Computational and Structural Biotechnology Journal

Article	Citations
Survival analysis across the entire transcriptome identifies biomarkers with the highest prognostic power in breast cancer	431
UCell: Robust and scalable single-cell gene signature scoring	238
The DisGeNET cytoscape app: Exploring and visualizing disease genomics data	227
Integration strategies of multi-omics data for machine learning analysis	196
From pyroptosis, apoptosis and necroptosis to PANoptosis: A mechanistic compendium of programmed cell death pathways	187
The language of proteins: NLP, machine learning & protein sequences	177
Review on circular RNAs and new insights into their roles in cancer	173
The oralome and its dysbiosis: New insights into oral microbiome-host interactions	173
A review on machine learning approaches and trends in drug discovery	167
Chemokines and chemokine receptors during COVID-19 infection	145
Network analysis methods for studying microbial communities: A mini review	131
Automated methods for cell type annotation on scRNA-seq data	122
Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring	110
Multi-omics approaches in cancer research with applications in tumor subtyping, prognosis, and diagnosis	109
Nanopore sequencing and its application to the study of microbial communities	103
An overview of current COVID-19 vaccine platforms	97
Farnesoid X receptor (FXR): Structures and ligands	94
Prediction of HER2-positive breast cancer recurrence and metastasis risk from histopathological images and clinical information via multimodal deep learning	90
Association of risk factors with type 2 diabetes: A systematic review	83
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data	80
The molecular feature of macrophages in tumor immune microenvironment of glioma patients	78
Recent advances in exploring the heavy metal(loid) resistant microbiome	69
Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes	68
Machine learning and deep learning methods that use omics data for metastasis prediction	67
Dependence of SARS-CoV-2 infection on cholesterol-rich lipid raft and endosomal acidification	66

Statistical methods for Mendelian randomization in genome-wide association studies: A review	61
Machine learning in the prediction of cancer therapy	59
A review on marine plastisphere: biodiversity, formation, and role in degradation	59
On the road to explainable AI in drug-drug interactions prediction: A systematic review	59
Artificial intelligence in clinical care amidst COVID-19 pandemic: A systematic review	58
Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing	57
Accurate brain tumor detection using deep convolutional neural network	53
Phycobiliproteins: Structural aspects, functional characteristics, and biotechnological perspectives	53
Statistical and machine learning methods for spatially resolved transcriptomics with histology	52
A review on compound-protein interaction prediction methods: Data, format, representation and model	51
Integrated metabolomics and network pharmacology to reveal the mechanisms of hydroxysafflor yellow A against acute traumatic brain injury	51
Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins	51
Skin microbiome transplantation and manipulation: Current state of the art	49
QuPath: The global impact of an open source digital pathology system	48
The genus Bifidobacterium: from genomics to functionality of an important component of the mammalian gut microbiota	47
Immune evasion of SARS-CoV-2 from interferon antiviral system	47
Advances in the development of therapeutic strategies against COVID-19 and perspectives in the drug design for emerging SARS-CoV-2 variants	47
Applied machine learning in cancer research: A systematic review for patient diagnosis, classification and prognosis	47
Stressed out: Bacterial response to high salinity using compatible solute biosynthesis and uptake systems, lessons from Vibrionaceae	45
Defining the wheat microbiome: Towards microbiome-facilitated crop production	45
Metabolic modelling approaches for describing and engineering microbial communities	44
Antioxidants and pentoxifylline as coadjuvant measures to standard therapy to improve prognosis of patients with pneumonia by COVID-19	43
Computational strategies for single-cell multi-omics integration	43
MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation	42
Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation	42
Protein domain identification methods and online resources	41
Identification of cyclin protein using gradient boost decision tree algorithm	40
Robustness of differential gene expression analysis of RNA-seq	40
Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor	39
