Computational and Structural Biotechnology Journal

Article	Citations
Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA	197
Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking	196
An integrated protein structure fitness scoring approach for identifying native-like model structures	154
Agreement and disagreement in pediatric functional neurological symptom disorders: Comparing patient reported outcome measures (PROMs) and clinician assessments	130
Identification of (Z)-2-benzylidene-dihydroimidazothiazolone derivatives as tyrosinase inhibitors: Anti-melanogenic effects and in silico studies	123
NGS allele counts versus called genotypes for testing genetic association	122
Network-based prioritization of cancer biomarkers by phenotype-driven module detection and ranking	109
Biomarker discovery process at binomial decision point (2BDP): Analytical pipeline to construct biomarker panel	96
The second intracellular loop of the yeast Trk1 potassium transporter is involved in regulation of activity, and interaction with 14–3-3 proteins	93
Comprehensive exploration of JQ1 and GSK2801 targets in breast cancer using network pharmacology and molecular modeling approaches	85
MUG: A mutation overview of GPCR subfamily A17 receptors	79
Integrated metabolomics and network analysis reveal changes in lipid metabolisms of tripterygium glycosides tablets in rats with collagen-induced arthritis	77
Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus	69
WUREN: Whole-modal union representation for epitope prediction	67
Corrigendum to “Cryo-EM reveals architectural diversity in active rotavirus particles” [Comput. Struct. Biotechnol. J. 17 (2019) 1178–1183]	63
Free energy landscape of the PI3Kα C-terminal activation	60
Nextcast: A software suite to analyse and model toxicogenomics data	57
Artificial intelligence predictive system of individual survival rate for lung adenocarcinoma	57
DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data	55
EthnoHERBS: Harnessing traditional herbal knowledge for biodiversity conservation and innovative health solutions	55
Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes	54
In silico and in vitro approaches allow the identification of the Prosystemin molecular network	54
dsCellNet: A new computational tool to infer cell–cell communication networks in the developing and aging brain	54
Using molecular dynamics simulations to interrogate T cell receptor non-equilibrium kinetics	52
Predictive dynamic control accurately maps the design space for 2,3-butanediol production	50

Automated machine learning in nanotoxicity assessment: A comparative study of predictive model performance	50
Consistencies and contradictions in different polymer models of chromatin architecture	49
Prediction of protein-ligand binding affinity with deep learning	49
What remains from living cells in bacterial lysate-based cell-free systems	48
Multi-omics landscape and clinical significance of a SMAD4-driven immune signature: Implications for risk stratification and frontline therapies in pancreatic cancer	48
Entropy-extreme model for predicting the development of cyber epidemics at early stages	46
VTAM: A robust pipeline for validating metabarcoding data using controls	43
Towards accurate and efficient diagnoses in nephropathology: An AI-based approach for assessing kidney transplant rejection	43
Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application.	42
Advanced biokinetic and hydrodynamic modelling to support and optimize the design of full-scale high rate algal ponds	42
UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets	42
The balance between photosynthesis and respiration explains the niche differentiation between Crocosphaera and Cyanothece	42
Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview	41
A novel exosome-derived prognostic signature and risk stratification for breast cancer based on multi-omics and systematic biological heterogeneity	41
A drug repurposing method based on inhibition effect on gene regulatory network	40
Improved inter-residue contact prediction via a hybrid generative model and dynamic loss function	40
Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects	40
MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants	39
Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants	39
Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations	38
Deep5mC: Predicting 5-methylcytosine (5mC) methylation status using a deep learning transformer approach	38
cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery	37
Data pre-processing for analyzing microbiome data – A mini review	37
From sequence to function through structure: Deep learning for protein design	36
Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species	36
Predicting zeta potential of liposomes from their structure: A nano-QSPR model for DOPE, DC-Chol, DOTAP, and EPC formulations	36
