Computational and Structural Biotechnology Journal

Papers
(The TQCC of Computational and Structural Biotechnology Journal is 10. 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 2022-08-01 to 2026-08-01.)
ArticleCitations
Predicting cellular adaptation proteins dependent on eIF2α regulation under stress conditions: Physiological and pathophysiological implications in neuronal function243
Corrigendum to “Maternal Clostridium butyricum supplementation during late gestation and lactation enhances gut bacterial communities, milk quality, and 211
Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species203
macpie: Scalable workflow for high-throughput transcriptomic profiling169
MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants161
A miRNA signature linked to high lipoprotein (a) and coronary calcification in familial hypercholesterolaemia157
Pseudotimecascade Visualizes Gene Expression Cascade in Pseudotime Analysis139
The influence of HIV sense and antisense transcripts on stochastic HIV transcription and reactivation121
Identification of a Novel Trifluoromethyl-Bearing Flavonoid as a Promising Androgen Receptor Antagonist: Structure-Based Virtual Screening and In Vitro Study110
SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis98
Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types86
Consistencies and contradictions in different polymer models of chromatin architecture84
In silico and in vitro approaches allow the identification of the Prosystemin molecular network81
MUG: A mutation overview of GPCR subfamily A17 receptors79
Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus79
Predictive dynamic control accurately maps the design space for 2,3-butanediol production77
cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery77
Free energy landscape of the PI3Kα C-terminal activation75
Corrigendum to “Cryo-EM reveals architectural diversity in active rotavirus particles” [Comput. Struct. Biotechnol. J. 17 (2019) 1178–1183]72
CRUSADE project: Recycling technologies for ELV components to create a sustainable source of market grade materials for EU applications71
From latent dynamics to data geometry: Nonlinear diffusion modelling for protein structures69
CKATool: A clinical kinematic analysis toolbox for upper limb rehabilitation68
Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview65
Biomarker discovery process at binomial decision point (2BDP): Analytical pipeline to construct biomarker panel65
Agreement and disagreement in pediatric functional neurological symptom disorders: Comparing patient reported outcome measures (PROMs) and clinician assessments64
The second intracellular loop of the yeast Trk1 potassium transporter is involved in regulation of activity, and interaction with 14–3-3 proteins63
Comprehensive exploration of JQ1 and GSK2801 targets in breast cancer using network pharmacology and molecular modeling approaches62
Computational fluid dynamics modeling and simulation of nanoparticle-tumor interaction: Systematic literature review61
Evolution is in the details: Regulatory differences in modern human and Neanderthal59
Integrative Multiomics and Single-Cell Profiling Identify TNFRSF1A + Macrophages as a Prognostic and Therapeutic Target in Diffuse Large B-cell Lymph59
Towards predicting implant-induced fibrosis: A standardized network model of macrophage-fibroblast interactions58
Cell segmentation and representation with shape priors56
Optimized Quantitative Bacterial Two-Hybrid (qB2H) for Protein–Protein Interaction Assessment55
VTAM: A robust pipeline for validating metabarcoding data using controls54
A novel exosome-derived prognostic signature and risk stratification for breast cancer based on multi-omics and systematic biological heterogeneity54
Radiomic clustering using graph network techniques coupled with unbalanced optimal transport52
DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data50
DiabetesOmic: A comprehensive multi-omics diabetes database50
Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants50
Prediction of protein-ligand binding affinity with deep learning48
Integrated metabolomics and network analysis reveal changes in lipid metabolisms of tripterygium glycosides tablets in rats with collagen-induced arthritis46
Gut microbiome enterotypes and temporal variations during a six-month inulin-supplemented weight loss randomized controlled trial in Thai children with obesity46
What remains from living cells in bacterial lysate-based cell-free systems45
A drug repurposing method based on inhibition effect on gene regulatory network45
Optimizing Histatin 5: Effects of K13 and K17 Substitutions on Proteolytic Stability and Antifungal Activity45
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
Data pre-processing for analyzing microbiome data – A mini review45
Predicting zeta potential of liposomes from their structure: A nano-QSPR model for DOPE, DC-Chol, DOTAP, and EPC formulations44
The balance between photosynthesis and respiration explains the niche differentiation between Crocosphaera and Cyanothece43
Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations43
WUREN: Whole-modal union representation for epitope prediction43
Automated machine learning in nanotoxicity assessment: A comparative study of predictive model performance42
Towards accurate and efficient diagnoses in nephropathology: An AI-based approach for assessing kidney transplant rejection42
Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes42
Deep5mC: Predicting 5-methylcytosine (5mC) methylation status using a deep learning transformer approach42
Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application.41
UNKAI: A protein functional identity prediction model based on ESM-C latent representations and the attention mechanism41
From sequence to function through structure: Deep learning for protein design41
EthnoHERBS: Harnessing traditional herbal knowledge for biodiversity conservation and innovative health solutions40
Over time analysis of the codon usage of SARS-CoV-2 and its variants39
Entropy-extreme model for predicting the development of cyber epidemics at early stages39
Self-supervised domain adaptation of protein language model based solely on positive enzyme-reaction pairs39
Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications38
A universal pipeline MosaicProt enables large-scale modeling and detection of chimeric protein sequences for studies on programmed ribosomal frameshifting38
PLO3S: Protein LOcal Surficial Similarity Screening38
ImmiR: A database of microRNAs associated with immune checkpoints and infiltrates37
Computational approaches in rheumatic diseases – Deciphering complex spatio-temporal cell interactions37
Mutation density analyses on long noncoding RNA reveal comparable patterns to protein-coding RNA and prognostic value37
Structural studies of protein–nucleic acid complexes: A brief overview of the selected techniques37
Prognostic iron-metabolism signature robustly stratifies single-cell characteristics of hepatocellular carcinoma37
Dual guide RNA-mediated concurrent C&G-to-T&A and A&T-to-G&C conversions using CRISPR base editors37
Inference of essential genes in Brugia malayi and Onchocerca volvulus by machine learning and the implicat36
Augusta: From RNA‐Seq to gene regulatory networks and Boolean models35
Multicopper oxidases with laccase-ferroxidase activity: Classification and study of ferroxidase activity determinants in a member from Heterobasidion annosum s. l.35
NaCTR: Natural product-derived compound-based drug discovery pipeline from traditional oriental medicine by search space reduction35
Empirical comparison and recent advances of computational prediction of hormone binding proteins using machine learning methods34
Co-expression of immune checkpoints in glioblastoma revealed by single-nucleus RNA sequencing and spatial transcriptomics34
The World of GPCR dimers – Mapping dopamine receptor D 2 homodimers in different activation states and configuration arrangements34
Review of protein structure-based analyses that illuminate plant stress mechanisms34
Single-cell multiome characterizing intercellular communication and intracellular regulation of epithelium and mesenchymal during secondary palate development in mice34
Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue33
Protein design accelerates the development and application of optogenetic tools33
STRUMP-I: Structure-based machine learning approach to pMHC-I binding prediction using force field energy features33
IsomiRome analysis reveals dysregulation of 5’ isomiRs during SARS-CoV-2 infection33
Epigenomics-Guided Multi-Omics Integration Uncovers a Lipid-Metabolic Signature with Translational Utility in Bladder Cancer32
SbD4Skin by EosCloud: Integrating multi-view molecular representation for predicting skin sensitization, irritation, and acute dermal toxicity32
Contagious infection-free medical interaction system with machine vision controlled by remote hand gesture during an operation32
Strengths and limitations of web servers for the modeling of TCRpMHC complexes32
Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems32
Toward Responsible and Privacy-Preserving Generation of Inpatient Clinical Discharge Notes Using Large Language Models31
ECGA: A web server to explore and analyze extrachromosomal gene in cancer31
Identification of genetic basis of brain imaging by group sparse multi-task learning leveraging summary statistics31
PCLDA: An interpretable cell annotation tool for single-cell RNA-sequencing data based on simple statistical methods31
Cat-E: A comprehensive web tool for exploring cancer targeting strategies31
PS-GO parametric protein search engine31
Thresholding Gini variable importance with a single-trained random forest: An empirical Bayes approach31
Impact of an irreversible β-galactosylceramidase inhibitor on the lipid profile of zebrafish embryos31
Pleiotropic expression quantitative trait loci are enriched in enhancers and transcription factor binding sites and impact more genes31
