Methods

Article	Citations
In silico trials: Verification, validation and uncertainty quantification of predictive models used in the regulatory evaluation of biomedical products	176
Magnetite nanoparticles: Synthesis methods – A comparative review	160
Radiomics for precision medicine: Current challenges, future prospects, and the proposal of a new framework	140
Methods for ChIP-seq analysis: A practical workflow and advanced applications	136
Modern epigenetics methods in biological research	126
DNA methylation methods: Global DNA methylation and methylomic analyses	101
Radiomics in neuro-oncology: Basics, workflow, and applications	87
The design and synthesis of circular RNAs	70
Deep transformers and convolutional neural network in identifying DNA N6-methyladenine sites in cross-species genomes	69
CRISPR-Cas systems for diagnosing infectious diseases	67
Methods for preparation of niosomes: A focus on thin-film hydration method	64
Variational graph auto-encoders for miRNA-disease association prediction	63
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy	61
A compact and interpretable convolutional neural network for cross-subject driver drowsiness detection from single-channel EEG	61
A hierarchical three-step superpixels and deep learning framework for skin lesion classification	55
SMAUG: Analyzing single-molecule tracks with nonparametric Bayesian statistics	52
Diagnosis of cholangiocarcinoma from microscopic hyperspectral pathological dataset by deep convolution neural networks	52
PET/CT radiomics in breast cancer: Mind the step	47
Large-scale phenotyping in dairy sector using milk MIR spectra: Key factors affecting the quality of predictions	45
Methods for analysis of specific DNA methylation status	45
Deep-4mCW2V: A sequence-based predictor to identify N4-methylcytosine sites in Escherichia coli	42
Amyloid-β oligomerization monitored by single-molecule stepwise photobleaching	42
Deep learning of brain magnetic resonance images: A brief review	41
Polymeric nanocapsules: A review on design and production methods for pharmaceutical purpose	41
DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions	41

StackDPPIV: A novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides	41
Automated ECG classification based on 1D deep learning network	39
Prediction and interpretation of cancer survival using graph convolution neural networks	38
Targeted bisulfite sequencing for biomarker discovery	38
Advanced glycation end products in musculoskeletal system and disorders	37
Prediction of drug response in multilayer networks based on fusion of multiomics data	36
A federated learning method for real-time emotion state classification from multi-modal streaming	36
Construction of disulfide containing redox-responsive polymeric nanomedicine	33
Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications	33
Integrating multi-omics data by learning modality invariant representations for improved prediction of overall survival of cancer	32
CRISPR-Cas12-based nucleic acids detection systems	32
Methods for preparation of nanostructured lipid carriers	32
CRISPR-based assays for rapid detection of SARS-CoV-2	32
Subject matching for cross-subject EEG-based recognition of driver states related to situation awareness	31
Intervening on psychopathology networks: Evaluating intervention targets through simulations	31
Reinventing radiation therapy with machine learning and imaging bio-markers (radiomics): State-of-the-art, challenges and perspectives	30
CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning	30
tRFTar: Prediction of tRF-target gene interactions via systemic re-analysis of Argonaute CLIP-seq datasets	30
TopoStats – A program for automated tracing of biomolecules from AFM images	29
RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features	28
Bisindolylmaleimide IX: A novel anti-SARS-CoV2 agent targeting viral main protease 3CLpro demonstrated by virtual screening pipeline and in-vitro validation assays	27
A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis	27
Investigating lymphangiogenesis in a sacrificially bioprinted volumetric model of breast tumor tissue	27
Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins	27
Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods	27
PrGeFNE: Predicting disease-related genes by fast network embedding	26
Methods to quantify heat stress in ruminants: Current status and future prospects	26
Machine learning-enabled optimization of extrusion-based 3D printing	26
