Application of Multilayer Network Models in Bioinformatics

Screening of Prospective Plant Compounds as H1R and CL1R Inhibitors and Its Antiallergic Efficacy through Molecular Docking Approach

(2021) Hasan Zulfiqar et al.   Computational and Mathematical Methods in Medicine

iBLP: An XGBoost-Based Predictor for Identifying Bioluminescent Proteins

(2021) Dan Zhang et al.   Computational and Mathematical Methods in Medicine

DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism

(2021) Duolin Wang et al.   NUCLEIC ACIDS RESEARCH

Application of deep learning methods in biological networks

(2020) Shuting Jin et al.   BRIEFINGS IN BIOINFORMATICS

FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network

(2020) Jiangyi Shao et al.   BRIEFINGS IN BIOINFORMATICS

Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning

(2020) Xiangxiang Zeng et al.   JOURNAL OF PROTEOME RESEARCH

Predicting preference of transcription factors for methylated DNA using sequence information

(2020) Meng-Lu Liu et al.   Molecular Therapy-Nucleic Acids

Deep-Kcr: accurate detection of lysine crotonylation sites using deep learning method

(2020) Hao Lv et al.   BRIEFINGS IN BIOINFORMATICS

ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm

(2020) Jiangyi Shao et al.   BRIEFINGS IN BIOINFORMATICS

A Method for Identifying Vesicle Transport Proteins Based on LibSVM and MRMD

(2020) Zhiyu Tao et al.   Computational and Mathematical Methods in Medicine

Identification of Drug–Target Interactions via Dual Laplacian Regularized Least Squares with Multiple Kernel Fusion

(2020) Yijie Ding et al.   KNOWLEDGE-BASED SYSTEMS

DeepAVP: A Dual-Channel Deep Neural Network for Identifying Variable-Length Antiviral Peptides

(2020) Jiawei Li et al.   IEEE Journal of Biomedical and Health Informatics

DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops

(2020) Fu-Ying Dao et al.   BRIEFINGS IN BIOINFORMATICS

Exploring associations of non-coding RNAs in human diseases via three-matrix factorization with hypergraph-regular terms on center kernel alignment

(2020) Hao Wang et al.   BRIEFINGS IN BIOINFORMATICS

A computational framework for identifying the transcription factors involved in enhancer-promoter loop formation

(2020) Li Liu et al.   Molecular Therapy-Nucleic Acids

Data integration of hybrid microarray and single cell expression data to enhance gene network inference

(2019) Wei Zhang et al.   Current Bioinformatics

Combining Sequence Entropy and Subgraph Topology for Complex Prediction in Protein Protein Interaction (PPI) Network

(2019) Aisha Sikandar et al.   Current Bioinformatics

Genetic variant rs17185536 regulates SIM1 gene expression in human brain hypothalamus

(2019) Guiyou Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep-Resp-Forest: A deep forest model to predict anti-cancer drug response

(2019) Ran Su et al.   METHODS

Adaptive Elman model of gene regulation network based on time series data

(2019) Shengxian Cao et al.   Current Bioinformatics

Comprehensive understanding of the interaction among stress hormones signalling pathways by gene co-expression network

(2019) Maryam Mortezaeefar et al.   Current Bioinformatics

The Expression Profiles of lncRNAs and Their Regulatory Network during Smek1/2 Knockout Mouse Neural Stem Cells Differentiation

(2019) Qichang Yang et al.   Current Bioinformatics

Predicting drug side effects with compact integration of heterogeneous networks

(2019) Xian Zhao et al.   Current Bioinformatics

Systems biology approaches reveal a multi-stress responsive WRKY transcription factor and stress associated gene co-expression networks in chickpea

(2019) Aravind K Kumar et al.   Current Bioinformatics

Computational methods for identifying the critical nodes in biological networks

(2019) Xiangrong Liu et al.   BRIEFINGS IN BIOINFORMATICS

DUNet: A deformable network for retinal vessel segmentation

(2019) Qiangguo Jin et al.   KNOWLEDGE-BASED SYSTEMS

Research on Gastric Cancer’s Drug-Resistant Gene Regulatory Network Model

(2019) Zhi Li et al.   Current Bioinformatics

BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Finding Community of Brain Networks Based on Neighbor Index and DPSO with Dynamic Crossover

(2019) Jie Zhang et al.   Current Bioinformatics

Complex Networks, Gene Expression and Cancer Complexity: A brief Review in Methodology and Applications.

