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 2022-08-01 to 2026-08-01.)

Article	Citations
A novel method for predicting DNA N⁴-methylcytosine sites based on deep forest algorithm	18
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection	15
NNDock2: A neural network-based scoring function for ranking protein–protein docking models	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	8
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model	6
Mendelian randomization and AlphaFold3 analysis suggest putative causal plasma proteins in graves’ disease	6
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model	5
Methods for cell-type annotation on scRNA-seq data: A recent overview	5
Predicting distant cancer metastasis using a weighted gene interaction network and sample-specific differential correlations	5
How much can ChatGPT really help computational biologists in programming?	4
A brief review and comparative analysis of RNA secondary structure prediction tools	4
Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM	4
Analysis of clonal evolution in cancer: A computational perspective	4
Polypharmacy side effect prediction based on semi-implicit graph variational auto-encoder	4
Learning long- and short-term dependencies for improving drug-target binding affinity prediction using transformer and edge contraction pooling	4
EnAMP: A novel deep learning ensemble antibacterial peptide recognition algorithm based on multi-features	4
Accounting for treatment during the development or validation of prediction models	4
Analysis of the regulation of model parameters on delay time in the p53 dynamical response to single-stranded breaks	3
ReinVar: A model-free paradigm-based reinforcement learning approach to detect copy number variation	3
Improving drug–target interaction prediction through dual-modality fusion with InteractNet	3
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
Bond-resolved graph-theoretic modeling of structural invariance and metabolic accessibility in drug molecules	3
Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation	3

Trap spaces as labelled ideals of SCC posets: A structural–functional theory of reachability in asynchronous boolean networks	2
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	2
When pipelines run but coordinates fail: A simple spatial specificity check for false locality in post-GWAS analysis	2
The use of 4D data-independent acquisition-based proteomic analysis and machine learning to reveal potential biomarkers for stress levels	2
Body plan evolvability: The role of variability in gene regulatory networks	2
Introduction to Selected Papers from InCoB 2021	2
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	2
Predicting ncRNA–Protein interactions with a graph attention model exploiting personalized subgraphs	2
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases	2
A pharmacokinetic model based on the SSA-1DCNN-Attention method	2
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties	2
M³-20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery	2
Author Index Volume 20 (2022)	2
Exploring relationship between hypercholesterolemia and instability of atherosclerotic plaque — An approach based on a matrix population model	2
A Scalable Pan-Genomic Pipeline for Annotation-Free Discovery of Species-Specific Markers: Application to Staphylococcus aureus	2
iAMY-RECMFF: Identifying amyloidgenic peptides by using residue pairwise energy content matrix and features fusion algorithm	2