Computational and Structural Biotechnology Journal

Article	Citations
Predicting cellular adaptation proteins dependent on eIF2α regulation under stress conditions: Physiological and pathophysiological implications in neuronal function	204
Corrigendum to “Maternal Clostridium butyricum supplementation during late gestation and lactation enhances gut bacterial communities, milk quality, and	185
Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species	173
Gut microbiome enterotypes and temporal variations during a six-month inulin-supplemented weight loss randomized controlled trial in Thai children with obesity	147
macpie: Scalable workflow for high-throughput transcriptomic profiling	141
Radiomic clustering using graph network techniques coupled with unbalanced optimal transport	129
Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants	110
DiabetesOmic: A comprehensive multi-omics diabetes database	108
Evolution is in the details: Regulatory differences in modern human and Neanderthal	105
Deep5mC: Predicting 5-methylcytosine (5mC) methylation status using a deep learning transformer approach	84
MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants	80
The influence of HIV sense and antisense transcripts on stochastic HIV transcription and reactivation	73
A miRNA signature linked to high lipoprotein (a) and coronary calcification in familial hypercholesterolaemia	73
Pseudotimecascade Visualizes Gene Expression Cascade in Pseudotime Analysis	73
Identification of a Novel Trifluoromethyl-Bearing Flavonoid as a Promising Androgen Receptor Antagonist: Structure-Based Virtual Screening and In Vitro Study	72
SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis	71
Data pre-processing for analyzing microbiome data – A mini review	68
Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types	68
Predicting zeta potential of liposomes from their structure: A nano-QSPR model for DOPE, DC-Chol, DOTAP, and EPC formulations	63
VTAM: A robust pipeline for validating metabarcoding data using controls	61
The balance between photosynthesis and respiration explains the niche differentiation between Crocosphaera and Cyanothece	59
Integrated metabolomics and network analysis reveal changes in lipid metabolisms of tripterygium glycosides tablets in rats with collagen-induced arthritis	59
Consistencies and contradictions in different polymer models of chromatin architecture	58
In silico and in vitro approaches allow the identification of the Prosystemin molecular network	57
MUG: A mutation overview of GPCR subfamily A17 receptors	56

DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data	56
cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery	53
Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus	53
Predictive dynamic control accurately maps the design space for 2,3-butanediol production	51
Free energy landscape of the PI3Kα C-terminal activation	51
WUREN: Whole-modal union representation for epitope prediction	50
Prediction of protein-ligand binding affinity with deep learning	49
Corrigendum to “Cryo-EM reveals architectural diversity in active rotavirus particles” [Comput. Struct. Biotechnol. J. 17 (2019) 1178–1183]	49
Ranking pre-trained speech embeddings in Parkinson's disease detection: Does Wav2Vec 2.0 outperform its 1.0 version across speech modes and languages?	49
Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations	49
EthnoHERBS: Harnessing traditional herbal knowledge for biodiversity conservation and innovative health solutions	48
CRUSADE project: Recycling technologies for ELV components to create a sustainable source of market grade materials for EU applications	48
From latent dynamics to data geometry: Nonlinear diffusion modelling for protein structures	46
CKATool: A clinical kinematic analysis toolbox for upper limb rehabilitation	45
Biomarker discovery process at binomial decision point (2BDP): Analytical pipeline to construct biomarker panel	44
Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview	44
Agreement and disagreement in pediatric functional neurological symptom disorders: Comparing patient reported outcome measures (PROMs) and clinician assessments	43
The second intracellular loop of the yeast Trk1 potassium transporter is involved in regulation of activity, and interaction with 14–3-3 proteins	43
Entropy-extreme model for predicting the development of cyber epidemics at early stages	43
A novel exosome-derived prognostic signature and risk stratification for breast cancer based on multi-omics and systematic biological heterogeneity	43
A drug repurposing method based on inhibition effect on gene regulatory network	43
Comprehensive exploration of JQ1 and GSK2801 targets in breast cancer using network pharmacology and molecular modeling approaches	41
Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes	40
Computational fluid dynamics modeling and simulation of nanoparticle-tumor interaction: Systematic literature review	40
What remains from living cells in bacterial lysate-based cell-free systems	39
Automated machine learning in nanotoxicity assessment: A comparative study of predictive model performance	39