Efficient production of large deletion and gene fragment knock-in mice mediated by genome editing with Cas9-mouse Cdt1 in mouse zygotes	26
Mass spectrometric analysis of protein deamidation – A focus on top-down and middle-down mass spectrometry	25
Signal and noise in circRNA translation	25
Deep6mAPred: A CNN and Bi-LSTM-based deep learning method for predicting DNA N6-methyladenosine sites across plant species	25
From tumour perfusion to drug delivery and clinical translation of in silico cancer models	25
CIRCexplorer pipelines for circRNA annotation and quantification from non-polyadenylated RNA-seq datasets	24
Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications	24
Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits	23
Additive manufacturing of bioactive glass biomaterials	23
Verification of CRISPR editing and finding transgenic inserts by Xdrop indirect sequence capture followed by short- and long-read sequencing	22
Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts	22
Detection of changes in the circadian rhythm of cattle in relation to disease, stress, and reproductive events	22
2-[18F]FDG PET/CT radiomics in lung cancer: An overview of the technical aspect and its emerging role in management of the disease	22
Hutchinson-Gilford progeria syndrome: Rejuvenating old drugs to fight accelerated ageing	22
Mapping the RNA structural landscape of viral genomes	21
Viral RNA structure analysis using DMS-MaPseq	21
dPromoter-XGBoost: Detecting promoters and strength by combining multiple descriptors and feature selection using XGBoost	21
The AGE Reader: A non-invasive method to assess long-term tissue damage	21
An in silico hybrid continuum-/agent-based procedure to modelling cancer development: Interrogating the interplay amongst glioma invasion, vascularity and necrosis	20
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	20
Resources for computational prediction of intrinsic disorder in proteins	20
Adversarial learning for semi-supervised pediatric sleep staging with single-EEG channel	19

Targeting cancer epigenetics with CRISPR-dCAS9: Principles and prospects	19
A practical guide for analysis of histone post-translational modifications by mass spectrometry: Best practices and pitfalls	19
Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies	19
Deep learning-based multimodal image analysis for cervical cancer detection	19
DeepTL-Ubi: A novel deep transfer learning method for effectively predicting ubiquitination sites of multiple species	19
Repeatability and ranking of long-term enteric methane emissions measurement on dairy cows across diets and time using GreenFeed system in farm-conditions	19
Functional imaging using radiomic features in assessment of lymphoma	18
Universal Southern blot protocol with cold or radioactive probes for the validation of alleles obtained by homologous recombination	18
Systematic review of radiomic biomarkers for predicting immune checkpoint inhibitor treatment outcomes	18
Drug repurposing for COVID-19 using computational screening: Is Fostamatinib/R406 a potential candidate?	18
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	18
Structural and molecular perspectives of SARS-CoV-2	18
Comparative analysis of network-based approaches and machine learning algorithms for predicting drug-target interactions	18
Penguin: A tool for predicting pseudouridine sites in direct RNA nanopore sequencing data	18
Smart biomaterials: From 3D printing to 4D bioprinting	18
Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis	17
Ensemble learning models that predict surface protein abundance from single-cell multimodal omics data	17
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	17
A brief review of machine learning methods for RNA methylation sites prediction	17
Structural and functional connectivity abnormalities of the default mode network in patients with Alzheimer's disease and mild cognitive impairment within two independent datasets	17
Predicting CircRNA disease associations using novel node classification and link prediction models on Graph Convolutional Networks	17
Digital PCR can augment the interpretation of RT-qPCR Cq values for SARS-CoV-2 diagnostics	17
A novel subnetwork representation learning method for uncovering disease-disease relationships	17
Nanopore long-read sequencing of circRNAs	17
CRISPR-mediated knock-in in the mouse embryo using long single stranded DNA donors synthesised by biotinylated PCR	16
Therapeutic approaches for SARS-CoV-2 infection	16
