OOIR: Observatory of International Research

Papers

(The TQCC of Current Bioinformatics is 5. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-04-01 to 2024-04-01.)

Article	Citations
Distance-based Support Vector Machine to Predict DNA N6- methyladenine Modification	134
MRMD2.0: A Python Tool for Machine Learning with Feature Ranking and Reduction	81
Relevance of Molecular Docking Studies in Drug Designing	72
Predicting Thermophilic Proteins by Machine Learning	53
MK-FSVM-SVDD: A Multiple Kernel-based Fuzzy SVM Model for Predicting DNA-binding Proteins via Support Vector Data Description	50
Identification of Drug-Disease Associations by Using Multiple Drug and Disease Networks	50
Sequence-based Identification of Arginine Amidation Sites in Proteins Using Deep Representations of Proteins and PseAAC	47
Identification of Lysine Carboxylation Sites in Proteins by Integrating Statistical Moments and Position Relative Features via General PseAAC	45
Sequence-based Identification of Allergen Proteins Developed by Integration of PseAAC and Statistical Moments via 5-Step Rule	41
Review of the Applications of Deep Learning in Bioinformatics	40
iATC-NFMLP: Identifying Classes of Anatomical Therapeutic Chemicals Based on Drug Networks, Fingerprints, and Multilayer Perceptron	38
ConvsPPIS: Identifying Protein-protein Interaction Sites by an Ensemble Convolutional Neural Network with Feature Graph	35
A Machine Learning-based Diagnosis of Thyroid Cancer Using Thyroid Nodules Ultrasound Images	34
NPalmitoylDeep-PseAAC: A Predictor of N-Palmitoylation Sites in Proteins Using Deep Representations of Proteins and PseAAC via Modified 5-Steps Rule	33
iTSP-PseAAC: Identifying Tumor Suppressor Proteins by Using Fully Connected Neural Network and PseAAC	32
Citrullination Site Prediction by Incorporating Sequence Coupled Effects into PseAAC and Resolving Data Imbalance Issue	27
Cervical Cancer Metastasis and Recurrence Risk Prediction Based on Deep Convolutional Neural Network	27
Identification of DNA-Binding Proteins via Hypergraph Based Laplacian Support Vector Machine	25
Leukocyte Image Segmentation Based on Adaptive Histogram Thresholding and Contour Detection	25
Predicting Protein Phosphorylation Sites Based on Deep Learning	24
Analysis of the Epigenetic Signature of Cell Reprogramming by Computational DNA Methylation Profiles	23
MD-LBP: An Efficient Computational Model for Protein Subcellular Localization from HeLa Cell Lines Using SVM	22
Fusing Multiple Biological Networks to Effectively Predict miRNA-disease Associations	21
Cancer Diagnosis and Disease Gene Identification via Statistical Machine Learning	21
Predicting LncRNA Subcellular Localization Using Unbalanced Pseudo-k Nucleotide Compositions	19

