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 2020-03-01 to 2024-03-01.)

Article	Citations
Modeling and simulation of spatial-temporal calcium distribution in T lymphocyte cell by using a reaction-diffusion equation	24
PROSPECT: A web server for predicting protein histidine phosphorylation sites	21
DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning	19
PDB-2-PBv3.0: An updated protein block database	18
Single-cell RNA-seq data clustering: A survey with performance comparison study	16
Denoising Protein–Protein interaction network via variational graph auto-encoder for protein complex detection	15
Comparing the topology of phylogenetic network generators	11
3D U-Net: A voxel-based method in binding site prediction of protein structure	11
EDeepSSP: Explainable deep neural networks for exact splice sites prediction	10
EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins	8
Constructing gene regulatory networks from microarray data using non-Gaussian pair-copula Bayesian networks	7
HemoNet: Predicting hemolytic activity of peptides with integrated feature learning	7
A protein succinylation sites prediction method based on the hybrid architecture of LSTM network and CNN	6
Incorporating intergenic regions into reversal and transposition distances with indels	6
BENIN: Biologically enhanced network inference	6
KFGRNI: A robust method to inference gene regulatory network from time-course gene data based on ensemble Kalman filter	5
iDNA6mA-Rice-DL: A local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method	5
Prediction of miRNA-disease associations based on Weighted K-Nearest known neighbors and network consistency projection	5
Unsupervised multi-instance learning for protein structure determination	5
DNN-Boost: Somatic mutation identification of tumor-only whole-exome sequencing data using deep neural network and XGBoost	4
Optimizing taxon addition order and branch lengths in the construction of phylogenetic trees using maximum likelihood	4
Distance matrices for nitrogenous bases and amino acids of SARS-CoV-2 via structural metric	4
DNA sequence, physics, and promoter function: Analysis of high-throughput data On T7 promoter variants activity	4
Approaches for the identification of driver mutations in cancer: A tutorial from a computational perspective	4
An integrated method for identifying essential proteins from multiplex network model of protein–protein interactions	4

Prediction of adverse drug reactions using drug convolutional neural networks	4
Transformation of FASTA files into feature vectors for unsupervised compression of short reads databases	4
O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine	3
Disease named entity recognition using long–short dependencies	3
Sparse robust graph-regularized non-negative matrix factorization based on correntropy	3
DEEPSMP: A deep learning model for predicting the ectodomain shedding events of membrane proteins	3
Network motif-based analysis of regulatory patterns in paralogous gene pairs	3
Small parsimony for natural genomes in the DCJ-indel model	3
ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets	3
Cascading classifier application for topology prediction of transmembrane beta-barrel proteins	3
Cell cycle period control through modulation of clock inputs	3
Protein–protein interaction site prediction using random forest proximity distance	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
A symmetry-inclusive algebraic approach to genome rearrangement	3
The potential of family-free rearrangements towards gene orthology inference	3
An evaluation of combined strategies for improving the performance of molecular docking	3
Population-specific adaptation in malaria-endemic regions of asia	3
PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures	3
SpliceViNCI: Visualizing the splicing of non-canonical introns through recurrent neural networks	2
ReHiC: Enhancing Hi-C data resolution via residual convolutional network	2
Detecting genetic associations with brain imaging phenotypes in Alzheimer’s disease via a novel structured KCCA approach	2
Prophage loci predictor for bacterial genomes	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
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	2
Genetic algorithm applied to simultaneous parameter estimation in bacterial growth	2
Scaling laws of graphs of 3D protein structures	2
A sequence-based two-layer predictor for identifying enhancers and their strength through enhanced feature extraction	2
Total evidence or taxonomic congruence? A comparison of methods for combining biological evidence	2
Sorting permutations by fragmentation-weighted operations	2
DeepBtoD: Improved RNA-binding proteins prediction via integrated deep learning	2
A deep imputation and inference framework for estimating personalized and race-specific causal effects of genomic alterations on PSA	2
Identifying protein complexes from protein–protein interaction networks based on the gene expression profile and core-attachment approach	2
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network	2
In silico de novo drug design of a therapeutic peptide inhibitor against UBE2C in breast cancer	2
PESM: A novel approach of tumor purity estimation based on sample specific methylation sites	2
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	2
BOPAL 2.0 and a study of tRNA and rRNA gene evolution in Clostridium	2
bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model	2
Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm	2
Quantificational evaluation of the resolving power of qualitative biomarkers with different cardinal numbers based on a magnitude-standardized index	2
Impact of low-confidence interactions on computational identification of protein complexes	2
Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets	2
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	2
A deep attention network for predicting amino acid signals in the formation of α-helices	2
Impacts of reference selection on the assembly of suspicious coronavirus genome	1
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases	1
Denoising of scanning electron microscope images for biological ultrastructure enhancement	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

ProgSIO-MSA: Progressive-based single iterative optimization framework for multiple sequence alignment using an effective scoring system	1
Evidence for exon shuffling is sensitive to model choice	1
Calculation of immune cell proportion from batch tumor gene expression profile based on support vector regression	1
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	1
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	1
Amino acid environment affinity model based on graph attention network	1
Flux balance network expansion predicts stage-specific human peri_implantation embryo metabolism	1
Transforming OMIC features for classification using siamese convolutional networks	1
RMI-DBG algorithm: A more agile iterative de Bruijn graph algorithm in short read genome assembly	1
Accounting for treatment during the development or validation of prediction models	1
Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins	1
Female reproduction-specific proteins, origins in marine species, and their evolution in the animal kingdom	1
Hot spots localization in proteins by optimized short time Ramanujan Fourier transform	1
EdClust: A heuristic sequence clustering method with higher sensitivity	1
An innovative method for the selection of inhibitors of the viral spike-glycoprotein of the SARS-CoV	1
Colorful orthology clustering in bounded-degree similarity graphs	1
Scalable classification of organisms into a taxonomy using hierarchical supervised learners	1
Obstacles to effective model deployment in healthcare	1
Mining of structural motifs in proteins using artificial bee colony optimization framework for druggability	1
RiRPSSP: A unified deep learning method for prediction of regular and irregular protein secondary structures	1
Regression based fast multi-trait genome-wide QTL analysis	1
Modeling the impact of point mutations on the stability of proteins	1
Structural profile matrices for predicting structural properties of proteins	1
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides	1
Involving repetitive regions in scaffolding improvement	1
Identification of cancer-related module in protein–protein interaction network based on gene prioritization	1
Overlapping group screening for binary cancer classification with TCGA high-dimensional genomic data	1
Influence of the go-based semantic similarity measures in multi-objective gene clustering algorithm performance	1
The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny	1
Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot	1
The impact of simulation time in predicting binding free energies using end-point approaches	1
RepeatsPlus — program for finding motifs and repeats in data sequences	1
DeepRT: Predicting compounds presence in pathway modules and classifying into module classes using deep neural networks based on molecular properties	1
Antimicrobial peptides recognition using weighted physicochemical property encoding	1
Optimized splitting of mixed-species RNA sequencing data	1
GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion	1
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	1