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 2020-11-01 to 2024-11-01.)

Article	Citations
Distance-based Support Vector Machine to Predict DNA N6- methyladenine Modification	227
MRMD2.0: A Python Tool for Machine Learning with Feature Ranking and Reduction	73
Identification of Drug-Disease Associations by Using Multiple Drug and Disease Networks	51
MK-FSVM-SVDD: A Multiple Kernel-based Fuzzy SVM Model for Predicting DNA-binding Proteins via Support Vector Data Description	47
Sequence-based Identification of Arginine Amidation Sites in Proteins Using Deep Representations of Proteins and PseAAC	47
Review of the Applications of Deep Learning in Bioinformatics	43
Sequence-based Identification of Allergen Proteins Developed by Integration of PseAAC and Statistical Moments via 5-Step Rule	42
iATC-NFMLP: Identifying Classes of Anatomical Therapeutic Chemicals Based on Drug Networks, Fingerprints, and Multilayer Perceptron	38
iTSP-PseAAC: Identifying Tumor Suppressor Proteins by Using Fully Connected Neural Network and PseAAC	32
NPalmitoylDeep-PseAAC: A Predictor of N-Palmitoylation Sites in Proteins Using Deep Representations of Proteins and PseAAC via Modified 5-Steps Rule	29
Identification of DNA-Binding Proteins via Hypergraph Based Laplacian Support Vector Machine	28
Cervical Cancer Metastasis and Recurrence Risk Prediction Based on Deep Convolutional Neural Network	28
Analysis of the Epigenetic Signature of Cell Reprogramming by Computational DNA Methylation Profiles	23
Cancer Diagnosis and Disease Gene Identification via Statistical Machine Learning	22
Modeling Hereditary Disease Behavior Using an Innovative Similarity Criterion and Ensemble Clustering	21
Predicting LncRNA Subcellular Localization Using Unbalanced Pseudo-k Nucleotide Compositions	21
Fusing Multiple Biological Networks to Effectively Predict miRNA-disease Associations	21
An Ensembled SVM Based Approach for Predicting Adverse Drug Reactions	20
Identification of Cancerlectins By Using Cascade Linear Discriminant Analysis and Optimal g-gap Tripeptide Composition	19
iAnt: Combination of Convolutional Neural Network and Random Forest Models Using PSSM and BERT Features to Identify Antioxidant Proteins	19
A Drug Target Interaction Prediction Based on LINE-RF Learning	19
BDselect: A Package for k-mer Selection Based on the Binomial Distribution	18
PMPTCE-HNEA: Predicting Metabolic Pathway Types of Chemicals and Enzymes with a Heterogeneous Network Embedding Algorithm	17
Early Prediction of Malignant Mesothelioma: An Approach Towards Non-invasive Method	16
Predicting lncRNA-protein Interactions by Machine Learning Methods: A Review	15

PoGB-pred: Prediction of Antifreeze Proteins Sequences Using Amino Acid Composition with Feature Selection Followed by a Sequential-based Ensemble Approach	15
Protein Secondary Structure Prediction Using Character Bi-gram Embedding and Bi-LSTM	15
Drug Design and Disease Diagnosis: The Potential of Deep Learning Models in Biology	14
Model with the GBDT for Colorectal Adenoma Risk Diagnosis	13
Exploiting XG Boost for Predicting Enhancer-promoter Interactions	12
A Deep Convolutional Neural Network to Improve the Prediction of Protein Secondary Structure	12
Identifying Breast Cancer-induced Gene Perturbations and its Application in Guiding Drug Repurposing	12
Enhanced Moth-flame Optimizer with Quasi-Reflection and Refraction Learning with Application to Image Segmentation and Medical Diagnosis	12
Exploring miRNA Sponge Networks of Breast Cancer by Combining miRNA-disease-lncRNA and miRNA-target Networks	12
Docking Techniques in Toxicology: An Overview	12
PEPRF: Identification of Essential Proteins by Integrating Topological Features of PPI Network and Sequence-based Features via Random Forest	11
Prediction of Microbe-drug Associations Based on Chemical Structures and the KATZ Measure	11
Identification of Most Relevant Features for Classification of Francisella tularensis using Machine Learning	11
An Efficient Multiple Kernel Support Vector Regression Model for Assessing Dry Weight of Hemodialysis Patients	11
