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 2022-06-01 to 2026-06-01.)

Article	Citations
A novel method for predicting DNA N⁴-methylcytosine sites based on deep forest algorithm	16
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection	14
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	12
NNDock2: A neural network-based scoring function for ranking protein–protein docking models	8
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks	7
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
Mendelian randomization and AlphaFold3 analysis suggest putative causal plasma proteins in graves’ disease	6
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model	5
Methods for cell-type annotation on scRNA-seq data: A recent overview	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
Predicting distant cancer metastasis using a weighted gene interaction network and sample-specific differential correlations	5
Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM	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
How much can ChatGPT really help computational biologists in programming?	4
Polypharmacy side effect prediction based on semi-implicit graph variational auto-encoder	3
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides	3
Improving drug–target interaction prediction through dual-modality fusion with InteractNet	3
Predicting ncRNA–Protein interactions with a graph attention model exploiting personalized subgraphs	3
A brief review and comparative analysis of RNA secondary structure prediction tools	3
Bond-resolved graph-theoretic modeling of structural invariance and metabolic accessibility in drug molecules	3
Behavioral dynamics of bacteriophage gene regulatory networks	3
ReinVar: A Model-Free Paradigm based Reinforcement Learning approach to Detect Copy Number Variation	3
Analysis of the regulation of model parameters on delay time in the p53 dynamical response to single-stranded breaks	3

Accounting for treatment during the development or validation of prediction models	3
Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation	3
Author Index Volume 20 (2022)	2
Introduction to Selected Papers from InCoB 2021	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
Early lifespan prediction in Caenorhabditis elegans via contrastive learning and channel attention	2
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations	2
When Pipelines Run but Coordinates Fail: A Simple Spatial Specificity Check for False Locality in post-GWAS Analysis	2
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	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
Body plan evolvability: The role of variability in gene regulatory networks	2
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	2
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases	2
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties	2
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	2
M³-20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery	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
Integrating temporal and spatial variabilities for identifying ion binding proteins in phage	2
Antimicrobial peptides recognition using weighted physicochemical property encoding	1
Identification of a seven autophagy-related gene pairs signature for the diagnosis of colorectal cancer using the RankComp algorithm	1
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	1
Integration of evolutionary computation and ensemble learning in bioinformatics (Case Study: Protein–Peptide Interaction Prediction)	1
CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data	1
Facilitating the drug repurposing with iC/E strategy: A practice on novel nNOS inhibitor discovery	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
Author Index Volume 21 (2023)	1
GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion	1
Parameter estimation analysis of the glioblastoma immune model	1
Author index Volume 23 (2025)	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
COLDLNA: Enhancing long-range node features extraction to improve robust generalization ability of drug-target binding affinity prediction in cold-start scenarios	1
A novel approach for the identification of single nucleotide polymorphisms	1
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	1
An alignment-independent three-dimensional quantitative structure–activity relationship study on ron receptor tyrosine kinase inhibitors	1
Multi-omics data analysis reveals the biological implications of alternative splicing events in lung adenocarcinoma	0
Algorithms for the Uniqueness of the Longest Common Subsequence	0
Prediction and annotation of alternative transcription starts and promoter shift in the chicken genome	0
bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model	0
PTGAC Model: A machine learning approach for constructing phylogenetic tree to compare protein sequences	0
Automated analysis of karyotype images	0
Gene representation bias in spatial transcriptomics	0
Editorial: Guidelines for Credible Machine Learning in Computational Biology	0
PLMABFW: A deep learning framework for predicting Antibody–Antigen interactions using protein language model	0
KANBind as a diagnostic probe for DNA-binding protein prediction: A prevalence-calibrated reality check under strict homology control	0
Integrating pharmacophore model and deep learning for activity prediction of molecules with BRCA1 gene	0
iCEED: Integrated customized extraction of enzyme data	0

SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction	0
DDINet: Drug–drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder	0
Multi-Classification of Drug–Drug interaction based on a complete graph convolutional neural network and explainable artificial intelligence	0
COYOTE: Sequence-derived structural descriptors-based computational identification of glycoproteins	0
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network	0
DeepRT: Predicting compounds presence in pathway modules and classifying into module classes using deep neural networks based on molecular properties	0
In silico de novo drug design of a therapeutic peptide inhibitor against UBE2C in breast cancer	0
Drug repurposing for non-small cell lung cancer by predicting drug response using pathway-level graph convolutional network	0
Comparative benchmarking of template-based, evolutionary-diffusion, and generative language models for ispetase structure prediction	0
iRNA5hmC-HOC: High-order correlation information for identifying RNA 5-hydroxymethylcytosine modification	0
Analyzing omics data by feature combinations based on kernel functions	0
ThermalProGAN: A sequence-based thermally stable protein generator trained using unpaired data	0
CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea	0
Modelling and optimizing combination therapeutic strategies for KRAS- and EGFR-mutant lung cancer	0
The impact of simulation time in predicting binding free energies using end-point approaches	0
The novel design of a multi-epitope vaccine candidate against the dengue virus using advanced immunoinformatics and structural analysis	0
RiRPSSP: A unified deep learning method for prediction of regular and irregular protein secondary structures	0
Small groups in multidimensional feature space: Two examples of supervised two-group classification from biomedicine	0
Integration of autoencoder and graph convolutional network for predicting breast cancer drug response	0
Imputation for Single-cell RNA-seq Data with Non-negative Matrix Factorization and Transfer Learning	0
Utilization of systematic error-assessment software to improve phylogenetic accuracy	0
Rearrangement distance with reversals, indels, and moves in intergenic regions on signed and unsigned permutations	0
Cancer classification and functional pathway discovery using TCGA transcriptomic profiles: A matched case-control framework	0
A technique for preserving network structure in randomized Hi-C data	0
PCA-constrained multi-core matrix fusion network: A novel approach for cancer subtype identification	0
An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra	0
A non-parametric Bayesian joint model for latent individual molecular profiles and survival in oncology	0
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	0
A model-based clustering algorithm with covariates adjustment and its application to lung cancer stratification	0
PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction	0
Analyzing omics data based on sample network	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
Overlapping group screening for binary cancer classification with TCGA high-dimensional genomic data	0
A network-based dynamic criterion for identifying prediction and early diagnosis biomarkers of complex diseases	0
AAindex-PPII: Predicting polyproline type II helix structure based on amino acid indexes with an improved BiGRU-TextCNN model	0
Predicting functional co-occurrence probability in PPI networks via multi-level participation expectation	0
Deep subspace fusion based on integrated self-supervision for cancer subtype identification	0
Author index Volume 22 (2024)	0
An ensemble approach for circular RNA-disease association prediction using variational autoencoder and genetic algorithm	0
Molecular dynamics simulations of ribosome-binding sites in theophylline-responsive riboswitch associated with improving the gene expression regulation in chloroplasts	0
NanoporeInspect: An Interactive Tool for Evaluating Nanopore Sequencing Quality and Ligation Efficiency	0
Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot	0
Predictive Recognition of DNA-binding Proteins Based on Pre-trained Language Model BERT	0
Gene regulatory network inference based on modified adaptive lasso	0
Drug synergy model for malignant diseases using deep learning	0
DNA sequences alignment method using sparse index on pan-genome graph	0
Designing of sorafenib analogs to target c-Raf for the management of hepatocellular carcinoma: Molecular dynamics and mmPBSA analysis	0
Study of the mechanism of step-by-step interaction of viral proteins during replication and transcription	0
Visual-SELEX: a technology ensemble for evaluating aptamer structural similarity via 3D visual spatial conformational analysis	0
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	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
Obstacles to effective model deployment in healthcare	0
Fractal dimensionality of a coiled helical coil	0
Deep learning inference of miRNA expression from bulk and single-cell mRNA expression	0
Quantification of the presence of enzymes in gelatin zymography using the Gini index	0
Research on similarity retrieval method based on mass spectral entropy	0
Gtie-Rt: A comprehensive graph learning model for predicting drugs targeting metabolic pathways in human	0