Computational and Structural Biotechnology Journal

Papers
(The TQCC of Computational and Structural Biotechnology Journal is 8. 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 2021-04-01 to 2025-04-01.)
ArticleCitations
UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets175
A DICOM-based standard for quantitative physical rehabilitation166
Transcriptomic investigations of polymyxins and colistin/sulbactam combination against carbapenem-resistant Acinetobacter baumannii142
A shared mechanism for TNP-ATP recognition by members of the P2X receptor family117
VIBES: A consensus subtyping of the vaginal microbiota reveals novel classification criteria109
Genome-wide analysis reveals the contributors to fast molecular evolution of the Chinese hook snout carp (Opsariichthys bidens)109
The molecular subtypes of autoimmune diseases91
Deep-HPI-pred: An R-Shiny applet for network-based classification and prediction of Host-Pathogen protein-protein interactions90
Enhancing prediction of short linear protein motifs with Wregex 3.084
cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery74
Network-based analysis of heterogeneous patient-matched brain and extracranial melanoma metastasis pairs reveals three homogeneous subgroups72
Comprehensive integration of single-cell RNA and transcriptome RNA sequencing to establish a pyroptosis-related signature for improving prognostic prediction of gastric cancer67
Stabilization of the retromer complex: Analysis of novel binding sites of bis-1,3-phenyl guanylhydrazone 2a to the VPS29/VPS35 interface63
RCDdb: A manually curated database and analysis platform for regulated cell death61
Personalized analysis of human cancer multi-omics for precision oncology58
Phosphopeptide binding to the N-SH2 domain of tyrosine phosphatase SHP2 correlates with the unzipping of its central β-sheet53
Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes51
Curvature-enhanced graph convolutional network for biomolecular interaction prediction50
Transnational learning and teaching activities: Smart Healthcare Engineering48
Revealing SARS-CoV-2 Mpro mutation cold and hot spots: Dynamic residue network analysis meets machine learning47
TCMM: A unified database for traditional Chinese medicine modernization and therapeutic innovations47
Cell-to-cell distance that combines gene expression and gene embeddings46
InTiCAR: Network-based identification of significant inter-tissue communicators for autoimmune diseases46
Protein allosteric site identification using machine learning and per amino acid residue reported internal protein nanoenvironment descriptors45
ppHiC: Interactive exploration of Hi-C results on the ProteinPaint web portal45
Landscape of intrinsically disordered proteins in mental disorder diseases45
Structural characteristics, functions, and counteracting strategies of biofilms in Staphylococcus aureus45
Rapid profiling of carcinogenic types of Helicobacter pylori infection via deep learning analysis of label-free SERS spectra of human serum44
Biased activation of the vasopressin V2 receptor probed by molecular dynamics simulations, NMR and pharmacological studies42
Nanopore sequencing of protozoa: Decoding biological information on a string of biochemical molecules into human-readable signals42
Structure-based protein and small molecule generation using EGNN and diffusion models: A comprehensive review41
A heterogeneous information network learning model with neighborhood-level structural representation for predicting lncRNA-miRNA interactions39
Free energy landscape of the PI3Kα C-terminal activation38
Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum38
WUREN: Whole-modal union representation for epitope prediction37
Insulin-related traits and prostate cancer: A Mendelian randomization study36
AFSC: A self-supervised augmentation-free spatial clustering method based on contrastive learning for identifying spatial domains36
Unsupervised machine learning for risk stratification and identification of relevant subgroups of ascending aorta dimensions using cardiac CT and clinical data36
Physical-aware model accuracy estimation for protein complex using deep learning method36
Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus36
Development of a new data management system for the study of the gut microbiome of children who are small for their gestational age36
The complement C3a/C3aR pathway is associated with treatment resistance to gemcitabine-based neoadjuvant therapy in pancreatic cancer35
HIV-1-envelope trimer transitions from prefusion-closed to CD4-bound-open conformations through an occluded-intermediate state35
DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures34
BrainCellR: A precise cell type nomenclature pipeline for comparative analysis across brain single-cell datasets34
Prolonged premature rupture of membranes with increased risk of infection is associated with gut accumulation of Pseudomonas from the environment34
C. perfringens enterotoxin-claudin pore complex: Models for structure, mechanism of pore assembly and cation permeability33
Predictive dynamic control accurately maps the design space for 2,3-butanediol production32
