Methods

Article	Citations
Methods and approaches to estimate B vitamin status in dairy cows: Knowledge, gaps and advances	193
Stereological estimation of cardiomyocyte number and proliferation	183
Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework	152
An integrated pipeline for high-throughput screening and profiling of spheroids using simple live image analysis of frame to frame variations	146
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	140
Hutchinson-Gilford progeria syndrome: Rejuvenating old drugs to fight accelerated ageing	110
Radiomics for precision medicine: Current challenges, future prospects, and the proposal of a new framework	87
TopoStats – A program for automated tracing of biomolecules from AFM images	77
Resources for computational prediction of intrinsic disorder in proteins	77
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	76
RDscan: Extracting RNA-disease relationship from the literature based on pre-training model	71
PET image reconstruction using physical and mathematical modelling for time of flight PET-MR scanners in the STIR library	70
Bacterial flagellar motor as a multimodal biosensor	64
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	61
SPIDE: A single cell potency inference method based on the local cell-specific network entropy	55
DMGL-MDA: A dual-modal graph learning method for microbe-drug association prediction	54
Editorial Board	52
Local augmented graph neural network for multi-omics cancer prognosis prediction and analysis	52
Editorial Board	51
Disease biomarker identification based on sample network optimization	48
Development of europium(III) complex functionalized silica nanoprobe for luminescence detection of tetracycline	47
Targeted mutagenesis in human iPSCs using CRISPR genome-editing tools	45
Approaches for the sensitive detection of rare base and prime editing events	44
Methods special issue: DNA and RNA helicases	43
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	42

Machine learning based identification of hub genes in renal clear cell carcinoma using multi-omics data	42
Toward drug-miRNA resistance association prediction by positional encoding graph neural network and multi-channel neural network	41
Split light up aptamers as a probing tool for nucleic acids	39
Special issue Methods: Nano-/bio-interface and biomedical applications	38
Predicting Drug-drug Interaction with Graph Mutual Interaction Attention Mechanism	38
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors	38
Point-of-care image-based quantitative urinalysis with commercial reagent strips: Design and clinical evaluation	37
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	36
Editorial Board	36
Advances in direct detection of lysine methylation and acetylation by nuclear magnetic resonance using 13C-enriched cofactors	33
An effective multi-task learning framework for drug repurposing based on graph representation learning	33
A method for assaying DNA flexibility	32
Editorial Board	32
A mutual promotion encoder-decoder method for ultrasonic hydronephrosis diagnosis	31
Design in biology and rational design in vaccinology: A conceptual analysis	31
Engineered U1 snRNAs to modulate alternatively spliced exons	30
GNPI: Graph normalization to integrate phylogenetic information for metagenomic host phenotype prediction	30
Editorial Board	30
Deep Learning in Bioinformatics and Biomedicine	29
Software defined radio frequency sensing framework for intelligent monitoring of sleep apnea syndrome	28
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	28
Editorial Board	27
Determining translocation orientations of nucleic acid helicases	27
Using inverse finite element analysis to identify spinal tissue behaviour in situ	27
Methods for preparation of nanoconstructs	27
Editorial Board	27
Methods for circular RNAs	27
Editorial Board	26
Test positivity – Evaluation of a new metric to assess epidemic dispersal mediated by non-symptomatic cases	26
Editorial	26
Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes	25
MultiscaleDTA: A multiscale-based method with a self-attention mechanism for drug-target binding affinity prediction	25
scSSA: A clustering method for single cell RNA-seq data based on semi-supervised autoencoder	24
Pan-methylarginine antibody generation using PEG linked GAR motifs as antigens	24
Brain controllability and morphometry similarity of internet gaming addiction	23
PDSM-LGCN: Prediction of drug sensitivity associated microRNAs via light graph convolution neural network	23
Method for the structural analysis of Twinkle mitochondrial DNA helicase by cryo-EM	22
MFF-DTA: Multi-scale feature fusion for drug-target affinity prediction	22
Machine learning for the analysis of multi-omics data	22
Fluorescent turn-on sensing of albumin proteins (BSA and ovalbumin) using vitamin B6 cofactor derived Schiff base	22
WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction	22
Editorial Board	21
Interpretable thoracic pathologic prediction via learning group-disentangled representation	21
Learning from imbalanced COVID-19 chest X-ray (CXR) medical imaging data	20
