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 2021-04-01 to 2025-04-01.)

Article	Citations
Involving repetitive regions in scaffolding improvement	29
A novel method for predicting DNA N⁴-methylcytosine sites based on deep forest algorithm	20
A new Bayesian approach for QTL mapping of family data	17
In silico de novo drug design of a therapeutic peptide inhibitor against UBE2C in breast cancer	11
Structural bioinformatics survey on disease-inducing missense mutations	9
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	8
Algorithms for the Uniqueness of the Longest Common Subsequence	5
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	5
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)	5
iRNA5hmC-HOC: High-order correlation information for identifying RNA 5-hydroxymethylcytosine modification	5
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases	4
Cross-cellular analysis of chromatin accessibility markers H3K4me3 and DNAse in the context of detecting cell-identity genes: an "all-or-nothing" approach	4
Construction of transcript regulation mechanism prediction models based on binding motif environment of transcription factor AoXlnR in Aspergillus oryzae	4
CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea	4
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection	4
RMI-DBG algorithm: A more agile iterative de Bruijn graph algorithm in short read genome assembly	4
Amino acid environment affinity model based on graph attention network	4
PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures	3
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	3
Improving drug–target interaction prediction through dual-modality fusion with InteractNet	3
Facilitating the drug repurposing with iC/E strategy: A practice on novel nNOS inhibitor discovery	3
Prediction and validation of avascular tumor growth pattern in different metabolic conditions using in silico and in vitro models	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction	3
Local RNA folding revisited	3

Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	3
Integrating temporal and spatial variabilities for identifying ion binding proteins in phage	3
Identifying duplications and lateral gene transfers simultaneously and rapidly	3
DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning	3
DNA sequences alignment method using sparse index on pan-genome graph	3
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network	2
Response of gene regulatory networks after infection of H3N2 virus	2
RepeatsPlus — program for finding motifs and repeats in data sequences	2
Imputation for Single-cell RNA-seq Data with Non-negative Matrix Factorization and Transfer Learning	2
Introduction to Selected Papers from InCoB 2021	2
Distance matrices for nitrogenous bases and amino acids of SARS-CoV-2 via structural metric	2
Author index Volume 22 (2024)	2
Compression for population genetic data through finite-state entropy	2
PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction	2
Mining sponge phenomena in RNA expression data	2
Obstacles to effective model deployment in healthcare	2
SAKit: An all-in-one analysis pipeline for identifying novel proteins resulting from variant events at both large and small scales	2
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	2
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	2
Trade-offs among transcription elongation rate, number, and duration of ubiquitous pauses on highly transcribed bacterial genes	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
Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets	2
Population-specific adaptation in malaria-endemic regions of asia	2
An alignment-independent three-dimensional quantitative structure–activity relationship study on ron receptor tyrosine kinase inhibitors	2
Introduction to the Special Issue of the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics	2
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks	2
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties	1
Drug repurposing for non-small cell lung cancer by predicting drug response using pathway-level graph convolutional network	1
Gene representation bias in spatial transcriptomics	1
Identification of a seven autophagy-related gene pairs signature for the diagnosis of colorectal cancer using the RankComp algorithm	1
Identifying protein complexes from protein–protein interaction networks based on the gene expression profile and core-attachment approach	1
Author Index Volume 20 (2022)	1
Molecular dynamics simulations of ribosome-binding sites in theophylline-responsive riboswitch associated with improving the gene expression regulation in chloroplasts	1
PTGAC Model: A machine learning approach for constructing phylogenetic tree to compare protein sequences	1
Predictive Recognition of DNA-binding Proteins Based on Pre-trained Language Model BERT	1
The impact of simulation time in predicting binding free energies using end-point approaches	1
Root locus-based stability analysis for biological systems	1
Clinical drug response prediction from preclinical cancer cell lines by logistic matrix factorization approach	1
The potential of family-free rearrangements towards gene orthology inference	1
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	1
Multi-omics data analysis reveals the biological implications of alternative splicing events in lung adenocarcinoma	1
Learning gene regulatory networks using gaussian process emulator and graphical LASSO	1
AAindex-PPII: Predicting polyproline type II helix structure based on amino acid indexes with an improved BiGRU-TextCNN model	1
Small groups in multidimensional feature space: Two examples of supervised two-group classification from biomedicine	1
Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot	1
The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny	1
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	1
Antimicrobial peptides recognition using weighted physicochemical property encoding	1
CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data	1
Research on similarity retrieval method based on mass spectral entropy	1

Rearrangement distance with reversals, indels, and moves in intergenic regions on signed and unsigned permutations	1
ThermalProGAN: A sequence-based thermally stable protein generator trained using unpaired data	1
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model	1
Evidence for exon shuffling is sensitive to model choice	1
Methods for cell-type annotation on scRNA-seq data: A recent overview	1
Colorful orthology clustering in bounded-degree similarity graphs	1
RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy	1
Utilization of systematic error-assessment software to improve phylogenetic accuracy	1
Computation and Analysis of Stationary and Periodic Solutions of the COVID-19 Infection Dynamics Model	1