OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Bioinformatics and Computational Biology is 0. 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 2022-08-01 to 2026-08-01.)

Article	Citations
A novel method for predicting DNA N⁴-methylcytosine sites based on deep forest algorithm	18
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection	15
NNDock2: A neural network-based scoring function for ranking protein–protein docking models	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	8
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model	6
Mendelian randomization and AlphaFold3 analysis suggest putative causal plasma proteins in graves’ disease	6
Methods for cell-type annotation on scRNA-seq data: A recent overview	5
Predicting distant cancer metastasis using a weighted gene interaction network and sample-specific differential correlations	5
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model	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
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
How much can ChatGPT really help computational biologists in programming?	4
A brief review and comparative analysis of RNA secondary structure prediction tools	4
Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM	4
Analysis of clonal evolution in cancer: A computational perspective	4
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
Bond-resolved graph-theoretic modeling of structural invariance and metabolic accessibility in drug molecules	3
Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation	3
Analysis of the regulation of model parameters on delay time in the p53 dynamical response to single-stranded breaks	3
ReinVar: A model-free paradigm-based reinforcement learning approach to detect copy number variation	3
Improving drug–target interaction prediction through dual-modality fusion with InteractNet	3

Introduction to Selected Papers from InCoB 2021	2
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	2
Predicting ncRNA–Protein interactions with a graph attention model exploiting personalized subgraphs	2
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases	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
M³-20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery	2
Author Index Volume 20 (2022)	2
Exploring relationship between hypercholesterolemia and instability of atherosclerotic plaque — An approach based on a matrix population model	2
A Scalable Pan-Genomic Pipeline for Annotation-Free Discovery of Species-Specific Markers: Application to Staphylococcus aureus	2
iAMY-RECMFF: Identifying amyloidgenic peptides by using residue pairwise energy content matrix and features fusion algorithm	2
Trap spaces as labelled ideals of SCC posets: A structural–functional theory of reachability in asynchronous boolean networks	2
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	2
When pipelines run but coordinates fail: A simple spatial specificity check for false locality in post-GWAS analysis	2
The use of 4D data-independent acquisition-based proteomic analysis and machine learning to reveal potential biomarkers for stress levels	2
Body plan evolvability: The role of variability in gene regulatory networks	2
A novel approach for the identification of single nucleotide polymorphisms	1
Integration of evolutionary computation and ensemble learning in bioinformatics (Case Study: Protein–Peptide Interaction Prediction)	1
Antimicrobial peptides recognition using weighted physicochemical property encoding	1
Early lifespan prediction in Caenorhabditis elegans via contrastive learning and channel attention	1
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	1
Identification of a seven autophagy-related gene pairs signature for the diagnosis of colorectal cancer using the RankComp algorithm	1
CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data	1
GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion	1
Author Index Volume 21 (2023)	1
Author index Volume 23 (2025)	1
Parameter estimation analysis of the glioblastoma immune model	1
Local RNA folding revisited	1
SAKit: An all-in-one analysis pipeline for identifying novel proteins resulting from variant events at both large and small scales	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
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	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
Facilitating the drug repurposing with iC/E strategy: A practice on novel nNOS inhibitor discovery	1
Integrating temporal and spatial variabilities for identifying ion binding proteins in phage	1
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	1
COLDLNA: Enhancing long-range node features extraction to improve robust generalization ability of drug-target binding affinity prediction in cold-start scenarios	1
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	1
iCEED: Integrated customized extraction of enzyme data	0
The impact of simulation time in predicting binding free energies using end-point approaches	0
DDINet: Drug–drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder	0
Predicting functional co-occurrence probability in PPI networks via multi-level participation expectation	0
Visual-SELEX: a technology ensemble for evaluating aptamer structural similarity via 3D visual spatial conformational analysis	0
Drug repurposing for non-small cell lung cancer by predicting drug response using pathway-level graph convolutional network	0
Cross-cellular analysis of chromatin accessibility markers H3K4me3 and DNase in the context of detecting cell-identity genes: An “all-or-nothing” approach	0
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	0
KANBind as a diagnostic probe for DNA-binding protein prediction: A prevalence-calibrated reality check under strict homology control	0
Multi-Classification of Drug–Drug interaction based on a complete graph convolutional neural network and explainable artificial intelligence	0
iRNA5hmC-HOC: High-order correlation information for identifying RNA 5-hydroxymethylcytosine modification	0
Overlapping group screening for binary cancer classification with TCGA high-dimensional genomic data	0