The variegated canalized-1 tomato mutant is linked to photosystem assembly32
Deep5mC: Predicting 5-methylcytosine (5mC) methylation status using a deep learning transformer approach32
Artificial intelligence in skeletal metastasis imaging31
MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants31
Deep learning-based characterization of neutrophil activation phenotypes in ex vivo human Candida blood infections30
NeuralBeds: Neural embeddings for efficient DNA data compression and optimized similarity search30
Cysteine hyperoxidation rewires communication pathways in the nucleosome and destabilizes the dyad30
Unraveling membrane properties at the organelle-level with LipidDyn29
PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data29
Path to normality: Assessing the level of social-distancing measures relaxation against antibody-resistant SARS-CoV-2 variants in a partially-vaccinated population29
Corrigendum to “Cryo-EM reveals architectural diversity in active rotavirus particles” [Comput. Struct. Biotechnol. J. 17 (2019) 1178–1183]29
Structural insight into the macrocyclic inhibitor TPX-0022 of c-Met and c-Src28
Confronting the data deluge: How artificial intelligence can be used in the study of plant stress28
Brain transcriptomic profiling reveals common alterations across neurodegenerative and psychiatric disorders28
TWN-FS method: A novel fragment screening method for drug discovery27
Discovery of compounds with viscosity-reducing effects on biopharmaceutical formulations with monoclonal antibodies27
Identification of feature genes and key biological pathways in immune-mediated necrotizing myopathy: High-throughput sequencing and bioinformatics analysis27
An integrated protein structure fitness scoring approach for identifying native-like model structures26
Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist26
Advances in the development of therapeutic strategies against COVID-19 and perspectives in the drug design for emerging SARS-CoV-2 variants26
Protons taken hostage: Dynamic H-bond networks of the pH-sensing GPR6826
Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects26
Non-monotonic fibril surface occlusion by GFP tags from coarse-grained molecular simulations25
PeakCNV: A multi-feature ranking algorithm-based tool for genome-wide copy number variation-association study25
The synergistic interaction landscape of chromatin regulators reveals their epigenetic regulation mechanisms across five cancer cell lines25
A comprehensive multi-omics analysis reveals molecular features associated with cancer via RNA cross-talks in the Notch signaling pathway25
BioCAT: Search for biosynthetic gene clusters producing nonribosomal peptides with known structure25
Identification of new head and neck squamous cell carcinoma subtypes and development of a novel score system (PGSscore) based on variations in pathway activity between tumor and adjacent non-tumor sam25
Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA25
Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking24
Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts24
Can we infer tumor presence of single cell transcriptomes and their tumor of origin from bulk transcriptomes by machine learning?24
Reconstruction of the origin of the first major SARS-CoV-2 outbreak in Germany24
Novelty detection for metabolic dynamics established on breast cancer tissue using 2D NMR TOCSY spectra24
LncRNA functional annotation with improved false discovery rate achieved by disease associations23
What remains from living cells in bacterial lysate-based cell-free systems23
Electron density is not spherical: the many applications of the transferable aspherical atom model23
Rapid intraoperative amplicon sequencing of CNS tumor markers23
Hepatic encephalopathy post-TIPS: Current status and prospects in predictive assessment23
Deciphering and designing microbial communities by genome-scale metabolic modelling23
Computational identification of differentially-expressed genes as suggested novel COVID-19 biomarkers: A bioinformatics analysis of expression profiles23
Designing CITOBOT: A portable device for cervical cancer screening using human-centered design, smart prototyping, and artificial intelligence23
Automated machine learning in nanotoxicity assessment: A comparative study of predictive model performance23
Agreement and disagreement in pediatric functional neurological symptom disorders: Comparing patient reported outcome measures (PROMs) and clinician assessments23
NanoConstruct: A web application builder of ellipsoidal nanoparticles for the investigation of their crystal growth, stability, and the calculation of atomistic descriptors23
BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications23
Keep it accurate and robust: An enhanced nuclei analysis framework23
Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations22
Critical assessment of structure-based approaches to improve protein resistance in aqueous ionic liquids by enzyme-wide saturation mutagenesis22
Machine learning for predicting Plasmodium liver stage development in vitro using microscopy imaging22
scCCTR: An iterative selection-based semi-supervised clustering model for single-cell RNA-seq data22
