Computational and Structural Biotechnology Journal

Papers
(The median citation count of Computational and Structural Biotechnology Journal is 4. 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 2022-01-01 to 2026-01-01.)
ArticleCitations
Agreement and disagreement in pediatric functional neurological symptom disorders: Comparing patient reported outcome measures (PROMs) and clinician assessments288
Corrigendum to “Cryo-EM reveals architectural diversity in active rotavirus particles” [Comput. Struct. Biotechnol. J. 17 (2019) 1178–1183]268
In silico and in vitro approaches allow the identification of the Prosystemin molecular network189
The balance between photosynthesis and respiration explains the niche differentiation between Crocosphaera and Cyanothece164
Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects161
NGS allele counts versus called genotypes for testing genetic association159
dsCellNet: A new computational tool to infer cell–cell communication networks in the developing and aging brain148
Network-based prioritization of cancer biomarkers by phenotype-driven module detection and ranking131
Biomarker discovery process at binomial decision point (2BDP): Analytical pipeline to construct biomarker panel119
An integrated protein structure fitness scoring approach for identifying native-like model structures119
Cell segmentation and representation with shape priors116
Comprehensive exploration of JQ1 and GSK2801 targets in breast cancer using network pharmacology and molecular modeling approaches100
Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking96
VTAM: A robust pipeline for validating metabarcoding data using controls95
Prediction of protein-ligand binding affinity with deep learning93
Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus92
Entropy-extreme model for predicting the development of cyber epidemics at early stages90
MUG: A mutation overview of GPCR subfamily A17 receptors83
Artificial intelligence predictive system of individual survival rate for lung adenocarcinoma82
A novel exosome-derived prognostic signature and risk stratification for breast cancer based on multi-omics and systematic biological heterogeneity79
Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA75
Predictive dynamic control accurately maps the design space for 2,3-butanediol production72
Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview71
Free energy landscape of the PI3Kα C-terminal activation70
Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes69
Integrated metabolomics and network analysis reveal changes in lipid metabolisms of tripterygium glycosides tablets in rats with collagen-induced arthritis68
The second intracellular loop of the yeast Trk1 potassium transporter is involved in regulation of activity, and interaction with 14–3-3 proteins67
Identification of (Z)-2-benzylidene-dihydroimidazothiazolone derivatives as tyrosinase inhibitors: Anti-melanogenic effects and in silico studies66
CKATool: A clinical kinematic analysis toolbox for upper limb rehabilitation65
Advanced biokinetic and hydrodynamic modelling to support and optimize the design of full-scale high rate algal ponds64
Nextcast: A software suite to analyse and model toxicogenomics data64
Multi-omics landscape and clinical significance of a SMAD4-driven immune signature: Implications for risk stratification and frontline therapies in pancreatic cancer63
Using molecular dynamics simulations to interrogate T cell receptor non-equilibrium kinetics62
Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations61
cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery60
The influence of HIV sense and antisense transcripts on stochastic HIV transcription and reactivation60
What remains from living cells in bacterial lysate-based cell-free systems58
UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets58
Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species57
Towards predicting implant-induced fibrosis: A standardized network model of macrophage-fibroblast interactions57
Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants56
Evolution is in the details: Regulatory differences in modern human and Neanderthal55
Deep5mC: Predicting 5-methylcytosine (5mC) methylation status using a deep learning transformer approach54
MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants54
A miRNA signature linked to high lipoprotein (a) and coronary calcification in familial hypercholesterolaemia54
macpie: Scalable workflow for high-throughput transcriptomic profiling53
Gut microbiome enterotypes and temporal variations during a six-month inulin-supplemented weight loss randomized controlled trial in Thai children with obesity52
Radiomic clustering using graph network techniques coupled with unbalanced optimal transport52
DiabetesOmic: A comprehensive multi-omics diabetes database52
DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data51
