OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Bioinformatics and Computational Biology is 2. 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
Modeling and simulation of spatial-temporal calcium distribution in T lymphocyte cell by using a reaction-diffusion equation	24
DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning	21
PROSPECT: A web server for predicting protein histidine phosphorylation sites	21
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
3D U-Net: A voxel-based method in binding site prediction of protein structure	11
Comparing the topology of phylogenetic network generators	11
EDeepSSP: Explainable deep neural networks for exact splice sites prediction	10
HemoNet: Predicting hemolytic activity of peptides with integrated feature learning	9
EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins	8
Incorporating intergenic regions into reversal and transposition distances with indels	7
Constructing gene regulatory networks from microarray data using non-Gaussian pair-copula Bayesian networks	7
BENIN: Biologically enhanced network inference	6
A protein succinylation sites prediction method based on the hybrid architecture of LSTM network and CNN	6
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
KFGRNI: A robust method to inference gene regulatory network from time-course gene data based on ensemble Kalman filter	5
DNA sequence, physics, and promoter function: Analysis of high-throughput data On T7 promoter variants activity	4
An evaluation of combined strategies for improving the performance of molecular docking	4
Transformation of FASTA files into feature vectors for unsupervised compression of short reads databases	4
An integrated method for identifying essential proteins from multiplex network model of protein–protein interactions	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

DNN-Boost: Somatic mutation identification of tumor-only whole-exome sequencing data using deep neural network and XGBoost	4
Prediction of adverse drug reactions using drug convolutional neural networks	4
Approaches for the identification of driver mutations in cancer: A tutorial from a computational perspective	4
A symmetry-inclusive algebraic approach to genome rearrangement	3
Sparse robust graph-regularized non-negative matrix factorization based on correntropy	3
The potential of family-free rearrangements towards gene orthology inference	3
DEEPSMP: A deep learning model for predicting the ectodomain shedding events of membrane proteins	3
PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures	3
Small parsimony for natural genomes in the DCJ-indel model	3
O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine	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
Sorting permutations by fragmentation-weighted operations	3
ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets	3
Disease named entity recognition using long–short dependencies	3
Population-specific adaptation in malaria-endemic regions of asia	3
Network motif-based analysis of regulatory patterns in paralogous gene pairs	3
Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets	2
A deep attention network for predicting amino acid signals in the formation of α-helices	2
PESM: A novel approach of tumor purity estimation based on sample specific methylation sites	2
ReHiC: Enhancing Hi-C data resolution via residual convolutional network	2
A sequence-based two-layer predictor for identifying enhancers and their strength through enhanced feature extraction	2
bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model	2
Shared ancestry of core-histone subunits and non-histone plant proteins containing the Histone Fold Motif (HFM)	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
In silico de novo drug design of a therapeutic peptide inhibitor against UBE2C in breast cancer	2
Genetic algorithm applied to simultaneous parameter estimation in bacterial growth	2
SpliceViNCI: Visualizing the splicing of non-canonical introns through recurrent neural networks	2
Total evidence or taxonomic congruence? A comparison of methods for combining biological evidence	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
A deep imputation and inference framework for estimating personalized and race-specific causal effects of genomic alterations on PSA	2
Identification of deregulation mechanisms specific to cancer subtypes	2
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network	2
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	2
Scaling laws of graphs of 3D protein structures	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
DeepBtoD: Improved RNA-binding proteins prediction via integrated deep learning	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