Sleep Staging Framework with Physiologically Harmonized Sub-Networks	20
SiBERT: A Siamese-based BERT network for Chinese medical entities alignment	20
Predicting CircRNA disease associations using novel node classification and link prediction models on Graph Convolutional Networks	20
Methods special issue: Recent advancement on fluorescent chemosensing and bioimaging	19
Editorial Board	19
NMR-based isotope editing, chemoselection and isotopomer distribution analysis in stable isotope resolved metabolomics	19

Current methodologies in studying chromatin and gene expression	19
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	19
Anle138b interaction in α-synuclein aggregates by dynamic nuclear polarization NMR	19
Editorial: Artificial intelligence in drug discovery and development	19
A new lysosome-targeted fluorescent probe for hydrogen peroxide based on a benzothiazole derivative	19
Using Drosophila to uncover molecular and physiological functions of circRNAs	19
Hydrogel-based hybrid membrane enhances in vitro ophthalmic drug evaluation in the OphthalMimic device	18
Repeatability and ranking of long-term enteric methane emissions measurement on dairy cows across diets and time using GreenFeed system in farm-conditions	18
Advanced deep learning approaches enable high-throughput biological and biomedicine data analysis	18
Systems dynamics and the uncertainties of diagnostics, testing and contact tracing for COVID-19	18
m6Adecom: Analysis of m6A profile matrix based on graph regularized non-negative matrix factorization	18
Heterogeneous graph attention networks for drug virus association prediction	18
A novel deep learning identifier for promoters and their strength using heterogeneous features	18
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	18
Additive manufacturing of bioactive glass biomaterials	18
PhosBERT: A self-supervised learning model for identifying phosphorylation sites in SARS-CoV-2-infected human cells	18
Minimal invasive fluorescence methods to quantify advanced glycation end products (AGEs) in skin and plasma of humans	17
Detection of changes in the circadian rhythm of cattle in relation to disease, stress, and reproductive events	17
Design of a 1 × 4 micro-magnetic stimulation device and its targeted, coordinated regulation on LTP of Schaffer-CA1 in the hippocampus of rats	17
A hierarchical three-step superpixels and deep learning framework for skin lesion classification	17
m6A-Maize: Weakly supervised prediction of m6A-carrying transcripts and m6A-affecting mutations in maize (Zea mays)	17
Trends in deamidation across archaeological bones, ceramics and dental calculus	17
DeepSADPr: A hybrid-learning architecture for serine ADP-ribosylation site prediction	17
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	16
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data	16
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	16
Fluorescent human RPA to track assembly dynamics on DNA	16
Triplex digital PCR assays for the quantification of intact proviral HIV-1 DNA	16
Design and characterization of hollow microneedles for localized intrascleral drug delivery of ocular formulations	16
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	15
MDL-CPI: Multi-view deep learning model for compound-protein interaction prediction	15
Microbiome metabolite quantification methods enabling insights into human health and disease	15
Identification of potential pan-coronavirus therapies using a computational drug repurposing platform	15
Subject matching for cross-subject EEG-based recognition of driver states related to situation awareness	15
A fluorescence turn “on-off” imaging probe for sequential detection of Al3+ and L-Cysteine in HeLa cells	15
m6Am RNA modification detection by m6Am-seq	15
Functional imaging using radiomic features in assessment of lymphoma	15
Movement recognition via channel-activation-wise sEMG attention	15
Editorial for methods special issue: Big data in digital health: methods, analysis and prospects	15
Methods to investigate nucleosome structure and dynamics with single-molecule FRET	14
Digital Intervention for behaviouR changE and Chronic disease prevenTION (DIRECTION): Study protocol for a randomized controlled trial of a web-based platform integrating nutrition, physical activity,	14
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	14
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	14
DNA shape features improve prediction of CRISPR/Cas9 activity	14
Methods to study circRNA-protein interactions	14
SMAUG: Analyzing single-molecule tracks with nonparametric Bayesian statistics	14
Does protein pretrained language model facilitate the prediction of protein–ligand interaction?	14
Intervening on psychopathology networks: Evaluating intervention targets through simulations	13
Targeted bisulfite sequencing for biomarker discovery	13
DNMG: Deep molecular generative model by fusion of 3D information for de novo drug design	13
On finding natural antibiotics based on TCM formulae	13
Introduction of mutations in plants with prime editing	13
