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 2021-05-01 to 2025-05-01.)

Article	Citations
Identification of genes associated with cancer prognosis in glioma: In silico data analyses of Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA)	29
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	17
PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures	11
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection	10
Involving repetitive regions in scaffolding improvement	9
A novel method for predicting DNA N⁴-methylcytosine sites based on deep forest algorithm	8
DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning	6
Colorful orthology clustering in bounded-degree similarity graphs	5
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	5
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model	5
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks	5
Analysis of clonal evolution in cancer: A computational perspective	4
EnAMP: A novel deep learning ensemble antibacterial peptide recognition algorithm based on multi-features	4
Accounting for treatment during the development or validation of prediction models	4
Methods for cell-type annotation on scRNA-seq data: A recent overview	4
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model	4
How much can ChatGPT really help computational biologists in programming?	4
Learning long- and short-term dependencies for improving drug-target binding affinity prediction using transformer and edge contraction pooling	4
Flux balance network expansion predicts stage-specific human peri_implantation embryo metabolism	4
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides	3
Author Index Volume 20 (2022)	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
Introduction to Selected Papers from InCoB 2021	3
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	3
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties	3

Identifying duplications and lateral gene transfers simultaneously and rapidly	3
Population-specific adaptation in malaria-endemic regions of asia	3
The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny	3
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	3
Polypharmacy side effect prediction based on semi-implicit graph variational auto-encoder	3
Improving drug–target interaction prediction through dual-modality fusion with InteractNet	3
O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine	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
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
Local RNA folding revisited	2
Transforming OMIC features for classification using siamese convolutional networks	2
iAMY-RECMFF: Identifying amyloidgenic peptides by using residue pairwise energy content matrix and features fusion algorithm	2
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	2
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	2
Mining sponge phenomena in RNA expression data	2
Prediction of nucleosome dynamic interval based on long–short-term memory network (LSTM)	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
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases	2
Introduction to the Special Issue of the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics	2
Facilitating the drug repurposing with iC/E strategy: A practice on novel nNOS inhibitor discovery	2
Amino acid environment affinity model based on graph attention network	1
Gene regulatory network inference based on modified adaptive lasso	1
Integrating pharmacophore model and deep learning for activity prediction of molecules with BRCA1 gene	1
RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families	1
Incorporating intergenic regions into reversal and transposition distances with indels	1
SAKit: An all-in-one analysis pipeline for identifying novel proteins resulting from variant events at both large and small scales	1
Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets	1
Impacts of reference selection on the assembly of suspicious coronavirus genome	1
DNA sequences alignment method using sparse index on pan-genome graph	1
iRNA5hmC-HOC: High-order correlation information for identifying RNA 5-hydroxymethylcytosine modification	1
SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction	1
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	1
A technique for preserving network structure in randomized Hi-C data	1
Impacts of high-quality public data: Special issue on integrating public and in-house biomedical data	1
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
Author Index Volume 21 (2023)	1
Antimicrobial peptides recognition using weighted physicochemical property encoding	1
RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy	1
CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data	1
Denoising of scanning electron microscope images for biological ultrastructure enhancement	1
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	1
A new Bayesian approach for QTL mapping of family data	1
Tensor decomposition based on the potential low-rank and p-shrinkage generalized threshold algorithm for analyzing cancer multiomics data	1
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	1
Prediction and validation of avascular tumor growth pattern in different metabolic conditions using in silico and in vitro models	1
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	1

A deep imputation and inference framework for estimating personalized and race-specific causal effects of genomic alterations on PSA	1
Identification of a seven autophagy-related gene pairs signature for the diagnosis of colorectal cancer using the RankComp algorithm	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
Trade-offs among transcription elongation rate, number, and duration of ubiquitous pauses on highly transcribed bacterial genes	1
GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion	1
iDNA6mA-Rice-DL: A local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method	1
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases	1