Atomistic and coarse-grained simulations of membrane proteins: A practical guide	16
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	16
DeepBindBC: A practical deep learning method for identifying native-like protein-ligand complexes in virtual screening	16
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	16
Methods for biomaterials printing: A short review and perspective	15
DNN-PNN: A parallel deep neural network model to improve anticancer drug sensitivity	15
Explore drug-like space with deep generative models	15
Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes	15
Decoding selective auditory attention with EEG using a transformer model	15
Glaucoma screening using an attention-guided stereo ensemble network	15
Microfabricated disk technology: Rapid scale up in midbrain organoid generation	15
Multi-targeting approach for nsp3, nsp9, nsp12 and nsp15 proteins of SARS-CoV-2 by Diosmin as illustrated by molecular docking and molecular dynamics simulation methodologies	15
PET image reconstruction using physical and mathematical modelling for time of flight PET-MR scanners in the STIR library	15
Protein domain microarrays as a platform to decipher signaling pathways and the histone code	15
Droplet digital PCR or quantitative PCR for in-depth genomic and functional validation of genetically altered rodents	15
Variability of computed tomography radiomics features of fibrosing interstitial lung disease: A test-retest study	15
From current knowledge to best practice: A primer on viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants	15
An integrated pipeline for high-throughput screening and profiling of spheroids using simple live image analysis of frame to frame variations	14
CRISPR-Cas, Argonaute proteins and the emerging landscape of amplification-free diagnostics	14
Potentials and caveats of AI in hybrid imaging	14
Methods to study circRNA-protein interactions	14
A network embedding based method for partial multi-omics integration in cancer subtyping	14
A brief review of RNA modification related database resources	14
Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation	14
Identifying and ranking potential cancer drivers using representation learning on attributed network	14
An interpretable deep learning model for classifying adaptor protein complexes from sequence information	14
MTGNN: Multi-Task Graph Neural Network based few-shot learning for disease similarity measurement	13
Action and function of helicases on RNA G-quadruplexes	13
Profiling of circRNAs using an enzyme-free digital counting method	13
MDL-CPI: Multi-view deep learning model for compound-protein interaction prediction	13
Estimation of dairy goat body composition: A direct calibration and comparison of eight methods	13
Application of CE-MS for the analysis of histones and histone modifications	13
Artificial intelligence and radiomics in pediatric molecular imaging	13
m6A-Maize: Weakly supervised prediction of m6A-carrying transcripts and m6A-affecting mutations in maize (Zea mays)	13
Production of knockout mouse lines with Cas9	13
Single-molecule and ensemble methods to probe RNP nucleation and condensate properties	13
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	13
A new lysosome-targeted fluorescent probe for hydrogen peroxide based on a benzothiazole derivative	13
Hyper-graph based sparse canonical correlation analysis for the diagnosis of Alzheimer’s disease from multi-dimensional genomic data	12
The cognitive science of COVID-19: Acceptance, denial, and belief change	12
RLDOCK method for predicting RNA-small molecule binding modes	12
DNMG: Deep molecular generative model by fusion of 3D information for de novo drug design	12
Ultrasensitive detection and quantification of viral nucleic acids with Raindance droplet digital PCR (ddPCR)	12
An assessment of the reproducibility of reverse transcription digital PCR quantification of HIV-1	12
Identifying and characterizing virus-encoded circular RNAs	12
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	12
m6AmPred: Identifying RNA N6, 2′-O-dimethyladenosine (m6Am) sites based on sequence-derived information	12
Targeted manipulation of m6A RNA modification through CRISPR-Cas-based strategies	12
Quantification of mRNA cap-modifications by means of LC-QqQ-MS	12
Visualization of the dynamics of histone modifications and their crosstalk using PTM-CrossTalkMapper	12
Systems dynamics and the uncertainties of diagnostics, testing and contact tracing for COVID-19	12