Application of Machine Learning in Animal Disease Analysis and Prediction	11
Rosetta and the Journey to Predict Proteins’ Structures, 20 Years on	11
Lung Cancer Classification and Gene Selection by Combining Affinity Propagation Clustering and Sparse Group Lasso	11
Densely Dilated Spatial Pooling Convolutional Network Using Benign Loss Functions for Imbalanced Volumetric Prostate Segmentation	10
A Review on the Methods of Peptide-MHC Binding Prediction	10
Robust Transcription Factor Binding Site Prediction Using Deep Neural Networks	10
HAMP: A Knowledge-base of Antimicrobial Peptides from Human Microbiome	10
Colorectal Cancer Classification and Survival Analysis Based on an Integrated RNA and DNA Molecular Signature	10
Prediction of Neddylation Sites Using the Composition of k-spaced Amino Acid Pairs and Fuzzy SVM	10
Prediction of lncRNA-disease Associations Based on Robust Multi-label Learning	10
Classification of Chromosomal DNA Sequences Using Hybrid Deep Learning Architectures	10
A Combined Feature Screening Approach of Random Forest and Filterbased Methods for Ultra-high Dimensional Data	10
A Novel Feature Selection Method Based on MRMR and Enhanced Flower Pollination Algorithm for High Dimensional Biomedical Data	10
Deep Learning Model for Pathogen Classification Using Feature Fusion and Data Augmentation	9
Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework	9
Identification of Potential Immune-related Biomarkers in Gastrointestinal Cancers	9
Feature Selection Algorithm for High-dimensional Biomedical Data Using Information Gain and Improved Chemical Reaction Optimization	9
The Regulation of Target Genes by Co-occupancy of Transcription Factors, c-Myc and Mxi1 with Max in the Mouse Cell Line	9
A Machine Learning-based Self-risk Assessment Technique for Cervical Cancer	9
TP-MV: Therapeutic Peptides Prediction by Multi-view Learning	9
An Unbiased Predictive Model to Detect DNA Methylation Propensity of CpG Islands in the Human Genome	9
A Review of Protein Inter-residue Distance Prediction	9
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	9
Introduction of Advanced Methods for Structure-based Drug Discovery	9
Complex Networks, Gene Expression and Cancer Complexity: A Brief Review of Methodology and Applications	8
Development of Machine Learning Based Blood-brain Barrier Permeability Prediction Models Using Physicochemical Properties, MACCS and Substructure Fingerprints	8
Whole-exome Sequencing of Tumor-only Samples Reveals the Association between Somatic Alterations and Clinical Features in Pancreatic Cancer	8
CSBPI_Site: Multi-Information Sources of Features to RNA Binding Sites Prediction	8
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	8
Bioluminescent Proteins Prediction with Voting Strategy	8
Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress	8
DeepFusion-RBP: Using Deep Learning to Fuse Multiple Features to Identify RNA-binding Protein Sequences	8
Artificial Intelligence for Bioinformatics and Biomedicine	8
Informative Gene Selection Based on Cost-Sensitive Fast Correlation- Based Filter Feature Selection	7
A Computational Framework to Identify Cross Association Between Complex Disorders by Protein-protein Interaction Network Analysis	7
PREDAIP: Computational Prediction and Analysis for Anti-inflammatory Peptide via a Hybrid Feature Selection Technique	7

MDAPlatform: A Component-based Platform for Constructing and Assessing miRNA-disease Association Prediction Methods	7
Integrative Analysis of miRNA-mediated Competing Endogenous RNA Network Reveals the lncRNAs-mRNAs Interaction in Glioblastoma Stem Cell Differentiation	7
Analysis and Validation of Differentially Expressed MicroRNAs with their Target Genes Involved in GLP-1RA Facilitated Osteogenesis	7
Identification of Disordered Regions of Intrinsically Disordered Proteins by Multi-features Fusion	7
A Path-based Method for Identification of Protein Phenotypic Annotations	7
