Computational and Structural Biotechnology Journal

Article	Citations
Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA	187
Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking	179
An integrated protein structure fitness scoring approach for identifying native-like model structures	149
Identification of (Z)-2-benzylidene-dihydroimidazothiazolone derivatives as tyrosinase inhibitors: Anti-melanogenic effects and in silico studies	119
Agreement and disagreement in pediatric functional neurological symptom disorders: Comparing patient reported outcome measures (PROMs) and clinician assessments	119
NGS allele counts versus called genotypes for testing genetic association	114
Network-based prioritization of cancer biomarkers by phenotype-driven module detection and ranking	102
Biomarker discovery process at binomial decision point (2BDP): Analytical pipeline to construct biomarker panel	92
The second intracellular loop of the yeast Trk1 potassium transporter is involved in regulation of activity, and interaction with 14–3-3 proteins	88
Comprehensive exploration of JQ1 and GSK2801 targets in breast cancer using network pharmacology and molecular modeling approaches	83
MUG: A mutation overview of GPCR subfamily A17 receptors	76
Integrated metabolomics and network analysis reveal changes in lipid metabolisms of tripterygium glycosides tablets in rats with collagen-induced arthritis	70
cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery	68
Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus	64
WUREN: Whole-modal union representation for epitope prediction	63
Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application.	56
Corrigendum to “Cryo-EM reveals architectural diversity in active rotavirus particles” [Comput. Struct. Biotechnol. J. 17 (2019) 1178–1183]	55
Free energy landscape of the PI3Kα C-terminal activation	54
Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects	54
VTAM: A robust pipeline for validating metabarcoding data using controls	53
Entropy-extreme model for predicting the development of cyber epidemics at early stages	53
The balance between photosynthesis and respiration explains the niche differentiation between Crocosphaera and Cyanothece	50
Artificial intelligence predictive system of individual survival rate for lung adenocarcinoma	50
DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data	49
Nextcast: A software suite to analyse and model toxicogenomics data	49

Predicting zeta potential of liposomes from their structure: A nano-QSPR model for DOPE, DC-Chol, DOTAP, and EPC formulations	48
EthnoHERBS: Harnessing traditional herbal knowledge for biodiversity conservation and innovative health solutions	48
In silico and in vitro approaches allow the identification of the Prosystemin molecular network	48
Multi-omics landscape and clinical significance of a SMAD4-driven immune signature: Implications for risk stratification and frontline therapies in pancreatic cancer	47
Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes	46
Advanced biokinetic and hydrodynamic modelling to support and optimize the design of full-scale high rate algal ponds	43
Improved inter-residue contact prediction via a hybrid generative model and dynamic loss function	42
dsCellNet: A new computational tool to infer cell–cell communication networks in the developing and aging brain	41
A novel exosome-derived prognostic signature and risk stratification for breast cancer based on multi-omics and systematic biological heterogeneity	40
Using molecular dynamics simulations to interrogate T cell receptor non-equilibrium kinetics	40
Data pre-processing for analyzing microbiome data – A mini review	39
Predictive dynamic control accurately maps the design space for 2,3-butanediol production	39
A drug repurposing method based on inhibition effect on gene regulatory network	39
Deep5mC: Predicting 5-methylcytosine (5mC) methylation status using a deep learning transformer approach	38
Automated machine learning in nanotoxicity assessment: A comparative study of predictive model performance	38
MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants	38
What remains from living cells in bacterial lysate-based cell-free systems	37
Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations	37
Prediction of protein-ligand binding affinity with deep learning	37
Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants	37
Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview	36
From sequence to function through structure: Deep learning for protein design	36
UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets	36
Consistencies and contradictions in different polymer models of chromatin architecture	35
Towards accurate and efficient diagnoses in nephropathology: An AI-based approach for assessing kidney transplant rejection	35
Cell segmentation and representation with shape priors	33
