Methods

Article	Citations
Editorial Board	132
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	87
Editorial Board	87
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	82
Interpretable thoracic pathologic prediction via learning group-disentangled representation	67
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm	66
Precision mapping of NF-κB-DNA binding: high-resolution insights via dynamic UV-laser footprinting	63
An overview of extracellular field potentials: Different potentiation and measurable components, interpretations, and hippocampal synaptic activity models	62
Predicting genes associated with ossification of the posterior longitudinal ligament using graph attention network	61
On finding natural antibiotics based on TCM formulae	54
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	51
The transformative role of single-cell analysis in multifactorial disorders research	48
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	47
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	40
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	40
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	38
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	38
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	36
Non-canonical amino acids and protein dynamics	35
Strategies for ocular drug delivery	35
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures	34
An Affordable paper based platform for eDNA Filtration, Concentration, and nucleic acid extraction	33
Unravelling cell heterogeneity and gene regulation mechanisms in multiple myeloma through single-cell RNA-seq	32
Atomic force microscope kymograph analysis: A case study of two membrane proteins	32
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	32

Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues	31
Viral-mediated fluorescent labelling of activated hippocampal memory engrams to study epigenetic dynamics associated with gene expression	31
Comprehensive evaluation of molecule property prediction with ChatGPT	30
Clinical analysis of eye movement-based data in the medical diagnosis of amblyopia	29
MRDFF: A deep forest based framework for CT whole heart segmentation	27
Electrochemical assay for the quantification of anticancer drugs and their inhibition mechanism	27
Editorial Board	27
Breaking barrier of binding buffer in colorimetric aptasensing of tetracycline in food fish using peroxidase mimic gold NanoZyme	26
MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models	25
Two minimally invasive strategies to implant guide cannulas for multiple injections in deep brain areas	25
DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions	25
MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction	25
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	25
Development and validation of a stability-indicating HPLC method for assay of tonabersat in pharmaceutical formulations	25
Advancing antisense oligonucleotide delivery through click chemistry based chemical conjugation with designed short non-cationic peptides for Duchenne muscular dystrophy	24
Multi-view contrastive clustering for cancer subtyping using fully and weakly paired multi-omics data	24
Exploring quantum frontiers in protein structure prediction: techniques, challenges, and opportunities	24
MLFA-UNet: A multi-level feature assembly UNet for medical image segmentation	24
Interpretable multimodal learning for tumor protein-metal binding: Progress, challenges, and perspectives	24
Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination	24
Guest Editor’s Introduction: Optical methods for characterisation of biomolecules	24
Editorial Board	24
Editorial Board	23
Measuring functional similarity of lncRNAs based on variable K-mer profiles of nucleotide sequences	23
A heterogeneous graph transformer framework for accurate cancer driver gene prediction and downstream analysis	22
Novel approaches to biomarker discover	22
Characterization of targeted knock-in achieved via tandem paired nicking mediated by CRISPR/Cas9 nickases	22
Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state	22
Model-agnostic confidence measurement for aggregating multimodal ensemble models in automatic diagnostic systems	21
Identification of immunoregulatory peptides from gut microbiota modulating Epstein-Barr virus-induced gene 3 (EBI3) using a novel specific AlphaLISA™ assay	20
A federated learning method for real-time emotion state classification from multi-modal streaming	20
Study protocol for a single-arm pilot trial investigating the feasibility of a multimodal digital technology for managing metabolic syndrome in patients with chronic obstructive pulmonary disease	20