A cellulose-degrading Bacillus altitudinis from Tibetan pigs improved the in vitro fermentation characteri30
OncoProExp: An interactive shiny web application for comprehensive cancer proteomics and phosphoproteomics analysis30
Bacillus subtilis spores displaying RBD domain of SARS-CoV-2 spike protein30
Functional Genomic Evidence for Candidate Small Viral RNA-Mediated Epigenetic Interference in SARS-CoV-1 and SARS-CoV-230
Machine learning in metastatic cancer research: Potentials, possibilities, and prospects29
Computationally derived structural insights into Rare Earth selectivity in lanmodulin and its variants29
Performance of a HER2 testing algorithm tailored for urothelial bladder cancer: A Bi-centre study29
Easy-MODA: Simplifying standardised registration of scientific simulation workflows through MODA template guidelines powered by the Enalos Cloud Platform29
Beyond the Scalpel: Assessing ChatGPT's potential as an auxiliary intelligent virtual assistant in oral surgery29
Structure-based identification of HNF4α agonists: Rosmarinic acid as a promising candidate for NAFLD treatment28
Oxidative stress-driven transcriptomic remodeling in human astrocytes reveals network signatures associated with neurodegenerative and cardiovascular processes28
Claudin-10b cation channels in tight junction strands: Octameric-interlocked pore barrels constitute paracellular channels with low water permeability28
CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction28
Experimental and Mechanistic Validation of PARP1pred for Identifying Potent Leads28
Fantastic genes and where to find them expressed in CHO28
Enhancing detection of epileptic seizures using transfer learning and EEG brain activity signals28
Short-chain fatty acids reprogram metabolic profiles with the induction of reactive oxygen species production in human colorectal adenocarcinoma cells28
Generic and queryable data integration schema for transcriptomics and epigenomics studies28
BioLogical: a universal analysis framework for biosystem logical dynamics28
A novel deep learning method for large-scale analysis of bone marrow adiposity using UK Biobank Dixon MRI data28
Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism27
Corrigendum to “TREAT: Therapeutic RNAs exploration inspired by artificial intelligence technology” [Comput Struct Biotechnol J 20 (2022) 5680–5689]27
PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics – catching the (un)usual suspects27
Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases26
HELLS modulates the stemness of intrahepatic cholangiocarcinoma through promoting senescence-associated secretory phenotype26
Comparative Analysis of Morphological and Acoustic Correlates of Bush-Cricket Tympanic Membranes26
Optimizing fountain codes for DNA data storage26
In-silico proteomic analysis of the role of IL-4 and IL-10 in IVD degeneration: Protein-protein interaction networks for candidate prioritisation26
scDemultiplex: An iterative beta-binomial model-based method for accurate demultiplexing with hashtag oligos26
Ion and water permeation through claudin-10b and claudin-15 paracellular channels26
The discovery of hidden guanylate cyclases (GCs) in the Homo sapiens proteome26
HIV infection detection using CRISPR/Cas systems: Present and future prospects26
Plasma cell-free extrachromosomal circular DNA is a molecular hallmark of preeclampsia25
Evaluation of the impact of printing and embroidery parameters in the process of obtaining utility comfort sensors used in protective clothing dedicated to premature babies25
TRRAP-mediated acetylation on Sp1 regulates adult neurogenesis25
Comparative analysis of amino acid auxotrophies and peptidase profiles in non-dysbiotic and dysbiotic small intestinal microbiomes25
Optimization of regulatory DNA with active learning25
Downregulation of ABLIM3 confers to the metastasis of neuroblastoma via regulating the cell adhesion molecules pathway25
Integrative geno-metabolomics of tenasserim turmeric ( Curcuma candida (Wall.) Techapr. & Škorničk.) with insights into volatile biosynthesis across 25
The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations25
Histone variants and chromatin structure, update of advances24
Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes24
Machine learning reveals STAT motifs as predictors for GR-mediated gene repression24
Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives24
EpiCas-DL : Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning24
EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks24
Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation24
Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations24
The Interaction between the Tyrosine Kinase Receptor EphA2 and RNF5: Structural Insights from an In Silico Approach24
Post-processing enhances protein secondary structure prediction with second order deep learning and embeddings23
Enhancing glucose level prediction of ICU patients through hierarchical modeling of irregular time-series23
