Methods

Article	Citations
In silico trials: Verification, validation and uncertainty quantification of predictive models used in the regulatory evaluation of biomedical products	145
Magnetite nanoparticles: Synthesis methods – A comparative review	130
Radiomics for precision medicine: Current challenges, future prospects, and the proposal of a new framework	125
Methods for ChIP-seq analysis: A practical workflow and advanced applications	115
Modern epigenetics methods in biological research	102
Radiomics in neuro-oncology: Basics, workflow, and applications	85
DNA methylation methods: Global DNA methylation and methylomic analyses	81
Methods for loading therapeutics into extracellular vesicles and generating extracellular vesicles mimetic-nanovesicles	68
Deep transformers and convolutional neural network in identifying DNA N6-methyladenine sites in cross-species genomes	66
SDLDA: lncRNA-disease association prediction based on singular value decomposition and deep learning	61
Recent trends in cell membrane-cloaked nanoparticles for therapeutic applications	61
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy	61
Variational graph auto-encoders for miRNA-disease association prediction	56
CRISPR-Cas systems for diagnosing infectious diseases	56
From laboratory to clinic: Translation of extracellular vesicle based cancer biomarkers	54
Improved library preparation with the new iCLIP2 protocol	52
A hierarchical three-step superpixels and deep learning framework for skin lesion classification	51
Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition	50
Methods for preparation of niosomes: A focus on thin-film hydration method	49
A compact and interpretable convolutional neural network for cross-subject driver drowsiness detection from single-channel EEG	49
SMAUG: Analyzing single-molecule tracks with nonparametric Bayesian statistics	48
Predicting drug-drug interactions using multi-modal deep auto-encoders based network embedding and positive-unlabeled learning	48
The design and synthesis of circular RNAs	47
iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites	46
Assessment of separation methods for extracellular vesicles from human and mouse brain tissues and human cerebrospinal fluids	45

Unraveling the mechanisms that specify molecules for secretion in extracellular vesicles	43
PET/CT radiomics in breast cancer: Mind the step	42
Diagnosis of cholangiocarcinoma from microscopic hyperspectral pathological dataset by deep convolution neural networks	41
Expression of eukaryotic membrane proteins in eukaryotic and prokaryotic hosts	41
Generation, purification and engineering of extracellular vesicles and their biomedical applications	40
Deep-4mCW2V: A sequence-based predictor to identify N4-methylcytosine sites in Escherichia coli	38
Methods for analysis of specific DNA methylation status	37
DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions	37
Large-scale phenotyping in dairy sector using milk MIR spectra: Key factors affecting the quality of predictions	36
Deep-Hipo: Multi-scale receptive field deep learning for histopathological image analysis	36
Amyloid-β oligomerization monitored by single-molecule stepwise photobleaching	36
CRISPR-based assays for rapid detection of SARS-CoV-2	34
StackDPPIV: A novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides	34
Deep learning of brain magnetic resonance images: A brief review	34
Extracellular blebs: Artificially-induced extracellular vesicles for facile production and clinical translation	33
Polymeric nanocapsules: A review on design and production methods for pharmaceutical purpose	33
Targeted bisulfite sequencing for biomarker discovery	33
Prediction of drug response in multilayer networks based on fusion of multiomics data	33
Prediction and interpretation of cancer survival using graph convolution neural networks	32
Advanced glycation end products in musculoskeletal system and disorders	32
The message passing neural networks for chemical property prediction on SMILES	29
Subject matching for cross-subject EEG-based recognition of driver states related to situation awareness	29
Automated ECG classification based on 1D deep learning network	28
Reinventing radiation therapy with machine learning and imaging bio-markers (radiomics): State-of-the-art, challenges and perspectives	28
Engineered extracellular vesicles and their mimetics for clinical translation	27
RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features	27
CRISPR-Cas12-based nucleic acids detection systems	27
tRFTar: Prediction of tRF-target gene interactions via systemic re-analysis of Argonaute CLIP-seq datasets	27
Nano-Ghosts: Biomimetic membranal vesicles, technology and characterization	26
Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications	26
CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning	26
Construction of disulfide containing redox-responsive polymeric nanomedicine	25
Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins	25
Fast and unbiased purification of RNA-protein complexes after UV cross-linking	25
Bisindolylmaleimide IX: A novel anti-SARS-CoV2 agent targeting viral main protease 3CLpro demonstrated by virtual screening pipeline and in-vitro validation assays	25
A federated learning method for real-time emotion state classification from multi-modal streaming	25
Integrating multi-omics data by learning modality invariant representations for improved prediction of overall survival of cancer	24
Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods	24