MPFFPSDC: A multi-pooling feature fusion model for predicting synergistic drug combinations	20
Improving domain generalization performance for medical image segmentation via random feature augmentation	20
CST-Based Molecular Profiling of Vaginal Microbiota Validated by qRT-PCR and 16S Amplicon Sequencing	19
Validation of combo ichroma as a reliable concentration-based alternative for AST and ALT measurement in liver disease monitoring	19
Materials-Based spatiotemporal analysis of microbial responses to glyphosate in Winogradsky columns	19
AntiT2DMP-Pred: Leveraging feature fusion and optimization for superior machine learning prediction of type 2 diabetes mellitus	19
Computational methods and strategies for combating COVID-19	18
SGAE-MDA: Exploring the MiRNA-disease associations in herbal medicines based on semi-supervised graph autoencoder	18
Syntenins at the crossroads of host–virus interactions	18
Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects	18
scGAAC: A graph attention autoencoder for clustering single-cell RNA-sequencing data	18
Corrigendum to “Decoding selective auditory attention with EEG using a transformer model” [Methods 204 (2022) 410–417]	17
Inner leaflet cationic lipid increases nucleic acid loading independently of outer leaflet lipid charge in asymmetric liposomes	17
Identification of DNase I hypersensitive sites in the human genome by multiple sequence descriptors	17
Deciphering cellular heterogeneity: Breakthroughs and prospects of single-cell-level SERS analysis in precision medicine	17
Microproteins transitioning into a new Phase: Defining the undefined	17
Editorial Board	17
Biomedical event causal relation extraction with deep knowledge fusion and Roberta-based data augmentation	17

Toward a rigorous assessment of the statistical performances of methods to estimate the Minimal Important Difference of Patient-Reported Outcomes: A protocol for a large-scale simulation study	17
HI-CeFSpot: High-throughput Immune Cell FluoroSpot assay	17
MDM2/p53-based live-cell quantitative FRET imaging for apoptosis drug discovery	16
Chromatin image-driven modelling	16
Exploring the artificial intelligence and machine learning models in the context of drug design difficulties and future potential for the pharmaceutical sectors	16
Probing excited state 1Hα chemical shifts in intrinsically disordered proteins with a triple resonance-based CEST experiment: Application to a disorder-to-order switch	16
Steric trapping strategy for studying the folding of helical membrane proteins	16
Gold nanoparticles for salivary-based sensors: A review	16
Renovating the Barnes maze for mouse models of dementia with STARR FIELD: A 4-day protocol for learning rate, retention, and cognitive flexibility	16
Baker’s yeast beta glucan supplementation was associated with an improved innate immune mRNA expression response after exercise	16
Modeling repeated self-reported outcome data: A continuous-time longitudinal Item Response Theory model	16
A dual-function fluorescence 'turn-on' probe that allows Zn (II) bioimaging and quantification of water in the organic solvent	15
CSSEC: An adaptive approach integrating consensus and specific self-expressive coefficients for multi-omics cancer subtyping	15
Hybrid multimodal fusion for graph learning in disease prediction	15
Authentication of Panax notoginseng with high-efficiency Proofman-LMTIA technology	15
Scale-adjusted distance transform and its applications to segmentation of multimodal images	15
A novel carboxyl polymer-modified upconversion luminescent nanoprobe for detection of prostate-specific antigen in the clinical gray zonebase by flow immunoassay strip	15
Single molecule methods for studying CRISPR Cas9-induced DNA unwinding	15
The coefficient of variation by image correlation spectroscopy (CV-ICS) quantifies chromatin compaction from images with low photon counts	15
Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing	15
Editorial Board	15
The semisynthesis of site-specifically modified histones and histone-based probes of chromatin-modifying enzymes	15
ZeRPI: A graph neural network model for zero-shot prediction of RNA-protein interactions	15
Detection and quantification of nanoparticle-induced intracellular ROS in live cells by laser scanning confocal microscopy	15
Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme	15
Meta-IL4: An ensemble learning approach for IL-4-inducing peptide prediction	14
Deep learning based method for predicting DNA N6-methyladenosine sites	14
Assessing the role of intrinsic disorder in RNA-binding protein function: hnRNP K as a case study	14
