Methods

Article	Citations
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	266
Predicting genes associated with ossification of the posterior longitudinal ligament using graph attention network	133
Interpretable thoracic pathologic prediction via learning group-disentangled representation	132
Editorial Board	105
An overview of extracellular field potentials: Different potentiation and measurable components, interpretations, and hippocampal synaptic activity models	92
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	87
Editorial Board	86
Editorial Board	82
On finding natural antibiotics based on TCM formulae	80
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	80
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors	72
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	70
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm	68
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	66
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	64
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	63
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	62
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	59
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	56
Non-canonical amino acids and protein dynamics	56
Strategies for ocular drug delivery	53
Synthesis of carbon nanotubes using pre-sintered oil fly ash via a reproducible process with large-scale potential	50
Pseudouridine RNA modification detection and quantification by RT-PCR	49
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	48
Two minimally invasive strategies to implant guide cannulas for multiple injections in deep brain areas	47

DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions	47
Breaking barrier of binding buffer in colorimetric aptasensing of tetracycline in food fish using peroxidase mimic gold NanoZyme	39
Electrochemical assay for the quantification of anticancer drugs and their inhibition mechanism	39
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures	38
The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years	37
Editorial Board	37
Isolation and culture of adult murine cardiac atrial and ventricular fibroblasts and myofibroblasts	37
Atomic force microscope kymograph analysis: A case study of two membrane proteins	36
Advancing antisense oligonucleotide delivery through click chemistry based chemical conjugation with designed short non-cationic peptides for Duchenne muscular dystrophy	36
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	35
Interpretable multimodal learning for tumor protein-metal binding: Progress, challenges, and perspectives	34
Development and validation of a stability-indicating HPLC method for assay of tonabersat in pharmaceutical formulations	34
Clinical analysis of eye movement-based data in the medical diagnosis of amblyopia	34
MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models	32
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	32
Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues	31
MRDFF: A deep forest based framework for CT whole heart segmentation	30
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis	30
MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction	30
Comprehensive evaluation of molecule property prediction with ChatGPT	29
Advanced glycation end products in musculoskeletal system and disorders	29
Editorial Board	29
Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination	28
scGAAC: A graph attention autoencoder for clustering single-cell RNA-sequencing data	28
Prediction of the transcription factor binding sites with meta-learning	28
Validation of combo ichroma as a reliable concentration-based alternative for AST and ALT measurement in liver disease monitoring	28
Guest Editor’s Introduction: Optical methods for characterisation of biomolecules	27
Novel approaches to biomarker discover	26
Model-agnostic confidence measurement for aggregating multimodal ensemble models in automatic diagnostic systems	26
UGDAS: Unsupervised graph-network based denoiser for abstractive summarization in biomedical domain	25
MPFFPSDC: A multi-pooling feature fusion model for predicting synergistic drug combinations	25
Editorial Board	24
Measuring functional similarity of lncRNAs based on variable K-mer profiles of nucleotide sequences	24
Characterization of targeted knock-in achieved via tandem paired nicking mediated by CRISPR/Cas9 nickases	23
A brief review of RNA modification related database resources	23
Improving domain generalization performance for medical image segmentation via random feature augmentation	23
Hybrid manifold-deep convolutional neural network for sleep staging	23
Materials-Based spatiotemporal analysis of microbial responses to glyphosate in Winogradsky columns	22
EpiHNet: Detecting epistasis by heterogeneous molecule network	22
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	22
A heterogeneous graph transformer framework for accurate cancer driver gene prediction and downstream analysis	22
Identification of immunoregulatory peptides from gut microbiota modulating Epstein-Barr virus-induced gene 3 (EBI3) using a novel specific AlphaLISA™ assay	22
COVID-19 lesion detection and segmentation–A deep learning method	22
Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state	21