Statistical methods for Mendelian randomization in genome-wide association studies: A review	33
NaCTR: Natural product-derived compound-based drug discovery pipeline from traditional oriental medicine by search space reduction	32
ECGA: A web server to explore and analyze extrachromosomal gene in cancer	32
Pleiotropic expression quantitative trait loci are enriched in enhancers and transcription factor binding sites and impact more genes	32
Inference of essential genes in Brugia malayi and Onchocerca volvulus by machine learning and the implications for discovering new interventions	31
Identification of genetic basis of brain imaging by group sparse multi-task learning leveraging summary statistics	31
Prognostic iron-metabolism signature robustly stratifies single-cell characteristics of hepatocellular carcinoma	31
Cat-E: A comprehensive web tool for exploring cancer targeting strategies	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	29
Machine learning in metastatic cancer research: Potentials, possibilities, and prospects	29
Mutation density analyses on long noncoding RNA reveal comparable patterns to protein-coding RNA and prognostic value	29
Co-expression of immune checkpoints in glioblastoma revealed by single-nucleus RNA sequencing and spatial transcriptomics	29
Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand	29
PS-GO parametric protein search engine	29
Contagious infection-free medical interaction system with machine vision controlled by remote hand gesture during an operation	28
Computational approaches in rheumatic diseases – Deciphering complex spatio-temporal cell interactions	28
Empirical comparison and recent advances of computational prediction of hormone binding proteins using machine learning methods	28
PLO3S: Protein LOcal Surficial Similarity Screening	28
Computationally derived structural insights into Rare Earth selectivity in lanmodulin and its variants	28
A cellulose-degrading Bacillus altitudinis from Tibetan pigs improved the in vitro fermentation characteristics of wheat bran	28
The World of GPCR dimers – Mapping dopamine receptor D2 homodimers in different activation states and configuration arrangements	28
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability	27
Identifying novel SMYD3 interactors on the trail of cancer hallmarks	27

Performance of a HER2 testing algorithm tailored for urothelial bladder cancer: A Bi-centre study	27
YTLR: Extracting yeast transcription factor-gene associations from the literature using automated literature readers	27
Literature-based translation from synthetic lethality screening into therapeutics targets: CD82 is a novel target for KRAS mutation in colon cancer	27
Multicopper oxidases with laccase-ferroxidase activity: Classification and study of ferroxidase activity determinants in a member from Heterobasidion annosum s. l.	27
Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems	27
Scale bar of aging trajectories for screening personal rejuvenation treatments	27
Drug repurposing in psoriasis, performed by reversal of disease-associated gene expression profiles	26
Thresholding Gini variable importance with a single-trained random forest: An empirical Bayes approach	26
Bacillus subtilis spores displaying RBD domain of SARS-CoV-2 spike protein	26
Population genomic analyses reveal evidence for limited recombination in the superbug Candida auris in nature	25
Machine learning reveals STAT motifs as predictors for GR-mediated gene repression	25
Survival estimation in patients with stomach and esophageal carcinoma using miRNA expression profiles	25
Beyond the Scalpel: Assessing ChatGPT's potential as an auxiliary intelligent virtual assistant in oral surgery	25
Protein design accelerates the development and application of optogenetic tools	25
Structural studies of protein–nucleic acid complexes: A brief overview of the selected techniques	25
Impact of an irreversible β-galactosylceramidase inhibitor on the lipid profile of zebrafish embryos	25
Strengths and limitations of web servers for the modeling of TCRpMHC complexes	25
Prediction of HER2-positive breast cancer recurrence and metastasis risk from histopathological images and clinical information via multimodal deep learning	25
Short-chain fatty acids reprogram metabolic profiles with the induction of reactive oxygen species production in human colorectal adenocarcinoma cells	24
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	24
Corrigendum to “Coupling the endophytic microbiome with the host transcriptome in olive roots” [Comput. Struct. Biotechnol. J. 19 (2021) 4777–4789]	24
INSIGHT: An integrated framework for safe and sustainable chemical and material assessment	24
HELLS modulates the stemness of intrahepatic cholangiocarcinoma through promoting senescence-associated secretory phenotype	24
