Computational and Structural Biotechnology Journal

Papers
(The TQCC of Computational and Structural Biotechnology Journal is 9. 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 2021-09-01 to 2025-09-01.)
ArticleCitations
Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA240
An integrated protein structure fitness scoring approach for identifying native-like model structures220
NGS allele counts versus called genotypes for testing genetic association170
The second intracellular loop of the yeast Trk1 potassium transporter is involved in regulation of activity, and interaction with 14–3-3 proteins147
Integrated metabolomics and network analysis reveal changes in lipid metabolisms of tripterygium glycosides tablets in rats with collagen-induced arthritis138
Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus138
WUREN: Whole-modal union representation for epitope prediction123
Corrigendum to “Cryo-EM reveals architectural diversity in active rotavirus particles” [Comput. Struct. Biotechnol. J. 17 (2019) 1178–1183]110
Nextcast: A software suite to analyse and model toxicogenomics data105
Comprehensive exploration of JQ1 and GSK2801 targets in breast cancer using network pharmacology and molecular modeling approaches96
Agreement and disagreement in pediatric functional neurological symptom disorders: Comparing patient reported outcome measures (PROMs) and clinician assessments89
A drug repurposing method based on inhibition effect on gene regulatory network85
Network-based prioritization of cancer biomarkers by phenotype-driven module detection and ranking77
Artificial intelligence predictive system of individual survival rate for lung adenocarcinoma75
Consistencies and contradictions in different polymer models of chromatin architecture72
Entropy-extreme model for predicting the development of cyber epidemics at early stages68
MUG: A mutation overview of GPCR subfamily A17 receptors66
Advanced biokinetic and hydrodynamic modelling to support and optimize the design of full-scale high rate algal ponds63
DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data60
Towards accurate and efficient diagnoses in nephropathology: An AI-based approach for assessing kidney transplant rejection59
Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview59
What remains from living cells in bacterial lysate-based cell-free systems59
The balance between photosynthesis and respiration explains the niche differentiation between Crocosphaera and Cyanothece59
Free energy landscape of the PI3Kα C-terminal activation59
Improved inter-residue contact prediction via a hybrid generative model and dynamic loss function58
Biomarker discovery process at binomial decision point (2BDP): Analytical pipeline to construct biomarker panel58
dsCellNet: A new computational tool to infer cell–cell communication networks in the developing and aging brain56
Identification of (Z)-2-benzylidene-dihydroimidazothiazolone derivatives as tyrosinase inhibitors: Anti-melanogenic effects and in silico studies55
Predictive dynamic control accurately maps the design space for 2,3-butanediol production55
VTAM: A robust pipeline for validating metabarcoding data using controls53
Using molecular dynamics simulations to interrogate T cell receptor non-equilibrium kinetics51
Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application.51
Data pre-processing for analyzing microbiome data – A mini review49
In silico and in vitro approaches allow the identification of the Prosystemin molecular network49
Multi-omics landscape and clinical significance of a SMAD4-driven immune signature: Implications for risk stratification and frontline therapies in pancreatic cancer49
EthnoHERBS: Harnessing traditional herbal knowledge for biodiversity conservation and innovative health solutions47
Towards predicting implant-induced fibrosis: A standardized network model of macrophage-fibroblast interactions47
Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects47
Predicting cellular adaptation proteins dependent on eIF2α regulation under stress conditions: Physiological and pathophysiological implications in neuronal function47
Evolution is in the details: Regulatory differences in modern human and Neanderthal46
Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations46
Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants46
DiabetesOmic: A comprehensive multi-omics diabetes database45
Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species44
Ranking pre-trained speech embeddings in Parkinson's disease detection: Does Wav2Vec 2.0 outperform its 1.0 version across speech modes and languages?44
MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants44
Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking44
Deep5mC: Predicting 5-methylcytosine (5mC) methylation status using a deep learning transformer approach44
A novel exosome-derived prognostic signature and risk stratification for breast cancer based on multi-omics and systematic biological heterogeneity43