Towards predicting implant-induced fibrosis: A standardized network model of macrophage-fibroblast interactions	39
Optimized Quantitative Bacterial Two-Hybrid (qB2H) for Protein–Protein Interaction Assessment	39
From sequence to function through structure: Deep learning for protein design	39
Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application.	38
Cell segmentation and representation with shape priors	38
Towards accurate and efficient diagnoses in nephropathology: An AI-based approach for assessing kidney transplant rejection	37
Single-cell multiome characterizing intercellular communication and intracellular regulation of epithelium and mesenchymal during secondary palate development in mice	37
Integrative Multiomics and Single-Cell Profiling Identify TNFRSF1A + Macrophages as a Prognostic and Therapeutic Target in Diffuse Large B-cell Lymph	37
IsomiRome analysis reveals dysregulation of 5’ isomiRs during SARS-CoV-2 infection	37
Over time analysis of the codon usage of SARS-CoV-2 and its variants	36
Self-supervised domain adaptation of protein language model based solely on positive enzyme-reaction pairs	36
A cellulose-degrading Bacillus altitudinis from Tibetan pigs improved the in vitro fermentation characteri	36
A universal pipeline MosaicProt enables large-scale modeling and detection of chimeric protein sequences for studies on programmed ribosomal frameshifting	36
Contagious infection-free medical interaction system with machine vision controlled by remote hand gesture during an operation	35
Protein design accelerates the development and application of optogenetic tools	35
Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems	35
Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications	35
Performance of a HER2 testing algorithm tailored for urothelial bladder cancer: A Bi-centre study	34
PLO3S: Protein LOcal Surficial Similarity Screening	34
SbD4Skin by EosCloud: Integrating multi-view molecular representation for predicting skin sensitization, irritation, and acute dermal toxicity	33
ImmiR: A database of microRNAs associated with immune checkpoints and infiltrates	33
Computational approaches in rheumatic diseases – Deciphering complex spatio-temporal cell interactions	33
OncoProExp: An interactive shiny web application for comprehensive cancer proteomics and phosphoproteomics analysis	33
Structural studies of protein–nucleic acid complexes: A brief overview of the selected techniques	33

NaCTR: Natural product-derived compound-based drug discovery pipeline from traditional oriental medicine by search space reduction	32
Strengths and limitations of web servers for the modeling of TCRpMHC complexes	31
Co-expression of immune checkpoints in glioblastoma revealed by single-nucleus RNA sequencing and spatial transcriptomics	31
Prognostic iron-metabolism signature robustly stratifies single-cell characteristics of hepatocellular carcinoma	31
Computationally derived structural insights into Rare Earth selectivity in lanmodulin and its variants	30
Augusta: From RNA‐Seq to gene regulatory networks and Boolean models	30
Dual guide RNA-mediated concurrent C&G-to-T&A and A&T-to-G&C conversions using CRISPR base editors	30
Inference of essential genes in Brugia malayi and Onchocerca volvulus by machine learning and the implicat	30
PCLDA: An interpretable cell annotation tool for single-cell RNA-sequencing data based on simple statistical methods	30
Impact of an irreversible β-galactosylceramidase inhibitor on the lipid profile of zebrafish embryos	29
Beyond the Scalpel: Assessing ChatGPT's potential as an auxiliary intelligent virtual assistant in oral surgery	29
Bacillus subtilis spores displaying RBD domain of SARS-CoV-2 spike protein	29
Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue	29
Machine learning in metastatic cancer research: Potentials, possibilities, and prospects	29
Identification of genetic basis of brain imaging by group sparse multi-task learning leveraging summary statistics	28
ECGA: A web server to explore and analyze extrachromosomal gene in cancer	28
Multicopper oxidases with laccase-ferroxidase activity: Classification and study of ferroxidase activity determinants in a member from Heterobasidion annosum s. l.	28
PS-GO parametric protein search engine	28
Pleiotropic expression quantitative trait loci are enriched in enhancers and transcription factor binding sites and impact more genes	28
Mutation density analyses on long noncoding RNA reveal comparable patterns to protein-coding RNA and prognostic value	28
Cat-E: A comprehensive web tool for exploring cancer targeting strategies	28
Review of protein structure-based analyses that illuminate plant stress mechanisms	27
The World of GPCR dimers – Mapping dopamine receptor D 2 homodimers in different activation states and configuration arrangements	27
Thresholding Gini variable importance with a single-trained random forest: An empirical Bayes approach	27
Comparative analysis of amino acid auxotrophies and peptidase profiles in non-dysbiotic and dysbiotic small intestinal microbiomes	27