The prognostic value of machine learning techniques versus cox regression model for head and neck cancer	14
DRCNNTLe: A deep recurrent convolutional neural network with transfer learning through pre-trained embeddings for automated ICD coding	14
CLCAP: Contrastive learning improves antigenicity prediction for influenza A virus using convolutional neural networks	14
Editorial Board	13
Kinetics measurements of G-quadruplex binding and unfolding by helicases	13
Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields	13
Towards transparent and interpretable screening: multi-biofluid FTIR spectroscopy with LLM-Augmented explainability for pancreatic cancer detection	13
Identification of adaptor proteins by incorporating deep learning and PSSM profiles	13
In silico identification of Histone Deacetylase inhibitors using Streamlined Masked Transformer-based Pretrained features	13
Predicting miRNA-lncRNA interactions on plant datasets based on bipartite network embedding method	13
m5c-iDeep: 5-Methylcytosine sites identification through deep learning	13
HistoSPACE: Histology-inspired spatial transcriptome prediction and characterization engine	13
Advances in biosensor technologies for early diagnosis of preeclampsia through molecular biomarkers	13
Convolutional autoencoder based on latent subspace projection for anomaly detection	13
Editorial Board	13
dsRNAPredictor-II: An improved predictor of identifying dsRNA and its silencing efficiency for Tribolium castaneum based on sequence length distribution	13
Smartphone-based low-cost and rapid quantitative detection of urinary creatinine with the Tyndall effect	13
Unveiling the pathogenicity of allosteric protein mutations via multifaceted feature ensembling	13
A comprehensive preanalytical protocol for fresh solid tumor biospecimens	13
Editorial Board	12
Natural language processing	12
Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET	12
Current methodologies in studying chromatin and gene expression	12
Resources for computational prediction of intrinsic disorder in proteins	12
Editorial Board	12
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer	12
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	12
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	11
Cell labeling approaches for tracking stromal vascular fraction fate	11
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	11
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	11
PCR-generated DNA templates enable efficient, rapid, and cost-effective mRNA synthesis	11
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	11
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data	11
A fluorescence turn “on-off” imaging probe for sequential detection of Al3+ and L-Cysteine in HeLa cells	11
Integrating a multi-omics strategy framework to screen potential targets in cognitive impairment-related epilepsy	11
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	11
An effective multi-task learning framework for drug repurposing based on graph representation learning	11
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications	11
Retraction notice to “Circularization enhances RNA aptamer binding and Stability: Evidence from in-cell NMR” [Methods 242 (2025) 72–79]	11
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies	11
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	11
Design of a 1 × 4 micro-magnetic stimulation device and its targeted, coordinated regulation on LTP of Schaffer-CA1 in the hippocampus of rats	11
Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors	11
Novel, standardized sample collection from the brain-nose interface	10
Clinical assessment of the diagnostic performance of the LIAISON® Legionella urinary antigen assay	10
Hexagonal image segmentation on spatially resolved transcriptomics	10
Low friction hydrogel with diclofenac eluting ability for dry eye therapeutic contact lenses	10
Fragile methods, fractured trust: rethinking scientific responsibility	10
Protocol for a pilot study: Feasibility of a web-based platform to improve nutrition, mindfulness, and physical function in people living with Post COVID-19 condition (BLEND)	10
Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review	10
Isothermal titration calorimetry and surface plasmon resonance methods to probe protein–protein interactions	10

Navigating the frontier of human microglia isolation—standardization and translational insight	10
Efficient experimental method for purifying allergens from aqueous extracts	10
Optimized CUT&Tag enables robust epigenome profiling in Schizosaccharomyces pombe	10
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome	10