Analyzing the human gut mycobiome – A short guide for beginners	24
Detecting differentially expressed circular RNAs from multiple quantification methods using a generalized linear mixed model	24
Claudin-10b cation channels in tight junction strands: Octameric-interlocked pore barrels constitute paracellular channels with low water permeability	24
Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins	24
Population-scale genotyping of structural variation in the era of long-read sequencing	24
EpiCas-DL: Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning	24
scDemultiplex: An iterative beta-binomial model-based method for accurate demultiplexing with hashtag oligos	24
Easy-MODA: Simplifying standardised registration of scientific simulation workflows through MODA template guidelines powered by the Enalos Cloud Platform	23
Structure-based identification of HNF4α agonists: Rosmarinic acid as a promising candidate for NAFLD treatment	23
EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks	23
MNNMDA: Predicting human microbe-disease association via a method to minimize matrix nuclear norm	23
In-silico proteomic analysis of the role of IL-4 and IL-10 in IVD degeneration: Protein-protein interaction networks for candidate prioritisation	23
Comparative analysis of amino acid auxotrophies and peptidase profiles in non-dysbiotic and dysbiotic small intestinal microbiomes	23
Interplay of starch debranching enzyme and its inhibitor is mediated by Redox-Activated SPL transcription factor	23
Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR-amplified glioblastoma	22
Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases	22
Post-processing enhances protein secondary structure prediction with second order deep learning and embeddings	22
Histone variants and chromatin structure, update of advances	22
Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases	22
Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation	22
HIV infection detection using CRISPR/Cas systems: Present and future prospects	22
Fantastic genes and where to find them expressed in CHO	22
A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis	21
MSPJ: Discovering potential biomarkers in small gene expression datasets via ensemble learning	21
SPARC: Structural properties associated with residue constraints	21
Role of Bmal1 in mediating the cholinergic system to regulate the behavioral rhythm of nocturnal marine molluscs	21
The seen and the unseen: Molecular classification and image based-analysis of gastrointestinal cancers	21
Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations	21
New insights empowered by single-cell sequencing: From neural crest to enteric nervous system	21
Structural insights into apoptotic regulation of human Bfk as a novel Bcl-2 family member	21
Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives	21
Reprogramming landscape highlighted by dynamic transcriptomes in therapy-induced neuroendocrine differentiation	20
The discovery of hidden guanylate cyclases (GCs) in the Homo sapiens proteome	20
Mysteries of gene regulation: Promoters are not the sole triggers of gene expression	20
Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis	20
CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction	20
Concentration-dependent thermodynamic analysis of the partition process of small ligands into proteins	20
The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations	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	19
TRRAP-mediated acetylation on Sp1 regulates adult neurogenesis	19
Modeling approaches for probing cross-feeding interactions in the human gut microbiome	19
PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics – catching the (un)usual suspects	19
Ion and water permeation through claudin-10b and claudin-15 paracellular channels	19
Targeting non-structural proteins of Hepatitis C virus for predicting repurposed drugs using QSAR and machine learning approaches	19
Protposer: The web server that readily proposes protein stabilizing mutations with high PPV	19
Corrigendum to “TREAT: Therapeutic RNAs exploration inspired by artificial intelligence technology” [Comput Struct Biotechnol J 20 (2022) 5680–5689]	19
Homologous cardiac calcium pump regulators phospholamban and sarcolipin adopt distinct oligomeric states in the membrane	19
Generic and queryable data integration schema for transcriptomics and epigenomics studies	19
Optimizing fountain codes for DNA data storage	19
Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism	19
A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics	19
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein–protein interaction network through integrative methods	19
Deep learning of antibody epitopes using positional permutation vectors	19
Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains	19
Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus	18
