Computational and Structural Biotechnology Journal

Article	Citations
Survival analysis across the entire transcriptome identifies biomarkers with the highest prognostic power in breast cancer	534
UCell: Robust and scalable single-cell gene signature scoring	351
The DisGeNET cytoscape app: Exploring and visualizing disease genomics data	300
Integration strategies of multi-omics data for machine learning analysis	263
From pyroptosis, apoptosis and necroptosis to PANoptosis: A mechanistic compendium of programmed cell death pathways	247
A review on machine learning approaches and trends in drug discovery	226
The language of proteins: NLP, machine learning & protein sequences	220
The oralome and its dysbiosis: New insights into oral microbiome-host interactions	219
Review on circular RNAs and new insights into their roles in cancer	212
Chemokines and chemokine receptors during COVID-19 infection	164
Network analysis methods for studying microbial communities: A mini review	161
Automated methods for cell type annotation on scRNA-seq data	142
Multi-omics approaches in cancer research with applications in tumor subtyping, prognosis, and diagnosis	142
Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring	131
Statistical methods for Mendelian randomization in genome-wide association studies: A review	126
Farnesoid X receptor (FXR): Structures and ligands	119
Nanopore sequencing and its application to the study of microbial communities	115
Prediction of HER2-positive breast cancer recurrence and metastasis risk from histopathological images and clinical information via multimodal deep learning	112
An overview of current COVID-19 vaccine platforms	111
Association of risk factors with type 2 diabetes: A systematic review	110
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data	108
Accurate brain tumor detection using deep convolutional neural network	108
Recent advances in exploring the heavy metal(loid) resistant microbiome	93
The molecular feature of macrophages in tumor immune microenvironment of glioma patients	93
Phycobiliproteins: Structural aspects, functional characteristics, and biotechnological perspectives	91

A review on marine plastisphere: biodiversity, formation, and role in degradation	90
Machine learning and deep learning methods that use omics data for metastasis prediction	80
Dependence of SARS-CoV-2 infection on cholesterol-rich lipid raft and endosomal acidification	79
Machine learning in the prediction of cancer therapy	79
Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing	73
On the road to explainable AI in drug-drug interactions prediction: A systematic review	72
Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes	72
A review on compound-protein interaction prediction methods: Data, format, representation and model	71
Benchmarking of Nanopore R10.4 and R9.4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing	66
Artificial intelligence in clinical care amidst COVID-19 pandemic: A systematic review	65
Metabolic modelling approaches for describing and engineering microbial communities	63
The genus Bifidobacterium: from genomics to functionality of an important component of the mammalian gut microbiota	63
Stressed out: Bacterial response to high salinity using compatible solute biosynthesis and uptake systems, lessons from Vibrionaceae	62
Integrated metabolomics and network pharmacology to reveal the mechanisms of hydroxysafflor yellow A against acute traumatic brain injury	62
Applied machine learning in cancer research: A systematic review for patient diagnosis, classification and prognosis	60
QuPath: The global impact of an open source digital pathology system	59
Protein–protein interaction prediction with deep learning: A comprehensive review	59
Computational solutions for spatial transcriptomics	58
Skin microbiome transplantation and manipulation: Current state of the art	58
N1-methyladenosine modification in cancer biology: Current status and future perspectives	56
Statistical and machine learning methods for spatially resolved transcriptomics with histology	56
From sequence to function through structure: Deep learning for protein design	55
Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins	54
DeepOmix: A scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis	54
Computational strategies for single-cell multi-omics integration	53
MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation	53
Protein domain identification methods and online resources	53
Defining the wheat microbiome: Towards microbiome-facilitated crop production	53
Statistical methods for mediation analysis in the era of high-throughput genomics: Current successes and future challenges	50