GCN-BMP: Investigating graph representation learning for DDI prediction task	24
PrGeFNE: Predicting disease-related genes by fast network embedding	24
Methods to quantify heat stress in ruminants: Current status and future prospects	24
Intervening on psychopathology networks: Evaluating intervention targets through simulations	24
Efficient production of large deletion and gene fragment knock-in mice mediated by genome editing with Cas9-mouse Cdt1 in mouse zygotes	23
Isolation and characterization of microvesicles from mesenchymal stem cells	23
Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts	23
Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications	23
From tumour perfusion to drug delivery and clinical translation of in silico cancer models	22
Detection of changes in the circadian rhythm of cattle in relation to disease, stress, and reproductive events	22
A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis	22
Mass spectrometric analysis of protein deamidation – A focus on top-down and middle-down mass spectrometry	22

TopoStats – A program for automated tracing of biomolecules from AFM images	22
Encoder-decoder CNN models for automatic tracking of tongue contours in real-time ultrasound data	22
Methods for preparation of nanostructured lipid carriers	22
Deep6mAPred: A CNN and Bi-LSTM-based deep learning method for predicting DNA N6-methyladenosine sites across plant species	21
Mapping the RNA structural landscape of viral genomes	21
Differential fluorescence nanoparticle tracking analysis for enumeration of the extracellular vesicle content in mixed particulate solutions	21
Signal and noise in circRNA translation	20
Machine learning-enabled optimization of extrusion-based 3D printing	20
Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits	20
2-[18F]FDG PET/CT radiomics in lung cancer: An overview of the technical aspect and its emerging role in management of the disease	20
TOP: A deep mixture representation learning method for boosting molecular toxicity prediction	19
Verification of CRISPR editing and finding transgenic inserts by Xdrop indirect sequence capture followed by short- and long-read sequencing	19
CIRCexplorer pipelines for circRNA annotation and quantification from non-polyadenylated RNA-seq datasets	19
An in silico hybrid continuum-/agent-based procedure to modelling cancer development: Interrogating the interplay amongst glioma invasion, vascularity and necrosis	19
Viral RNA structure analysis using DMS-MaPseq	19
Additive manufacturing of bioactive glass biomaterials	19
A deep metric learning approach for histopathological image retrieval	18
DeepTL-Ubi: A novel deep transfer learning method for effectively predicting ubiquitination sites of multiple species	18
Adversarial learning for semi-supervised pediatric sleep staging with single-EEG channel	18
icSHAPE-pipe: A comprehensive toolkit for icSHAPE data analysis and evaluation	18
A novel graph attention adversarial network for predicting disease-related associations	17
A novel subnetwork representation learning method for uncovering disease-disease relationships	17
Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies	17
Structural and molecular perspectives of SARS-CoV-2	17
A practical guide for analysis of histone post-translational modifications by mass spectrometry: Best practices and pitfalls	17
Resources for computational prediction of intrinsic disorder in proteins	17
Universal Southern blot protocol with cold or radioactive probes for the validation of alleles obtained by homologous recombination	17
The AGE Reader: A non-invasive method to assess long-term tissue damage	17
Interpretable machine learning in bioinformatics	16
Systematic review of radiomic biomarkers for predicting immune checkpoint inhibitor treatment outcomes	16
Repeatability and ranking of long-term enteric methane emissions measurement on dairy cows across diets and time using GreenFeed system in farm-conditions	16
Reprogramming extracellular vesicles with engineered proteins	16
CRISPR-mediated knock-in in the mouse embryo using long single stranded DNA donors synthesised by biotinylated PCR	16
Functional imaging using radiomic features in assessment of lymphoma	16
Drug repurposing for COVID-19 using computational screening: Is Fostamatinib/R406 a potential candidate?	16
Targeting cancer epigenetics with CRISPR-dCAS9: Principles and prospects	16
Comparative analysis of network-based approaches and machine learning algorithms for predicting drug-target interactions	15
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	15
dPromoter-XGBoost: Detecting promoters and strength by combining multiple descriptors and feature selection using XGBoost	15
Structural and functional connectivity abnormalities of the default mode network in patients with Alzheimer's disease and mild cognitive impairment within two independent datasets	15
PET image reconstruction using physical and mathematical modelling for time of flight PET-MR scanners in the STIR library	15
Digital PCR can augment the interpretation of RT-qPCR Cq values for SARS-CoV-2 diagnostics	15
Atomistic and coarse-grained simulations of membrane proteins: A practical guide	15
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	15
A network embedding based method for partial multi-omics integration in cancer subtyping	14
Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis	14
Solid-supported lipid bilayers – A versatile tool for the structural and functional characterization of membrane proteins	14