DiabetesOmic: A comprehensive multi-omics diabetes database	35
Evolution is in the details: Regulatory differences in modern human and Neanderthal	35
Statistical methods for Mendelian randomization in genome-wide association studies: A review	35
ECGA: A web server to explore and analyze extrachromosomal gene in cancer	33
Cell segmentation and representation with shape priors	33
Prognostic iron-metabolism signature robustly stratifies single-cell characteristics of hepatocellular carcinoma	32
NaCTR: Natural product-derived compound-based drug discovery pipeline from traditional oriental medicine by search space reduction	32
Inference of essential genes in Brugia malayi and Onchocerca volvulus by machine learning and the implications for discovering new interventions	32
Identification of genetic basis of brain imaging by group sparse multi-task learning leveraging summary statistics	32
Pleiotropic expression quantitative trait loci are enriched in enhancers and transcription factor binding sites and impact more genes	32
Co-expression of immune checkpoints in glioblastoma revealed by single-nucleus RNA sequencing and spatial transcriptomics	31
Machine learning in metastatic cancer research: Potentials, possibilities, and prospects	31
Cat-E: A comprehensive web tool for exploring cancer targeting strategies	31
Scale bar of aging trajectories for screening personal rejuvenation treatments	30
PLO3S: Protein LOcal Surficial Similarity Screening	30
Multicopper oxidases with laccase-ferroxidase activity: Classification and study of ferroxidase activity determinants in a member from Heterobasidion annosum s. l.	30
Contagious infection-free medical interaction system with machine vision controlled by remote hand gesture during an operation	30
Dual guide RNA-mediated concurrent C&G-to-T&A and A&T-to-G&C conversions using CRISPR base editors	30
PS-GO parametric protein search engine	30
Empirical comparison and recent advances of computational prediction of hormone binding proteins using machine learning methods	30
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability	29
Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems	29
Literature-based translation from synthetic lethality screening into therapeutics targets: CD82 is a novel target for KRAS mutation in colon cancer	29
Performance of a HER2 testing algorithm tailored for urothelial bladder cancer: A Bi-centre study	29

Identifying novel SMYD3 interactors on the trail of cancer hallmarks	29
Population genomic analyses reveal evidence for limited recombination in the superbug Candida auris in nature	28
Bacillus subtilis spores displaying RBD domain of SARS-CoV-2 spike protein	28
Computational approaches in rheumatic diseases – Deciphering complex spatio-temporal cell interactions	28
Thresholding Gini variable importance with a single-trained random forest: An empirical Bayes approach	28
Survival estimation in patients with stomach and esophageal carcinoma using miRNA expression profiles	28
A cellulose-degrading Bacillus altitudinis from Tibetan pigs improved the in vitro fermentation characteristics of wheat bran	28
Impact of an irreversible β-galactosylceramidase inhibitor on the lipid profile of zebrafish embryos	28
Strengths and limitations of web servers for the modeling of TCRpMHC complexes	28
Protein design accelerates the development and application of optogenetic tools	28
The World of GPCR dimers – Mapping dopamine receptor D2 homodimers in different activation states and configuration arrangements	27
Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand	27
Over time analysis of the codon usage of SARS-CoV-2 and its variants	27
Computationally derived structural insights into Rare Earth selectivity in lanmodulin and its variants	27
YTLR: Extracting yeast transcription factor-gene associations from the literature using automated literature readers	27
Structural studies of protein–nucleic acid complexes: A brief overview of the selected techniques	27
Augusta: From RNA‐Seq to gene regulatory networks and Boolean models	26
Detecting differentially expressed circular RNAs from multiple quantification methods using a generalized linear mixed model	26
Corrigendum to “Coupling the endophytic microbiome with the host transcriptome in olive roots” [Comput. Struct. Biotechnol. J. 19 (2021) 4777–4789]	26
Mutation density analyses on long noncoding RNA reveal comparable patterns to protein-coding RNA and prognostic value	26
Prediction of HER2-positive breast cancer recurrence and metastasis risk from histopathological images and clinical information via multimodal deep learning	26
INSIGHT: An integrated framework for safe and sustainable chemical and material assessment	26
Drug repurposing in psoriasis, performed by reversal of disease-associated gene expression profiles	26
