Methods

Article	Citations
Methods and approaches to estimate B vitamin status in dairy cows: Knowledge, gaps and advances	183
Movement recognition via channel-activation-wise sEMG attention	152
Interpretable thoracic pathologic prediction via learning group-disentangled representation	146
Advances in direct detection of lysine methylation and acetylation by nuclear magnetic resonance using 13C-enriched cofactors	140
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	110
Software defined radio frequency sensing framework for intelligent monitoring of sleep apnea syndrome	87
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies	77
An effective multi-task learning framework for drug repurposing based on graph representation learning	77
MFF-DTA: Multi-scale feature fusion for drug-target affinity prediction	76
Editorial Board	71
Retraction notice to “A methodological framework for rigorous systematic reviews: Tailoring comprehensive analyses to clinicians and healthcare professionals” [Methods 225 (2024) 38–43]	70
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	64
Stereological estimation of cardiomyocyte number and proliferation	61
Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework	55
An integrated pipeline for high-throughput screening and profiling of spheroids using simple live image analysis of frame to frame variations	54
Hutchinson-Gilford progeria syndrome: Rejuvenating old drugs to fight accelerated ageing	52
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	52
Radiomics for precision medicine: Current challenges, future prospects, and the proposal of a new framework	51
TopoStats – A program for automated tracing of biomolecules from AFM images	48
Resources for computational prediction of intrinsic disorder in proteins	47
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	45
RDscan: Extracting RNA-disease relationship from the literature based on pre-training model	44
Bacterial flagellar motor as a multimodal biosensor	43
SPIDE: A single cell potency inference method based on the local cell-specific network entropy	42
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	42

DMGL-MDA: A dual-modal graph learning method for microbe-drug association prediction	41
Editorial Board	39
Editorial Board	38
Local augmented graph neural network for multi-omics cancer prognosis prediction and analysis	38
Disease biomarker identification based on sample network optimization	38
Development of europium(III) complex functionalized silica nanoprobe for luminescence detection of tetracycline	37
Targeted mutagenesis in human iPSCs using CRISPR genome-editing tools	36
Approaches for the sensitive detection of rare base and prime editing events	36
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	33
Methods special issue: DNA and RNA helicases	33
Toward drug-miRNA resistance association prediction by positional encoding graph neural network and multi-channel neural network	32
Machine learning based identification of hub genes in renal clear cell carcinoma using multi-omics data	32
Split light up aptamers as a probing tool for nucleic acids	31
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors	31
Special issue Methods: Nano-/bio-interface and biomedical applications	30
Predicting Drug-drug Interaction with Graph Mutual Interaction Attention Mechanism	30
Point-of-care image-based quantitative urinalysis with commercial reagent strips: Design and clinical evaluation	30
Editorial Board	29
A method for assaying DNA flexibility	28
Editorial Board	28
Deep Learning in Bioinformatics and Biomedicine	27
Editorial Board	27
Engineered U1 snRNAs to modulate alternatively spliced exons	27
Design in biology and rational design in vaccinology: A conceptual analysis	27
GNPI: Graph normalization to integrate phylogenetic information for metagenomic host phenotype prediction	27
A mutual promotion encoder-decoder method for ultrasonic hydronephrosis diagnosis	27
Editorial Board	26
Methods for circular RNAs	26
Editorial Board	26
Determining translocation orientations of nucleic acid helicases	25
Editorial	24
Methods for preparation of nanoconstructs	24
Test positivity – Evaluation of a new metric to assess epidemic dispersal mediated by non-symptomatic cases	23
Editorial Board	23
MultiscaleDTA: A multiscale-based method with a self-attention mechanism for drug-target binding affinity prediction	22
Brain controllability and morphometry similarity of internet gaming addiction	22
Pan-methylarginine antibody generation using PEG linked GAR motifs as antigens	22
scSSA: A clustering method for single cell RNA-seq data based on semi-supervised autoencoder	22
Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes	22
Machine learning for the analysis of multi-omics data	21
PDSM-LGCN: Prediction of drug sensitivity associated microRNAs via light graph convolution neural network	21
WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction	20
Fluorescent turn-on sensing of albumin proteins (BSA and ovalbumin) using vitamin B6 cofactor derived Schiff base	20
Method for the structural analysis of Twinkle mitochondrial DNA helicase by cryo-EM	20
Predicting CircRNA disease associations using novel node classification and link prediction models on Graph Convolutional Networks	19
Learning from imbalanced COVID-19 chest X-ray (CXR) medical imaging data	19
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	19
Editorial: Artificial intelligence in drug discovery and development	19
Current methodologies in studying chromatin and gene expression	19
