OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Bioinformatics and Computational Biology is 1. 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 2022-01-01 to 2026-01-01.)

Article	Citations
A novel method for predicting DNA N⁴-methylcytosine sites based on deep forest algorithm	15
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection	11
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	10
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
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	6
Analysis of clonal evolution in cancer: A computational perspective	6
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
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model	5
How much can ChatGPT really help computational biologists in programming?	4
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
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
Accounting for treatment during the development or validation of prediction models	3
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	3
Flux balance network expansion predicts stage-specific human peri_implantation embryo metabolism	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
M³-20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery	3
A brief review and comparative analysis of RNA secondary structure prediction tools	3
Behavioral dynamics of bacteriophage gene regulatory networks	3

Introduction to Selected Papers from InCoB 2021	3
Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation	3
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
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases	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
Local RNA folding revisited	2
An alignment-independent three-dimensional quantitative structure–activity relationship study on ron receptor tyrosine kinase inhibitors	2
Body plan evolvability: The role of variability in gene regulatory networks	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
Author Index Volume 20 (2022)	2
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	2
RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy	2
Prediction of nucleosome dynamic interval based on long–short-term memory network (LSTM)	2
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties	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
Parameter estimation analysis of the glioblastoma immune model	2
Antimicrobial peptides recognition using weighted physicochemical property encoding	2
Clarifying real receptor binding site between coronavirus HCoV-HKU1 and 9-O-Ac-Sia based on molecular docking	1
Denoising of scanning electron microscope images for biological ultrastructure enhancement	1
Tensor decomposition based on the potential low-rank and p-shrinkage generalized threshold algorithm for analyzing cancer multiomics data	1
Gene regulatory network inference based on modified adaptive lasso	1
COLDLNA: Enhancing long-range node features extraction to improve robust generalization ability of drug-target binding affinity prediction in cold-start scenarios	1
Construction of a multi-tissue compound–target interaction network of Qingfei Paidu decoction in COVID-19 treatment based on deep learning and transcriptomic analysis	1
Author Index Volume 21 (2023)	1
SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction	1
DNA sequences alignment method using sparse index on pan-genome graph	1
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	1
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	1
RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families	1
CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data	1
SAKit: An all-in-one analysis pipeline for identifying novel proteins resulting from variant events at both large and small scales	1
Author index Volume 23 (2025)	1
GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion	1
iRNA5hmC-HOC: High-order correlation information for identifying RNA 5-hydroxymethylcytosine modification	1
Integrating pharmacophore model and deep learning for activity prediction of molecules with BRCA1 gene	1
A technique for preserving network structure in randomized Hi-C data	1
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	1
Identification of a seven autophagy-related gene pairs signature for the diagnosis of colorectal cancer using the RankComp algorithm	1
Facilitating the drug repurposing with iC/E strategy: A practice on novel nNOS inhibitor discovery	1