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Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning

Briefings in bioinformatics, 2023-01, Vol.24 (1)

2023

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Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning

Bioinformatics (Oxford, England), 2024-03, Vol.40 (4)

2024

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Incorporating prior information into differential network analysis using non-paranormal graphical models

Bioinformatics (Oxford, England), 2017-08, Vol.33 (16), p.2436-2445

2017

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Equivariant Line Graph Neural Network for Protein-Ligand Binding Affinity Prediction

IEEE journal of biomedical and health informatics, 2024-07, Vol.28 (7), p.4336-4347

2024

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DEMOC: a deep embedded multi-omics learning approach for clustering single-cell CITE-seq data

Briefings in bioinformatics, 2022-09, Vol.23 (5)

2022

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A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks

Bioinformatics, 2020-06, Vol.36 (11), p.3474-3481

2020

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Sparse regularized low-rank tensor regression with applications in genomic data analysis

Pattern recognition, 2020-11, Vol.107, p.107516, Article 107516

2020

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MARS: a motif-based autoregressive model for retrosynthesis prediction

Bioinformatics (Oxford, England), 2024-03, Vol.40 (3)

2024

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Self-representative kernel concept factorization

Knowledge-based systems, 2023-01, Vol.259, p.110051, Article 110051

2023

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EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning

Bioinformatics, 2019-11, Vol.35 (22), p.4827-4829

2019

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DiffNetFDR: differential network analysis with false discovery rate control

Bioinformatics (Oxford, England), 2019-09, Vol.35 (17), p.3184-3186

2019

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Recent advances in network-based methods for disease gene prediction

Briefings in bioinformatics, 2021-07, Vol.22 (4)

2021

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RepLong: de novo repeat identification using long read sequencing data

Bioinformatics, 2018-04, Vol.34 (7), p.1099-1107

2018

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Predicting synthetic lethal interactions in human cancers using graph regularized self-representative matrix factorization

BMC bioinformatics, 2019-12, Vol.20 (Suppl 19), p.657-8, Article 657

2019

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Differential network analysis by simultaneously considering changes in gene interactions and gene expression

Bioinformatics, 2021-12, Vol.37 (23), p.4414-4423

2021

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Determining minimum set of driver nodes in protein-protein interaction networks

BMC bioinformatics, 2015-05, Vol.16 (1), p.146-146, Article 146

2015

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A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks

BMC bioinformatics, 2017-12, Vol.18 (Suppl 13), p.463-463, Article 463

2017

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Predicting the impacts of mutations on protein-ligand binding affinity based on molecular dynamics simulations and machine learning methods

Computational and structural biotechnology journal, 2020-01, Vol.18, p.439-454

2020

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Differential network analysis from cross-platform gene expression data

Scientific reports, 2016-09, Vol.6 (1), p.34112-34112, Article 34112

2016

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WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values

Briefings in bioinformatics, 2021-11, Vol.22 (6)

2021

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WMLRR: A Weighted Multi-View Low Rank Representation to Identify Cancer Subtypes From Multiple Types of Omics Data

IEEE/ACM transactions on computational biology and bioinformatics, 2021-11, Vol.18 (6), p.2891-2897

2021

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scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation

Bioinformatics, 2020-05, Vol.36 (10), p.3131-3138

2020

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Node-based learning of differential networks from multi-platform gene expression data

Methods (San Diego, Calif.), 2017-10, Vol.129, p.41-49

2017

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Detecting temporal protein complexes from dynamic protein-protein interaction networks

BMC bioinformatics, 2014-10, Vol.15 (1), p.335-335, Article 335

2014

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DiffGraph: an R package for identifying gene network rewiring using differential graphical models

Bioinformatics, 2018-05, Vol.34 (9), p.1571-1573

2018

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Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning

Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning

Incorporating prior information into differential network analysis using non-paranormal graphical models

Equivariant Line Graph Neural Network for Protein-Ligand Binding Affinity Prediction

DEMOC: a deep embedded multi-omics learning approach for clustering single-cell CITE-seq data

A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks

Sparse regularized low-rank tensor regression with applications in genomic data analysis

MARS: a motif-based autoregressive model for retrosynthesis prediction

Self-representative kernel concept factorization

EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning

DiffNetFDR: differential network analysis with false discovery rate control

Recent advances in network-based methods for disease gene prediction

RepLong: de novo repeat identification using long read sequencing data

Predicting synthetic lethal interactions in human cancers using graph regularized self-representative matrix factorization

Differential network analysis by simultaneously considering changes in gene interactions and gene expression

Determining minimum set of driver nodes in protein-protein interaction networks

A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks

Predicting the impacts of mutations on protein-ligand binding affinity based on molecular dynamics simulations and machine learning methods

Differential network analysis from cross-platform gene expression data

WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values

WMLRR: A Weighted Multi-View Low Rank Representation to Identify Cancer Subtypes From Multiple Types of Omics Data

scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation

Node-based learning of differential networks from multi-platform gene expression data

Detecting temporal protein complexes from dynamic protein-protein interaction networks

DiffGraph: an R package for identifying gene network rewiring using differential graphical models

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