Towards advanced bioprocess optimization: A multiscale modelling approach22
Genomic evidence for divergent co-infections of co-circulating SARS-CoV-2 lineages22
Biomarker discovery process at binomial decision point (2BDP): Analytical pipeline to construct biomarker panel22
Stability of human gut microbiome: Comparison of ecological modelling and observational approaches21
Comparative evaluation of AlphaFold2 and disorder predictors for prediction of intrinsic disorder, disorder content and fully disordered proteins21
Structures and implications of the nuclease domain of human parvovirus B19 NS1 protein21
Multiple transcription auto regulatory loops can act as robust oscillators and decision-making motifs21
NanoBioAccumulate: Modelling the uptake and bioaccumulation of nanomaterials in soil and aquatic invertebrates via the Enalos DIAGONAL Cloud Platform20
Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites20
D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-120
Predicting the effects of cultivation condition on gene regulation in Escherichia coli by using deep learning20
Multiscale modeling of drug resistance in glioblastoma with gene mutations and angiogenesis20
Towards mechanistic models of mutational effects: Deep learning on Alzheimer’s Aβ peptide20
Histone modification in Saccharomyces cerevisiae: A review of the current status20
Critical evaluation of the use of artificial data for machine learning based de novo peptide identification20
Automated sample annotation for diabetes mellitus in healthcare integrated biobanking20
A pathway-based mutation signature to predict the clinical outcomes and response to CTLA-4 inhibitors in melanoma20
Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals20
Identification of (Z)-2-benzylidene-dihydroimidazothiazolone derivatives as tyrosinase inhibitors: Anti-melanogenic effects and in silico studies19
Prediction of protein-ligand binding affinity with deep learning19
DeepMC-iNABP: Deep learning for multiclass identification and classification of nucleic acid-binding proteins19
Assessing comparative importance of DNA sequence and epigenetic modifications on gene expression using a deep convolutional neural network19
Flow cytometry-based study of model marine microalgal consortia revealed an ecological advantage of siderophore utilization by the dinoflagellate Amphidinium carterae19
A novel integrative computational framework for breast cancer radiogenomic biomarker discovery19
Multi-omics landscape and clinical significance of a SMAD4-driven immune signature: Implications for risk stratification and frontline therapies in pancreatic cancer19
Network-based prioritization of cancer biomarkers by phenotype-driven module detection and ranking19
Beta-diversity distance matrices for microbiome sample size and power calculations — How to obtain good estimates19
Sequence variety in the CC’ loop of Siglec-8/9/3 determines the recognitions to sulfated oligosaccharides19
SRIQ clustering: A fusion of Random Forest, QT clustering, and KNN concepts19
Classification of lung adenocarcinoma based on stemness scores in bulk and single cell transcriptomes19
Artificial intelligence and deep learning: New tools for histopathological diagnosis of nonalcoholic fatty liver disease/nonalcoholic steatohepatitis18
Comprehensive exploration of JQ1 and GSK2801 targets in breast cancer using network pharmacology and molecular modeling approaches18
Clinical Decision Support systems: A step forward in establishing the clinical laboratory as a decision maker hub - A CDS system protocol implementation in the clinical laboratory18
First thermostable CLIP-tag by rational design applied to an archaeal O-alkyl-guanine-DNA-alkyl-transferase18
Beyond sequence: Structure-based machine learning18
In silico analyses of isoniazid and streptomycin resistance-associated mutations in Mycobacterium tuberculosis18
IHGA: An interactive web server for large-scale and comprehensive discovery of genes of interest in hepatocellular carcinoma18
Predicting zeta potential of liposomes from their structure: A nano-QSPR model for DOPE, DC-Chol, DOTAP, and EPC formulations18
TF-COMB – Discovering grammar of transcription factor binding sites18
IMFSegNet: Cost-effective and objective quantification of intramuscular fat in histological sections by deep learning18
Caffeine causes cell cycle arrest at G0/G1 and increases of ubiquitinated proteins, ATP and mitochondrial membrane potential in renal cells18
Consistencies and contradictions in different polymer models of chromatin architecture18
Crystallographic mining of ASK1 regulators to unravel the intricate PPI interfaces for the discovery of small molecule18
dsCellNet: A new computational tool to infer cell–cell communication networks in the developing and aging brain18
Recognition of the ligand-induced spatiotemporal residue pair pattern of β2-adrenergic receptors using 3-D residual networks trained by the time series of protein distance maps17
Mechanistic insights into multiple-step transport of mitochondrial ADP/ATP carrier17
Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA17
Light-sheet laser speckle imaging for cilia motility assessment17
