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 2022-06-01 to 2026-06-01.)

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	14
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	12
NNDock2: A neural network-based scoring function for ranking protein–protein docking models	8
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks	7
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
Mendelian randomization and AlphaFold3 analysis suggest putative causal plasma proteins in graves’ disease	6
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	5
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model	5
Analysis of clonal evolution in cancer: A computational perspective	5
Predicting distant cancer metastasis using a weighted gene interaction network and sample-specific differential correlations	5
Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM	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
How much can ChatGPT really help computational biologists in programming?	4
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
A brief review and comparative analysis of RNA secondary structure prediction tools	3
Bond-resolved graph-theoretic modeling of structural invariance and metabolic accessibility in drug molecules	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
ReinVar: A Model-Free Paradigm based Reinforcement Learning approach to Detect Copy Number Variation	3
Analysis of the regulation of model parameters on delay time in the p53 dynamical response to single-stranded breaks	3

Accounting for treatment during the development or validation of prediction models	3
Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation	3
Author Index Volume 20 (2022)	2
Introduction to Selected Papers from InCoB 2021	2
Exploring relationship between hypercholesterolemia and instability of atherosclerotic plaque — An approach based on a matrix population model	2
Transforming OMIC features for classification using siamese convolutional networks	2
Early lifespan prediction in Caenorhabditis elegans via contrastive learning and channel attention	2
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	2
When Pipelines Run but Coordinates Fail: A Simple Spatial Specificity Check for False Locality in post-GWAS Analysis	2
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	2
iAMY-RECMFF: Identifying amyloidgenic peptides by using residue pairwise energy content matrix and features fusion algorithm	2
Trap Spaces as Labelled Ideals of SCC Posets: A Structural-Functional Theory of Reachability in Asynchronous Boolean Networks	2
Body plan evolvability: The role of variability in gene regulatory networks	2
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	2
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases	2
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties	2
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	2
M³-20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery	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
Integrating temporal and spatial variabilities for identifying ion binding proteins in phage	2