Empirical comparison and recent advances of computational prediction of hormone binding proteins using machine learning methods	27
Plasma cell-free extrachromosomal circular DNA is a molecular hallmark of preeclampsia	26
Enhancing detection of epileptic seizures using transfer learning and EEG brain activity signals	26
Post-processing enhances protein secondary structure prediction with second order deep learning and embeddings	26
Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes	26
Comparative Analysis of Morphological and Acoustic Correlates of Bush-Cricket Tympanic Membranes	26
Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation	26
Structure-based identification of HNF4α agonists: Rosmarinic acid as a promising candidate for NAFLD treatment	26
Integrative geno-metabolomics of tenasserim turmeric ( Curcuma candida (Wall.) Techapr. & Škorničk.) with insights into volatile biosynthesis across	26
Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases	26
Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism	25
In-silico proteomic analysis of the role of IL-4 and IL-10 in IVD degeneration: Protein-protein interaction networks for candidate prioritisation	25
EpiCas-DL : Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning	25
PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics – catching the (un)usual suspects	25
CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction	25
EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks	24
Optimizing fountain codes for DNA data storage	24
Machine learning reveals STAT motifs as predictors for GR-mediated gene repression	24
Ion and water permeation through claudin-10b and claudin-15 paracellular channels	24
The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations	24
Fantastic genes and where to find them expressed in CHO	24
Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives	24
Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases	24
Enhancing glucose level prediction of ICU patients through hierarchical modeling of irregular time-series	24
Easy-MODA: Simplifying standardised registration of scientific simulation workflows through MODA template guidelines powered by the Enalos Cloud Platform	24
HELLS modulates the stemness of intrahepatic cholangiocarcinoma through promoting senescence-associated secretory phenotype	23
Claudin-10b cation channels in tight junction strands: Octameric-interlocked pore barrels constitute paracellular channels with low water permeability	23
Oxidative stress-driven transcriptomic remodeling in human astrocytes reveals network signatures associated with neurodegenerative and cardiovascular processes	23
Corrigendum to “TREAT: Therapeutic RNAs exploration inspired by artificial intelligence technology” [Comput Struct Biotechnol J 20 (2022) 5680–5689]	23
HIV infection detection using CRISPR/Cas systems: Present and future prospects	23
scDemultiplex: An iterative beta-binomial model-based method for accurate demultiplexing with hashtag oligos	23
INSIGHT: An integrated framework for safe and sustainable chemical and material assessment	23
The discovery of hidden guanylate cyclases (GCs) in the Homo sapiens proteome	23
Evaluation of the impact of printing and embroidery parameters in the process of obtaining utility comfort sensors used in protective clothing dedicated to premature babies	23
The potential of Real-Time volume-rendered 3D Imaging in immersive virtual-reality (VR) for surgical planning in infants with congenital thoracic malformation (CTM)	23
Histone variants and chromatin structure, update of advances	22
Generic and queryable data integration schema for transcriptomics and epigenomics studies	22
TRRAP-mediated acetylation on Sp1 regulates adult neurogenesis	22
A novel deep learning method for large-scale analysis of bone marrow adiposity using UK Biobank Dixon MRI data	22
Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations	22
BioLogical: a universal analysis framework for biosystem logical dynamics	22
Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains	22
MNNMDA: Predicting human microbe-disease association via a method to minimize matrix nuclear norm	22
Downregulation of ABLIM3 confers to the metastasis of neuroblastoma via regulating the cell adhesion molecules pathway	22
New targets for the treatment of ulcerative colitis: Gut microbiota and its metabolites	22
Deep learning of antibody epitopes using positional permutation vectors	21
CPRCSdb: A comprehensive phenotype-associated single-cell transcriptomic database for human cancer	21
Corrigendum to “Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin” [Comput Struct Biotechnol J 27 (2025) 1286–1295]	21
Deep learning based deconvolution methods: A systematic review	21
Short-chain fatty acids reprogram metabolic profiles with the induction of reactive oxygen species production in human colorectal adenocarcinoma cells	21
Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231-luc-GFP cell line	21
A potent nonapeptide inhibitor for the CXCL12/HMGB1 heterocomplex: A computational and experimental approach	21