Bioinformatics Analysis Identifies CPZ as a Tumor Immunology Biomarker for Gastric Cancer	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
PsePSSM-based Prediction for the Protein-ATP Binding Sites	7
Identification of Biomarkers and Functional Modules from Genomic Data in Stage-wise Breast Cancer	7
NLP-MeTaxa: A Natural Language Processing Approach for Metagenomic Taxonomic Binning Based on Deep Learning	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
Development and Application of Artificial Intelligence Methods in Biological and Medical Data	6
An Information Gain-based Method for Evaluating the Classification Power of Features Towards Identifying Enhancers	6
High-density Genetic Linkage Map Construction in Sunflower (Helianthus annuus L.) Using SNP and SSR Markers	6
Bioinformatics Analysis Reveals Centromere Protein K Can Serve as Potential Prognostic Biomarker and Therapeutic Target for Non-small Cell Lung Cancer	6
DILI-Stk: An Ensemble Model for the Prediction of Drug-induced Liver Injury of Drug Candidates	6
Screening of SLE-susceptible SNPs in One Chinese Family with Systemic Lupus Erythematosus	6
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	6
Salient Features, Data and Algorithms for MicroRNA Screening from Plants: A Review on the Gains and Pitfalls of Machine Learning Techniques	6
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	6
Intelligent Techniques Analysis for Glycosylation Site Prediction	6
Feature-scML: An Open-source Python Package for the Feature Importance Visualization of Single-Cell Omics with Machine Learning	6
Using the Chou’s Pseudo Component to Predict the ncRNA Locations Based on the Improved K-Nearest Neighbor (iKNN) Classifier	6
Comprehensive Analysis Reveals GPRIN1 is a Potential Biomarker for Non-sm all Cell Lung Cancer	6
An Algorithm to Improve the Speed of Semi and Non-specific Enzyme Searches in Proteomics	6
The Prospect of Bioactive Peptide Research: A Review on Databases and Tools	6
Classifying Cognitive Normal and Early Mild Cognitive Impairment of Alzheimer’s Disease by Applying Restricted Boltzmann Machine to fMRI Data	5
Predicting Chromosome Flexibility from the Genomic Sequence Based on Deep Learning Neural Networks	5
A Novel Hybrid Filter/Wrapper Feature Selection Approach Based on Improved Fruit Fly Optimization Algorithm and Chi-square Test for High Dimensional Microarray Data	5
Prediction of Drug Pathway-based Disease Classes using Multiple Properties of Drugs	5
A Review: Computational Approaches to Design sgRNA of CRISPR-Cas9	5
A Cross-entropy-based Method for Essential Protein Identification in Yeast Protein-protein Interaction Network	5
A Constrained Probabilistic Matrix Decomposition Method for Predicting miRNA-disease Associations	5
Survival Prediction of Esophageal Squamous Cell Carcinoma Based on the Prognostic Index and Sparrow Search Algorithm-Support Vector Machine	5
ConvChrome: Predicting Gene Expression Based on Histone Modifications Using Deep Learning Techniques	5
Genome-wide Characterization Deciphers Distinct Properties of Aquaporins in Six Phytophthora Species	5
Ensemble Adaptive Total Variation Graph Regularized NMF for Singlecell RNA-seq Data Analysis	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
Genome-wide Identification of Differently Expressed lncRNAs, mRNAs, and circRNAs in Patients with Osteoarthritis	5
Incorporating K-mers Highly Correlated to Epigenetic Modifications for Bayesian Inference of Gene Interactions	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
Identification of Key mRNAs, miRNAs, and mRNA-miRNA Network Involved in Papillary Thyroid Carcinoma	5
DSAE-Impute: Learning Discriminative Stacked Autoencoders for Imputing Single-cell RNA-seq Data	5
Structural and Functional Analyses of SARS COV-2 RNA-dependent RNA Polymerase Protein and Complementary vs. Synthetic Drugs against COVID-19 and the Exploration of Binding Sites for Docking, Molecular	5
LPLSG: Prediction of lncRNA-protein Interaction Based on Local Network Structure	5
Recognition of CRISPR Off-Target Cleavage Sites with SeqGAN	5