Recent progress in the analysis of protein deamidation using mass spectrometry	21
Glaucoma screening using an attention-guided stereo ensemble network	20
AntiT2DMP-Pred: Leveraging feature fusion and optimization for superior machine learning prediction of type 2 diabetes mellitus	20
Scale-adjusted distance transform and its applications to segmentation of multimodal images	20
A federated learning method for real-time emotion state classification from multi-modal streaming	20
Chromatin image-driven modelling	20

Multi-view contrastive clustering for cancer subtyping using fully and weakly paired multi-omics data	20
MLFA-UNet: A multi-level feature assembly UNet for medical image segmentation	20
Probing excited state 1Hα chemical shifts in intrinsically disordered proteins with a triple resonance-based CEST experiment: Application to a disorder-to-order switch	20
HI-CeFSpot: High-throughput Immune Cell FluoroSpot assay	20
Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects	19
Identification of DNase I hypersensitive sites in the human genome by multiple sequence descriptors	19
Corrigendum to “Decoding selective auditory attention with EEG using a transformer model” [Methods 204 (2022) 410–417]	19
Biomedical event causal relation extraction with deep knowledge fusion and Roberta-based data augmentation	19
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	19
Deciphering cellular heterogeneity: Breakthroughs and prospects of single-cell-level SERS analysis in precision medicine	19
Computational methods and strategies for combating COVID-19	19
Inner leaflet cationic lipid increases nucleic acid loading independently of outer leaflet lipid charge in asymmetric liposomes	18
Exploring the artificial intelligence and machine learning models in the context of drug design difficulties and future potential for the pharmaceutical sectors	18
Steric trapping strategy for studying the folding of helical membrane proteins	18
SGAE-MDA: Exploring the MiRNA-disease associations in herbal medicines based on semi-supervised graph autoencoder	18
Baker’s yeast beta glucan supplementation was associated with an improved innate immune mRNA expression response after exercise	18
Deep learning based method for predicting DNA N6-methyladenosine sites	17
The semisynthesis of site-specifically modified histones and histone-based probes of chromatin-modifying enzymes	17
Microproteins transitioning into a new Phase: Defining the undefined	17
Editorial Board	17
Modeling repeated self-reported outcome data: A continuous-time longitudinal Item Response Theory model	17
Convolutional autoencoder based on latent subspace projection for anomaly detection	16
Hybrid multimodal fusion for graph learning in disease prediction	16
Single molecule methods for studying CRISPR Cas9-induced DNA unwinding	16
Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts	16
Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing	16
CSSEC: An adaptive approach integrating consensus and specific self-expressive coefficients for multi-omics cancer subtyping	16
Authentication of Panax notoginseng with high-efficiency Proofman-LMTIA technology	16
DRCNNTLe: A deep recurrent convolutional neural network with transfer learning through pre-trained embeddings for automated ICD coding	16
A novel carboxyl polymer-modified upconversion luminescent nanoprobe for detection of prostate-specific antigen in the clinical gray zonebase by flow immunoassay strip	16
A compact and interpretable convolutional neural network for cross-subject driver drowsiness detection from single-channel EEG	15
The prognostic value of machine learning techniques versus cox regression model for head and neck cancer	15
Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme	15
A comprehensive preanalytical protocol for fresh solid tumor biospecimens	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
CLCAP: Contrastive learning improves antigenicity prediction for influenza A virus using convolutional neural networks	15
Methods for preparation of niosomes: A focus on thin-film hydration method	15
In silico identification of Histone Deacetylase inhibitors using Streamlined Masked Transformer-based Pretrained features	15
A dual-function fluorescence 'turn-on' probe that allows Zn (II) bioimaging and quantification of water in the organic solvent	15
Meta-IL4: An ensemble learning approach for IL-4-inducing peptide prediction	15
Assessing the role of intrinsic disorder in RNA-binding protein function: hnRNP K as a case study	15
Graph matching survey for medical imaging: On the way to deep learning	15
HistoSPACE: Histology-inspired spatial transcriptome prediction and characterization engine	14
Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields	14
Predicting miRNA-lncRNA interactions on plant datasets based on bipartite network embedding method	14
Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET	14
m5c-iDeep: 5-Methylcytosine sites identification through deep learning	14
Identification of adaptor proteins by incorporating deep learning and PSSM profiles	14
Kinetics measurements of G-quadruplex binding and unfolding by helicases	14
Smartphone-based low-cost and rapid quantitative detection of urinary creatinine with the Tyndall effect	14