Droplet digital PCR or quantitative PCR for in-depth genomic and functional validation of genetically altered rodents	14
Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation	14
From current knowledge to best practice: A primer on viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants	14
Smart biomaterials: From 3D printing to 4D bioprinting	14
A brief review of RNA modification related database resources	14
Microfabricated disk technology: Rapid scale up in midbrain organoid generation	14
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	14
An integrated pipeline for high-throughput screening and profiling of spheroids using simple live image analysis of frame to frame variations	14
A brief review of machine learning methods for RNA methylation sites prediction	14
Glaucoma screening using an attention-guided stereo ensemble network	14
Nanopore long-read sequencing of circRNAs	14
Therapeutic approaches for SARS-CoV-2 infection	14
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	14
CRISPR-Cas, Argonaute proteins and the emerging landscape of amplification-free diagnostics	13
Lipid exchange among polymer-encapsulated nanodiscs by time-resolved Förster resonance energy transfer	13
Predicting CircRNA disease associations using novel node classification and link prediction models on Graph Convolutional Networks	13
m6A-Maize: Weakly supervised prediction of m6A-carrying transcripts and m6A-affecting mutations in maize (Zea mays)	13
CLIP and RNA interactome studies to unravel genome-wide RNA-protein interactions in vivo in Arabidopsis thaliana	13
Ensemble learning models that predict surface protein abundance from single-cell multimodal omics data	13
Biophysical analysis of lipidic nanoparticles	13
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	13
Potentials and caveats of AI in hybrid imaging	13
Variability of computed tomography radiomics features of fibrosing interstitial lung disease: A test-retest study	13
RNA-centric approaches to study RNA-protein interactions in vitro and in silico	13
m6AmPred: Identifying RNA N6, 2′-O-dimethyladenosine (m6Am) sites based on sequence-derived information	12
Protein domain microarrays as a platform to decipher signaling pathways and the histone code	12
Quantification of mRNA cap-modifications by means of LC-QqQ-MS	12
DeepBindBC: A practical deep learning method for identifying native-like protein-ligand complexes in virtual screening	12
Production of knockout mouse lines with Cas9	12
An assessment of the reproducibility of reverse transcription digital PCR quantification of HIV-1	12
Visualization of the dynamics of histone modifications and their crosstalk using PTM-CrossTalkMapper	12
Ultrasensitive detection and quantification of viral nucleic acids with Raindance droplet digital PCR (ddPCR)	12
Penguin: A tool for predicting pseudouridine sites in direct RNA nanopore sequencing data	12

Artificial intelligence and radiomics in pediatric molecular imaging	12
Systems dynamics and the uncertainties of diagnostics, testing and contact tracing for COVID-19	12
Application of CE-MS for the analysis of histones and histone modifications	11
Identifying and ranking potential cancer drivers using representation learning on attributed network	11
Explore drug-like space with deep generative models	11
Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes	11
Estimation of dairy goat body composition: A direct calibration and comparison of eight methods	11
Action and function of helicases on RNA G-quadruplexes	11
Graph convolutional network approach to discovering disease-related circRNA-miRNA-mRNA axes	11
Aggregated network centrality shows non-random structure of genomic and proteomic networks	11
Decoding selective auditory attention with EEG using a transformer model	11
Profiling of circRNAs using an enzyme-free digital counting method	11
Methods for biomaterials printing: A short review and perspective	11
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	11
Triplex digital PCR assays for the quantification of intact proviral HIV-1 DNA	11
Deep learning-based multimodal image analysis for cervical cancer detection	11
Targeted manipulation of m6A RNA modification through CRISPR-Cas-based strategies	10
Multi-scale approaches for the simulation of cardiac electrophysiology: II – Tissue-level structure and function	10
Prediction of coronary heart disease based on combined reinforcement multitask progressive time-series networks	10
Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets	10
Inference of chromosome 3D structures from GAM data by a physics computational approach	10
An interpretable deep learning model for classifying adaptor protein complexes from sequence information	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
Hybrid manifold-deep convolutional neural network for sleep staging	10
Model-based autoencoders for imputing discrete single-cell RNA-seq data	10
Generating therapeutic monoclonal antibodies to complex multi-spanning membrane targets: Overcoming the antigen challenge and enabling discovery strategies	10
MTGNN: Multi-Task Graph Neural Network based few-shot learning for disease similarity measurement	10
Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS	10
Single-molecule and ensemble methods to probe RNP nucleation and condensate properties	10
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	10
Identifying and characterizing virus-encoded circular RNAs	10
Methods to study circRNA-protein interactions	10