The potential of Real-Time volume-rendered 3D Imaging in immersive virtual-reality (VR) for surgical planning in infants with congenital thoracic malformation (CTM)23
Deep learning of antibody epitopes using positional permutation vectors23
Structural Modeling of Protein–DNA Interactions Underlying Genome Copy Number Variation in Nanoviruses23
Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains23
Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases23
MNNMDA: Predicting human microbe-disease association via a method to minimize matrix nuclear norm23
New targets for the treatment of ulcerative colitis: Gut microbiota and its metabolites23
INSIGHT: An integrated framework for safe and sustainable chemical and material assessment23
Detection and prioritization of COVID-19 infected patients from CXR images: Analysis of AI-assisted diagnosis in clinical settings22
Salivary Proteomic Signatures Reveal Novel Mechanistic Insights into Moderate Dental Fluorosis Pathogenesis and Oral Homeostasis Disruption22
Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231-luc-GFP cell line22
Deciphering mitochondrial dysfunction in keratoconus: Insights into ACSL4 from machine learning-based bulk and single-cell transcriptome analyses and experimental validation22
Tevenvirinae phages encode a family of LSm-like fold proteins22
CPRCSdb: A comprehensive phenotype-associated single-cell transcriptomic database for human cancer22
Improving doublet cell removal efficiency through multiple algorithm runs22
Corrigendum to “Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin” [Comput Struct Biotechnol J 27 (2025) 1286–1295]22
Design, proof-of-concept of single robotic hair transplant mechanisms for both harvest and implant of hair grafts21
Metabolomic and lipidomic insights into the impact of Euglena gracilis -derived β-glucan supplementation on sow colostrum and milk composition21
Data recovery methods for DNA storage based on fountain codes21
Deep learning based deconvolution methods: A systematic review21
Increased risk of arrhythmias, heart failure, and thrombosis in SARS-CoV-2 positive individuals persists at one year post-infection21
Reference-based read clustering improves the de novo genome assembly of microbial strains21
Cluster parameter-based DBSCAN maps for image characterization21
RNA secondary structure prediction by conducting multi-class classifications21
Osmolyte-induced protein stability changes explained by graph theory21
Quercetin: A promising drug candidate against the potential SARS-CoV-2-Spike mutants with high viral infectivity20
Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation20
Dynamics of spindle assembly and position checkpoints: Integrating molecular mechanisms with computational models20
A method for analyzing the ERP associated with high frequency ANT DBS offset20
The effect of long-term ambient storage on the morphology of adhered DNA origami20
A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer20
MUC13-Associated Molecular Interactome in Pancreatic Cancer20
HYG-mol: An Interpretable Multimodal Hypergraph Framework for Molecular Property Prediction20
MACRAMÉ – Advanced characterisation methodologies to assess and predict the health and environmental risks of advanced materials20
HELENA project: Driving innovation in high energy density Li-metal halide solid-state batteries for electric vehicles and aircrafts19
ALDH2 as a potential stem cell-related biomarker in lung adenocarcinoma: Comprehensive multi-omics analysis19
Family-wide analysis of integrin structures predicted by AlphaFold219
Computational design of α-amylase from Bacillus licheniformis to increase its activity and stability at high temperatures19
Low-calorie diet intervention ameliorates gut microbiota dysbiosis and metabolic changes in obese patients with type 2 diabetes under standard care19
iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data19
Shared and divergent contribution of vitamin A and oxytocin to the aetiology of autism spectrum disorder19
How to describe the time-dependent dissolution of engineered nanomaterials?19
Overcoming the cognition-reality gap in robot-to-human handovers with anisotropic variable force guidance19
Artificial intelligence-large language models (AI-LLMs) for reliable and accurate cardiotocography (CTG) interpretation in obstetric practice19
Identifying the risk of Kawasaki disease based solely on routine blood test features through novel construction of machine learning models19
Pathway-guided architectures for interpretable AI in biological research19
A Nano Risk Governance Portal supporting risk governance of nanomaterials and nano-enabled products19
f RNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data19
TOAST: A novel method for identifying topologically associated domains based on graph auto-encoders and clustering19
Controllability analysis of intercellular protein–protein interaction networks19
iResNetDM: An interpretable deep learning approach for four types of DNA methylation modification prediction19
Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus19