Corrigendum to “Maternal Clostridium butyricum supplementation during late gestation and lactation enhances gut bacterial communities, milk quality, and reduces piglet diarrhea” [Comput Struct Biotech51
Consistencies and contradictions in different polymer models of chromatin architecture50
Computational fluid dynamics modeling and simulation of nanoparticle-tumor interaction: Systematic literature review50
A drug repurposing method based on inhibition effect on gene regulatory network49
From latent dynamics to data geometry: Nonlinear diffusion modelling for protein structures48
WUREN: Whole-modal union representation for epitope prediction47
Predicting zeta potential of liposomes from their structure: A nano-QSPR model for DOPE, DC-Chol, DOTAP, and EPC formulations46
Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application.46
Improved inter-residue contact prediction via a hybrid generative model and dynamic loss function46
Ranking pre-trained speech embeddings in Parkinson's disease detection: Does Wav2Vec 2.0 outperform its 1.0 version across speech modes and languages?45
From sequence to function through structure: Deep learning for protein design45
CRUSADE project: Recycling technologies for ELV components to create a sustainable source of market grade materials for EU applications44
Towards accurate and efficient diagnoses in nephropathology: An AI-based approach for assessing kidney transplant rejection44
Data pre-processing for analyzing microbiome data – A mini review43
Automated machine learning in nanotoxicity assessment: A comparative study of predictive model performance43
Predicting cellular adaptation proteins dependent on eIF2α regulation under stress conditions: Physiological and pathophysiological implications in neuronal function42
Identification of genetic basis of brain imaging by group sparse multi-task learning leveraging summary statistics42
EthnoHERBS: Harnessing traditional herbal knowledge for biodiversity conservation and innovative health solutions42
Statistical methods for Mendelian randomization in genome-wide association studies: A review42
Contagious infection-free medical interaction system with machine vision controlled by remote hand gesture during an operation41
Prognostic iron-metabolism signature robustly stratifies single-cell characteristics of hepatocellular carcinoma41
PS-GO parametric protein search engine41
ECGA: A web server to explore and analyze extrachromosomal gene in cancer40
Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems40
Impact of an irreversible β-galactosylceramidase inhibitor on the lipid profile of zebrafish embryos39
Survival estimation in patients with stomach and esophageal carcinoma using miRNA expression profiles39
The World of GPCR dimers – Mapping dopamine receptor D2 homodimers in different activation states and configuration arrangements39
Literature-based translation from synthetic lethality screening into therapeutics targets: CD82 is a novel target for KRAS mutation in colon cancer39
Inference of essential genes in Brugia malayi and Onchocerca volvulus by machine learning and the implications for discovering new interventions39
Identifying novel SMYD3 interactors on the trail of cancer hallmarks39
SbD4Skin by EosCloud: Integrating multi-view molecular representation for predicting skin sensitization, irritation, and acute dermal toxicity38
Pleiotropic expression quantitative trait loci are enriched in enhancers and transcription factor binding sites and impact more genes38
Population genomic analyses reveal evidence for limited recombination in the superbug Candida auris in nature38
Performance of a HER2 testing algorithm tailored for urothelial bladder cancer: A Bi-centre study38
Multicopper oxidases with laccase-ferroxidase activity: Classification and study of ferroxidase activity determinants in a member from Heterobasidion annosum s. l.38
Drug repurposing in psoriasis, performed by reversal of disease-associated gene expression profiles38
PCLDA: An interpretable cell annotation tool for single-cell RNA-sequencing data based on simple statistical methods37
Protein design accelerates the development and application of optogenetic tools37
Augusta: From RNA‐Seq to gene regulatory networks and Boolean models37
Structural studies of protein–nucleic acid complexes: A brief overview of the selected techniques37
PLO3S: Protein LOcal Surficial Similarity Screening37
Co-expression of immune checkpoints in glioblastoma revealed by single-nucleus RNA sequencing and spatial transcriptomics37
Cat-E: A comprehensive web tool for exploring cancer targeting strategies36
YTLR: Extracting yeast transcription factor-gene associations from the literature using automated literature readers36
A cellulose-degrading Bacillus altitudinis from Tibetan pigs improved the in vitro fermentation characteristics of wheat bran36
IsomiRome analysis reveals dysregulation of 5’ isomiRs during SARS-CoV-2 infection35
Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications35