Beyond the Scalpel: Assessing ChatGPT's potential as an auxiliary intelligent virtual assistant in oral surgery	26
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	26
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein–protein interaction network through integrative methods	25
Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations	25
Short-chain fatty acids reprogram metabolic profiles with the induction of reactive oxygen species production in human colorectal adenocarcinoma cells	25
Interplay of starch debranching enzyme and its inhibitor is mediated by Redox-Activated SPL transcription factor	25
Population-scale genotyping of structural variation in the era of long-read sequencing	25
Machine learning reveals STAT motifs as predictors for GR-mediated gene repression	25
The discovery of hidden guanylate cyclases (GCs) in the Homo sapiens proteome	25
Analyzing the human gut mycobiome – A short guide for beginners	25
Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases	24
MSPJ: Discovering potential biomarkers in small gene expression datasets via ensemble learning	24
Structural insights into apoptotic regulation of human Bfk as a novel Bcl-2 family member	24
New insights empowered by single-cell sequencing: From neural crest to enteric nervous system	24
The seen and the unseen: Molecular classification and image based-analysis of gastrointestinal cancers	24
Role of Bmal1 in mediating the cholinergic system to regulate the behavioral rhythm of nocturnal marine molluscs	23
Concentration-dependent thermodynamic analysis of the partition process of small ligands into proteins	23
Corrigendum to “TREAT: Therapeutic RNAs exploration inspired by artificial intelligence technology” [Comput Struct Biotechnol J 20 (2022) 5680–5689]	23
Generic and queryable data integration schema for transcriptomics and epigenomics studies	23
Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis	23
Reprogramming landscape highlighted by dynamic transcriptomes in therapy-induced neuroendocrine differentiation	23
A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics	23
TRRAP-mediated acetylation on Sp1 regulates adult neurogenesis	23
Mysteries of gene regulation: Promoters are not the sole triggers of gene expression	23
Protposer: The web server that readily proposes protein stabilizing mutations with high PPV	23
PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics – catching the (un)usual suspects	23
Ion and water permeation through claudin-10b and claudin-15 paracellular channels	22
HELLS modulates the stemness of intrahepatic cholangiocarcinoma through promoting senescence-associated secretory phenotype	22
Optimizing fountain codes for DNA data storage	22
Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains	22
Targeted removal of mitochondrial DNA from mouse and human extrachromosomal circular DNA with CRISPR-Cas9	22
Deep learning of antibody epitopes using positional permutation vectors	22
In-silico proteomic analysis of the role of IL-4 and IL-10 in IVD degeneration: Protein-protein interaction networks for candidate prioritisation	22
Downregulation of ABLIM3 confers to the metastasis of neuroblastoma via regulating the cell adhesion molecules pathway	22
Structure-based identification of HNF4α agonists: Rosmarinic acid as a promising candidate for NAFLD treatment	21
scDemultiplex: An iterative beta-binomial model-based method for accurate demultiplexing with hashtag oligos	21
Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives	21
EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks	21
Claudin-10b cation channels in tight junction strands: Octameric-interlocked pore barrels constitute paracellular channels with low water permeability	21
Targeting non-structural proteins of Hepatitis C virus for predicting repurposed drugs using QSAR and machine learning approaches	21
Fantastic genes and where to find them expressed in CHO	21
New targets for the treatment of ulcerative colitis: Gut microbiota and its metabolites	20
Easy-MODA: Simplifying standardised registration of scientific simulation workflows through MODA template guidelines powered by the Enalos Cloud Platform	20
CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction	20
Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases	20
A novel deep learning method for large-scale analysis of bone marrow adiposity using UK Biobank Dixon MRI data	20
Comparative analysis of amino acid auxotrophies and peptidase profiles in non-dysbiotic and dysbiotic small intestinal microbiomes	20
Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies	20
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 variants	20
Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation	20
Post-processing enhances protein secondary structure prediction with second order deep learning and embeddings	20
Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR-amplified glioblastoma	19
Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism	19
Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins	19
Overcoming the cognition-reality gap in robot-to-human handovers with anisotropic variable force guidance	19
MNNMDA: Predicting human microbe-disease association via a method to minimize matrix nuclear norm	19
Modeling approaches for probing cross-feeding interactions in the human gut microbiome	19

EpiCas-DL: Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning	19
HIV infection detection using CRISPR/Cas systems: Present and future prospects	19
Homologous cardiac calcium pump regulators phospholamban and sarcolipin adopt distinct oligomeric states in the membrane	19
Evaluation of protein descriptors in computer-aided rational protein engineering tasks and its application in property prediction in SARS-CoV-2 spike glycoprotein	19
SPARC: Structural properties associated with residue constraints	19
The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations	19
Histone variants and chromatin structure, update of advances	19
A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis	19
CNNSplice: Robust models for splice site prediction using convolutional neural networks	19
Design, proof-of-concept of single robotic hair transplant mechanisms for both harvest and implant of hair grafts	18
Shared and divergent contribution of vitamin A and oxytocin to the aetiology of autism spectrum disorder	18
Transcriptomic signatures associated with autoimmune thyroiditis in papillary thyroid carcinoma and cancer immunotherapy-induced thyroid dysfunction	18
How to describe the time-dependent dissolution of engineered nanomaterials?	18
Data recovery methods for DNA storage based on fountain codes	18
Demystifying extrachromosomal DNA circles: Categories, biogenesis, and cancer therapeutics	18
Detection and prioritization of COVID-19 infected patients from CXR images: Analysis of AI-assisted diagnosis in clinical settings	18
MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks	18
fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data	18
MM-DRPNet: A multimodal dynamic radial partitioning network for enhanced protein–ligand binding affinity prediction	18
Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation	18
Prediction and validation of host-pathogen interactions by a versatile inference approach using Aspergillus fumigatus as a case study	18
Reference-based read clustering improves the de novo genome assembly of microbial strains	18
Binding modes of prothrombin cleavage site sequences to the factor Xa catalytic triad: Insights from atomistic simulations	18
Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1	18
MACRAMÉ – Advanced characterisation methodologies to assess and predict the health and environmental risks of advanced materials	18
A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer	18
TOAST: A novel method for identifying topologically associated domains based on graph auto-encoders and clustering	18
Relative flux trade-offs and optimization of metabolic network functionalities	18
Unleashing high content screening in hit detection – Benchmarking AI workflows including novelty detection	17
Quercetin: A promising drug candidate against the potential SARS-CoV-2-Spike mutants with high viral infectivity	17
ALDH2 as a potential stem cell-related biomarker in lung adenocarcinoma: Comprehensive multi-omics analysis	17
Computational design of α-amylase from Bacillus licheniformis to increase its activity and stability at high temperatures	17
SpatialPPIv2: Enhancing protein–protein interaction prediction through graph neural networks with protein language models	17
Establishment and validation of a cholesterol metabolism-related prognostic signature for hepatocellular carcinoma	17
Family-wide analysis of integrin structures predicted by AlphaFold2	17
IBPred: A sequence-based predictor for identifying ion binding protein in phage	17
BioPrediction-RPI: Democratizing the prediction of interaction between non-coding RNA and protein with end-to-end machine learning	17
Starch granules and their size distribution in wheat: Biosynthesis, physicochemical properties and their effect on flour-based food systems	17
Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins	17
Deep learning frameworks for protein–protein interaction prediction	17
Determining key residues of engineered scFv antibody variants with improved MMP-9 binding using deep sequencing and machine learning	17
Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma	17
Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life	17
iResNetDM: An interpretable deep learning approach for four types of DNA methylation modification prediction	17
Deciphering mitochondrial dysfunction in keratoconus: Insights into ACSL4 from machine learning-based bulk and single-cell transcriptome analyses and experimental validation	17