Inhibition of the main protease of SARS-CoV-2 (Mpro) by repurposing/designing drug-like substances and utilizing nature’s toolbox of bioactive compounds	50
A guide to multi-omics data collection and integration for translational medicine	50
Immune evasion of SARS-CoV-2 from interferon antiviral system	50
Advances in the development of therapeutic strategies against COVID-19 and perspectives in the drug design for emerging SARS-CoV-2 variants	50
Secrete or perish: The role of secretion systems in Xanthomonas biology	48
Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation	48
Robustness of differential gene expression analysis of RNA-seq	48
Antioxidants and pentoxifylline as coadjuvant measures to standard therapy to improve prognosis of patients with pneumonia by COVID-19	48
Codon-based indices for modeling gene expression and transcript evolution	47
Representation learning applications in biological sequence analysis	47
AI applications in functional genomics	47
Identification of cyclin protein using gradient boost decision tree algorithm	46
The mechanism of activation of monomeric B-Raf V600E	45
N-terminal domain mutations of the spike protein are structurally implicated in epitope recognition in emerging SARS-CoV-2 strains	45
Diet-gut microbiota interactions on cardiovascular disease	44
Subtypes of tail spike proteins predicts the host range of Ackermannviridae phages	44
Structural and molecular biology of hepatitis E virus	44
Human endogenous retroviruses in development and disease	44
Gut microbial metabolome in inflammatory bowel disease: From association to therapeutic perspectives	44
Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor	43
Modelling microbial communities: Harnessing consortia for biotechnological applications	43

AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae	43
Automatic cell type identification methods for single-cell RNA sequencing	42
An overview of potential inhibitors targeting non-structural proteins 3 (PLpro and Mac1) and 5 (3CLpro/Mpro) of SARS-CoV-2	41
Soil under stress: The importance of soil life and how it is influenced by (micro)plastic pollution	41
Machine learning application in personalised lung cancer recurrence and survivability prediction	41
Deimmunization of protein therapeutics – Recent advances in experimental and computational epitope prediction and deletion	40
Identification of multipotent drugs for COVID-19 therapeutics with the evaluation of their SARS-CoV2 inhibitory activity	40
ADP-ribosylation systems in bacteria and viruses	40
Dynamic progression of the calf’s microbiome and its influence on host health	40
COVID-19 pandemic: Can zinc supplementation provide an additional shield against the infection?	40
Chaos game representation and its applications in bioinformatics	39
The role of solute binding proteins in signal transduction	39
New approaches for the characterization of plastic-associated microbial communities and the discovery of plastic-degrading microorganisms and enzymes	38
Novel coronavirus disease (COVID-19) pandemic: A recent mini review	38
Computational design of a cutinase for plastic biodegradation by mining molecular dynamics simulations trajectories	38
Advances in multi-omics study of biomarkers of glycolipid metabolism disorder	37
MLACP 2.0: An updated machine learning tool for anticancer peptide prediction	37
Rhizosphere microbiome: Functional compensatory assembly for plant fitness	37
Insights into the biosynthesis pathway of phenolic compounds in microalgae	36
Advances in flux balance analysis by integrating machine learning and mechanism-based models	36
Identifies microtubule-binding protein CSPP1 as a novel cancer biomarker associated with ferroptosis and tumor microenvironment	36
Intense bitterness of molecules: Machine learning for expediting drug discovery	36
Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6	35
Deciphering extrachromosomal circular DNA in Arabidopsis	35
Microorganisms in the reproductive system and probiotic's regulatory effects on reproductive health	35
The ecological roles of microbial lipopeptides: Where are we going?	35
Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain	35
Bacterial species identification using MALDI-TOF mass spectrometry and machine learning techniques: A large-scale benchmarking study	35
Prediction of repurposed drugs for Coronaviruses using artificial intelligence and machine learning	34
DCNN-4mC: Densely connected neural network based N4-methylcytosine site prediction in multiple species	34
Ecological distribution and potential roles of Woesearchaeota in anaerobic biogeochemical cycling unveiled by genomic analysis	34
