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 2022-05-01 to 2026-05-01.)

Article	Citations
A novel method for predicting DNA N⁴-methylcytosine sites based on deep forest algorithm	16
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection	12
NNDock2: A neural network-based scoring function for ranking protein–protein docking models	12
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	8
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks	7
Mendelian randomization and AlphaFold3 analysis suggest putative causal plasma proteins in graves’ disease	6
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	6
Predicting distant cancer metastasis using a weighted gene interaction network and sample-specific differential correlations	5
Analysis of clonal evolution in cancer: A computational perspective	5
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model	5
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model	5
Methods for cell-type annotation on scRNA-seq data: A recent overview	4
Learning long- and short-term dependencies for improving drug-target binding affinity prediction using transformer and edge contraction pooling	4
How much can ChatGPT really help computational biologists in programming?	4
Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM	3
A brief review and comparative analysis of RNA secondary structure prediction tools	3
Flux balance network expansion predicts stage-specific human peri_implantation embryo metabolism	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
Analysis of the regulation of model parameters on delay time in the p53 dynamical response to single-stranded breaks	3
EnAMP: A novel deep learning ensemble antibacterial peptide recognition algorithm based on multi-features	3
Accounting for treatment during the development or validation of prediction models	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
Polypharmacy side effect prediction based on semi-implicit graph variational auto-encoder	3
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides	3

Improving drug–target interaction prediction through dual-modality fusion with InteractNet	3
Predicting ncRNA–Protein interactions with a graph attention model exploiting personalized subgraphs	3
iAMY-RECMFF: Identifying amyloidgenic peptides by using residue pairwise energy content matrix and features fusion algorithm	2
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	2
Early lifespan prediction in Caenorhabditis elegans via contrastive learning and channel attention	2
Integrating temporal and spatial variabilities for identifying ion binding proteins in phage	2
Introduction to Selected Papers from InCoB 2021	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
Body plan evolvability: The role of variability in gene regulatory networks	2
Prediction of nucleosome dynamic interval based on long–short-term memory network (LSTM)	2
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	2
M³-20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery	2
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties	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
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	2
Transforming OMIC features for classification using siamese convolutional networks	2
The use of 4D data-independent acquisition-based proteomic analysis and machine learning to reveal potential biomarkers for stress levels	2
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	2