Methods special issue: Recent advancement on fluorescent chemosensing and bioimaging	19

Sleep Staging Framework with Physiologically Harmonized Sub-Networks	19
SiBERT: A Siamese-based BERT network for Chinese medical entities alignment	19
Editorial Board	19
PhosBERT: A self-supervised learning model for identifying phosphorylation sites in SARS-CoV-2-infected human cells	18
A new lysosome-targeted fluorescent probe for hydrogen peroxide based on a benzothiazole derivative	18
Heterogeneous graph attention networks for drug virus association prediction	18
Hydrogel-based hybrid membrane enhances in vitro ophthalmic drug evaluation in the OphthalMimic device	18
NMR-based isotope editing, chemoselection and isotopomer distribution analysis in stable isotope resolved metabolomics	18
Advanced deep learning approaches enable high-throughput biological and biomedicine data analysis	18
Additive manufacturing of bioactive glass biomaterials	18
Using Drosophila to uncover molecular and physiological functions of circRNAs	18
Anle138b interaction in α-synuclein aggregates by dynamic nuclear polarization NMR	18
A novel deep learning identifier for promoters and their strength using heterogeneous features	18
DeepSADPr: A hybrid-learning architecture for serine ADP-ribosylation site prediction	17
Repeatability and ranking of long-term enteric methane emissions measurement on dairy cows across diets and time using GreenFeed system in farm-conditions	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
Systems dynamics and the uncertainties of diagnostics, testing and contact tracing for COVID-19	17
m6A-Maize: Weakly supervised prediction of m6A-carrying transcripts and m6A-affecting mutations in maize (Zea mays)	17
m6Adecom: Analysis of m6A profile matrix based on graph regularized non-negative matrix factorization	17
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	17
Detection of changes in the circadian rhythm of cattle in relation to disease, stress, and reproductive events	16
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	16
A hierarchical three-step superpixels and deep learning framework for skin lesion classification	16
Minimal invasive fluorescence methods to quantify advanced glycation end products (AGEs) in skin and plasma of humans	16
Trends in deamidation across archaeological bones, ceramics and dental calculus	16
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
MDL-CPI: Multi-view deep learning model for compound-protein interaction prediction	15
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	15
Fluorescent human RPA to track assembly dynamics on DNA	15
Functional imaging using radiomic features in assessment of lymphoma	15
m6Am RNA modification detection by m6Am-seq	15
Triplex digital PCR assays for the quantification of intact proviral HIV-1 DNA	15
Editorial for methods special issue: Big data in digital health: methods, analysis and prospects	15
Identification of potential pan-coronavirus therapies using a computational drug repurposing platform	15
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data	15
Subject matching for cross-subject EEG-based recognition of driver states related to situation awareness	14
Microbiome metabolite quantification methods enabling insights into human health and disease	14
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	14
Methods to study circRNA-protein interactions	14
SMAUG: Analyzing single-molecule tracks with nonparametric Bayesian statistics	14
A fluorescence turn “on-off” imaging probe for sequential detection of Al3+ and L-Cysteine in HeLa cells	14
Methods to investigate nucleosome structure and dynamics with single-molecule FRET	14
DNA shape features improve prediction of CRISPR/Cas9 activity	14
Does protein pretrained language model facilitate the prediction of protein–ligand interaction?	13
m6Acancer-Net: Identification of m6A-mediated cancer driver genes from gene-site heterogeneous network	13
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	13
On finding natural antibiotics based on TCM formulae	13
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	13
Intervening on psychopathology networks: Evaluating intervention targets through simulations	13
Targeted bisulfite sequencing for biomarker discovery	13
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	13
An interpretable deep learning model for classifying adaptor protein complexes from sequence information	13
Introduction of mutations in plants with prime editing	13
Advances in base editing with an emphasis on an AAV-based strategy	12
Prediction and interpretation of cancer survival using graph convolution neural networks	12
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	12
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	12
Explore drug-like space with deep generative models	12
An aggregation-induced emission-based ratiometric fluorescent chemosensor for Hg(II) and its application in Caenorhabditis elegans imaging	12
Deep6mAPred: A CNN and Bi-LSTM-based deep learning method for predicting DNA N6-methyladenosine sites across plant species	12
DNMG: Deep molecular generative model by fusion of 3D information for de novo drug design	12
Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies	12
The platform development, adherence and efficacy to a digital Brief therapy for insomnia (dBTI) during the COVID-19 pandemic	12
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer	11
Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data	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