Design, proof-of-concept of single robotic hair transplant mechanisms for both harvest and implant of hair grafts	18
Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life	18

Targeted removal of mitochondrial DNA from mouse and human extrachromosomal circular DNA with CRISPR-Cas9	18
Evaluation of protein descriptors in computer-aided rational protein engineering tasks and its application in property prediction in SARS-CoV-2 spike glycoprotein	18
Detection and prioritization of COVID-19 infected patients from CXR images: Analysis of AI-assisted diagnosis in clinical settings	18
Reference-based read clustering improves the de novo genome assembly of microbial strains	18
Downregulation of ABLIM3 confers to the metastasis of neuroblastoma via regulating the cell adhesion molecules pathway	18
A novel deep learning method for large-scale analysis of bone marrow adiposity using UK Biobank Dixon MRI data	18
Overcoming the cognition-reality gap in robot-to-human handovers with anisotropic variable force guidance	18
MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks	18
CNNSplice: Robust models for splice site prediction using convolutional neural networks	18
Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies	18
Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1	17
Prediction and validation of host-pathogen interactions by a versatile inference approach using Aspergillus fumigatus as a case study	17
iResNetDM: An interpretable deep learning approach for four types of DNA methylation modification prediction	17
Data recovery methods for DNA storage based on fountain codes	17
fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data	17
Machine learning for metabolic pathway optimization: A review	17
Binding modes of prothrombin cleavage site sequences to the factor Xa catalytic triad: Insights from atomistic simulations	17
TOAST: A novel method for identifying topologically associated domains based on graph auto-encoders and clustering	17
A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer	17
Relative flux trade-offs and optimization of metabolic network functionalities	17
Demystifying extrachromosomal DNA circles: Categories, biogenesis, and cancer therapeutics	17
Shared and divergent contribution of vitamin A and oxytocin to the aetiology of autism spectrum disorder	17
Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation	17
MM-DRPNet: A multimodal dynamic radial partitioning network for enhanced protein–ligand binding affinity prediction	17
Computational design of α-amylase from Bacillus licheniformis to increase its activity and stability at high temperatures	16
Discovery of a new generation of angiotensin receptor blocking drugs: Receptor mechanisms and in silico binding to enzymes relevant to SARS-CoV-2	16
Noninvasive detection and interpretation of gastrointestinal diseases by collaborative serum metabolite and magnetically controlled capsule endoscopy	16
Increased risk of arrhythmias, heart failure, and thrombosis in SARS-CoV-2 positive individuals persists at one year post-infection	16
Metabolomic and lipidomic insights into the impact of Euglena gracilis-derived β-glucan supplementation on sow colostrum and milk composition	16
Dynamics of spindle assembly and position checkpoints: Integrating molecular mechanisms with computational models	16
MACRAMÉ – Advanced characterisation methodologies to assess and predict the health and environmental risks of advanced materials	16
Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins	16
Transcriptomic signatures associated with autoimmune thyroiditis in papillary thyroid carcinoma and cancer immunotherapy-induced thyroid dysfunction	16
RNA secondary structure prediction by conducting multi-class classifications	16
Improving doublet cell removal efficiency through multiple algorithm runs	16
Cluster parameter-based DBSCAN maps for image characterization	16
Osmolyte-induced protein stability changes explained by graph theory	16
Non-coding antisense transcripts: fine regulation of gene expression in cancer	16
HELENA project: Driving innovation in high energy density Li-metal halide solid-state batteries for electric vehicles and aircrafts	16
Starch granules and their size distribution in wheat: Biosynthesis, physicochemical properties and their effect on flour-based food systems	16
Artificial intelligence-large language models (AI-LLMs) for reliable and accurate cardiotocography (CTG) interpretation in obstetric practice	16
How to describe the time-dependent dissolution of engineered nanomaterials?	16
IBPred: A sequence-based predictor for identifying ion binding protein in phage	15
Establishment and validation of a cholesterol metabolism-related prognostic signature for hepatocellular carcinoma	15
A potent nonapeptide inhibitor for the CXCL12/HMGB1 heterocomplex: A computational and experimental approach	15
Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma	15
Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review	15
AmiCa: Atlas of miRNA-gene correlations in cancer	15
SCInter: A comprehensive single-cell transcriptome integration database for human and mouse	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
Integrating whole genome sequencing, methylation, gene expression, topologically associated domain information in regulatory mutation prediction: A study of follicular lymphoma	15
Deep learning frameworks for protein–protein interaction prediction	15
Family-wide analysis of integrin structures predicted by AlphaFold2	15
Quercetin: A promising drug candidate against the potential SARS-CoV-2-Spike mutants with high viral infectivity	15
SpatialPPIv2: Enhancing protein–protein interaction prediction through graph neural networks with protein language models	15
Determining key residues of engineered scFv antibody variants with improved MMP-9 binding using deep sequencing and machine learning	15
iKcr_CNN: A novel computational tool for imbalance classification of human nonhistone crotonylation sites based on convolutional neural networks with focal loss	15
Spontaneous regeneration of cholecystokinergic reticulospinal axons after a complete spinal cord injury in sea lampreys	15
The optimal metric for viral genome space	15
Single-cell 5′ RNA sequencing of camelid peripheral B cells provides insights into cellular basis of heavy-chain antibody production	15
Analysis of the galactomannan binding ability of β-mannosidases, BtMan2A and CmMan5A, regarding their activity and synergism with a β-mannanase	15
An evaluation of homeostatic plasticity for ecosystems using an analytical data science approach	15
ALDH2 as a potential stem cell-related biomarker in lung adenocarcinoma: Comprehensive multi-omics analysis	15
Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton	15
BioPrediction-RPI: Democratizing the prediction of interaction between non-coding RNA and protein with end-to-end machine learning	15
Unleashing high content screening in hit detection – Benchmarking AI workflows including novelty detection	15
iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data	15
Assessing the effect of selective serotonin reuptake inhibitors in the prevention of post-acute sequelae of COVID-19	15
Investigating how HIV-1 antiretrovirals differentially behave as substrates and inhibitors of P-glycoprotein via molecular dynamics simulations	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
The nucleotide landscape of polyXY regions	15
LncCat: An ORF attention model to identify LncRNA based on ensemble learning strategy and fused sequence information	15
The natural product biosynthesis potential of the microbiomes of Earth – Bioprospecting for novel anti-microbial agents in the meta-omics era	14
Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin	14
Unlocking the specificity of antimicrobial peptide interactions for membrane-targeted therapies	14
Conserved FimH mutations in the global Escherichia coli ST131 multi-drug resistant lineage weaken interdomain interactions and alter adhesin function	14
Systematic screening and dynamic profiling of germline regulatory pathways and spermatogonial surface markers in a bivalve mollusc	14
GENI: A web server to identify gene set enrichments in tumor samples	14
Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics	14
Breast MRI radiomics and machine learning-based predictions of response to neoadjuvant chemotherapy – How are they affected by variations in tumor delineation?	14
VarMeter2: An enhanced structure-based method for predicting pathogenic missense variants through Mahalanobis distance	14
Microorganisms in the reproductive system and probiotic's regulatory effects on reproductive health	14
Liquid-liquid phase separation in hair cell stereocilia development and maintenance	14
Interactions between gut microbes and NLRP3 inflammasome in the gut-brain axis	14
Accurate protein stability predictions from homology models	14
An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus	14
SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information	14
Kinase-substrate prediction using an autoregressive model	14
Modeling omics dose-response at the pathway level with DoseRider	14
Comprehensive analysis of circulating cell-free RNAs in blood for diagnosing non-small cell lung cancer	14
3D chromatin structure changes during spermatogenesis and oogenesis	14
Random survival forest model identifies novel biomarkers of event-free survival in high-risk pediatric acute lymphoblastic leukemia	14
Multidimensional morphological analysis of live sperm based on multiple-target tracking	14
A novel cathelicidin TS-CATH derived from Thamnophis sirtalis combats drug-resistant gram-negative bacteria in vitro and in vivo	14