The intratumor microbiome predicts prognosis across gender and subtypes in papillary thyroid carcinoma	34
Temperature dependence of the SARS-CoV-2 affinity to human ACE2 determines COVID-19 progression and clinical outcome	33
ALDH2 as a potential stem cell-related biomarker in lung adenocarcinoma: Comprehensive multi-omics analysis	33
INPUT: An intelligent network pharmacology platform unique for traditional Chinese medicine	33
Co-crystallization and structure determination: An effective direction for anti-SARS-CoV-2 drug discovery	32
Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next ch	32
Structure-based molecular modeling in SAR analysis and lead optimization	32
Considerations for constructing a protein sequence database for metaproteomics	32
Deep learning in prediction of intrinsic disorder in proteins	32
Targeting protein-protein interaction interfaces in COVID-19 drug discovery	32
Molecular dynamics simulations of the delta and omicron SARS-CoV-2 spike – ACE2 complexes reveal distinct changes between both variants	31
Exploring the impact of intestinal ion transport on the gut microbiota	31
De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology	31
Gene expression data analysis using Hellinger correlation in weighted gene co-expression networks (WGCNA)	31
Phosphotyrosine couples peptide binding and SHP2 activation via a dynamic allosteric network	31
Boolean modelling as a logic-based dynamic approach in systems medicine	31
ggVolcanoR: A Shiny app for customizable visualization of differential expression datasets	31
2D Zernike polynomial expansion: Finding the protein-protein binding regions	30
Richness estimation in microbiome data obtained from denoising pipelines	30
An extracellular lipase from Amycolatopsis mediterannei is a cutinase with plastic degrading activity	30
Application of long-read sequencing to the detection of structural variants in human cancer genomes	30
Computational prediction of secreted proteins in gram-negative bacteria	29
A mathematical model of the circadian clock and drug pharmacology to optimize irinotecan administration timing in colorectal cancer	29
Eleven routine clinical features predict COVID-19 severity uncovered by machine learning of longitudinal measurements	29
Superspreading and heterogeneity in transmission of SARS, MERS, and COVID-19: A systematic review	29
Computational modelling supports that dengue virus envelope antibodies can bind to SARS-CoV-2 receptor binding sites: Is pre-exposure to dengue virus protective against COVID-19 severity?	28
Antibiotic resistance: Time of synthesis in a post-genomic age	28
Exploiting cheminformatic and machine learning to navigate the available chemical space of potential small molecule inhibitors of SARS-CoV-2	28
Oral microbiota transplantation fights against head and neck radiotherapy-induced oral mucositis in mice	28
MXD3 as an onco-immunological biomarker encompassing the tumor microenvironment, disease staging, prognoses, and therapeutic responses in multiple cancer types	28
Deep learning frameworks for protein–protein interaction prediction	28
Synthetic gut microbiome: Advances and challenges	28
Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine	28
Predicted structural mimicry of spike receptor-binding motifs from highly pathogenic human coronaviruses	27
Reconstructing Boolean network ensembles from single-cell data for unraveling dynamics in the aging of human hematopoietic stem cells	27
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures	27
Discovery of a new generation of angiotensin receptor blocking drugs: Receptor mechanisms and in silico binding to enzymes relevant to SARS-CoV-2	27
Contribution of hydrophobic interactions to protein mechanical stability	27
Staphylococcus aureus induces neutrophil extracellular traps (NETs) and neutralizes their bactericidal potential	27
Advances in integrative structural biology: Towards understanding protein complexes in their cellular context	27
Protein conformational switch discerned via network centrality properties	27
Deep learning for COVID-19 chest CT (computed tomography) image analysis: A lesson from lung cancer	26
MetaCancer: A deep learning-based pan-cancer metastasis prediction model developed using multi-omics data	26
Structure-based peptide design targeting intrinsically disordered proteins: Novel histone H4 and H2A peptidic inhibitors	26
Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification	26
From structure to function – Ligand recognition by myeloid C-type lectin receptors	26
Rhizosphere microbes enhance plant salt tolerance: Toward crop production in saline soil	26
TS-m6A-DL: Tissue-specific identification of N6-methyladenosine sites using a universal deep learning model	25