Integrated analyses of prognostic and immunotherapeutic significance of EZH2 in uveal melanoma	10
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph	10
Coffee – a ubiquitous substitute for uranyl acetate in staining of biological ultrathin sections for electron microscopy studies	10
Enhancing RNA Delivery: Practical insights into NeoLNPTM transfection reagent	10
3D printing of calcium doped Isomalt via custom-made Extruder: Facile approach for creating blood vascular like networks within tissue mimicking hydrogel matrix	10
Validation of plasmonic-based biosensors for rapid and in depth characterization of monoclonal antibodies directed against rabbit haemorrhagic and foot-and-mouth disease viruses in biological samples	10
GCHN-DTI: Predicting drug-target interactions by graph convolution on heterogeneous networks	10
Temperature-jump microscopy and interaction of Hsp70 heat shock protein with a client protein in vivo	10
Development and validation of a new and rapid molecular diagnostic tool based on RT-LAMP for Hepatitis C virus detection at point-of-care	9
Triazole-linked amidopyrene-tagged fluorometric probe for Au3+ ions and pH control aggregation-induced emission	9
Machine learning aided single cell image analysis improves understanding of morphometric heterogeneity of human mesenchymal stem cells	9
Sensitive and specific detection of ctDNA using Copper-Free click chemistry and magnetic bead Technology	9
Dimensional emotion recognition from camera-based PRV features	9
Multimodal contrastive representation learning for drug-target binding affinity prediction	9
Corrigendum to “Smart biomaterials: From 3D printing to 4D bioprinting” [Methods 205 (2022) 191–199]	9
MSO-GP: 3-D segmentation of large and complex conjoined tree structures	9
AntiMF: A deep learning framework for predicting anticancer peptides based on multi-view feature extraction	9
Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq	9
Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms	9
Editorial Board	9
Protocol for partial heart transplantation of the pulmonary valve in a swine model: surgical technique, postoperative care, assessments and outcomes	9
Editorial Board	9
Imaging flow cytometry reveals LPS-induced changes to intracellular intensity and distribution of α-synuclein in a TLR4-dependent manner in STC-1 cells	9
LiteMamba-Bound: A lightweight Mamba-based model with boundary-aware and normalized active contour loss for skin lesion segmentation	9
Fluorescence-based ratiometric sensors as emerging tools for CN− detection: Chemical structures, sensing mechanisms and applications	9
LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm	9
Exploring drug-target interaction prediction on cold-start scenarios via meta-learning-based graph transformer	9
Prediction of drug-induced hepatotoxicity based on histopathological whole slide images	9
Copper catalyzed cycloaddition for the synthesis of non isomerisable 2′ and 3′-regioisomers of arg-tRNAarg	9
Site-specific incorporation of biophysical probes into NF-ĸB with non-canonical amino acids	8
A prognostic gene signature and subtype-specific drug sensitivity in TNBC revealed by single-cell and bulk RNA sequencing: Insights into stemness and tumor heterogeneity	8
Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13	8
Real-time, label-free assessment of cell fusion dynamics by high-content imaging	8
SGMFQP: An ontology-based Swine Gut Microbiota Federated Query Platform	8
A posterior probability based Bayesian method for single-cell RNA-seq data imputation	8
DNA-regulated structural engineering of metal nanomaterials: A strategy for advanced optical biosensing	8
Rapid in vitro and computer-aided method for assessing synergistic interactions between NSAIDs and analgesics	8
Generation of site-specifically labelled fluorescent human XPA to investigate DNA binding dynamics during nucleotide excision repair	8
Editorial Board	8
Strain promoted click labeling of oligonucleotides on solid-phase support	8
Proteomics method for identifying POT1-associated complexes at telomeres using ChIP-Mass spectrometry	8
Machine learning algorithms for prediction of entrapment efficiency in nanomaterials	8
Optimizing Retinal Imaging: Evaluation of ultrasmall TiO2 nanoparticle- fluorescein conjugates for improved Fundus Fluorescein Angiography	8
What’s the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry	8
First report of CRISPR/Cas13a-based rapid detection of groundnut bud necrosis virus without amplification	8
Artificial intelligence and computer-aided drug discovery: Methods development and application	8