Single-cell multiome characterizing intercellular communication and intracellular regulation of epithelium and mesenchymal during secondary palate development in mice35
Review of protein structure-based analyses that illuminate plant stress mechanisms35
Over time analysis of the codon usage of SARS-CoV-2 and its variants35
ImmiR: A database of microRNAs associated with immune checkpoints and infiltrates35
Mutation density analyses on long noncoding RNA reveal comparable patterns to protein-coding RNA and prognostic value35
A universal pipeline MosaicProt enables large-scale modeling and detection of chimeric protein sequences for studies on programmed ribosomal frameshifting34
Dual guide RNA-mediated concurrent C&G-to-T&A and A&T-to-G&C conversions using CRISPR base editors34
Self-supervised domain adaptation of protein language model based solely on positive enzyme-reaction pairs34
Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand34
OncoProExp: An interactive shiny web application for comprehensive cancer proteomics and phosphoproteomics analysis34
Computationally derived structural insights into Rare Earth selectivity in lanmodulin and its variants33
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability33
Strengths and limitations of web servers for the modeling of TCRpMHC complexes33
Thresholding Gini variable importance with a single-trained random forest: An empirical Bayes approach33
Scale bar of aging trajectories for screening personal rejuvenation treatments33
Machine learning in metastatic cancer research: Potentials, possibilities, and prospects33
Empirical comparison and recent advances of computational prediction of hormone binding proteins using machine learning methods33
NaCTR: Natural product-derived compound-based drug discovery pipeline from traditional oriental medicine by search space reduction33
Bacillus subtilis spores displaying RBD domain of SARS-CoV-2 spike protein33
Prediction of HER2-positive breast cancer recurrence and metastasis risk from histopathological images and clinical information via multimodal deep learning32
Computational approaches in rheumatic diseases – Deciphering complex spatio-temporal cell interactions32
The discovery of hidden guanylate cyclases (GCs) in the Homo sapiens proteome31
A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis31
TRRAP-mediated acetylation on Sp1 regulates adult neurogenesis31
Machine learning reveals STAT motifs as predictors for GR-mediated gene repression31
HELLS modulates the stemness of intrahepatic cholangiocarcinoma through promoting senescence-associated secretory phenotype31
Beyond the Scalpel: Assessing ChatGPT's potential as an auxiliary intelligent virtual assistant in oral surgery31
Optimizing fountain codes for DNA data storage31
SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants31
Corrigendum to “TREAT: Therapeutic RNAs exploration inspired by artificial intelligence technology” [Comput Struct Biotechnol J 20 (2022) 5680–5689]30
Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism30
Corrigendum to “Coupling the endophytic microbiome with the host transcriptome in olive roots” [Comput. Struct. Biotechnol. J. 19 (2021) 4777–4789]30
SPARC: Structural properties associated with residue constraints30
Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR-amplified glioblastoma30
Generic and queryable data integration schema for transcriptomics and epigenomics studies30
Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations30
Concentration-dependent thermodynamic analysis of the partition process of small ligands into proteins30
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein–protein interaction network through integrative methods30
Short-chain fatty acids reprogram metabolic profiles with the induction of reactive oxygen species production in human colorectal adenocarcinoma cells30
The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations30
Detecting differentially expressed circular RNAs from multiple quantification methods using a generalized linear mixed model30
MSPJ: Discovering potential biomarkers in small gene expression datasets via ensemble learning30
The seen and the unseen: Molecular classification and image based-analysis of gastrointestinal cancers30
Protposer: The web server that readily proposes protein stabilizing mutations with high PPV29
Deep learning of antibody epitopes using positional permutation vectors29
Role of Bmal1 in mediating the cholinergic system to regulate the behavioral rhythm of nocturnal marine molluscs29
Mysteries of gene regulation: Promoters are not the sole triggers of gene expression29
Plasma cell-free extrachromosomal circular DNA is a molecular hallmark of preeclampsia29
scDemultiplex: An iterative beta-binomial model-based method for accurate demultiplexing with hashtag oligos29
PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics – catching the (un)usual suspects29
Claudin-10b cation channels in tight junction strands: Octameric-interlocked pore barrels constitute paracellular channels with low water permeability29