Spontaneous binding of potential COVID-19 drugs (Camostat and Nafamostat) to human serine protease TMPRSS2	25

Effective use of sequence information to predict CRISPR-Cas9 off-target	25
Insight into membraneless organelles and their associated proteins: Drivers, Clients and Regulators	25
Strategies for mitochondrial gene editing	25
Exploiting the molecular basis of age and gender differences in outcomes of SARS-CoV-2 infections	25
Dysbiosis and relapse-related microbiome in inflammatory bowel disease: A shotgun metagenomic approach	25
CRISPR/Cas9 based genome editing for targeted transcriptional control in triple-negative breast cancer	25
Identifying DNA N4-methylcytosine sites in the rosaceae genome with a deep learning model relying on distributed feature representation	25
Machine learning analysis of SERS fingerprinting for the rapid determination of Mycobacterium tuberculosis infection and drug resistance	25
The life and death of RNA across temperatures	25
MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics	24
Machine learning assisted analysis of breast cancer gene expression profiles reveals novel potential prognostic biomarkers for triple-negative breast cancer	24
Gut eukaryotic virome in colorectal carcinogenesis: Is that a trigger?	24
Systematic review of computational methods for drug combination prediction	24
Drug repurposing in psoriasis, performed by reversal of disease-associated gene expression profiles	24
A brief review of protein–ligand interaction prediction	24
Reversal of the unique Q493R mutation increases the affinity of Omicron S1-RBD for ACE2	24
Binding characteristics of staphylococcal protein A and streptococcal protein G for fragment crystallizable portion of human immunoglobulin G	24
A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics	24
Virulence factor-related gut microbiota genes and immunoglobulin A levels as novel markers for machine learning-based classification of autism spectrum disorder	24
Network metrics, structural dynamics and density functional theory calculations identified a novel Ursodeoxycholic Acid derivative against therapeutic target Parkin for Parkinson's disease	24
Employing hypoxia characterization to predict tumour immune microenvironment, treatment sensitivity and prognosis in hepatocellular carcinoma	24
High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance	24
Modeling approaches for probing cross-feeding interactions in the human gut microbiome	24
Application of interpretable machine learning for early prediction of prognosis in acute kidney injury	23
Deep learning for microscopic examination of protozoan parasites	23
Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand	23
Metabolomics and biochemical assays reveal the metabolic responses to hypo-salinity stress and osmoregulatory role of cAMP-PKA pathway in Mercenaria mercenaria	23
Integrative approaches for analysis of mRNA and microRNA high-throughput data	23
FangNet: Mining herb hidden knowledge from TCM clinical effective formulas using structure network algorithm	23
Endocytosis of nutrient transporters in fungi: The ART of connecting signaling and trafficking	23
The mitogenomes of two saprophytic Boletales species (Coniophora) reveals intron dynamics and accumulation of plasmid-derived and non-conserved genes	23
Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning	23
Distinguishing between PTEN clinical phenotypes through mutation analysis	23
Lactobacillus casei Zhang exerts probiotic effects to antibiotic-treated rats	23
Machine learning applications in RNA modification sites prediction	23
The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains	22
Association between intestinal microbiome and inflammatory bowel disease: Insights from bibliometric analysis	22
Prediction of CRISPR/Cas9 single guide RNA cleavage efficiency and specificity by attention-based convolutional neural networks	22
Gut microbiome signatures distinguish type 2 diabetes mellitus from non-alcoholic fatty liver disease	22
Binding affinity and mechanisms of SARS-CoV-2 variants	22
PSNtools for standalone and web-based structure network analyses of conformational ensembles	22
The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour	22
Exploring the universal healthy human gut microbiota around the World	22
Dynamic sensitivity analysis: Defining personalised strategies to drive brain state transitions via whole brain modelling	21
Identification of SHCBP1 as a potential biomarker involving diagnosis, prognosis, and tumor immune microenvironment across multiple cancers	21
Integrating pan-genome with metagenome for microbial community profiling	21