Optimising multiplex immunofluorescence staining for characterising the tumour immune micro-environment	8
DNA base order parameter determination without influence of chemical exchange	8
The clinical potential and limitations of metal-organic frameworks (MOFs) in dentistry	8
Fluorescent molecular probes for imaging and detection of oxidases and peroxidases in biological samples	8
Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays	8
Trans-m5C: A transformer-based model for predicting 5-methylcytosine (m5C) sites	8
Multifunctional nanophotonic photoacoustic biosensors: a new era in molecular imaging–guided deep-tissue cancer monitoring	8
StackDPPIV: A novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides	7
Challenges, optimization strategies, and future horizons of advanced deep learning approaches for brain lesion segmentation	7
Capturing G protein-coupled receptors into native lipid-bilayer nanodiscs using new diisobutylene/maleic acid (DIBMA) copolymers	7
Corrigendum to “Design principles for LAMP–CRISPR molecular diagnostics” [Methods 251 (2026) 1–22]	7
Adversarial learning for semi-supervised pediatric sleep staging with single-EEG channel	7
Applicability analysis of immunotherapy for lung cancer patients based on deep learning	7
Advances in machine learning for epigenetics and biomedical applications	7
Surface-enhanced Raman scattering (SERS) technology: Emerging applications in cancer imaging and precision medicine	7
Guide to studying intrinsically disordered proteins by high-speed atomic force microscopy	7
cfDNAFE: Comprehensively extracting multi-omics features of cell-free DNA for noninvasive diagnosis	7
Prediction of drug protein interactions based on variable scale characteristic pyramid convolution network	7
DBPboost:A method of classification of DNA-binding proteins based on improved differential evolution algorithm and feature extraction	7
Disease-related omics data analysis	7
Multitask learning model for predicting non-coding RNA-disease associations: Incorporating local and global context	7
AI-augmented prediction of high-risk PINK1 variants associated with Parkinson’s disease: integrating multilayered bioinformatics, MD simulation, and deep learning	7
Biochemical analysis of DNA synthesis blockage by G-quadruplex structure and bypass facilitated by a G4-resolving helicase	7
A domain-label-guided translation model for molecular optimization	7
Development and validation of a machine learning model for predicting drug-drug interactions with oral diabetes medications	7
Ratiometric lysosome-targeting luminescent probe based on a coumarin-ruthenium(II) complex for formaldehyde detection and imaging in living cells and mouse brain tissues	7
Evaluation of unitary conductance of gap junction channels based on stationary fluctuation analysis	7
Does protein pretrained language model facilitate the prediction of protein–ligand interaction?	6
Development of capillary electrophoresis method to measure albumin thiol oxidation in dystrophic humans and animal models of Duchenne muscular dystrophy	6
PENet: Prior evidence deep neural network for bladder cancer staging	6
ReLume: Enhancing DNA storage data reconstruction with flow network and graph partitioning	6
RETRACTED: Circularization enhances RNA aptamer binding and Stability: Evidence from in-cell NMR	6
Movement recognition via channel-activation-wise sEMG attention	6
A simple and accurate high throughput evaluation method for larval zebrafish xenografts	6
MPEMDA: A multi-similarity integration approach with pre-completion and error correction for predicting microbe-drug associations	6
Digital choices as emotional Mirrors: Mapping psychosocial profiles through smartphone app usage patterns	6
Recent developments for the analysis of latent constructs using measurement scales in health research	6
CAMKMT knockdown delays myopia progression by reducing calcium Ion-mediated ER Stress-induced apoptosis	6
Anle138b interaction in α-synuclein aggregates by dynamic nuclear polarization NMR	6
DeepDBS: Identification of DNA-binding sites in protein sequences by using deep representations and random forest	6
N-GlycoPred: A hybrid deep learning model for accurate identification of N-glycosylation sites	6
RETRACTED: A methodological framework for rigorous systematic reviews: Tailoring comprehensive analyses to clinicians and healthcare professionals	6
Emulation of Quantitative Systems Pharmacology models to accelerate virtual population inference in immuno-oncology	6
Explainable machine learning-based prediction of psoriatic arthritis flares using heterogenous real-world data for personalised patient care	6
Editorial Board	6