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 2022-05-01 to 2026-05-01.)

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	12
NNDock2: A neural network-based scoring function for ranking protein–protein docking models	12
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	8
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks	7
Mendelian randomization and AlphaFold3 analysis suggest putative causal plasma proteins in graves’ disease	6
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
Analysis of clonal evolution in cancer: A computational perspective	5
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model	5
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model	5
Predicting distant cancer metastasis using a weighted gene interaction network and sample-specific differential correlations	5
Learning long- and short-term dependencies for improving drug-target binding affinity prediction using transformer and edge contraction pooling	4
How much can ChatGPT really help computational biologists in programming?	4
Methods for cell-type annotation on scRNA-seq data: A recent overview	4
EnAMP: A novel deep learning ensemble antibacterial peptide recognition algorithm based on multi-features	3
Accounting for treatment during the development or validation of prediction models	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
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
Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM	3
A brief review and comparative analysis of RNA secondary structure prediction tools	3
Flux balance network expansion predicts stage-specific human peri_implantation embryo metabolism	3

Behavioral dynamics of bacteriophage gene regulatory networks	3
Analysis of the regulation of model parameters on delay time in the p53 dynamical response to single-stranded breaks	3
Body plan evolvability: The role of variability in gene regulatory networks	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
M³-20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery	2
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties	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
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities	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
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
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data	2
Early lifespan prediction in Caenorhabditis elegans via contrastive learning and channel attention	2
Integrating temporal and spatial variabilities for identifying ion binding proteins in phage	2
Introduction to Selected Papers from InCoB 2021	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
Parameter estimation analysis of the glioblastoma immune model	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
Gene regulatory network inference based on modified adaptive lasso	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
Identification of a seven autophagy-related gene pairs signature for the diagnosis of colorectal cancer using the RankComp algorithm	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
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	1
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	1
Integration of evolutionary computation and ensemble learning in bioinformatics (Case Study: Protein–Peptide Interaction Prediction)	1
An alignment-independent three-dimensional quantitative structure–activity relationship study on ron receptor tyrosine kinase inhibitors	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
Integrating pharmacophore model and deep learning for activity prediction of molecules with BRCA1 gene	1
GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion	1
Author Index Volume 21 (2023)	1
Multi-Classification of Drug–Drug interaction based on a complete graph convolutional neural network and explainable artificial intelligence	0
Construction of transcript regulation mechanism prediction models based on binding motif environment of transcription factor AoXlnR in Aspergillus oryzae	0
iRNA5hmC-HOC: High-order correlation information for identifying RNA 5-hydroxymethylcytosine modification	0
Predicting functional co-occurrence probability in PPI networks via multi-level participation expectation	0
Deep learning inference of miRNA expression from bulk and single-cell mRNA expression	0
Gtie-Rt: A comprehensive graph learning model for predicting drugs targeting metabolic pathways in human	0
Research on similarity retrieval method based on mass spectral entropy	0
Quantification of the presence of enzymes in gelatin zymography using the Gini index	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
Integration of autoencoder and graph convolutional network for predicting breast cancer drug response	0

Prediction and annotation of alternative transcription starts and promoter shift in the chicken genome	0
PTGAC Model: A machine learning approach for constructing phylogenetic tree to compare protein sequences	0
Utilization of systematic error-assessment software to improve phylogenetic accuracy	0
Gene representation bias in spatial transcriptomics	0
Drug synergy model for malignant diseases using deep learning	0
Overlapping group screening for binary cancer classification with TCGA high-dimensional genomic data	0
Rearrangement distance with reversals, indels, and moves in intergenic regions on signed and unsigned permutations	0
Designing of sorafenib analogs to target c-Raf for the management of hepatocellular carcinoma: Molecular dynamics and mmPBSA analysis	0
PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction	0
Visual-SELEX: a technology ensemble for evaluating aptamer structural similarity via 3D visual spatial conformational analysis	0
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	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
An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra	0
Fractal dimensionality of a coiled helical coil	0
A technique for preserving network structure in randomized Hi-C data	0
Analyzing omics data by feature combinations based on kernel functions	0
DNA sequences alignment method using sparse index on pan-genome graph	0
CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea	0
Predictive Recognition of DNA-binding Proteins Based on Pre-trained Language Model BERT	0
Imputation for Single-cell RNA-seq Data with Non-negative Matrix Factorization and Transfer Learning	0
RiRPSSP: A unified deep learning method for prediction of regular and irregular protein secondary structures	0
Modelling and optimizing combination therapeutic strategies for KRAS- and EGFR-mutant lung cancer	0
NanoporeInspect: An Interactive Tool for Evaluating Nanopore Sequencing Quality and Ligation Efficiency	0
The novel design of a multi-epitope vaccine candidate against the dengue virus using advanced immunoinformatics and structural analysis	0
Small groups in multidimensional feature space: Two examples of supervised two-group classification from biomedicine	0
ThermalProGAN: A sequence-based thermally stable protein generator trained using unpaired data	0
Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot	0
iCEED: Integrated customized extraction of enzyme data	0
Analyzing omics data based on sample network	0
Drug repurposing for non-small cell lung cancer by predicting drug response using pathway-level graph convolutional network	0
DDINet: Drug–drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder	0
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network	0
COYOTE: Sequence-derived structural descriptors-based computational identification of glycoproteins	0
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases	0
In silico de novo drug design of a therapeutic peptide inhibitor against UBE2C in breast cancer	0
SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction	0
A model-based clustering algorithm with covariates adjustment and its application to lung cancer stratification	0
DeepRT: Predicting compounds presence in pathway modules and classifying into module classes using deep neural networks based on molecular properties	0
PLMABFW: A deep learning framework for predicting Antibody–Antigen interactions using protein language model	0
A network-based dynamic criterion for identifying prediction and early diagnosis biomarkers of complex diseases	0
Cancer classification and functional pathway discovery using TCGA transcriptomic profiles: A matched case-control framework	0
Algorithms for the Uniqueness of the Longest Common Subsequence	0
bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model	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
Automated analysis of karyotype images	0
Editorial: Guidelines for Credible Machine Learning in Computational Biology	0
Deep subspace fusion based on integrated self-supervision for cancer subtype identification	0
Molecular dynamics simulations of ribosome-binding sites in theophylline-responsive riboswitch associated with improving the gene expression regulation in chloroplasts	0
KANBind as a diagnostic probe for DNA-binding protein prediction: A prevalence-calibrated reality check under strict homology control	0
The impact of simulation time in predicting binding free energies using end-point approaches	0
Study of the mechanism of step-by-step interaction of viral proteins during replication and transcription	0
PCA-constrained multi-core matrix fusion network: A novel approach for cancer subtype identification	0
Obstacles to effective model deployment in healthcare	0
A non-parametric Bayesian joint model for latent individual molecular profiles and survival in oncology	0
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	0
Comparative benchmarking of template-based, evolutionary-diffusion, and generative language models for ispetase structure prediction	0