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 2021-09-01 to 2025-09-01.)

Article	Citations
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
Involving repetitive regions in scaffolding improvement	9
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks	7
Analysis of clonal evolution in cancer: A computational perspective	6
Methods for cell-type annotation on scRNA-seq data: A recent overview	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
Colorful orthology clustering in bounded-degree similarity graphs	5
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model	5
Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM	5
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model	5
EnAMP: A novel deep learning ensemble antibacterial peptide recognition algorithm based on multi-features	5
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
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
Accounting for treatment during the development or validation of prediction models	4
How much can ChatGPT really help computational biologists in programming?	4
A brief review and comparative analysis of RNA secondary structure prediction tools	3
Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation	3
Improving drug–target interaction prediction through dual-modality fusion with InteractNet	3
Author Index Volume 20 (2022)	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
Population-specific adaptation in malaria-endemic regions of asia	3

NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	3
The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny	3
Identifying duplications and lateral gene transfers simultaneously and rapidly	3
M³-20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery	3
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	3
Introduction to Selected Papers from InCoB 2021	3
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases	2
Body plan evolvability: The role of variability in gene regulatory networks	2
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	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
The use of 4D data-independent acquisition-based proteomic analysis and machine learning to reveal potential biomarkers for stress levels	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
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
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	2
iAMY-RECMFF: Identifying amyloidgenic peptides by using residue pairwise energy content matrix and features fusion algorithm	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
Parameter estimation analysis of the glioblastoma immune 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
Integrating temporal and spatial variabilities for identifying ion binding proteins in phage	2
O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine	2
Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm	1
Clarifying real receptor binding site between coronavirus HCoV-HKU1 and 9-O-Ac-Sia based on molecular docking	1
CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data	1
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	1
RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families	1
A technique for preserving network structure in randomized Hi-C data	1
Amino acid environment affinity model based on graph attention network	1
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases	1
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	1
Tensor decomposition based on the potential low-rank and p-shrinkage generalized threshold algorithm for analyzing cancer multiomics data	1
Denoising of scanning electron microscope images for biological ultrastructure enhancement	1
Author Index Volume 21 (2023)	1
COLDLNA: Enhancing long-range node features extraction to improve robust generalization capability of drug-target binding affinity prediction in cold-start scenarios	1
SAKit: An all-in-one analysis pipeline for identifying novel proteins resulting from variant events at both large and small scales	1
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	1
Integrating pharmacophore model and deep learning for activity prediction of molecules with BRCA1 gene	1
A new Bayesian approach for QTL mapping of family data	1
An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra	1
iRNA5hmC-HOC: High-order correlation information for identifying RNA 5-hydroxymethylcytosine modification	1
Gene regulatory network inference based on modified adaptive lasso	1
GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion	1
Incorporating intergenic regions into reversal and transposition distances with indels	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
DNA sequences alignment method using sparse index on pan-genome graph	1
Compression for population genetic data through finite-state entropy	1
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	1
Prediction and validation of avascular tumor growth pattern in different metabolic conditions using in silico and in vitro models	1
SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction	1