SpaInGNN: Enhanced clustering and integration of spatial transcriptomics based on refined graph neural networks	11
Therapeutic approaches for SARS-CoV-2 infection	11
Prediction of YY1 loop anchor based on multi-omics features	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
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	11
A fitness training optimization system based on heart rate prediction under different activities	11
Design and characterization of hollow microneedles for localized intrascleral drug delivery of ocular formulations	10
Nanopore long-read sequencing of circRNAs	10
Emulation of Quantitative Systems Pharmacology models to accelerate virtual population inference in immuno-oncology	10
Structure-function analysis of DEAD-box helicase DDX43	10
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,	10
Variability of computed tomography radiomics features of fibrosing interstitial lung disease: A test-retest study	10

Structural and functional connectivity abnormalities of the default mode network in patients with Alzheimer's disease and mild cognitive impairment within two independent datasets	10
AAPred-CNN: Accurate predictor based on deep convolution neural network for identification of anti-angiogenic peptides	10
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy	10
MRDFF: A deep forest based framework for CT whole heart segmentation	10
A roadmap to cysteine specific labeling of membrane proteins for single-molecule photobleaching studies	10
Isothermal titration calorimetry and surface plasmon resonance methods to probe protein–protein interactions	10
HCI-modelling for improving the clinical usability of digital health technologies	10
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis	9
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	9
MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models	9
Novel, standardized sample collection from the brain-nose interface	9
DeepDBS: Identification of DNA-binding sites in protein sequences by using deep representations and random forest	9
N-GlycoPred: A hybrid deep learning model for accurate identification of N-glycosylation sites	9
PENet: Prior evidence deep neural network for bladder cancer staging	9
RETRACTED: A methodological framework for rigorous systematic reviews: Tailoring comprehensive analyses to clinicians and healthcare professionals	9
Single-cell RNA-seq data analysis based on directed graph neural network	9
Multi-sample dual-decoder graph autoencoder	9
Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues	9
Verification of CRISPR editing and finding transgenic inserts by Xdrop indirect sequence capture followed by short- and long-read sequencing	9
The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years	9
Development and validation of a stability-indicating HPLC method for assay of tonabersat in pharmaceutical formulations	9
Non-canonical amino acids and protein dynamics	9
Detection and Segmentation of Breast Masses Based on Multi-Layer Feature Fusion	9
Editorial Board	9
Comprehensive evaluation of molecule property prediction with ChatGPT	9
Advances in the exact nuclear Overhauser effect 2018–2022	9
Efficient experimental method for purifying allergens from aqueous extracts	9
Artificial intelligence and computer-aided drug discovery: Methods development and application	9
Relaxation and single site multiple mutations to identify and control allosteric networks	9
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph	9
CHiTA: A scarless high-throughput pipeline for characterization of ribozymes	9
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	9
Guest Editor introduction	8
Recent developments for the analysis of latent constructs using measurement scales in health research	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
Atomic force microscope kymograph analysis: A case study of two membrane proteins	8
Hexagonal image segmentation on spatially resolved transcriptomics	8
Basic techniques associated with studying transcription elongation both in vitro and in vivo within mammalian cells	8
Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data	8
High-throughput genotyping of high-homology mutant mouse strains by next-generation sequencing	8
Editorial Board	8
Editorial Board	8
Utilization of passive visual perception task in detecting patients with major depressive disorder for active health	8
Editorial Board	8
Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets	8
Trans ligation of RNAs to generate hybrid circular RNAs using highly efficient autocatalytic transcripts	8
NetAUC: A network-based multi-biomarker identification method by AUC optimization	8
Advances in optical and electrochemical sensing of bisphenol a (BPA) utilizing microfluidic Technology: A mini perspective	8
Detecting circRNA in purified spliceosomal P complex	8
A heat diffusion multilayer network approach for the identification of functional biomarkers in rumen methane emissions	8
Synthesis of carbon nanotubes using pre-sintered oil fly ash via a reproducible process with large-scale potential	8
Bioinformatics resources for understanding RNA modifications	8
Determination of rate constants for conformational changes of RNA helicases by single-molecule FRET TIRF microscopy	8
rPAC: Route based pathway analysis for cohorts of gene expression data sets	8
Study of circular RNA translation using reporter systems in living cells	8
Editorial Board	8
Site-specific protein conjugates incorporating Para-Azido-L-Phenylalanine for cellular and in vivo imaging	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