dsRNAPredictor-II: An improved predictor of identifying dsRNA and its silencing efficiency for Tribolium castaneum based on sequence length distribution	14
Atrial-specific hiPSC-derived cardiomyocytes in drug discovery and disease modeling	14
Editorial Board	14
Editorial Board	14
Unveiling the pathogenicity of allosteric protein mutations via multifaceted feature ensembling	14
Editorial Board	13
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	13
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies	13
Design of a 1 × 4 micro-magnetic stimulation device and its targeted, coordinated regulation on LTP of Schaffer-CA1 in the hippocampus of rats	13
Editorial Board	13
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications	13
MTGNN: Multi-Task Graph Neural Network based few-shot learning for disease similarity measurement	13
Editorial Board	13
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer	13
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	13
Integrating a multi-omics strategy framework to screen potential targets in cognitive impairment-related epilepsy	13
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	13
A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis	13
Current methodologies in studying chromatin and gene expression	13
PCR-generated DNA templates enable efficient, rapid, and cost-effective mRNA synthesis	13
Natural language processing	13
Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data	13
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	13
Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review	12
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	12
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	12
An effective multi-task learning framework for drug repurposing based on graph representation learning	12
Low friction hydrogel with diclofenac eluting ability for dry eye therapeutic contact lenses	12
Coffee – a ubiquitous substitute for uranyl acetate in staining of biological ultrathin sections for electron microscopy studies	12

Resources for computational prediction of intrinsic disorder in proteins	12
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	12
Efficient experimental method for purifying allergens from aqueous extracts	12
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome	12
Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors	12
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data	12
A fluorescence turn “on-off” imaging probe for sequential detection of Al3+ and L-Cysteine in HeLa cells	12
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	12
Novel, standardized sample collection from the brain-nose interface	11
Enhancing RNA Delivery: Practical insights into NeoLNPTM transfection reagent	11
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy	11
Isothermal titration calorimetry and surface plasmon resonance methods to probe protein–protein interactions	11
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph	11
3D printing of calcium doped Isomalt via custom-made Extruder: Facile approach for creating blood vascular like networks within tissue mimicking hydrogel matrix	11
Temperature-jump microscopy and interaction of Hsp70 heat shock protein with a client protein in vivo	11
Optimized CUT&Tag enables robust epigenome profiling in Schizosaccharomyces pombe	11
Hexagonal image segmentation on spatially resolved transcriptomics	11
Integrated analyses of prognostic and immunotherapeutic significance of EZH2 in uveal melanoma	11
Multimodal contrastive representation learning for drug-target binding affinity prediction	10
Triazole-linked amidopyrene-tagged fluorometric probe for Au3+ ions and pH control aggregation-induced emission	10
Prediction of drug-induced hepatotoxicity based on histopathological whole slide images	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
Fragile methods, fractured trust: rethinking scientific responsibility	10
LiteMamba-Bound: A lightweight Mamba-based model with boundary-aware and normalized active contour loss for skin lesion segmentation	10
Fluorescence-based ratiometric sensors as emerging tools for CN− detection: Chemical structures, sensing mechanisms and applications	10
MSO-GP: 3-D segmentation of large and complex conjoined tree structures	10
Editorial Board	10
Exploring drug-target interaction prediction on cold-start scenarios via meta-learning-based graph transformer	10
Machine learning aided single cell image analysis improves understanding of morphometric heterogeneity of human mesenchymal stem cells	10
Prediction of coronary heart disease based on combined reinforcement multitask progressive time-series networks	10
Corrigendum to “Smart biomaterials: From 3D printing to 4D bioprinting” [Methods 205 (2022) 191–199]	10
RLDOCK method for predicting RNA-small molecule binding modes	10
Imaging flow cytometry reveals LPS-induced changes to intracellular intensity and distribution of α-synuclein in a TLR4-dependent manner in STC-1 cells	10
Guitar2: An improved version of the Guitar for sketching the transcriptomic view of RNA-related biological features	10
Editorial Board	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	10
Machine learning algorithms for prediction of entrapment efficiency in nanomaterials	9
Editorial	9
DNA building blocks for AFM tip functionalization: An easy, fast and stable strategy	9
Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms	9
NGOME-Lite: Proteome-wide prediction of spontaneous protein deamidation highlights differences between taxa	9
Fluorescent molecular probes for imaging and detection of oxidases and peroxidases in biological samples	9
Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13	9
DNA base order parameter determination without influence of chemical exchange	9
Surface-enhanced Raman scattering (SERS) technology: Emerging applications in cancer imaging and precision medicine	9
Multifunctional nanophotonic photoacoustic biosensors: a new era in molecular imaging–guided deep-tissue cancer monitoring	9
Artificial intelligence and computer-aided drug discovery: Methods development and application	9
AntiMF: A deep learning framework for predicting anticancer peptides based on multi-view feature extraction	9
What’s the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry	9
Copper catalyzed cycloaddition for the synthesis of non isomerisable 2′ and 3′-regioisomers of arg-tRNAarg	9
GCHN-DTI: Predicting drug-target interactions by graph convolution on heterogeneous networks	9
LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm	9
Publisher’s note	9
Strain promoted click labeling of oligonucleotides on solid-phase support	9
Site-specific incorporation of biophysical probes into NF-ĸB with non-canonical amino acids	9
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	9
Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays	9
SGMFQP: An ontology-based Swine Gut Microbiota Federated Query Platform	9
Dimensional emotion recognition from camera-based PRV features	9
Trans-m5C: A transformer-based model for predicting 5-methylcytosine (m5C) sites	9
Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq	9
High resolution imaging of viruses: Scanning probe microscopy and related techniques	9
A posterior probability based Bayesian method for single-cell RNA-seq data imputation	9
Editorial Board	9
Rapid in vitro and computer-aided method for assessing synergistic interactions between NSAIDs and analgesics	9
Optimizing Retinal Imaging: Evaluation of ultrasmall TiO2 nanoparticle- fluorescein conjugates for improved Fundus Fluorescein Angiography	9
Prediction of drug protein interactions based on variable scale characteristic pyramid convolution network	8
DBPboost:A method of classification of DNA-binding proteins based on improved differential evolution algorithm and feature extraction	8
Adversarial learning for semi-supervised pediatric sleep staging with single-EEG channel	8
CRISPR-Cas systems for diagnosing infectious diseases	8
Generation of site-specifically labelled fluorescent human XPA to investigate DNA binding dynamics during nucleotide excision repair	8
RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features	8
Guide to studying intrinsically disordered proteins by high-speed atomic force microscopy	8
Editorial for methods special issue: Big data in digital health: methods, analysis and prospects	8
Development and validation of a machine learning model for predicting drug-drug interactions with oral diabetes medications	8
Ultrasensitive detection and quantification of viral nucleic acids with Raindance droplet digital PCR (ddPCR)	8
Weighted hypergraph learning and adaptive inductive matrix completion for SARS-CoV-2 drug repositioning	8
Evaluation of unitary conductance of gap junction channels based on stationary fluctuation analysis	8
Optimising multiplex immunofluorescence staining for characterising the tumour immune micro-environment	8
Challenges, optimization strategies, and future horizons of advanced deep learning approaches for brain lesion segmentation	8
Biochemical analysis of DNA synthesis blockage by G-quadruplex structure and bypass facilitated by a G4-resolving helicase	8
cfDNAFE: Comprehensively extracting multi-omics features of cell-free DNA for noninvasive diagnosis	8
Comprehensive method for isolation and functional characterization of bacterial vesicles from human biological samples	8
Applicability analysis of immunotherapy for lung cancer patients based on deep learning	8
A domain-label-guided translation model for molecular optimization	8
AI-augmented prediction of high-risk PINK1 variants associated with Parkinson’s disease: integrating multilayered bioinformatics, MD simulation, and deep learning	8
Measuring hypertrophy in neonatal rat primary cardiomyocytes and human iPSC-derived cardiomyocytes	8
Advances in machine learning for epigenetics and biomedical applications	8
StackDPPIV: A novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides	8
Multitask learning model for predicting non-coding RNA-disease associations: Incorporating local and global context	8
Immunological methods for the determination of AGE-RAGE axis generated glutathionylated and carbonylated proteins as oxidative stress markers	8
Ratiometric lysosome-targeting luminescent probe based on a coumarin-ruthenium(II) complex for formaldehyde detection and imaging in living cells and mouse brain tissues	8
Capturing G protein-coupled receptors into native lipid-bilayer nanodiscs using new diisobutylene/maleic acid (DIBMA) copolymers	8
CRISPR-ENHANCE: An enhanced nucleic acid detection platform using Cas12a	8
Movement recognition via channel-activation-wise sEMG attention	7