Advances in base editing with an emphasis on an AAV-based strategy	13
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	13
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	13
m6Acancer-Net: Identification of m6A-mediated cancer driver genes from gene-site heterogeneous network	13
Explore drug-like space with deep generative models	13
An aggregation-induced emission-based ratiometric fluorescent chemosensor for Hg(II) and its application in Caenorhabditis elegans imaging	12
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	12
Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data	12
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	12
Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies	12
Deep6mAPred: A CNN and Bi-LSTM-based deep learning method for predicting DNA N6-methyladenosine sites across plant species	12
A fitness training optimization system based on heart rate prediction under different activities	12
Prediction and interpretation of cancer survival using graph convolution neural networks	12
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	12
The platform development, adherence and efficacy to a digital Brief therapy for insomnia (dBTI) during the COVID-19 pandemic	12
Therapeutic approaches for SARS-CoV-2 infection	12
Advances in the exact nuclear Overhauser effect 2018–2022	11
Prediction of YY1 loop anchor based on multi-omics features	11
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer	11
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy	11
SpaInGNN: Enhanced clustering and integration of spatial transcriptomics based on refined graph neural networks	11
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications	11
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm	11
Identifying and characterizing virus-encoded circular RNAs	11
Variability of computed tomography radiomics features of fibrosing interstitial lung disease: A test-retest study	11
WITHDRAWN: Deep networks and network representation in bioinformatics	11
MVCLST: A spatial transcriptome data analysis pipeline for cell type classification based on multi-view comparative learning	11
An interpretable deep learning model for classifying adaptor protein complexes from sequence information	11

HCI-modelling for improving the clinical usability of digital health technologies	10
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	10
Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues	10
Data-driven case fatality rate estimation for the primary lineage of SARS-CoV-2 in Poland	10
A self-supervised feature-standardization-block for cross-domain lung disease classification	10
Emulation of Quantitative Systems Pharmacology models to accelerate virtual population inference in immuno-oncology	10
Single-cell RNA-seq data analysis based on directed graph neural network	10
Comprehensive evaluation of molecule property prediction with ChatGPT	10
Alleviation of neurological disease by RNA editing	10
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	10
CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning	10
TPQCI: A topology potential-based method to quantify functional influence of copy number variations	10
MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models	10
AAPred-CNN: Accurate predictor based on deep convolution neural network for identification of anti-angiogenic peptides	10
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	9
Integrating multi-omics data by learning modality invariant representations for improved prediction of overall survival of cancer	9
Naphthalimide-based new architecture for fluorescence turn-on sensing of Cu2+ and colorimetric detection of F-/CN–	9
MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction	9
Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review	9
Model-based autoencoders for imputing discrete single-cell RNA-seq data	9
PrGeFNE: Predicting disease-related genes by fast network embedding	9
Editorial Board	9
The fine art of preparing membrane transport proteins for biomolecular simulations: Concepts and practical considerations	9
Verification of CRISPR editing and finding transgenic inserts by Xdrop indirect sequence capture followed by short- and long-read sequencing	9
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph	9
In vitro production and multiplex quantification of 2′,3′-cyclic phosphate-containing 5′-tRNA half molecules	9
Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors	9
Atomistic and coarse-grained simulations of membrane proteins: A practical guide	9
DNN-PNN: A parallel deep neural network model to improve anticancer drug sensitivity	9
Efficient experimental method for purifying allergens from aqueous extracts	9
MRDFF: A deep forest based framework for CT whole heart segmentation	9
Non-canonical amino acids and protein dynamics	9
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis	9
Novel, standardized sample collection from the brain-nose interface	9
N-GlycoPred: A hybrid deep learning model for accurate identification of N-glycosylation sites	9