Automated machine learning in nanotoxicity assessment: A comparative study of predictive model performance43
The influence of HIV sense and antisense transcripts on stochastic HIV transcription and reactivation42
From sequence to function through structure: Deep learning for protein design41
Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes41
CKATool: A Clinical Kinematic Analysis Toolbox for Upper Limb Rehabilitation40
cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery40
UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets40
Cell segmentation and representation with shape priors39
Prediction of protein-ligand binding affinity with deep learning39
Statistical methods for Mendelian randomization in genome-wide association studies: A review38
Predicting zeta potential of liposomes from their structure: A nano-QSPR model for DOPE, DC-Chol, DOTAP, and EPC formulations37
Identification of genetic basis of brain imaging by group sparse multi-task learning leveraging summary statistics37
Inference of essential genes in Brugia malayi and Onchocerca volvulus by machine learning and the implications for discovering new interventions37
NaCTR: Natural product-derived compound-based drug discovery pipeline from traditional oriental medicine by search space reduction37
Contagious infection-free medical interaction system with machine vision controlled by remote hand gesture during an operation36
Cat-E: A comprehensive web tool for exploring cancer targeting strategies36
PS-GO parametric protein search engine35
ECGA: A web server to explore and analyze extrachromosomal gene in cancer35
Scale bar of aging trajectories for screening personal rejuvenation treatments35
Prognostic iron-metabolism signature robustly stratifies single-cell characteristics of hepatocellular carcinoma34
Strengths and limitations of web servers for the modeling of TCRpMHC complexes34
Bacillus subtilis spores displaying RBD domain of SARS-CoV-2 spike protein34
The World of GPCR dimers – Mapping dopamine receptor D2 homodimers in different activation states and configuration arrangements34
Mutation density analyses on long noncoding RNA reveal comparable patterns to protein-coding RNA and prognostic value33
Population genomic analyses reveal evidence for limited recombination in the superbug Candida auris in nature33
YTLR: Extracting yeast transcription factor-gene associations from the literature using automated literature readers33
SbD4Skin by EosCloud: Integrating multi-view molecular representation for predicting skin sensitization, irritation, and acute dermal toxicity33
Pleiotropic expression quantitative trait loci are enriched in enhancers and transcription factor binding sites and impact more genes33
Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand33
A cellulose-degrading Bacillus altitudinis from Tibetan pigs improved the in vitro fermentation characteristics of wheat bran32
Augusta: From RNA‐Seq to gene regulatory networks and Boolean models32
PCLDA: An interpretable cell annotation tool for single-cell RNA-sequencing data based on simple statistical methods32
Computational approaches in rheumatic diseases – Deciphering complex spatio-temporal cell interactions32
Literature-based translation from synthetic lethality screening into therapeutics targets: CD82 is a novel target for KRAS mutation in colon cancer31
PLO3S: Protein LOcal Surficial Similarity Screening31
Identifying novel SMYD3 interactors on the trail of cancer hallmarks31
Performance of a HER2 testing algorithm tailored for urothelial bladder cancer: A Bi-centre study31
Drug repurposing in psoriasis, performed by reversal of disease-associated gene expression profiles31
Dual guide RNA-mediated concurrent C&G-to-T&A and A&T-to-G&C conversions using CRISPR base editors31
Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems31
Empirical comparison and recent advances of computational prediction of hormone binding proteins using machine learning methods30
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability30
Co-expression of immune checkpoints in glioblastoma revealed by single-nucleus RNA sequencing and spatial transcriptomics30
Structural studies of protein–nucleic acid complexes: A brief overview of the selected techniques30
Impact of an irreversible β-galactosylceramidase inhibitor on the lipid profile of zebrafish embryos29
Survival estimation in patients with stomach and esophageal carcinoma using miRNA expression profiles29
Review of protein structure-based analyses that illuminate plant stress mechanisms29
Prediction of HER2-positive breast cancer recurrence and metastasis risk from histopathological images and clinical information via multimodal deep learning29
Multicopper oxidases with laccase-ferroxidase activity: Classification and study of ferroxidase activity determinants in a member from Heterobasidion annosum s. l.29