Statistical methods for mediation analysis in the era of high-throughput genomics: Current successes and future challenges	39
N-terminal domain mutations of the spike protein are structurally implicated in epitope recognition in emerging SARS-CoV-2 strains	39
Secrete or perish: The role of secretion systems in Xanthomonas biology	38
Inhibition of the main protease of SARS-CoV-2 (Mpro) by repurposing/designing drug-like substances and utilizing nature’s toolbox of bioactive compounds	38
Identification of multipotent drugs for COVID-19 therapeutics with the evaluation of their SARS-CoV2 inhibitory activity	38
Representation learning applications in biological sequence analysis	38
DeepOmix: A scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis	38
Protein–protein interaction prediction with deep learning: A comprehensive review	37
Structural and molecular biology of hepatitis E virus	37
Human endogenous retroviruses in development and disease	37
COVID-19 pandemic: Can zinc supplementation provide an additional shield against the infection?	37
Subtypes of tail spike proteins predicts the host range of Ackermannviridae phages	37
An overview of potential inhibitors targeting non-structural proteins 3 (PLpro and Mac1) and 5 (3CLpro/Mpro) of SARS-CoV-2	37
AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae	37
The mechanism of activation of monomeric B-Raf V600E	36
Novel coronavirus disease (COVID-19) pandemic: A recent mini review	35
AI applications in functional genomics	35
Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6	35
Codon-based indices for modeling gene expression and transcript evolution	34
Diet-gut microbiota interactions on cardiovascular disease	34
ADP-ribosylation systems in bacteria and viruses	34

The role of solute binding proteins in signal transduction	34
DCNN-4mC: Densely connected neural network based N4-methylcytosine site prediction in multiple species	33
Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain	33
Deimmunization of protein therapeutics – Recent advances in experimental and computational epitope prediction and deletion	32
Ecological distribution and potential roles of Woesearchaeota in anaerobic biogeochemical cycling unveiled by genomic analysis	32
Gut microbial metabolome in inflammatory bowel disease: From association to therapeutic perspectives	32
Dynamic progression of the calf’s microbiome and its influence on host health	32
Deciphering extrachromosomal circular DNA in Arabidopsis	31
The ecological roles of microbial lipopeptides: Where are we going?	31
N1-methyladenosine modification in cancer biology: Current status and future perspectives	31
Prediction of repurposed drugs for Coronaviruses using artificial intelligence and machine learning	31
Soil under stress: The importance of soil life and how it is influenced by (micro)plastic pollution	31
Computational solutions for spatial transcriptomics	31
Temperature dependence of the SARS-CoV-2 affinity to human ACE2 determines COVID-19 progression and clinical outcome	31
Molecular dynamics simulations of the delta and omicron SARS-CoV-2 spike – ACE2 complexes reveal distinct changes between both variants	31
From sequence to function through structure: Deep learning for protein design	31
Intense bitterness of molecules: Machine learning for expediting drug discovery	30
Rhizosphere microbiome: Functional compensatory assembly for plant fitness	30
The intratumor microbiome predicts prognosis across gender and subtypes in papillary thyroid carcinoma	30
Automatic cell type identification methods for single-cell RNA sequencing	29
New approaches for the characterization of plastic-associated microbial communities and the discovery of plastic-degrading microorganisms and enzymes	28
2D Zernike polynomial expansion: Finding the protein-protein binding regions	28
Phosphotyrosine couples peptide binding and SHP2 activation via a dynamic allosteric network	28
Chaos game representation and its applications in bioinformatics	27
Computational design of a cutinase for plastic biodegradation by mining molecular dynamics simulations trajectories	27
Eleven routine clinical features predict COVID-19 severity uncovered by machine learning of longitudinal measurements	27
Co-crystallization and structure determination: An effective direction for anti-SARS-CoV-2 drug discovery	27
Targeting protein-protein interaction interfaces in COVID-19 drug discovery	27
Insights into the biosynthesis pathway of phenolic compounds in microalgae	27
Superspreading and heterogeneity in transmission of SARS, MERS, and COVID-19: A systematic review	27
Advances in flux balance analysis by integrating machine learning and mechanism-based models	27
