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 2021-02-01 to 2025-02-01.)

Article	Citations
Integrating temporal and spatial variabilities for identifying ion binding proteins in phage	27
Prediction and validation of avascular tumor growth pattern in different metabolic conditions using in silico and in vitro models	17
Involving repetitive regions in scaffolding improvement	15
A novel method for predicting DNA N⁴-methylcytosine sites based on deep forest algorithm	11
PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures	9
Amino acid environment affinity model based on graph attention network	6
A new Bayesian approach for QTL mapping of family data	6
In silico de novo drug design of a therapeutic peptide inhibitor against UBE2C in breast cancer	6
Identifying duplications and lateral gene transfers simultaneously and rapidly	6
Structural bioinformatics survey on disease-inducing missense mutations	5
RMI-DBG algorithm: A more agile iterative de Bruijn graph algorithm in short read genome assembly	5
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	4
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection	4
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)	4
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	4
iRNA5hmC-HOC: High-order correlation information for identifying RNA 5-hydroxymethylcytosine modification	4
Construction of transcript regulation mechanism prediction models based on binding motif environment of transcription factor AoXlnR in Aspergillus oryzae	4
SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction	3
DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning	3
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	3
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	3
CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea	3
RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy	3
Algorithms for the Uniqueness of the Longest Common Subsequence	3
DNA sequences alignment method using sparse index on pan-genome graph	3

Improving drug–target interaction prediction through dual-modality fusion with InteractNet	3
Facilitating the drug repurposing with iC/E strategy: A practice on novel nNOS inhibitor discovery	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases	3
RepeatsPlus — program for finding motifs and repeats in data sequences	2
Introduction to the Special Issue of the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics	2
Mining sponge phenomena in RNA expression data	2
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	2
Response of gene regulatory networks after infection of H3N2 virus	2
SAKit: An all-in-one analysis pipeline for identifying novel proteins resulting from variant events at both large and small scales	2
Construction of a multi-tissue compound–target interaction network of Qingfei Paidu decoction in COVID-19 treatment based on deep learning and transcriptomic analysis	2
PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction	2
An alignment-independent three-dimensional quantitative structure–activity relationship study on ron receptor tyrosine kinase inhibitors	2
Population-specific adaptation in malaria-endemic regions of asia	2
Distance matrices for nitrogenous bases and amino acids of SARS-CoV-2 via structural metric	2
Introduction to Selected Papers from InCoB 2021	2
Imputation for Single-cell RNA-seq Data with Non-negative Matrix Factorization and Transfer Learning	2
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network	2
Antimicrobial peptides recognition using weighted physicochemical property encoding	2
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	2
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	2
The impact of simulation time in predicting binding free energies using end-point approaches	2
Root locus-based stability analysis for biological systems	2
Trade-offs among transcription elongation rate, number, and duration of ubiquitous pauses on highly transcribed bacterial genes	2
Local RNA folding revisited	2
Obstacles to effective model deployment in healthcare	2
ASAP-DTA: Predicting Drug-Target Binding Affinity with Adaptive Structure Aware Networks	2
Compression for population genetic data through finite-state entropy	2
Utilization of systematic error-assessment software to improve phylogenetic accuracy	2
Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets	2