Computationally derived structural insights into Rare Earth selectivity in lanmodulin and its variants29
Machine learning in metastatic cancer research: Potentials, possibilities, and prospects29
Protein design accelerates the development and application of optogenetic tools29
Over time analysis of the codon usage of SARS-CoV-2 and its variants29
Thresholding Gini variable importance with a single-trained random forest: An empirical Bayes approach28
Homologous cardiac calcium pump regulators phospholamban and sarcolipin adopt distinct oligomeric states in the membrane28
Corrigendum to “Coupling the endophytic microbiome with the host transcriptome in olive roots” [Comput. Struct. Biotechnol. J. 19 (2021) 4777–4789]28
Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases28
Beyond the Scalpel: Assessing ChatGPT's potential as an auxiliary intelligent virtual assistant in oral surgery28
Detecting differentially expressed circular RNAs from multiple quantification methods using a generalized linear mixed model28
Interplay of starch debranching enzyme and its inhibitor is mediated by Redox-Activated SPL transcription factor28
Reprogramming landscape highlighted by dynamic transcriptomes in therapy-induced neuroendocrine differentiation27
Structural insights into apoptotic regulation of human Bfk as a novel Bcl-2 family member27
Targeted removal of mitochondrial DNA from mouse and human extrachromosomal circular DNA with CRISPR-Cas927
Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis27
The seen and the unseen: Molecular classification and image based-analysis of gastrointestinal cancers27
EpiCas-DL: Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning27
MSPJ: Discovering potential biomarkers in small gene expression datasets via ensemble learning27
A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis27
A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics26
Downregulation of ABLIM3 confers to the metastasis of neuroblastoma via regulating the cell adhesion molecules pathway26
Protposer: The web server that readily proposes protein stabilizing mutations with high PPV26
PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics – catching the (un)usual suspects26
HELLS modulates the stemness of intrahepatic cholangiocarcinoma through promoting senescence-associated secretory phenotype26
Corrigendum to “TREAT: Therapeutic RNAs exploration inspired by artificial intelligence technology” [Comput Struct Biotechnol J 20 (2022) 5680–5689]26
Deep learning of antibody epitopes using positional permutation vectors26
Generic and queryable data integration schema for transcriptomics and epigenomics studies26
Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies25
SPARC: Structural properties associated with residue constraints25
HIV infection detection using CRISPR/Cas systems: Present and future prospects25
Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism25
The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations25
CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction25
Optimizing fountain codes for DNA data storage24
The discovery of hidden guanylate cyclases (GCs) in the Homo sapiens proteome24
INSIGHT: An integrated framework for safe and sustainable chemical and material assessment24
Population-scale genotyping of structural variation in the era of long-read sequencing24
Concentration-dependent thermodynamic analysis of the partition process of small ligands into proteins24
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
Machine learning reveals STAT motifs as predictors for GR-mediated gene repression24
Easy-MODA: Simplifying standardised registration of scientific simulation workflows through MODA template guidelines powered by the Enalos Cloud Platform24
New insights empowered by single-cell sequencing: From neural crest to enteric nervous system23
Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains23
Modeling approaches for probing cross-feeding interactions in the human gut microbiome23
Mysteries of gene regulation: Promoters are not the sole triggers of gene expression23
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein–protein interaction network through integrative methods23
Role of Bmal1 in mediating the cholinergic system to regulate the behavioral rhythm of nocturnal marine molluscs23
Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR-amplified glioblastoma23
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 variants23
Analyzing the human gut mycobiome – A short guide for beginners23
Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation22
In-silico proteomic analysis of the role of IL-4 and IL-10 in IVD degeneration: Protein-protein interaction networks for candidate prioritisation22
Plasma cell-free extrachromosomal circular DNA is a molecular hallmark of preeclampsia22
scDemultiplex: An iterative beta-binomial model-based method for accurate demultiplexing with hashtag oligos22