Osmolyte-induced protein stability changes explained by graph theory	17
Non-coding antisense transcripts: fine regulation of gene expression in cancer	16
Artificial intelligence-large language models (AI-LLMs) for reliable and accurate cardiotocography (CTG) interpretation in obstetric practice	16
Dynamics of spindle assembly and position checkpoints: Integrating molecular mechanisms with computational models	16
Cluster parameter-based DBSCAN maps for image characterization	16
A potent nonapeptide inhibitor for the CXCL12/HMGB1 heterocomplex: A computational and experimental approach	16
iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data	16
HELENA project: Driving innovation in high energy density Li-metal halide solid-state batteries for electric vehicles and aircrafts	16
Improving doublet cell removal efficiency through multiple algorithm runs	16
Tevenvirinae phages encode a family of LSm-like fold proteins	16
Metabolomic and lipidomic insights into the impact of Euglena gracilis-derived β-glucan supplementation on sow colostrum and milk composition	16
RNA secondary structure prediction by conducting multi-class classifications	16
Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton	16
LncCat: An ORF attention model to identify LncRNA based on ensemble learning strategy and fused sequence information	15
Discovery of a new generation of angiotensin receptor blocking drugs: Receptor mechanisms and in silico binding to enzymes relevant to SARS-CoV-2	15
SCInter: A comprehensive single-cell transcriptome integration database for human and mouse	15
Machine learning for metabolic pathway optimization: A review	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
Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin	15
The natural product biosynthesis potential of the microbiomes of Earth – Bioprospecting for novel anti-microbial agents in the meta-omics era	15
An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus	15
A novel cathelicidin TS-CATH derived from Thamnophis sirtalis combats drug-resistant gram-negative bacteria in vitro and in vivo	15
The optimal metric for viral genome space	15
The nucleotide landscape of polyXY regions	15
AmiCa: Atlas of miRNA-gene correlations in cancer	15
iKcr_CNN: A novel computational tool for imbalance classification of human nonhistone crotonylation sites based on convolutional neural networks with focal loss	15
Noninvasive detection and interpretation of gastrointestinal diseases by collaborative serum metabolite and magnetically controlled capsule endoscopy	15
Investigating how HIV-1 antiretrovirals differentially behave as substrates and inhibitors of P-glycoprotein via molecular dynamics simulations	15
Spontaneous regeneration of cholecystokinergic reticulospinal axons after a complete spinal cord injury in sea lampreys	15
Modeling omics dose-response at the pathway level with DoseRider	15
Systematic screening and dynamic profiling of germline regulatory pathways and spermatogonial surface markers in a bivalve mollusc	15
VarMeter2: An enhanced structure-based method for predicting pathogenic missense variants through Mahalanobis distance	15
Analysis of the galactomannan binding ability of β-mannosidases, BtMan2A and CmMan5A, regarding their activity and synergism with a β-mannanase	15
Liquid-liquid phase separation in hair cell stereocilia development and maintenance	15
Conserved FimH mutations in the global Escherichia coli ST131 multi-drug resistant lineage weaken interdomain interactions and alter adhesin function	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
Interspecific and intraspecific Taylor's laws for frog skin microbes	15
Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review	15
Increased risk of arrhythmias, heart failure, and thrombosis in SARS-CoV-2 positive individuals persists at one year post-infection	15
Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus	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
Accurate protein stability predictions from homology models	15
Kinase-substrate prediction using an autoregressive model	15
Plasticity of BioPhi-driven humanness optimization in ScFv-CD99 binding affinity validated through AlphaFold, HADDOCK, and MD simulations	15
Microorganisms in the reproductive system and probiotic's regulatory effects on reproductive health	15
Unlocking the specificity of antimicrobial peptide interactions for membrane-targeted therapies	15
Single-cell 5′ RNA sequencing of camelid peripheral B cells provides insights into cellular basis of heavy-chain antibody production	15
Breast MRI radiomics and machine learning-based predictions of response to neoadjuvant chemotherapy – How are they affected by variations in tumor delineation?	15
An evaluation of homeostatic plasticity for ecosystems using an analytical data science approach	15