(2019) A. C. Iliopoulos et al.   Current Bioinformatics

Protein Network Analysis using Small World Concepts

(2019) Neetu Kumari et al.   Current Bioinformatics

Identification of drug–target interactions via fuzzy bipartite local model

(2019) Yijie Ding et al.   NEURAL COMPUTING & APPLICATIONS

Fold-LTR-TCP: protein fold recognition based on triadic closure principle

(2019) Bin Liu et al.   BRIEFINGS IN BIOINFORMATICS

Identification of membrane protein types via multivariate information fusion with Hilbert–Schmidt Independence Criterion

(2019) Hao Wang et al.   NEUROCOMPUTING

Network-based method for mining novel HPV infection related genes using random walk with restart algorithm

(2018) Liucun Zhu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Prediction of potential disease-associated microRNAs using structural perturbation method

(2018) Xiangxiang Zeng et al.   BIOINFORMATICS

DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function

(2018) Liang Cheng et al.   BIOINFORMATICS

A Novel Model for Predicting LncRNA-disease Associations based on the LncRNA-MiRNA-Disease Interactive Network

(2018) Lei Wang et al.   Current Bioinformatics

Prediction of human protein subcellular localization using deep learning

(2018) Leyi Wei et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

Developing a Multi-Dose Computational Model for Drug-induced Hepatotoxicity Prediction based on Toxicogenomics Data

(2018) Ran Su et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Brief Survey of Biological Network Alignment and a Variant with Incorporation of Functional Annotations

(2018) Fang Jing et al.   Current Bioinformatics

In-silico identification of drug lead molecule against pesticide-exposed neurodevelopmental disorders through the network-based computational model approach

(2018) Neha Srivastava et al.   Current Bioinformatics

Identification of drug-side effect association via multiple information integration with centered kernel alignment

(2018) Yijie Ding et al.   NEUROCOMPUTING

LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse

(2018) Liang Cheng et al.   NUCLEIC ACIDS RESEARCH

Disease status affects the association between rs4813620 and the expression of Alzheimer’s disease susceptibility geneTRIB3

(2018) Guiyou Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying sigma70 promoters with novel pseudo nucleotide composition

(2017) Hao Lin et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Fast prediction of protein methylation sites using a sequence-based feature selection technique

(2017) Leyi Wei et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Local-DPP: An improved DNA-binding protein prediction method by exploring local evolutionary information

(2017) Leyi Wei et al.   INFORMATION SCIENCES

Identification of drug-target interactions via multiple information integration

(2017) Yijie Ding et al.   INFORMATION SCIENCES

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

(2017) Guohua Wang et al.   NUCLEIC ACIDS RESEARCH

Methods of MicroRNA Promoter Prediction and Transcription Factor Mediated Regulatory Network

(2017) Yuming Zhao et al.   Biomed Research International

Spiking Neural P Systems with Colored Spikes

(2017) Tao Song et al.   IEEE Transactions on Cognitive and Developmental Systems

Alzheimer’s Disease Variants with the Genome-Wide Significance are Significantly Enriched in Immune Pathways and Active in Immune Cells

(2016) Qinghua Jiang et al.   MOLECULAR NEUROBIOLOGY

Integrating genome-wide association studies and gene expression data highlights dysregulated multiple sclerosis risk pathways

(2016) Guiyou Liu et al.   Multiple Sclerosis Journal

Alzheimer’s diseaseCD33rs3865444 variant does not contribute to cognitive performance: Table 1.

(2016) Guiyou Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating genome-wide association studies and gene expression data highlights dysregulated multiple sclerosis risk pathways

(2016) Guiyou Liu et al.   Multiple Sclerosis Journal

Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks

(2015) Xiangxiang Zeng et al.   BRIEFINGS IN BIOINFORMATICS

Probabilistic Models for Capturing More Physicochemical Properties on Protein–Protein Interface

(2014) Fei Guo et al.   Journal of Chemical Information and Modeling

TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data

(2014) Qinghua Jiang et al.   Biomed Research International

Improved and Promising Identification of Human MicroRNAs by Incorporating a High-Quality Negative Set

(2013) Leyi Wei et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Predicting human microRNA-disease associations based on support vector machine

(2013) Qinghua Jiang et al.   International Journal of Data Mining and Bioinformatics

Detecting Protein Conformational Changes in Interactions via Scaling Known Structures

(2013) Fei Guo et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Entropy Production Rate Changes in Lysogeny/Lysis Switch Regulation of Bacteriophage Lambda

(2011) Hui Ding et al.   COMMUNICATIONS IN THEORETICAL PHYSICS

Protein–Protein Binding Sites Prediction by 3D Structural Similarities

(2011) Fei Guo et al.   Journal of Chemical Information and Modeling

Prioritization of disease microRNAs through a human phenome-microRNAome network

(2010) Qinghua Jiang et al.   BMC Systems Biology

Signal Transducers and Activators of Transcription-1 (STAT1) Regulates microRNA Transcription in Interferon γ-Stimulated HeLa Cells

(2010) Guohua Wang et al.   PLoS One

Transcription factor and microRNA regulation in androgen-dependent and -independent prostate cancer cells

(2008) Guohua Wang et al.   BMC GENOMICS