New targets for the treatment of ulcerative colitis: Gut microbiota and its metabolites22
Enhancing glucose level prediction of ICU patients through hierarchical modeling of irregular time-series22
EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks22
Comparative analysis of amino acid auxotrophies and peptidase profiles in non-dysbiotic and dysbiotic small intestinal microbiomes22
Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives22
Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes22
Structure-based identification of HNF4α agonists: Rosmarinic acid as a promising candidate for NAFLD treatment22
Post-processing enhances protein secondary structure prediction with second order deep learning and embeddings22
Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases22
Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations21
A novel deep learning method for large-scale analysis of bone marrow adiposity using UK Biobank Dixon MRI data21
Histone variants and chromatin structure, update of advances21
Demystifying extrachromosomal DNA circles: Categories, biogenesis, and cancer therapeutics21
MNNMDA: Predicting human microbe-disease association via a method to minimize matrix nuclear norm21
TRRAP-mediated acetylation on Sp1 regulates adult neurogenesis21
Claudin-10b cation channels in tight junction strands: Octameric-interlocked pore barrels constitute paracellular channels with low water permeability21
CNNSplice: Robust models for splice site prediction using convolutional neural networks21
Relative flux trade-offs and optimization of metabolic network functionalities21
Short-chain fatty acids reprogram metabolic profiles with the induction of reactive oxygen species production in human colorectal adenocarcinoma cells21
Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins21
Fantastic genes and where to find them expressed in CHO21
Ion and water permeation through claudin-10b and claudin-15 paracellular channels21
Targeting non-structural proteins of Hepatitis C virus for predicting repurposed drugs using QSAR and machine learning approaches21
Reference-based read clustering improves the de novo genome assembly of microbial strains21
Prediction and validation of host-pathogen interactions by a versatile inference approach using Aspergillus fumigatus as a case study21
Noninvasive detection and interpretation of gastrointestinal diseases by collaborative serum metabolite and magnetically controlled capsule endoscopy20
fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data20
A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer20
AmiCa: Atlas of miRNA-gene correlations in cancer20
BioPrediction-RPI: Democratizing the prediction of interaction between non-coding RNA and protein with end-to-end machine learning20
Family-wide analysis of integrin structures predicted by AlphaFold220
A Nano Risk Governance Portal supporting risk governance of nanomaterials and nano-enabled products20
MACRAMÉ – Advanced characterisation methodologies to assess and predict the health and environmental risks of advanced materials20
Binding modes of prothrombin cleavage site sequences to the factor Xa catalytic triad: Insights from atomistic simulations20
Structural and functional mapping of ars gene cluster in Deinococcus indicus DR120
Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life20
Quercetin: A promising drug candidate against the potential SARS-CoV-2-Spike mutants with high viral infectivity20
Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma20
Transcriptomic signatures associated with autoimmune thyroiditis in papillary thyroid carcinoma and cancer immunotherapy-induced thyroid dysfunction20
Determining key residues of engineered scFv antibody variants with improved MMP-9 binding using deep sequencing and machine learning20
Data recovery methods for DNA storage based on fountain codes20
TOAST: A novel method for identifying topologically associated domains based on graph auto-encoders and clustering20
MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks20
MM-DRPNet: A multimodal dynamic radial partitioning network for enhanced protein–ligand binding affinity prediction20
iResNetDM: An interpretable deep learning approach for four types of DNA methylation modification prediction20
Unleashing high content screening in hit detection – Benchmarking AI workflows including novelty detection20
How to describe the time-dependent dissolution of engineered nanomaterials?20
IBPred: A sequence-based predictor for identifying ion binding protein in phage20
Design, proof-of-concept of single robotic hair transplant mechanisms for both harvest and implant of hair grafts19
Non-coding antisense transcripts: fine regulation of gene expression in cancer19
Cluster parameter-based DBSCAN maps for image characterization19
Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231-luc-GFP cell line19
Osmolyte-induced protein stability changes explained by graph theory19
