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 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
Colorful orthology clustering in bounded-degree similarity graphs	5
How much can ChatGPT really help computational biologists in programming?	5
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
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
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
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	3
Author Index Volume 20 (2022)	3
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
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
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
iRNA5hmC-HOC: High-order correlation information for identifying RNA 5-hydroxymethylcytosine modification	1
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases	1
Integrating pharmacophore model and deep learning for activity prediction of molecules with BRCA1 gene	1
Denoising of scanning electron microscope images for biological ultrastructure enhancement	1
RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families	1
Identification of a seven autophagy-related gene pairs signature for the diagnosis of colorectal cancer using the RankComp algorithm	1
A technique for preserving network structure in randomized Hi-C data	1
SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction	1
PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction	1
Amino acid environment affinity model based on graph attention network	1
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network	1
DNA sequences alignment method using sparse index on pan-genome graph	1
Author Index Volume 21 (2023)	1
GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion	1
Trade-offs among transcription elongation rate, number, and duration of ubiquitous pauses on highly transcribed bacterial genes	1
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	1
Clarifying real receptor binding site between coronavirus HCoV-HKU1 and 9-O-Ac-Sia based on molecular docking	1
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	1
Obstacles to effective model deployment in healthcare	1
A new Bayesian approach for QTL mapping of family data	1
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	1
Prediction and validation of avascular tumor growth pattern in different metabolic conditions using in silico and in vitro models	1

Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm	1
Incorporating intergenic regions into reversal and transposition distances with indels	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
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
An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra	1
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	1