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 2021-08-01 to 2025-08-01.)

Article	Citations
Involving repetitive regions in scaffolding improvement	17
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection	13
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	13
A novel method for predicting DNA N⁴-methylcytosine sites based on deep forest algorithm	12
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks	9
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	7
Methods for cell-type annotation on scRNA-seq data: A recent overview	6
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model	6
Analysis of clonal evolution in cancer: A computational perspective	6
EnAMP: A novel deep learning ensemble antibacterial peptide recognition algorithm based on multi-features	5
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model	5
Learning long- and short-term dependencies for improving drug-target binding affinity prediction using transformer and edge contraction pooling	5
Colorful orthology clustering in bounded-degree similarity graphs	5
How much can ChatGPT really help computational biologists in programming?	5
Polypharmacy side effect prediction based on semi-implicit graph variational auto-encoder	4
A brief review and comparative analysis of RNA secondary structure prediction tools	4
Improving drug–target interaction prediction through dual-modality fusion with InteractNet	4
Accounting for treatment during the development or validation of prediction models	4
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides	4
Flux balance network expansion predicts stage-specific human peri_implantation embryo metabolism	4
Identifying duplications and lateral gene transfers simultaneously and rapidly	3
Introduction to Selected Papers from InCoB 2021	3
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties	3
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	3
Population-specific adaptation in malaria-endemic regions of asia	3

Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation	3
The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
M³-20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery	3
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	3
Author Index Volume 20 (2022)	3
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
Local RNA folding revisited	2
Facilitating the drug repurposing with iC/E strategy: A practice on novel nNOS inhibitor discovery	2
O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine	2
The use of 4D data-independent acquisition-based proteomic analysis and machine learning to reveal potential biomarkers for stress levels	2
A pharmacokinetic model based on the SSA-1DCNN-Attention method	2
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	2
Antimicrobial peptides recognition using weighted physicochemical property encoding	2
Mining sponge phenomena in RNA expression data	2
Introduction to the Special Issue of the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics	2
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	2
Parameter estimation analysis of the glioblastoma immune model	2
iAMY-RECMFF: Identifying amyloidgenic peptides by using residue pairwise energy content matrix and features fusion algorithm	2
Body plan evolvability: The role of variability in gene regulatory networks	2
Integrating temporal and spatial variabilities for identifying ion binding proteins in phage	2
An alignment-independent three-dimensional quantitative structure–activity relationship study on ron receptor tyrosine kinase inhibitors	2
Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets	2
RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy	2
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases	2
Transforming OMIC features for classification using siamese convolutional networks	2
Prediction of nucleosome dynamic interval based on long–short-term memory network (LSTM)	2
Exploring relationship between hypercholesterolemia and instability of atherosclerotic plaque — An approach based on a matrix population model	2