Evaluation of protein descriptors in computer-aided rational protein engineering tasks and its application in property prediction in SARS-CoV-2 spike glycoprotein19
Computational design of α-amylase from Bacillus licheniformis to increase its activity and stability at high temperatures19
Metabolomic and lipidomic insights into the impact of Euglena gracilis-derived β-glucan supplementation on sow colostrum and milk composition19
Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins19
Overcoming the cognition-reality gap in robot-to-human handovers with anisotropic variable force guidance19
Increased risk of arrhythmias, heart failure, and thrombosis in SARS-CoV-2 positive individuals persists at one year post-infection19
Corrigendum to “Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin” [Comput Struct Biotechnol J 27 (2025) 1286–1295]19
Dynamics of spindle assembly and position checkpoints: Integrating molecular mechanisms with computational models19
Deep learning based deconvolution methods: A systematic review18
Establishment and validation of a cholesterol metabolism-related prognostic signature for hepatocellular carcinoma18
RNA secondary structure prediction by conducting multi-class classifications18
Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton18
A potent nonapeptide inhibitor for the CXCL12/HMGB1 heterocomplex: A computational and experimental approach18
Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation18
Identifying the risk of Kawasaki disease based solely on routine blood test features through novel construction of machine learning models18
Improving doublet cell removal efficiency through multiple algorithm runs18
Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus18
Shared and divergent contribution of vitamin A and oxytocin to the aetiology of autism spectrum disorder18
Discovery of a new generation of angiotensin receptor blocking drugs: Receptor mechanisms and in silico binding to enzymes relevant to SARS-CoV-218
Deep learning frameworks for protein–protein interaction prediction18
Detection and prioritization of COVID-19 infected patients from CXR images: Analysis of AI-assisted diagnosis in clinical settings18
Artificial intelligence-large language models (AI-LLMs) for reliable and accurate cardiotocography (CTG) interpretation in obstetric practice18
SpatialPPIv2: Enhancing protein–protein interaction prediction through graph neural networks with protein language models18
iKcr_CNN: A novel computational tool for imbalance classification of human nonhistone crotonylation sites based on convolutional neural networks with focal loss18
ALDH2 as a potential stem cell-related biomarker in lung adenocarcinoma: Comprehensive multi-omics analysis18
Deciphering mitochondrial dysfunction in keratoconus: Insights into ACSL4 from machine learning-based bulk and single-cell transcriptome analyses and experimental validation18
HELENA project: Driving innovation in high energy density Li-metal halide solid-state batteries for electric vehicles and aircrafts18
Tevenvirinae phages encode a family of LSm-like fold proteins18
iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data17
Investigating how HIV-1 antiretrovirals differentially behave as substrates and inhibitors of P-glycoprotein via molecular dynamics simulations17
Optical genome mapping reveals novel structural variations in an autism spectrum disorder cohort17
Kinase-substrate prediction using an autoregressive model17
VarMeter2: An enhanced structure-based method for predicting pathogenic missense variants through Mahalanobis distance17
An integrated analysis of dysregulated SCD1 in human cancers and functional verification of miR-181a-5p/SCD1 axis in esophageal squamous cell carcinoma17
Machine learning for metabolic pathway optimization: A review17
Analysis of the galactomannan binding ability of β-mannosidases, BtMan2A and CmMan5A, regarding their activity and synergism with a β-mannanase17
Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin17
The natural product biosynthesis potential of the microbiomes of Earth – Bioprospecting for novel anti-microbial agents in the meta-omics era17
Comprehensive analysis of circulating cell-free RNAs in blood for diagnosing non-small cell lung cancer17
Starch granules and their size distribution in wheat: Biosynthesis, physicochemical properties and their effect on flour-based food systems17
The nucleotide landscape of polyXY regions17
Interspecific and intraspecific Taylor's laws for frog skin microbes17
Plasticity of BioPhi-driven humanness optimization in ScFv-CD99 binding affinity validated through AlphaFold, HADDOCK, and MD simulations17
Conserved FimH mutations in the global Escherichia coli ST131 multi-drug resistant lineage weaken interdomain interactions and alter adhesin function17
Spontaneous regeneration of cholecystokinergic reticulospinal axons after a complete spinal cord injury in sea lampreys17
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