Comparative analysis of amino acid auxotrophies and peptidase profiles in non-dysbiotic and dysbiotic small intestinal microbiomes28
Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes28
Enhancing glucose level prediction of ICU patients through hierarchical modeling of irregular time-series28
In-silico proteomic analysis of the role of IL-4 and IL-10 in IVD degeneration: Protein-protein interaction networks for candidate prioritisation28
Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives28
Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases28
Post-processing enhances protein secondary structure prediction with second order deep learning and embeddings28
HIV infection detection using CRISPR/Cas systems: Present and future prospects27
Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation27
EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks27
Ion and water permeation through claudin-10b and claudin-15 paracellular channels27
Optimization of regulatory DNA with active learning27
Structure-based identification of HNF4α agonists: Rosmarinic acid as a promising candidate for NAFLD treatment27
Fantastic genes and where to find them expressed in CHO27
Analyzing the human gut mycobiome – A short guide for beginners27
Integrative geno-metabolomics of tenasserim turmeric (Curcuma candida (Wall.) Techapr. & Škorničk.) with insights into volatile biosynthesis across the turmeric genus27
Enhancing detection of epileptic seizures using transfer learning and EEG brain activity signals27
INSIGHT: An integrated framework for safe and sustainable chemical and material assessment26
Modeling approaches for probing cross-feeding interactions in the human gut microbiome26
Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies26
The potential of Real-Time volume-rendered 3D Imaging in immersive virtual-reality (VR) for surgical planning in infants with congenital thoracic malformation (CTM)26
BioLogical: a universal analysis framework for biosystem logical dynamics26
Population-scale genotyping of structural variation in the era of long-read sequencing25
Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins25
Reprogramming landscape highlighted by dynamic transcriptomes in therapy-induced neuroendocrine differentiation25
Targeted removal of mitochondrial DNA from mouse and human extrachromosomal circular DNA with CRISPR-Cas925
A novel deep learning method for large-scale analysis of bone marrow adiposity using UK Biobank Dixon MRI data25
Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis25
New insights empowered by single-cell sequencing: From neural crest to enteric nervous system25
Homologous cardiac calcium pump regulators phospholamban and sarcolipin adopt distinct oligomeric states in the membrane25
Histone variants and chromatin structure, update of advances25
CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction25
A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics25
Structural insights into apoptotic regulation of human Bfk as a novel Bcl-2 family member25
Easy-MODA: Simplifying standardised registration of scientific simulation workflows through MODA template guidelines powered by the Enalos Cloud Platform24
Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases24
Oxidative Stress-Driven Transcriptomic Remodeling in Human Astrocytes Reveals Network Signatures Associated with Neurodegenerative and Cardiovascular Processes24
TOAST: A novel method for identifying topologically associated domains based on graph auto-encoders and clustering24
MNNMDA: Predicting human microbe-disease association via a method to minimize matrix nuclear norm24
Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains24
Targeting non-structural proteins of Hepatitis C virus for predicting repurposed drugs using QSAR and machine learning approaches24
EpiCas-DL: Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning24
A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer24
Downregulation of ABLIM3 confers to the metastasis of neuroblastoma via regulating the cell adhesion molecules pathway24
New targets for the treatment of ulcerative colitis: Gut microbiota and its metabolites24
Evaluation of the impact of printing and embroidery parameters in the process of obtaining utility comfort sensors used in protective clothing dedicated to premature babies24
CNNSplice: Robust models for splice site prediction using convolutional neural networks24
Interplay of starch debranching enzyme and its inhibitor is mediated by Redox-Activated SPL transcription factor24
BioPrediction-RPI: Democratizing the prediction of interaction between non-coding RNA and protein with end-to-end machine learning23
Reference-based read clustering improves the de novo genome assembly of microbial strains23
Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation23
Structural and functional mapping of ars gene cluster in Deinococcus indicus DR123
Unleashing high content screening in hit detection – Benchmarking AI workflows including novelty detection23