A Sequential Ensemble Model for Communicable Disease Forecasting	19
Modeling Hereditary Disease Behavior Using an Innovative Similarity Criterion and Ensemble Clustering	19
Identification of Novel Key Targets and Candidate Drugs in Oral Squamous Cell Carcinoma	18
A Drug Target Interaction Prediction Based on LINE-RF Learning	18
Identification of Cancerlectins By Using Cascade Linear Discriminant Analysis and Optimal g-gap Tripeptide Composition	18
An Ensembled SVM Based Approach for Predicting Adverse Drug Reactions	17
Protein Secondary Structure Prediction Using Character Bi-gram Embedding and Bi-LSTM	17
iAnt: Combination of Convolutional Neural Network and Random Forest Models Using PSSM and BERT Features to Identify Antioxidant Proteins	15
BDselect: A Package for k-mer Selection Based on the Binomial Distribution	15
Predicting lncRNA-protein Interactions by Machine Learning Methods: A Review	14
PMPTCE-HNEA: Predicting Metabolic Pathway Types of Chemicals and Enzymes with a Heterogeneous Network Embedding Algorithm	14
PoGB-pred: Prediction of Antifreeze Proteins Sequences Using Amino Acid Composition with Feature Selection Followed by a Sequential-based Ensemble Approach	13
Early Prediction of Malignant Mesothelioma: An Approach Towards Non-invasive Method	13
Research on Gastric Cancer’s Drug-resistant Gene Regulatory Network Model	13
Exploring miRNA Sponge Networks of Breast Cancer by Combining miRNA-disease-lncRNA and miRNA-target Networks	12
Model with the GBDT for Colorectal Adenoma Risk Diagnosis	12
Current State of the Art for Survival Prediction in Cancer Using Data Mining Techniques	12
Identifying Breast Cancer-induced Gene Perturbations and its Application in Guiding Drug Repurposing	12
Docking Techniques in Toxicology: An Overview	11
Exploiting XG Boost for Predicting Enhancer-promoter Interactions	11
Identification of Most Relevant Features for Classification of Francisella tularensis using Machine Learning	11
Application of Machine Learning in Animal Disease Analysis and Prediction	10
An Efficient Multiple Kernel Support Vector Regression Model for Assessing Dry Weight of Hemodialysis Patients	10
Prediction of lncRNA-disease Associations Based on Robust Multi-label Learning	10
PEPRF: Identification of Essential Proteins by Integrating Topological Features of PPI Network and Sequence-based Features via Random Forest	10
Lung Cancer Classification and Gene Selection by Combining Affinity Propagation Clustering and Sparse Group Lasso	10
Classification of Chromosomal DNA Sequences Using Hybrid Deep Learning Architectures	10
Prediction of Microbe-drug Associations Based on Chemical Structures and the KATZ Measure	10
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	10
The Regulation of Target Genes by Co-occupancy of Transcription Factors, c-Myc and Mxi1 with Max in the Mouse Cell Line	9
Robust Transcription Factor Binding Site Prediction Using Deep Neural Networks	9
TP-MV: Therapeutic Peptides Prediction by Multi-view Learning	9
Elastic Net Regularized Softmax Regression Methods for Multi-subtype Classification in Cancer	9
Deep Learning Model for Pathogen Classification Using Feature Fusion and Data Augmentation	9
A Deep Convolutional Neural Network to Improve the Prediction of Protein Secondary Structure	9
Identification of Potential Immune-related Biomarkers in Gastrointestinal Cancers	9
Introduction of Advanced Methods for Structure-based Drug Discovery	9
Rosetta and the Journey to Predict Proteins’ Structures, 20 Years on	9
Genetic Algorithm-based Feature Selection Approach for Enhancing the Effectiveness of Similarity Searching in Ligand-based Virtual Screening	9
Prediction of Neddylation Sites Using the Composition of k-spaced Amino Acid Pairs and Fuzzy SVM	9
HAMP: A Knowledge-base of Antimicrobial Peptides from Human Microbiome	9
A Review of Protein Inter-residue Distance Prediction	9
Densely Dilated Spatial Pooling Convolutional Network Using Benign Loss Functions for Imbalanced Volumetric Prostate Segmentation	8
An Unbiased Predictive Model to Detect DNA Methylation Propensity of CpG Islands in the Human Genome	8
A Combined Feature Screening Approach of Random Forest and Filterbased Methods for Ultra-high Dimensional Data	8
A Novel Feature Selection Method Based on MRMR and Enhanced Flower Pollination Algorithm for High Dimensional Biomedical Data	8
Artificial Intelligence for Bioinformatics and Biomedicine	8
CSBPI_Site: Multi-Information Sources of Features to RNA Binding Sites Prediction	8
Complex Networks, Gene Expression and Cancer Complexity: A Brief Review of Methodology and Applications	8
DeepFusion-RBP: Using Deep Learning to Fuse Multiple Features to Identify RNA-binding Protein Sequences	8

Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework	8
Bioluminescent Proteins Prediction with Voting Strategy	8
SimExact – An Efficient Method to Compute Function Similarity Between Proteins Using Gene Ontology	8
Colorectal Cancer Classification and Survival Analysis Based on an Integrated RNA and DNA Molecular Signature	8
Feature Selection Algorithm for High-dimensional Biomedical Data Using Information Gain and Improved Chemical Reaction Optimization	8
A Review on the Methods of Peptide-MHC Binding Prediction	8
A Sequence-segment Neighbor Encoding Schema for Protein Hotspot Residue Prediction	8
Whole-exome Sequencing of Tumor-only Samples Reveals the Association between Somatic Alterations and Clinical Features in Pancreatic Cancer	8
A Path-based Method for Identification of Protein Phenotypic Annotations	7
Bioinformatics Analysis Identifies CPZ as a Tumor Immunology Biomarker for Gastric Cancer	7
A Machine Learning-based Self-risk Assessment Technique for Cervical Cancer	7
A Novel Integrative Approach for Non-coding RNA Classification Based on Deep Learning	7
Mutation Mechanisms of Breast Cancer among the Female Population in China	7
Identification of Biomarkers and Functional Modules from Genomic Data in Stage-wise Breast Cancer	7
Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress	7
MDAPlatform: A Component-based Platform for Constructing and Assessing miRNA-disease Association Prediction Methods	7
PsePSSM-based Prediction for the Protein-ATP Binding Sites	7
Development of Machine Learning Based Blood-brain Barrier Permeability Prediction Models Using Physicochemical Properties, MACCS and Substructure Fingerprints	7
The Human OncoBiome Database: A Database of Cancer Microbiome Datasets	7
Identification of Disordered Regions of Intrinsically Disordered Proteins by Multi-features Fusion	7
High-dimensional Causal Mediation Analysis with a Large Number of Mediators Clumping at Zero to Assess the Contribution of the Microbiome to the Risk of Bacterial Pathogen Colonization in Older Adults	7
Intelligent Techniques Analysis for Glycosylation Site Prediction	6
Integrative Analysis of miRNA-mediated Competing Endogenous RNA Network Reveals the lncRNAs-mRNAs Interaction in Glioblastoma Stem Cell Differentiation	6
PREDAIP: Computational Prediction and Analysis for Anti-inflammatory Peptide via a Hybrid Feature Selection Technique	6
Sequence-based Structural B-cell Epitope Prediction by Using Two Layer SVM Model and Association Rule Features	6
Drug Design and Disease Diagnosis: The Potential of Deep Learning Models in Biology	6
Comprehensive Analysis Reveals GPRIN1 is a Potential Biomarker for Non-sm all Cell Lung Cancer	6
Bioinformatics Analysis Reveals Centromere Protein K Can Serve as Potential Prognostic Biomarker and Therapeutic Target for Non-small Cell Lung Cancer	6
Bioinformatics Analysis of The Rhizosphere Microbiota of Dangshan Su Pear in Different Soil Types	6
Screening of SLE-susceptible SNPs in One Chinese Family with Systemic Lupus Erythematosus	6
A Computational Framework to Identify Cross Association Between Complex Disorders by Protein-protein Interaction Network Analysis	6
Development and Application of Artificial Intelligence Methods in Biological and Medical Data	6
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	6
An Information Gain-based Method for Evaluating the Classification Power of Features Towards Identifying Enhancers	6
DILI-Stk: An Ensemble Model for the Prediction of Drug-induced Liver Injury of Drug Candidates	6
Delineating Characteristic Sequence and Structural Features of Precursor and Mature Piwi-interacting RNAs of Epithelial Ovarian Cancer	6
GASPIDs Versus Non-GASPIDs - Differentiation Based on Machine Learning Approach	6
Using the Chou’s Pseudo Component to Predict the ncRNA Locations Based on the Improved K-Nearest Neighbor (iKNN) Classifier	6
Analysis and Validation of Differentially Expressed MicroRNAs with their Target Genes Involved in GLP-1RA Facilitated Osteogenesis	6
Informative Gene Selection Based on Cost-Sensitive Fast Correlation- Based Filter Feature Selection	6
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	6
High-density Genetic Linkage Map Construction in Sunflower (Helianthus annuus L.) Using SNP and SSR Markers	6
Recognition of CRISPR Off-Target Cleavage Sites with SeqGAN	5
Ensemble Adaptive Total Variation Graph Regularized NMF for Singlecell RNA-seq Data Analysis	5
An Algorithm to Improve the Speed of Semi and Non-specific Enzyme Searches in Proteomics	5
Multi-label Learning for the Diagnosis of Cancer and Identification of Novel Biomarkers with High-throughput Omics	5
Natural Scene Nutrition Information Acquisition and Analysis Based on Deep Learning	5
Feature-scML: An Open-source Python Package for the Feature Importance Visualization of Single-Cell Omics with Machine Learning	5
Comparisons of MicroRNA Set Enrichment Analysis Tools on Cancer De-regulated miRNAs from TCGA Expression Datasets	5
Construction and Analysis of mRNA and lncRNA Regulatory Networks Reveal the Key Genes Associated with Prostate Cancer Related Fatigue During Localized Radiation Therapy	5
Stability Analysis at Key Positions of EGFR Related to Non-small Cell Lung Cancer	5
The Prospect of Bioactive Peptide Research: A Review on Databases and Tools	5
Genome-wide Identification of Differently Expressed lncRNAs, mRNAs, and circRNAs in Patients with Osteoarthritis	5
A Constrained Probabilistic Matrix Decomposition Method for Predicting miRNA-disease Associations	5
White Blood Cell Image Segmentation Based on Color Component Combination and Contour Fitting	5
Predicting Chromosome Flexibility from the Genomic Sequence Based on Deep Learning Neural Networks	5
DSAE-Impute: Learning Discriminative Stacked Autoencoders for Imputing Single-cell RNA-seq Data	5
Salient Features, Data and Algorithms for MicroRNA Screening from Plants: A Review on the Gains and Pitfalls of Machine Learning Techniques	5
A Cross-entropy-based Method for Essential Protein Identification in Yeast Protein-protein Interaction Network	5
Incorporating K-mers Highly Correlated to Epigenetic Modifications for Bayesian Inference of Gene Interactions	5