MM-DRPNet: A multimodal dynamic radial partitioning network for enhanced protein–ligand binding affinity prediction19
Single-cell 5′ RNA sequencing of camelid peripheral B cells provides insights into cellular basis of heavy-chain antibody production18
Modeling omics dose-response at the pathway level with DoseRider18
SpatialPPIv2: Enhancing protein–protein interaction prediction through graph neural networks with protein language models18
AmiCa: Atlas of miRNA-gene correlations in cancer18
CHIASMA: Advancing chemicals and materials safety and sustainability assessments through innovative integration of in vitro and in silico (new approach) methodologies18
CNNSplice: Robust models for splice site prediction using convolutional neural networks18
PathoEye: A deep learning framework for the whole-slide image analysis of skin tissue18
A numerical approach to bio-mechanics analysis based on live micro-CT images in the rat temporomandibular joint18
VarMeter2: An enhanced structure-based method for predicting pathogenic missense variants through Mahalanobis distance18
KG-DFI: A prediction of drug–food interactions based on knowledge graph embedding18
A potent nonapeptide inhibitor for the CXCL12/HMGB1 heterocomplex: A computational and experimental approach18
BioPrediction-RPI: Democratizing the prediction of interaction between non-coding RNA and protein with end-to-end machine learning18
Starch granules and their size distribution in wheat: Biosynthesis, physicochemical properties and their effect on flour-based food systems18
Determining key residues of engineered scFv antibody variants with improved MMP-9 binding using deep sequencing and machine learning18
Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review18
Improving Face Age Prediction by Using Multiple-Angle Photos18
Kinase-substrate prediction using an autoregressive model18
Cavity-Filling Mutations as a Strategy to Stabilize Prefusion Viral Fusion Proteins for Vaccine Design18
Machine-Learning-Based Prediction of Clinical Outcomes in Gliomas Using Glycomic Features18
Structural and functional mapping of ars gene cluster in Deinococcus indicus DR118
A scalable MNase-seq framework for reproducible nucleosome profiling across pluripotent stem cell and cardiomyocyte models18
Machine learning for metabolic pathway optimization: A review18
Low magnetic fields stimulate cardiac mitochondrial bioenergetics with a bell-shaped response: Possibly via a radical pair mechanism17
An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus17
Exploring novel furochochicine derivatives as promising JAK2 inhibitors in HeLa cells: Integrating docking, QSAR-ML, MD simulations, and experiments17
Machine learning and gene network integration reveal prognostic subnetworks and biomarkers in pancreatic cancer17
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-1917
Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin17
DNA Methylation in Blood Samples from Malignant Mammary Tumors of Companion Dogs: A Pilot Study17
Integrated metabolome and transcriptome analysis reveals ferroptosis involvement in cisplatin resistance of esophageal squamous cancer cell17
The nucleotide landscape of polyXY regions17
An integrated analysis of dysregulated SCD1 in human cancers and functional verification of miR-181a-5p/SCD1 axis in esophageal squamous cell carcinoma17
Estimating the effect of tissue- and blood-derived cell reference matrices on deconvolving bulk transcriptomic datasets17
Comprehensive analysis of circulating cell-free RNAs in blood for diagnosing non-small cell lung cancer17
Multi-matrix metabolomics in rare monogenic diabetes syndromes: Analysis of oral fluids and serum in carriers of pathogenic variants in the ALMS1/BBS gen17
Interspecific and intraspecific Taylor's laws for frog skin microbes17
Enhancing surgical object detection in laparoscopic cholecystectomy with explicit positional relationship modeling17
Systematic screening and dynamic profiling of germline regulatory pathways and spermatogonial surface markers in a bivalve mollusc17
Cross-species multi-task learning with molecular and ADME descriptors for liver microsomal metabolic stability16
Plasticity of BioPhi-driven humanness optimization in ScFv-CD99 binding affinity validated through AlphaFold, HADDOCK, and MD simulations16
Lateral walking gait phase recognition for hip exoskeleton by denoising autoencoder-LSTM16
A semi-mechanistic mathematical framework for simulating multi-hormone dynamics in reproductive endocrinology16
Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics16
GENI: A web server to identify gene set enrichments in tumor samples16
The optimal metric for viral genome space16
A comprehensive review on computational metabolomics: Advancing multiscale analysis through in-silico approaches16
Computational modeling of cotranscriptional RNA folding16
LncCat: An ORF attention model to identify LncRNA based on ensemble learning strategy and fused sequence information16
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