Luciferase-based GloSensor™ cAMP assay: Temperature optimization and application to cell-based kinetic studies	11
Multi-scale approaches for the simulation of cardiac electrophysiology: II – Tissue-level structure and function	11
Method for highly selective, ultrasensitive fluorimetric detection of Cu2+ and Al3+ by Schiff bases containing o-phenylenediamine and o-aminophenol	11

Graph convolutional network approach to discovering disease-related circRNA-miRNA-mRNA axes	11
Heterogeneous graph attention networks for drug virus association prediction	11
Identification of adaptor proteins using the ANOVA feature selection technique	11
Absolute quantification of SARS-CoV-2 with Clarity Plus™ digital PCR	11
Recent progress in the analysis of protein deamidation using mass spectrometry	11
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	11
PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features	11
Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS	11
Stimulated emission depletion (STED) super resolution imaging of RNA- and protein-containing domains in fixed cells	11
Hybrid manifold-deep convolutional neural network for sleep staging	11
Triplex digital PCR assays for the quantification of intact proviral HIV-1 DNA	11
Molecular characterization and RSV Co-infection of Nicotiana benthamiana with three distinct begomoviruses	10
Model-based autoencoders for imputing discrete single-cell RNA-seq data	10
Introduction of mutations in plants with prime editing	10
Methods to investigate advanced glycation end-product and their application in clinical practice	10
Multi-scale approaches for the simulation of cardiac electrophysiology: I – Sub-cellular and stochastic calcium dynamics from cell to organ	10
Prediction of coronary heart disease based on combined reinforcement multitask progressive time-series networks	10
Isolation and culture of adult murine cardiac atrial and ventricular fibroblasts and myofibroblasts	10
WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction	10
An open-access computer image analysis (CIA) method to predict meat and fat content from an android smartphone-derived picture of the bovine 5th-6th rib	10
Continuum mechanical parameterisation of cytoplasmic dynein from atomistic simulation	10
An epileptic seizure prediction model based on a time-wise attention simulation module and a pretrained ResNet	10
Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets	10
Deep learning in preclinical antibody drug discovery and development	10
Computational modelling of flavivirus dynamics: The ins and outs	9
Analysis of coordinated NMR chemical shifts to map allosteric regulatory networks in proteins	9
Progression and application of CRISPR-Cas genomic editors	9
PAQMAN: Protein-nucleic acid affinity quantification by MAss spectrometry in nuclear extracts	9
Identification and detection of mecciRNAs	9
Use of CRISPR/Cas ribonucleoproteins for high throughput gene editing of induced pluripotent stem cells	9
DeepSADPr: A hybrid-learning architecture for serine ADP-ribosylation site prediction	9
Methods and approaches to estimate B vitamin status in dairy cows: Knowledge, gaps and advances	9
A correlative super-resolution protocol to visualise structural underpinnings of fast second-messenger signalling in primary cell types	9
Guide for starting or optimizing a 3D printing clinical service	9
Correlating single-molecule characteristics of the yeast aquaglyceroporin Fps1 with environmental perturbations directly in living cells	9
Quantitative mass spectrometry-based analysis of proteins related to cattle and their products – Focus on cows’ milk beta-casein proteoforms	9
Discover novel disease-associated genes based on regulatory networks of long-range chromatin interactions	9
rPAC: Route based pathway analysis for cohorts of gene expression data sets	9
Fluorescent turn-on sensing of albumin proteins (BSA and ovalbumin) using vitamin B6 cofactor derived Schiff base	9
Applicability analysis of immunotherapy for lung cancer patients based on deep learning	9
Single-molecule FRET dynamics of molecular motors in an ABEL trap	9
Analysis of pseudouridines and other RNA modifications using HydraPsiSeq protocol	9
Mapping circular RNA structures in living cells by SHAPE-MaP	9
Exploring the artificial intelligence and machine learning models in the context of drug design difficulties and future potential for the pharmaceutical sectors	9
Imaging the fibroblast growth factor receptor network on the plasma membrane with DNA-assisted single-molecule super-resolution microscopy	9