Antibiotic resistance: Time of synthesis in a post-genomic age	26
Application of long-read sequencing to the detection of structural variants in human cancer genomes	26
Exploiting cheminformatic and machine learning to navigate the available chemical space of potential small molecule inhibitors of SARS-CoV-2	26
An extracellular lipase from Amycolatopsis mediterannei is a cutinase with plastic degrading activity	26
De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology	26
Machine learning application in personalised lung cancer recurrence and survivability prediction	26
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	26
Benchmarking of Nanopore R10.4 and R9.4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing	26
INPUT: An intelligent network pharmacology platform unique for traditional Chinese medicine	26
Boolean modelling as a logic-based dynamic approach in systems medicine	25
Modelling microbial communities: Harnessing consortia for biotechnological applications	25
Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification	25
Staphylococcus aureus induces neutrophil extracellular traps (NETs) and neutralizes their bactericidal potential	25
Microorganisms in the reproductive system and probiotic's regulatory effects on reproductive health	25
Spontaneous binding of potential COVID-19 drugs (Camostat and Nafamostat) to human serine protease TMPRSS2	25
MXD3 as an onco-immunological biomarker encompassing the tumor microenvironment, disease staging, prognoses, and therapeutic responses in multiple cancer types	25
Predicted structural mimicry of spike receptor-binding motifs from highly pathogenic human coronaviruses	25
MLACP 2.0: An updated machine learning tool for anticancer peptide prediction	25
Advances in multi-omics study of biomarkers of glycolipid metabolism disorder	24
A mathematical model of the circadian clock and drug pharmacology to optimize irinotecan administration timing in colorectal cancer	24
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?	24
Deep learning in prediction of intrinsic disorder in proteins	23
Reconstructing Boolean network ensembles from single-cell data for unraveling dynamics in the aging of human hematopoietic stem cells	23
Insight into membraneless organelles and their associated proteins: Drivers, Clients and Regulators	23
Deep learning for COVID-19 chest CT (computed tomography) image analysis: A lesson from lung cancer	23
Computational prediction of secreted proteins in gram-negative bacteria	23
TS-m6A-DL: Tissue-specific identification of N6-methyladenosine sites using a universal deep learning model	23
Advances in integrative structural biology: Towards understanding protein complexes in their cellular context	23
A guide to multi-omics data collection and integration for translational medicine	23
Gene expression data analysis using Hellinger correlation in weighted gene co-expression networks (WGCNA)	22
Deep learning frameworks for protein–protein interaction prediction	22
Protein conformational switch discerned via network centrality properties	22
FangNet: Mining herb hidden knowledge from TCM clinical effective formulas using structure network algorithm	22
Structure-based peptide design targeting intrinsically disordered proteins: Novel histone H4 and H2A peptidic inhibitors	22
Considerations for constructing a protein sequence database for metaproteomics	22
CRISPR/Cas9 based genome editing for targeted transcriptional control in triple-negative breast cancer	22
Structure-based molecular modeling in SAR analysis and lead optimization	22
Strategies for mitochondrial gene editing	22
Exploiting the molecular basis of age and gender differences in outcomes of SARS-CoV-2 infections	22
The mitogenomes of two saprophytic Boletales species (Coniophora) reveals intron dynamics and accumulation of plasmid-derived and non-conserved genes	22
Employing hypoxia characterization to predict tumour immune microenvironment, treatment sensitivity and prognosis in hepatocellular carcinoma	22
Identifying DNA N4-methylcytosine sites in the rosaceae genome with a deep learning model relying on distributed feature representation	21
Lactobacillus casei Zhang exerts probiotic effects to antibiotic-treated rats	21
Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus	21
Gut eukaryotic virome in colorectal carcinogenesis: Is that a trigger?	21
Bacterial species identification using MALDI-TOF mass spectrometry and machine learning techniques: A large-scale benchmarking study	21
Dysbiosis and relapse-related microbiome in inflammatory bowel disease: A shotgun metagenomic approach	21
ggVolcanoR: A Shiny app for customizable visualization of differential expression datasets	21