Demystifying extrachromosomal DNA circles: Categories, biogenesis, and cancer therapeutics23
Overcoming the cognition-reality gap in robot-to-human handovers with anisotropic variable force guidance23
IBPred: A sequence-based predictor for identifying ion binding protein in phage23
Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life23
Binding modes of prothrombin cleavage site sequences to the factor Xa catalytic triad: Insights from atomistic simulations23
Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma23
Evaluation of protein descriptors in computer-aided rational protein engineering tasks and its application in property prediction in SARS-CoV-2 spike glycoprotein23
Shared and divergent contribution of vitamin A and oxytocin to the aetiology of autism spectrum disorder23
Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton23
Relative flux trade-offs and optimization of metabolic network functionalities23
Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins23
iKcr_CNN: A novel computational tool for imbalance classification of human nonhistone crotonylation sites based on convolutional neural networks with focal loss22
Non-coding antisense transcripts: fine regulation of gene expression in cancer22
Design, proof-of-concept of single robotic hair transplant mechanisms for both harvest and implant of hair grafts22
HELENA project: Driving innovation in high energy density Li-metal halide solid-state batteries for electric vehicles and aircrafts22
MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks22
Detection and prioritization of COVID-19 infected patients from CXR images: Analysis of AI-assisted diagnosis in clinical settings22
A method for analyzing the ERP associated with high frequency ANT DBS offset22
Data recovery methods for DNA storage based on fountain codes22
MACRAMÉ – Advanced characterisation methodologies to assess and predict the health and environmental risks of advanced materials22
Transcriptomic signatures associated with autoimmune thyroiditis in papillary thyroid carcinoma and cancer immunotherapy-induced thyroid dysfunction22
iResNetDM: An interpretable deep learning approach for four types of DNA methylation modification prediction22
Noninvasive detection and interpretation of gastrointestinal diseases by collaborative serum metabolite and magnetically controlled capsule endoscopy22
Family-wide analysis of integrin structures predicted by AlphaFold222
Prediction and validation of host-pathogen interactions by a versatile inference approach using Aspergillus fumigatus as a case study22
fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data22
ALDH2 as a potential stem cell-related biomarker in lung adenocarcinoma: Comprehensive multi-omics analysis22
CHIASMA: Advancing chemicals and materials safety and sustainability assessments through innovative integration of in vitro and in silico (new approach) methodologies22
MM-DRPNet: A multimodal dynamic radial partitioning network for enhanced protein–ligand binding affinity prediction22
A Nano Risk Governance Portal supporting risk governance of nanomaterials and nano-enabled products22
Deep learning frameworks for protein–protein interaction prediction21
Increased risk of arrhythmias, heart failure, and thrombosis in SARS-CoV-2 positive individuals persists at one year post-infection21
Metabolomic and lipidomic insights into the impact of Euglena gracilis-derived β-glucan supplementation on sow colostrum and milk composition21
Improving doublet cell removal efficiency through multiple algorithm runs21
Dynamics of spindle assembly and position checkpoints: Integrating molecular mechanisms with computational models21
Tevenvirinae phages encode a family of LSm-like fold proteins21
Osmolyte-induced protein stability changes explained by graph theory21
Low-calorie diet intervention ameliorates gut microbiota dysbiosis and metabolic changes in obese patients with type 2 diabetes under standard care21
Pathway-guided architectures for interpretable AI in biological research21
CPRCSdb: A comprehensive phenotype-associated single-cell transcriptomic database for human cancer21
SpatialPPIv2: Enhancing protein–protein interaction prediction through graph neural networks with protein language models21
Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231-luc-GFP cell line21
A potent nonapeptide inhibitor for the CXCL12/HMGB1 heterocomplex: A computational and experimental approach21
Deep learning based deconvolution methods: A systematic review21
Identifying the risk of Kawasaki disease based solely on routine blood test features through novel construction of machine learning models21
Quercetin: A promising drug candidate against the potential SARS-CoV-2-Spike mutants with high viral infectivity20
Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus20
Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review20
Machine learning for metabolic pathway optimization: A review20
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