RETRACTED: A methodological framework for rigorous systematic reviews: Tailoring comprehensive analyses to clinicians and healthcare professionals	9
Isothermal titration calorimetry and surface plasmon resonance methods to probe protein–protein interactions	9
Efficient allele conversion in mouse zygotes and primary cells based on electroporation of Cre protein	9
Microfabricated disk technology: Rapid scale up in midbrain organoid generation	9
Atomic force microscope kymograph analysis: A case study of two membrane proteins	8
Editorial Board	8
Hexagonal image segmentation on spatially resolved transcriptomics	8
Guest Editor introduction	8
Multi-sample dual-decoder graph autoencoder	8
Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data	8
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome	8
Isolation and culture of adult murine cardiac atrial and ventricular fibroblasts and myofibroblasts	8
Synthesis of carbon nanotubes using pre-sintered oil fly ash via a reproducible process with large-scale potential	8
Measuring occupancies of the nucleosome and nucleosome-interacting factors in vivo in Saccharomyces cerevisiae genome-wide	8
Basic techniques associated with studying transcription elongation both in vitro and in vivo within mammalian cells	8
Editorial Board	8
High-throughput genotyping of high-homology mutant mouse strains by next-generation sequencing	8
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures	8
Sizing, stabilising, and cloning repeat-expansions for gene targeting constructs	8
Editorial Board	8
Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets	8
Editorial Board	8
Relaxation and single site multiple mutations to identify and control allosteric networks	8
Site-specific protein conjugates incorporating Para-Azido-L-Phenylalanine for cellular and in vivo imaging	8
Advances in optical and electrochemical sensing of bisphenol a (BPA) utilizing microfluidic Technology: A mini perspective	8
NetAUC: A network-based multi-biomarker identification method by AUC optimization	8
A heat diffusion multilayer network approach for the identification of functional biomarkers in rumen methane emissions	8
Detecting circRNA in purified spliceosomal P complex	8
rPAC: Route based pathway analysis for cohorts of gene expression data sets	8
Trans ligation of RNAs to generate hybrid circular RNAs using highly efficient autocatalytic transcripts	8
Study of circular RNA translation using reporter systems in living cells	8
Furan-based (photo)oxidation reactions and their application in nucleic acid and protein targeting	8
Targeting cancer epigenetics with CRISPR-dCAS9: Principles and prospects	7
Use of CRISPR/Cas ribonucleoproteins for high throughput gene editing of induced pluripotent stem cells	7
Low-dose CT imaging via cascaded ResUnet with spectrum loss	7
Machine learning methods for bio-medical image and signal processing: Recent advances	7
COVID-19 related interdisciplinary methods: Preventing errors and detecting research opportunities	7
Detection and Segmentation of Breast Masses Based on Multi-Layer Feature Fusion	7
An in silico hybrid continuum-/agent-based procedure to modelling cancer development: Interrogating the interplay amongst glioma invasion, vascularity and necrosis	7
The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years	7
An epileptic seizure prediction model based on a time-wise attention simulation module and a pretrained ResNet	7
Machine learning-enabled optimization of extrusion-based 3D printing	7
Imaging the fibroblast growth factor receptor network on the plasma membrane with DNA-assisted single-molecule super-resolution microscopy	7
Advanced glycation end products in musculoskeletal system and disorders	7
Cervical lesion image enhancement based on conditional entropy generative adversarial network framework	7
M−CDC: Magnetic pull-down-assisted colorimetric method based on the CRISPR/Cas12a system	7
Bioinformatics resources for understanding RNA modifications	7
Utilization of passive visual perception task in detecting patients with major depressive disorder for active health	7
Droplet digital PCR or quantitative PCR for in-depth genomic and functional validation of genetically altered rodents	7
Nucleic acid sample preparation techniques for bead-based suspension arrays	7
Structure-function analysis of DEAD-box helicase DDX43	7
Nanopore long-read sequencing of circRNAs	7
Structural and functional connectivity abnormalities of the default mode network in patients with Alzheimer's disease and mild cognitive impairment within two independent datasets	7
Multiple analyte profiling (MAP) index as a powerful diagnostic and therapeutic monitoring tool	7
Determination of rate constants for conformational changes of RNA helicases by single-molecule FRET TIRF microscopy	7
Recent developments for the analysis of latent constructs using measurement scales in health research	7
Editorial Board	7
Engineering natural based nanocomposite inks via interface interaction for extrusion 3D printing	7
Pyrene-based fluorescent chemosensor for rapid detection of water and its applications	7
The evolution of N6-methyladenosine regulators in plants	7