Comprehensive characterization of human–virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs17
The impact of noise and missing fragmentation cleavages on de novo peptide identification algorithms17
In silico screening of phenylethanoid glycosides, a class of pharmacologically active compounds as natural inhibitors of SARS-CoV-2 proteases17
Using patient-generated health data more efficient and effectively to facilitate the implementation of value-based healthcare in the EU – Innovation report17
Analysis methods for the gut microbiome in neuropsychiatric and neurodegenerative disorders17
Highly effective batch effect correction method for RNA-seq count data17
Functional convergence of Yunnan snub-nosed monkey and bamboo-eating panda gut microbiomes revealing the driving by dietary flexibility on mammal gut microbiome17
Hybrid computational models of multicellular tumour growth considering glucose metabolism16
The NPR/Hal family of protein kinases in yeasts: biological role, phylogeny and regulation under environmental challenges16
TWN-RENCOD: A novel method for protein binding site comparison16
SARS-CoV-2 virus classification based on stacked sparse autoencoder16
CCLHunter: An efficient toolkit for cancer cell line authentication16
NGS allele counts versus called genotypes for testing genetic association16
Unravelling hierarchical levels of structure in lipid membranes16
Open quantum systems theory of ultraweak ultraviolet photon emissions: Revisiting Gurwitsch's onion experiment as a prototype for quantum biology16
LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries16
The chromatin remodeling factors EP300 and TRRAP are novel SMYD3 interactors involved in the emerging ‘nonmutational epigenetic reprogramming’ cancer hallmark16
CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins16
Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles16
Exploring the patient-microbiome interaction patterns for pan-cancer16
A pilot reverse virtual screening study suggests toxic exposures caused long-term epigenetic changes in Gulf War Illness16
The second intracellular loop of the yeast Trk1 potassium transporter is involved in regulation of activity, and interaction with 14–3-3 proteins16
Methods to mechanically perturb and characterize GUV-based minimal cell models16
Dynamic alternative polyadenylation during iPSC differentiation into cardiomyocytes16
Classifying breast cancer and fibroadenoma tissue biopsies from paraffined stain-free slides by fractal biomarkers in Fourier Ptychographic Microscopy16
GSPHI: A novel deep learning model for predicting phage-host interactions via multiple biological information15
Nanomechanics combined with HDX reveals allosteric drug binding sites of CFTR NBD115
Exploring the landscape of tools and resources for the analysis of long non-coding RNAs15
Exploring chemical space for lead identification by propagating on chemical similarity network15
Extending arterial stiffness assessment along the circumference using beam-steered ARFI and wave-tracking: A proof-of-principle study in phantoms and ex vivo15
Databases and prospects of dynamic gene regulation in eukaryotes: A mini review15
Unitig level assembly graph based metagenome-assembled genome refiner (UGMAGrefiner): A tool to increase completeness and resolution of metagenome-assembled genomes15
The impact of pathogenic and artificial mutations on Claudin-5 selectivity from molecular dynamics simulations15
Genetically predicted telomere length and its relationship with neurodegenerative diseases and life expectancy15
Epigenetic modifications: Allusive clues of lncRNA functions in plants15
Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein15
The evolutionary diversification and antimicrobial potential of MPEG1 in Metazoa15
Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview15
Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study15
Discovery of a highly efficient TylF methyltransferase via random mutagenesis for improving tylosin production15
Exploring long non-coding RNA networks from single cell omics data15
Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships15
In silico and in vitro approaches allow the identification of the Prosystemin molecular network15
A drug repurposing method based on inhibition effect on gene regulatory network15
Structural characterization of a cross-protective natural chimera of factor H binding protein from meningococcal serogroup B strain NL09615
MUG: A mutation overview of GPCR subfamily A17 receptors14
OrganelX web server for sub-peroxisomal and sub-mitochondrial protein localization and peroxisomal target signal detection14
Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism14
Entropy-extreme model for predicting the development of cyber epidemics at early stages14
ProFeatX: A parallelized protein feature extraction suite for machine learning14
ProxyBind: A compendium of binding sites for proximity-induced pharmacology14
Improved inter-residue contact prediction via a hybrid generative model and dynamic loss function14
Integration of transcriptomics data into agent-based models of solid tumor metastasis14
Modeling incomplete penetrance in arrhythmogenic cardiomyopathy by human induced pluripotent stem cell derived cardiomyocytes14
Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark study14
Computational Analysis of the Gut Microbiota-Mediated Drug Metabolism14
Targeted protein degradation in mammalian cells: A promising avenue toward future14
Genome mining of metabolic gene clusters in the Rubiaceae family14
Metabolomics and biochemical assays reveal the metabolic responses to hypo-salinity stress and osmoregulatory role of cAMP-PKA pathway in Mercenaria mercenaria14
Corrigendum to “AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships” [Comput Struct Biotechnol J 27 (2025) 265–277]14
Network Proximity-based computational pipeline identifies drug candidates for different pathological stages of Alzheimer's disease14
VTAM: A robust pipeline for validating metabarcoding data using controls14
Cell segmentation and representation with shape priors14
Integrated metabolomics and network analysis reveal changes in lipid metabolisms of tripterygium glycosides tablets in rats with collagen-induced arthritis14
Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants14
Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application.14
Exploring the universal healthy human gut microbiota around the World14
Computational modelling of bone growth and mineralization surrounding biodegradable Mg-based and permanent Ti implants14
Corrigendum to “In silico and in vitro approaches allow the identification of the Prosystemin molecular network” [Comput Struct Biotechnol J 21 (2023) 212–223]14
Landscape of the intratumroal microenvironment in bladder cancer: Implications for prognosis and immunotherapy14
Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations13
EccBase: A high-quality database for exploration and characterization of extrachromosomal circular DNAs in cancer13
Language models can identify enzymatic binding sites in protein sequences13
RNAME: A comprehensive database of RNA modification enzymes13
Network-based identification and mechanism exploration of active ingredients against Alzheimer’s disease via targeting endoplasmic reticulum stress from traditional chinese medicine13
Cross-kingdom analyses of transmembrane protein kinases show their functional diversity and distinct origins in protists13
Hinge region mediates signal transmission of luteinizing hormone and chorionic gonadotropin receptor13
From sequence to function through structure: Deep learning for protein design13
Richness estimation in microbiome data obtained from denoising pipelines13
SoluProtMutDB: A manually curated database of protein solubility changes upon mutations13
Computational modeling for deciphering tissue microenvironment heterogeneity from spatially resolved transcriptomics13
A guide to multi-omics data collection and integration for translational medicine13
A roadmap towards safe and sustainable by design nanotechnology: Implementation for nano-silver-based antimicrobial textile coatings production by ASINA project13
MLSP: A bioinformatics tool for predicting molecular subtypes and prognosis in patients with breast cancer13
Artificial intelligence-driven meta-analysis of brain gene expression identifies novel gene candidates and a role for mitochondria in Alzheimer’s disease13
A novel exosome-derived prognostic signature and risk stratification for breast cancer based on multi-omics and systematic biological heterogeneity13
Using molecular dynamics simulations to interrogate T cell receptor non-equilibrium kinetics13
Quantifying fecal and plasma short-chain fatty acids in healthy Thai individuals13
Predicting the location of coordinated metal ion-ligand binding sites using geometry-aware graph neural networks13
Advances in multi-omics study of biomarkers of glycolipid metabolism disorder13
Nanopore sequencing enables novel detection of deuterium incorporation in DNA13
Using metagenomic data to boost protein structure prediction and discovery13
Model-based prediction of optogenetic sound encoding in the human cochlea by future optical cochlear implants13
TetraRNA, a tetra-class machine learning model for deciphering the coding potential derivation of RNA world12
An ecological and stochastic perspective on persisters resuscitation12
CHAPERONg: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses12
Soil under stress: The importance of soil life and how it is influenced by (micro)plastic pollution12
Biotic interactions and environmental modifications determine symbiotic microbial diversity and stability12
Smad4 regulates TGF-β1-mediated hedgehog activation to promote epithelial-to-mesenchymal transition in pancreatic cancer cells by suppressing Gli1 activity12
Advanced biokinetic and hydrodynamic modelling to support and optimize the design of full-scale high rate algal ponds12
Challenges and opportunities in processing NanoString nCounter data12
Improving generalization capability of deep learning-based nuclei instance segmentation by non-deterministic train time and deterministic test time stain normalization12
Fever temperatures modulate intraprotein dynamics and enhance the binding affinity between monoclonal antibodies and the spike protein from SARS-CoV-212
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