Modeling approaches for probing cross-feeding interactions in the human gut microbiome	20

Oral microbiota transplantation fights against head and neck radiotherapy-induced oral mucositis in mice	20
Binding affinity and mechanisms of SARS-CoV-2 variants	20
Integrative approaches for analysis of mRNA and microRNA high-throughput data	20
Identifies microtubule-binding protein CSPP1 as a novel cancer biomarker associated with ferroptosis and tumor microenvironment	20
MetaCancer: A deep learning-based pan-cancer metastasis prediction model developed using multi-omics data	20
Evolution, correlation, structural impact and dynamics of emerging SARS-CoV-2 variants	20
Distinguishing between PTEN clinical phenotypes through mutation analysis	20
Synthetic gut microbiome: Advances and challenges	20
A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics	20
Machine learning applications in RNA modification sites prediction	20
Effective use of sequence information to predict CRISPR-Cas9 off-target	19
Exploring the impact of intestinal ion transport on the gut microbiota	19
Prediction of CRISPR/Cas9 single guide RNA cleavage efficiency and specificity by attention-based convolutional neural networks	19
Endocytosis of nutrient transporters in fungi: The ART of connecting signaling and trafficking	19
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures	19
FIREcaller: Detecting frequently interacting regions from Hi-C data	19
Association between intestinal microbiome and inflammatory bowel disease: Insights from bibliometric analysis	19
Virulence factor-related gut microbiota genes and immunoglobulin A levels as novel markers for machine learning-based classification of autism spectrum disorder	19
Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum	18
Network metrics, structural dynamics and density functional theory calculations identified a novel Ursodeoxycholic Acid derivative against therapeutic target Parkin for Parkinson's disease	18
A data-driven methodology towards evaluating the potential of drug repurposing hypotheses	18
In silico and in vitro insights into tyrosinase inhibitors with a 2-thioxooxazoline-4-one template	18
Richness estimation in microbiome data obtained from denoising pipelines	18
The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains	18
ALDH2 as a potential stem cell-related biomarker in lung adenocarcinoma: Comprehensive multi-omics analysis	18
Discovery of a new generation of angiotensin receptor blocking drugs: Receptor mechanisms and in silico binding to enzymes relevant to SARS-CoV-2	18
Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering	18
A brief review of protein–ligand interaction prediction	18
Gut microbiome signatures distinguish type 2 diabetes mellitus from non-alcoholic fatty liver disease	18
Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs	18
Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises	18
Application of interpretable machine learning for early prediction of prognosis in acute kidney injury	17
A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis	17
MutTMPredictor: Robust and accurate cascade XGBoost classifier for prediction of mutations in transmembrane proteins	17
The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour	17
The life and death of RNA across temperatures	17
Metabolomics reveals sex-specific metabolic shifts and predicts the duration from positive to negative in non-severe COVID-19 patients during recovery process	17
Machine learning assisted analysis of breast cancer gene expression profiles reveals novel potential prognostic biomarkers for triple-negative breast cancer	17
Neuroprotective derivatives of tacrine that target NMDA receptor and acetyl cholinesterase – Design, synthesis and biological evaluation	17
High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance	17
WADDAICA: A webserver for aiding protein drug design by artificial intelligence and classical algorithm	17
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	17
Transcriptomic signatures and repurposing drugs for COVID-19 patients: findings of bioinformatics analyses	17
Identification of SHCBP1 as a potential biomarker involving diagnosis, prognosis, and tumor immune microenvironment across multiple cancers	17
PSNtools for standalone and web-based structure network analyses of conformational ensembles	17
Rational engineering of the lccβ T. versicolor laccase for the mediator-less oxidation of large polycyclic aromatic hydrocarbons	17
Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine	17
Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life	17
Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family	17
MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics	17
