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 2021-06-01 to 2025-06-01.)

Article	Citations
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	30
PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures	17
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection	11
Involving repetitive regions in scaffolding improvement	10
A novel method for predicting DNA N⁴-methylcytosine sites based on deep forest algorithm	9
DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning	8
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
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks	6
Methods for cell-type annotation on scRNA-seq data: A recent overview	5
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model	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
Polypharmacy side effect prediction based on semi-implicit graph variational auto-encoder	4
How much can ChatGPT really help computational biologists in programming?	4
EnAMP: A novel deep learning ensemble antibacterial peptide recognition algorithm based on multi-features	4
Flux balance network expansion predicts stage-specific human peri_implantation embryo metabolism	4
Colorful orthology clustering in bounded-degree similarity graphs	4
Accounting for treatment during the development or validation of prediction models	4
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides	4
Learning long- and short-term dependencies for improving drug-target binding affinity prediction using transformer and edge contraction pooling	4
Identifying duplications and lateral gene transfers simultaneously and rapidly	3
Introduction to Selected Papers from InCoB 2021	3
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	3
Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation	3
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	3

The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
Improving drug–target interaction prediction through dual-modality fusion with InteractNet	3
M³-20M: A Large-Scale Multi-Modal Molecule Dataset for AI-driven Drug Design and Discovery	3
Population-specific adaptation in malaria-endemic regions of asia	3
O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine	2
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases	2
Prediction of nucleosome dynamic interval based on long–short-term memory network (LSTM)	2
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	2
Local RNA folding revisited	2
RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy	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
The use of 4D data-independent acquisition-based proteomic analysis and machine learning to reveal potential biomarkers for stress levels	2
Introduction to the Special Issue of the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics	2
Trade-offs among transcription elongation rate, number, and duration of ubiquitous pauses on highly transcribed bacterial genes	2
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	2
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties	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
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
Antimicrobial peptides recognition using weighted physicochemical property encoding	2
Author Index Volume 20 (2022)	2
GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion	1
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	1
Facilitating the drug repurposing with iC/E strategy: A practice on novel nNOS inhibitor discovery	1
Denoising of scanning electron microscope images for biological ultrastructure enhancement	1
SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction	1
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural 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
Amino acid environment affinity model based on graph attention network	1
Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm	1
Integrating pharmacophore model and deep learning for activity prediction of molecules with BRCA1 gene	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
Identification of a seven autophagy-related gene pairs signature for the diagnosis of colorectal cancer using the RankComp algorithm	1
Mining sponge phenomena in RNA expression data	1
CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data	1
Tensor decomposition based on the potential low-rank and p-shrinkage generalized threshold algorithm for analyzing cancer multiomics data	1
Compression for population genetic data through finite-state entropy	1
iRNA5hmC-HOC: High-order correlation information for identifying RNA 5-hydroxymethylcytosine modification	1
An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra	1
Prediction and validation of avascular tumor growth pattern in different metabolic conditions using in silico and in vitro models	1
iDNA6mA-Rice-DL: A local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method	1
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	1
A deep imputation and inference framework for estimating personalized and race-specific causal effects of genomic alterations on PSA	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
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
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	1
Gene regulatory network inference based on modified adaptive lasso	1
Response of gene regulatory networks after infection of H3N2 virus	1
A new Bayesian approach for QTL mapping of family data	1
DNA sequences alignment method using sparse index on pan-genome graph	1
Incorporating intergenic regions into reversal and transposition distances with indels	1
A technique for preserving network structure in randomized Hi-C data	1
RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families	1