HYG-mol: An Interpretable Multimodal Hypergraph Framework for Molecular Property Prediction	21
Optimization of regulatory DNA with active learning	21
SpatialPPIv2: Enhancing protein–protein interaction prediction through graph neural networks with protein language models	21

Tevenvirinae phages encode a family of LSm-like fold proteins	21
MUC13-Associated Molecular Interactome in Pancreatic Cancer	20
The effect of long-term ambient storage on the morphology of adhered DNA origami	20
CHIASMA: Advancing chemicals and materials safety and sustainability assessments through innovative integration of in vitro and in silico (new approach) methodologies	20
Low-calorie diet intervention ameliorates gut microbiota dysbiosis and metabolic changes in obese patients with type 2 diabetes under standard care	20
Identifying the risk of Kawasaki disease based solely on routine blood test features through novel construction of machine learning models	20
HELENA project: Driving innovation in high energy density Li-metal halide solid-state batteries for electric vehicles and aircrafts	20
Dynamics of spindle assembly and position checkpoints: Integrating molecular mechanisms with computational models	20
MACRAMÉ – Advanced characterisation methodologies to assess and predict the health and environmental risks of advanced materials	20
Detection and prioritization of COVID-19 infected patients from CXR images: Analysis of AI-assisted diagnosis in clinical settings	19
Family-wide analysis of integrin structures predicted by AlphaFold2	19
CNNSplice: Robust models for splice site prediction using convolutional neural networks	19
Quercetin: A promising drug candidate against the potential SARS-CoV-2-Spike mutants with high viral infectivity	19
How to describe the time-dependent dissolution of engineered nanomaterials?	19
TOAST: A novel method for identifying topologically associated domains based on graph auto-encoders and clustering	19
A method for analyzing the ERP associated with high frequency ANT DBS offset	19
AmiCa: Atlas of miRNA-gene correlations in cancer	18
Overcoming the cognition-reality gap in robot-to-human handovers with anisotropic variable force guidance	18
Shared and divergent contribution of vitamin A and oxytocin to the aetiology of autism spectrum disorder	18
Design, proof-of-concept of single robotic hair transplant mechanisms for both harvest and implant of hair grafts	18
Machine learning for metabolic pathway optimization: A review	18
Increased risk of arrhythmias, heart failure, and thrombosis in SARS-CoV-2 positive individuals persists at one year post-infection	18
f RNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data	18
Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1	18
Pathway-guided architectures for interpretable AI in biological research	18
Reference-based read clustering improves the de novo genome assembly of microbial strains	18
ALDH2 as a potential stem cell-related biomarker in lung adenocarcinoma: Comprehensive multi-omics analysis	18
Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus	18
A Nano Risk Governance Portal supporting risk governance of nanomaterials and nano-enabled products	18
BioPrediction-RPI: Democratizing the prediction of interaction between non-coding RNA and protein with end-to-end machine learning	17
A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer	17
Osmolyte-induced protein stability changes explained by graph theory	17
Artificial intelligence-large language models (AI-LLMs) for reliable and accurate cardiotocography (CTG) interpretation in obstetric practice	17
Starch granules and their size distribution in wheat: Biosynthesis, physicochemical properties and their effect on flour-based food systems	17
iResNetDM: An interpretable deep learning approach for four types of DNA methylation modification prediction	17
MM-DRPNet: A multimodal dynamic radial partitioning network for enhanced protein–ligand binding affinity prediction	17
Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation	17
Metabolomic and lipidomic insights into the impact of Euglena gracilis -derived β-glucan supplementation on sow colostrum and milk composition	17
Data recovery methods for DNA storage based on fountain codes	17
Computational design of α-amylase from Bacillus licheniformis to increase its activity and stability at high temperatures	17
Determining key residues of engineered scFv antibody variants with improved MMP-9 binding using deep sequencing and machine learning	17
iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data	17
RNA secondary structure prediction by conducting multi-class classifications	17
Cluster parameter-based DBSCAN maps for image characterization	17
A semi-mechanistic mathematical framework for simulating multi-hormone dynamics in reproductive endocrinology	16
LC-MS/MS identifies elevated imidazole propionate and gut-derived metabolite alterations in peritoneal dialysis patients	16
Low magnetic fields stimulate cardiac mitochondrial bioenergetics with a bell-shaped response: Possibly via a radical pair mechanism	16