Reversal of the unique Q493R mutation increases the affinity of Omicron S1-RBD for ACE2	16
OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization	16
SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants	16
Active phase prebiotic feeding alters gut microbiota, induces weight-independent alleviation of hepatic steatosis and serum cholesterol in high-fat diet-fed mice	16
Automated and semi-automated enhancement, segmentation and tracing of cytoskeletal networks in microscopic images: A review	16
Emerging frontiers in human milk microbiome research and suggested primers for 16S rRNA gene analysis	16
Temperature effect on the SARS-CoV-2: A molecular dynamics study of the spike homotrimeric glycoprotein	16
Drug repurposing in psoriasis, performed by reversal of disease-associated gene expression profiles	16
DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species	16
Metabolomics and biochemical assays reveal the metabolic responses to hypo-salinity stress and osmoregulatory role of cAMP-PKA pathway in Mercenaria mercenaria	16
Contribution of sample processing to gut microbiome analysis in the model Lepidoptera, silkworm Bombyx mori	16
Binding characteristics of staphylococcal protein A and streptococcal protein G for fragment crystallizable portion of human immunoglobulin G	16
Comparative host transcriptome in response to pathogenic fungi identifies common and species-specific transcriptional antifungal host response pathways	16
Dissecting the role of glutamine in seeding peptide aggregation	16
Prediction of GPCR activity using machine learning	16
Maize specialized metabolome networks reveal organ-preferential mixed glycosides	16
Profiling of host genetic alterations and intra-tumor microbiomes in colorectal cancer	15
Integrating pan-genome with metagenome for microbial community profiling	15
Systems biology reveals key tissue-specific metabolic and transcriptional signatures involved in the response of Medicago truncatula plant genotypes to salt stress	15
Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction	15
DeepMC-iNABP: Deep learning for multiclass identification and classification of nucleic acid-binding proteins	15
A comparative study of multiple instance learning methods for cancer detection using T-cell receptor sequences	15
Drug repositioning in drug discovery of T2DM and repositioning potential of antidiabetic agents	15
SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information	15
A tandem motif-based and structural approach can identify hidden functional phosphodiesterases	15
Neuropilins: C-end rule peptides and their association with nociception and COVID-19	15
Exploring the universal healthy human gut microbiota around the World	15
Microbial interaction-driven community differences as revealed by network analysis	15
Substantial cell apoptosis provoked by naked PAMAM dendrimers in HER2-positive human breast cancer via JNK and ERK1/ERK2 signalling pathways	15
High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance	15
FSL-Kla: A few-shot learning-based multi-feature hybrid system for lactylation site prediction	15
TF-COMB – Discovering grammar of transcription factor binding sites	15
Machine learning analysis of SERS fingerprinting for the rapid determination of Mycobacterium tuberculosis infection and drug resistance	14
Deep learning for microscopic examination of protozoan parasites	14
Machine learning applied to serum and cerebrospinal fluid metabolomes revealed altered arginine metabolism in neonatal sepsis with meningoencephalitis	14
Strategies for structure elucidation of small molecules based on LC–MS/MS data from complex biological samples	14
The emerging potential of microbiome transplantation on human health interventions	14
Dynamic sensitivity analysis: Defining personalised strategies to drive brain state transitions via whole brain modelling	14
Mini-review: Recent advances in post-translational modification site prediction based on deep learning	14
Transcriptional and translational landscape of Candida auris in response to caspofungin	14
PySTACHIO: Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn, a flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy data	14
Rhizosphere microbes enhance plant salt tolerance: Toward crop production in saline soil	14
The constrained disorder principle defines living organisms and provides a method for correcting disturbed biological systems	14
Functional convergence of Yunnan snub-nosed monkey and bamboo-eating panda gut microbiomes revealing the driving by dietary flexibility on mammal gut microbiome	14
Transcriptomic and genomic changes associated with radioadaptation in Exophiala dermatitidis	14