OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Bioinformatics and Computational Biology is 1. 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
DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning	25
3D U-Net: A voxel-based method in binding site prediction of protein structure	15
HemoNet: Predicting hemolytic activity of peptides with integrated feature learning	12
Comparing the topology of phylogenetic network generators	11
Incorporating intergenic regions into reversal and transposition distances with indels	9
Prediction of adverse drug reactions using drug convolutional neural networks	7
Prediction of miRNA-disease associations based on Weighted K-Nearest known neighbors and network consistency projection	6
KFGRNI: A robust method to inference gene regulatory network from time-course gene data based on ensemble Kalman filter	6
Unsupervised multi-instance learning for protein structure determination	6
An evaluation of combined strategies for improving the performance of molecular docking	6
A protein succinylation sites prediction method based on the hybrid architecture of LSTM network and CNN	6
Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets	5
iDNA6mA-Rice-DL: A local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method	5
DNN-Boost: Somatic mutation identification of tumor-only whole-exome sequencing data using deep neural network and XGBoost	4
Transformation of FASTA files into feature vectors for unsupervised compression of short reads databases	4
SpliceViNCI: Visualizing the splicing of non-canonical introns through recurrent neural networks	4
The potential of family-free rearrangements towards gene orthology inference	4
PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures	4
Small parsimony for natural genomes in the DCJ-indel model	4
Distance matrices for nitrogenous bases and amino acids of SARS-CoV-2 via structural metric	4
A symmetry-inclusive algebraic approach to genome rearrangement	3
DeepBtoD: Improved RNA-binding proteins prediction via integrated deep learning	3
Sparse robust graph-regularized non-negative matrix factorization based on correntropy	3
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases	3
RMI-DBG algorithm: A more agile iterative de Bruijn graph algorithm in short read genome assembly	3

RiRPSSP: A unified deep learning method for prediction of regular and irregular protein secondary structures	3
O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine	3
TemporalGSSA: A numerically robust R-wrapper to facilitate computation of a metabolite-specific and simulation time-dependent trajectory from stochastic simulation algorithm (SSA)-generated datasets	3
Protein–protein interaction site prediction using random forest proximity distance	3
bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model	3
Evidence for exon shuffling is sensitive to model choice	3
Population-specific adaptation in malaria-endemic regions of asia	3
Identification of genes associated with cancer prognosis in glioma: In silico data analyses of Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA)	3
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	2
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	2
Prediction of nucleosome dynamic interval based on long–short-term memory network (LSTM)	2
BOPAL 2.0 and a study of tRNA and rRNA gene evolution in Clostridium	2
Total evidence or taxonomic congruence? A comparison of methods for combining biological evidence	2
Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm	2
Shared ancestry of core-histone subunits and non-histone plant proteins containing the Histone Fold Motif (HFM)	2
Identification of deregulation mechanisms specific to cancer subtypes	2
Clinical drug response prediction from preclinical cancer cell lines by logistic matrix factorization approach	2
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network	2
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	2
Genetic algorithm applied to simultaneous parameter estimation in bacterial growth	2
Detecting genetic associations with brain imaging phenotypes in Alzheimer’s disease via a novel structured KCCA approach	2
A sequence-based two-layer predictor for identifying enhancers and their strength through enhanced feature extraction	2
Denoising of scanning electron microscope images for biological ultrastructure enhancement	2
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides	2
A deep imputation and inference framework for estimating personalized and race-specific causal effects of genomic alterations on PSA	2
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	2
Antimicrobial peptides recognition using weighted physicochemical property encoding	2
RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy	2
Scaling laws of graphs of 3D protein structures	2
In silico de novo drug design of a therapeutic peptide inhibitor against UBE2C in breast cancer	2
ReHiC: Enhancing Hi-C data resolution via residual convolutional network	2
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	2
Prophage loci predictor for bacterial genomes	2
Overlapping group screening for binary cancer classification with TCGA high-dimensional genomic data	2
EdClust: A heuristic sequence clustering method with higher sensitivity	2
Identifying protein complexes from protein–protein interaction networks based on the gene expression profile and core-attachment approach	2
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	2
The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny	1
GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion	1
RepeatsPlus — program for finding motifs and repeats in data sequences	1
Behavioral dynamics of bacteriophage gene regulatory networks	1
Accounting for treatment during the development or validation of prediction models	1
Female reproduction-specific proteins, origins in marine species, and their evolution in the animal kingdom	1
Analyzing omics data based on sample network	1
Hot spots localization in proteins by optimized short time Ramanujan Fourier transform	1
Molecular Dynamics Simulations of Ribosome-Binding Sites in Theophylline-Responsive Riboswitch Associated with Improving the gene Expression Regulation in Chloroplasts	1
Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot	1
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	1
Compression for population genetic data through finite-state entropy	1
Transforming OMIC features for classification using siamese convolutional networks	1

Obstacles to effective model deployment in healthcare	1
Amino acid environment affinity model based on graph attention network	1
Optimized splitting of mixed-species RNA sequencing data	1
iAMY-RECMFF: Identifying amyloidgenic peptides by using residue pairwise energy content matrix and features fusion algorithm	1
Quantification of the presence of enzymes in gelatin zymography using the Gini index	1
RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families	1
Influence of the go-based semantic similarity measures in multi-objective gene clustering algorithm performance	1
Colorful orthology clustering in bounded-degree similarity graphs	1
Mining of structural motifs in proteins using artificial bee colony optimization framework for druggability	1
The impact of simulation time in predicting binding free energies using end-point approaches	1
Impacts of reference selection on the assembly of suspicious coronavirus genome	1
Regression based fast multi-trait genome-wide QTL analysis	1
Involving repetitive regions in scaffolding improvement	1
Flux balance network expansion predicts stage-specific human peri_implantation embryo metabolism	1
Identification of cancer-related module in protein–protein interaction network based on gene prioritization	1
Reversals and transpositions distance with proportion restriction	1
AAindex-PPII: Predicting polyproline type II helix structure based on amino acid indexes with an improved BiGRU-TextCNN model	1
DeepRT: Predicting compounds presence in pathway modules and classifying into module classes using deep neural networks based on molecular properties	1
An innovative method for the selection of inhibitors of the viral spike-glycoprotein of the SARS-CoV	1