.

[BibT_eX]

[DOI]

Genom. Proteom. Bioinform., April, 2023

Unsupervised construction of gene regulatory network based on single-cell multi-omics data of colorectal cancer.

[BibT_eX]

[DOI]

Briefings Bioinform., March, 2023

MCANet: shared-weight-based MultiheadCrossAttention network for drug-target interaction prediction.

[BibT_eX]

[DOI]

Briefings Bioinform., March, 2023

Feature selection combined with top-down and bottom-up strategies for survival analysis: A case of prognostic prediction in glioblastoma.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, February, 2023

CanMethdb: a database for genome-wide DNA methylation annotation in cancers.

[BibT_eX]

[DOI]

Bioinform., January, 2023

MicroRNA Promoter Identification in Human With a Three-level Prediction Method.

[BibT_eX]

[DOI]

Xin Wang

Jie Li

Guohua Wang

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

A Clustering Ensemble Method for Cell Type Detection by Multiobjective Particle Optimization.

[BibT_eX]

[DOI]

Qiaoming Liu

Xudong Zhao

Guohua Wang

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

MTGDC: A Multi-Scale Tensor Graph Diffusion Clustering for Single-Cell RNA Sequencing Data.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

scWECTA: A weighted ensemble classification framework for cell type assignment based on single cell transcriptome.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, 2023

2022

StackCirRNAPred: computational classification of long circRNA from other lncRNA based on stacking strategy.

[BibT_eX]

[DOI]

BMC Bioinform., December, 2022

An interpretable deep learning workflow for discovering subvisual abnormalities in CT scans of COVID-19 inpatients and survivors.

[BibT_eX]

[DOI]

Nat. Mach. Intell., 2022

IOFS-SA: An interactive online feature selection tool for survival analysis.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, 2022

Supervised graph co-contrastive learning for drug-target interaction prediction.

[BibT_eX]

[DOI]

Bioinform., 2022

Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

Ensemble classification based signature discovery for cancer diagnosis in RNA expression profiles across different platforms.

[BibT_eX]

[DOI]

Xudong Zhao

Tong Liu

Guohua Wang

Briefings Bioinform., 2022

Complex genome assembly based on long-read sequencing.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

A survey on computational methods in discovering protein inhibitors of SARS-CoV-2.

[BibT_eX]

[DOI]

Qiaoming Liu

Jun Wan

Guohua Wang

Briefings Bioinform., 2022

scESI: evolutionary sparse imputation for single-cell transcriptomes from nearest neighbor cells.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

Drug-target interaction predication via multi-channel graph neural networks.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

Detection of transcription factors binding to methylated DNA by deep recurrent neural network.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

2021

Correction to: Efficient iterative Hi-C scaffolder based on N-best neighbors.

[BibT_eX]

[DOI]

BMC Bioinform., December, 2021

ReRF-Pred: predicting amyloidogenic regions of proteins based on their pseudo amino acid composition and tripeptide composition.

[BibT_eX]

[DOI]

BMC Bioinform., 2021

Efficient iterative Hi-C scaffolder based on N-best neighbors.

[BibT_eX]

[DOI]

BMC Bioinform., 2021

BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method.

[BibT_eX]

[DOI]

Bioinform., 2021

Evaluating disease similarity based on gene network reconstruction and representation.

[BibT_eX]

[DOI]

Yang Li

Keqi Wang

Guohua Wang

Bioinform., 2021

The stacking strategy-based hybrid framework for identifying non-coding RNAs.

[BibT_eX]

[DOI]

Briefings Bioinform., 2021

CHTKC: a robust and efficient k-mer counting algorithm based on a lock-free chaining hash table.

[BibT_eX]

[DOI]

Briefings Bioinform., 2021

A deep learning approach for filtering structural variants in short read sequencing data.

[BibT_eX]

[DOI]

Briefings Bioinform., 2021

AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads.

[BibT_eX]

[DOI]

Briefings Bioinform., 2021

2020

ECFS-DEA: an ensemble classifier-based feature selection for differential expression analysis on expression profiles.

[BibT_eX]

[DOI]

BMC Bioinform., 2020

Evaluating individual genome similarity with a topic model.

[BibT_eX]

[DOI]

Bioinform., 2020

BYASE: a Python library for estimating gene and isoform level allele-specific expression.

[BibT_eX]

[DOI]

Lili Dong

Jianan Wang

Guohua Wang

Bioinform., 2020

AFS-DEA: An automatic feature selection platform for differential expression analysis.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

2018

MeDReaders: a database for transcription factors that bind to methylated DNA.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2018

2017

Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility.

[BibT_eX]

[DOI]

BMC Bioinform., 2017

2016

Preface.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

HAlign: Fast multiple similar DNA/RNA sequence alignment based on the centre star strategy.

[BibT_eX]

[DOI]

Bioinform., 2015

2011

A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2011

2010

Prioritization of disease microRNAs through a human phenome-microRNAome network.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2010

2009

miR2Disease: a manually curated database for microRNA deregulation in human disease.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2009

2007

Refining Detection of RNA-Protein Binding Regions by Pyrosequencing of RNA Fragments.

[BibT_eX]

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007

Identification of Transcription Factor and microRNA Binding Sites from Array-derived Gene Expression Data.

[BibT_eX]

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007

Guohua Wang

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