MRDFF: A deep forest based framework for CT whole heart segmentation	9
Bacterial flagellar motor as a multimodal biosensor	9
Automation of data analysis in molecular cancer imaging and its potential impact on future clinical practice	8
An approach to measuring protein turnover in human induced pluripotent stem cell organoids by mass spectrometry	8
Clip for studying protein-RNA interactions that regulate virus replication	8
Paired dCas9 design as a nucleic acid detection platform for pathogenic strains	8
A high-throughput screening platform to identify nanocarriers for efficient delivery of RNA-based therapies	8
Promoter prediction in nannochloropsis based on densely connected convolutional neural networks	8
AntiMF: A deep learning framework for predicting anticancer peptides based on multi-view feature extraction	8
Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data	8
Trends in deamidation across archaeological bones, ceramics and dental calculus	8
Emerging tools to investigate bromodomain functions	8
Development of europium(III) complex functionalized silica nanoprobe for luminescence detection of tetracycline	8
Latest progress in the study of nanoparticle-based delivery of the CRISPR/Cas9 system	8
ATRANET – Automated generation of transition networks for the structural characterization of intrinsically disordered proteins	8
The prognostic value of machine learning techniques versus cox regression model for head and neck cancer	8
A multi-objective optimization method for identification of module biomarkers for disease diagnosis	8
Can alternative PET reconstruction schemes improve the prognostic value of radiomic features in non-small cell lung cancer?	8
A pseudo-Siamese framework for circRNA-RBP binding sites prediction integrating BiLSTM and soft attention mechanism	8
Efficient allele conversion in mouse zygotes and primary cells based on electroporation of Cre protein	8
Antisense probing of dynamic RNA structures	8
Using Drosophila to uncover molecular and physiological functions of circRNAs	8
Comprehensive analysis of histone-binding proteins with multi-angle light scattering	8
Atrial-specific hiPSC-derived cardiomyocytes in drug discovery and disease modeling	8
A network biology approach to identify crucial host targets for COVID-19	8
DREAM: Drug-drug interaction extraction with enhanced dependency graph and attention mechanism	8
A near-infrared emitted fluorescence probe for the detection of biosulfite in live zebrafish, mouse and real food samples	8
Topographically smooth and stable supported lipid bilayer for high-resolution AFM studies	8
Joint models for the longitudinal analysis of measurement scales in the presence of informative dropout	8
COVID-19 lesion detection and segmentation–A deep learning method	8
Structure-function analysis of DEAD-box helicase DDX43	8
m6Am RNA modification detection by m6Am-seq	8
A fitness training optimization system based on heart rate prediction under different activities	8
Engineered U1 snRNAs to modulate alternatively spliced exons	8
Methods in isolation and characterization of bovine monocytes and macrophages	7
Low-dose CT imaging via cascaded ResUnet with spectrum loss	7
Integrated approaches to reveal mechanisms by which RNA viruses reprogram the cellular environment	7
Pseudouridine RNA modification detection and quantification by RT-PCR	7
Brain controllability and morphometry similarity of internet gaming addiction	7
Test positivity – Evaluation of a new metric to assess epidemic dispersal mediated by non-symptomatic cases	7
iEnhancer-MRBF: Identifying enhancers and their strength with a multiple Laplacian-regularized radial basis function network	7
Pyrene-based fluorescent chemosensor for rapid detection of water and its applications	7
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome	7
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	7
Pan-methylarginine antibody generation using PEG linked GAR motifs as antigens	7
Cervical lesion image enhancement based on conditional entropy generative adversarial network framework	7
Data-driven case fatality rate estimation for the primary lineage of SARS-CoV-2 in Poland	7
AAPred-CNN: Accurate predictor based on deep convolution neural network for identification of anti-angiogenic peptides	7
SiBERT: A Siamese-based BERT network for Chinese medical entities alignment	7
MultiscaleDTA: A multiscale-based method with a self-attention mechanism for drug-target binding affinity prediction	7