Analyzing omics data by feature combinations based on kernel functions	0
Deep learning inference of miRNA expression from bulk and single-cell mRNA expression	0
The novel design of a multi-epitope vaccine candidate against the dengue virus using advanced immunoinformatics and structural analysis	0
A network-based dynamic criterion for identifying prediction and early diagnosis biomarkers of complex diseases	0
An ensemble approach for circular RNA-disease association prediction using variational autoencoder and genetic algorithm	0
Multi-omics data analysis reveals the biological implications of alternative splicing events in lung adenocarcinoma	0
PLMABFW: A deep learning framework for predicting Antibody–Antigen interactions using protein language model	0
ThermalProGAN: A sequence-based thermally stable protein generator trained using unpaired data	0
PTGAC Model: A machine learning approach for constructing phylogenetic tree to compare protein sequences	0
Predictive Recognition of DNA-binding Proteins Based on Pre-trained Language Model BERT	0
Gene representation bias in spatial transcriptomics	0
PCA-constrained multi-core matrix fusion network: A novel approach for cancer subtype identification	0
Cancer classification and functional pathway discovery using TCGA transcriptomic profiles: A matched case-control framework	0
A non-parametric Bayesian joint model for latent individual molecular profiles and survival in oncology	0
Study of the mechanism of step-by-step interaction of viral proteins during replication and transcription	0
COYOTE: Sequence-derived structural descriptors-based computational identification of glycoproteins	0
Obstacles to effective model deployment in healthcare	0
Construction of transcript regulation mechanism prediction models based on binding motif environment of transcription factor AoXlnR in Aspergillus oryzae	0
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases	0
A model-based clustering algorithm with covariates adjustment and its application to lung cancer stratification	0
An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra	0
A technique for preserving network structure in randomized Hi-C data	0
DNA sequences alignment method using sparse index on pan-genome graph	0
CNV-ECOD: A copy number variation detection method based on ECOD algorithm using next-generation sequencing data	0
Integration of autoencoder and graph convolutional network for predicting breast cancer drug response	0
Deep subspace fusion based on integrated self-supervision for cancer subtype identification	0
CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea	0
RiRPSSP: A unified deep learning method for prediction of regular and irregular protein secondary structures	0
Research on similarity retrieval method based on mass spectral entropy	0
Imputation for Single-cell RNA-seq Data with Non-negative Matrix Factorization and Transfer Learning	0
Prediction and annotation of alternative transcription starts and promoter shift in the chicken genome	0
Small groups in multidimensional feature space: Two examples of supervised two-group classification from biomedicine	0
Designing of sorafenib analogs to target c-Raf for the management of hepatocellular carcinoma: Molecular dynamics and mmPBSA analysis	0
Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot	0
In silico de novo drug design of a therapeutic peptide inhibitor against UBE2C in breast cancer	0
Quantification of the presence of enzymes in gelatin zymography using the Gini index	0
Drug synergy model for malignant diseases using deep learning	0
Rearrangement distance with reversals, indels, and moves in intergenic regions on signed and unsigned permutations	0
Comparative benchmarking of template-based, evolutionary-diffusion, and generative language models for IsPETase structure prediction	0
PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction	0
Fractal dimensionality of a coiled helical coil	0
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	0
SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction	0
Analyzing omics data based on sample network	0
DeepRT: Predicting compounds presence in pathway modules and classifying into module classes using deep neural networks based on molecular properties	0
NanoporeInspect: An Interactive Tool for Evaluating Nanopore Sequencing Quality and Ligation Efficiency	0
Gtie-Rt: A comprehensive graph learning model for predicting drugs targeting metabolic pathways in human	0
Erratum — DDINet: Drug–drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder	0
Modelling and optimizing combination therapeutic strategies for KRAS- and EGFR-mutant lung cancer	0
Algorithms for the Uniqueness of the Longest Common Subsequence	0
Editorial: Guidelines for Credible Machine Learning in Computational Biology	0
AAindex-PPII: Predicting polyproline type II helix structure based on amino acid indexes with an improved BiGRU-TextCNN model	0
Author index Volume 22 (2024)	0
Utilization of systematic error-assessment software to improve phylogenetic accuracy	0
Molecular dynamics simulations of ribosome-binding sites in theophylline-responsive riboswitch associated with improving the gene expression regulation in chloroplasts	0