Modeling omics dose-response at the pathway level with DoseRider	16
Plasticity of BioPhi-driven humanness optimization in ScFv-CD99 binding affinity validated through AlphaFold, HADDOCK, and MD simulations	16
Deciphering mitochondrial dysfunction in keratoconus: Insights into ACSL4 from machine learning-based bulk and single-cell transcriptome analyses and experimental validation	16
PathoEye: A deep learning framework for the whole-slide image analysis of skin tissue	16
Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics	16
Improving Face Age Prediction by Using Multiple-Angle Photos	16
An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus	16
DNA Methylation in Blood Samples from Malignant Mammary Tumors of Companion Dogs: A Pilot Study	16
Kinase-substrate prediction using an autoregressive model	16
Improving doublet cell removal efficiency through multiple algorithm runs	16
Salivary Proteomic Signatures Reveal Novel Mechanistic Insights into Moderate Dental Fluorosis Pathogenesis and Oral Homeostasis Disruption	16
Multi-matrix metabolomics in rare monogenic diabetes syndromes: Analysis of oral fluids and serum in carriers of pathogenic variants in the ALMS1/BBS gen	16
GENI: A web server to identify gene set enrichments in tumor samples	16
A numerical approach to bio-mechanics analysis based on live micro-CT images in the rat temporomandibular joint	16
Comprehensive analysis of circulating cell-free RNAs in blood for diagnosing non-small cell lung cancer	16
Estimating the effect of tissue- and blood-derived cell reference matrices on deconvolving bulk transcriptomic datasets	16
VarMeter2: An enhanced structure-based method for predicting pathogenic missense variants through Mahalanobis distance	16
Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review	16
Optical genome mapping reveals novel structural variations in an autism spectrum disorder cohort	16
Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin	16
Systematic screening and dynamic profiling of germline regulatory pathways and spermatogonial surface markers in a bivalve mollusc	15
Machine learning and gene network integration reveal prognostic subnetworks and biomarkers in pancreatic cancer	15
Direct antiglobulin test type, red blood cell distribution width, and estimated glomerular filtration rate for early prediction of in-hospital mortality of patients with COVID-19	15
Liquid-liquid phase separation in hair cell stereocilia development and maintenance	15
Spontaneous regeneration of cholecystokinergic reticulospinal axons after a complete spinal cord injury in sea lampreys	15
Investigating how HIV-1 antiretrovirals differentially behave as substrates and inhibitors of P-glycoprotein via molecular dynamics simulations	15
The optimal metric for viral genome space	15
Accurate protein stability predictions from homology models	15
The nucleotide landscape of polyXY regions	15
An integrated analysis of dysregulated SCD1 in human cancers and functional verification of miR-181a-5p/SCD1 axis in esophageal squamous cell carcinoma	15
LncCat: An ORF attention model to identify LncRNA based on ensemble learning strategy and fused sequence information	15
Lateral walking gait phase recognition for hip exoskeleton by denoising autoencoder-LSTM	15
Assessing the effect of selective serotonin reuptake inhibitors in the prevention of post-acute sequelae of COVID-19	15
Breast MRI radiomics and machine learning-based predictions of response to neoadjuvant chemotherapy – How are they affected by variations in tumor delineation?	15
Interspecific and intraspecific Taylor's laws for frog skin microbes	15
Enhancing surgical object detection in laparoscopic cholecystectomy with explicit positional relationship modeling	15
Integrated metabolome and transcriptome analysis reveals ferroptosis involvement in cisplatin resistance of esophageal squamous cancer cell	15
SCInter: A comprehensive single-cell transcriptome integration database for human and mouse	15
A novel cathelicidin TS-CATH derived from Thamnophis sirtalis combats drug-resistant gram-negative bacteria in vitro	15
Multidimensional morphological analysis of live sperm based on multiple-target tracking	15
scBlood: A comprehensive single-cell accessible chromatin database of blood cells	14
DeepNeuropePred: A robust and universal tool to predict cleavage sites from neuropeptide precursors by protein language model	14
Numerical simulation study of nanoparticle diffusion in gray matter	14
EnsembleDL-ATG: Identifying autophagy proteins by integrating their sequence and evolutionary information using an ensemble deep learning framework	14
One path, two solutions: Network-based analysis identifies targetable pathways for the treatment of comorbid type II diabetes and neuropsychiatric disorders	14
Topological embedding and directional feature importance in ensemble classifiers for multi-class classification	14
A review of Ribosome profiling and tools used in Ribo-seq data analysis	14
Rational design of monomeric IL37 variants guided by stability and dynamical analyses of IL37 dimers	14