Rational engineering of the lccβ T. versicolor laccase for the mediator-less oxidation of large polycyclic aromatic hydrocarbons	21
SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information	21
Establishment and validation of a cholesterol metabolism-related prognostic signature for hepatocellular carcinoma	21
A guidebook of spatial transcriptomic technologies, data resources and analysis approaches	21
Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus	21
Profiling of host genetic alterations and intra-tumor microbiomes in colorectal cancer	21
WADDAICA: A webserver for aiding protein drug design by artificial intelligence and classical algorithm	21
Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs	21
Correction of out-of-focus microscopic images by deep learning	21
FSL-Kla: A few-shot learning-based multi-feature hybrid system for lactylation site prediction	21
Emerging artificial intelligence applications in Spatial Transcriptomics analysis	21
A data-driven methodology towards evaluating the potential of drug repurposing hypotheses	21
Temperature effect on the SARS-CoV-2: A molecular dynamics study of the spike homotrimeric glycoprotein	21
A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis	20
In silico and in vitro insights into tyrosinase inhibitors with a 2-thioxooxazoline-4-one template	20
Mathematical-based microbiome analytics for clinical translation	20
DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species	20
HDAC2 as a target for developing anti-cancer drugs	20
Microbial interaction-driven community differences as revealed by network analysis	20
Single-cell analysis of multiple cancer types reveals differences in endothelial cells between tumors and normal tissues	20
Comparative host transcriptome in response to pathogenic fungi identifies common and species-specific transcriptional antifungal host response pathways	20
Insights into the molecular mechanism of positive cooperativity between partial agonist MK-8666 and full allosteric agonist AP8 of hGPR40 by Gaussian accelerated molecular dynamics (GaMD) simulations	20
Evolution, correlation, structural impact and dynamics of emerging SARS-CoV-2 variants	20
Computational methods for protein localization prediction	20
Emerging frontiers in human milk microbiome research and suggested primers for 16S rRNA gene analysis	20
OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization	20
Pervasive genome duplications across the plant tree of life and their links to major evolutionary innovations and transitions	20
Integrative RNA profiling of TBEV-infected neurons and astrocytes reveals potential pathogenic effectors	20
Evolutionary coupling-inspired engineering of alcohol dehydrogenase reveals the influence of distant sites on its catalytic efficiency for stereospecific synthesis of chiral alcohols	20
Functional convergence of Yunnan snub-nosed monkey and bamboo-eating panda gut microbiomes revealing the driving by dietary flexibility on mammal gut microbiome	20
Deep learning for protein secondary structure prediction: Pre and post-AlphaFold	19
DeepMC-iNABP: Deep learning for multiclass identification and classification of nucleic acid-binding proteins	19
Structural inspection and protein motions modelling of a fungal glycoside hydrolase family 18 chitinase by crystallography depicts a dynamic enzymatic mechanism	19
Deconvolution algorithms for inference of the cell-type composition of the spatial transcriptome	19
The emerging potential of microbiome transplantation on human health interventions	19
Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data	19
Identification of piRNA disease associations using deep learning	19
Neuroprotective derivatives of tacrine that target NMDA receptor and acetyl cholinesterase – Design, synthesis and biological evaluation	19
Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life	19
Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction	19
Dissecting the role of glutamine in seeding peptide aggregation	19
CHAPERONg: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses	19
MutTMPredictor: Robust and accurate cascade XGBoost classifier for prediction of mutations in transmembrane proteins	19
Secondary structures in RNA synthesis, splicing and translation	19
scDrug: From single-cell RNA-seq to drug response prediction	19
Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum	18
Structural and functional characterization of the receptor binding proteins of Escherichia coli O157 phages EP75 and EP335	18
Using molecular dynamics simulations to interrogate T cell receptor non-equilibrium kinetics	18
Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering	18