Methods

Article	Citations
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	214
Editorial Board	102
Editorial Board	100
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm	99
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	79
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	76
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	74
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	72
Interpretable thoracic pathologic prediction via learning group-disentangled representation	66
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	64
On finding natural antibiotics based on TCM formulae	59
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	57
Approaches for the sensitive detection of rare base and prime editing events	55
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors	55
Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies	55
Brain controllability and morphometry similarity of internet gaming addiction	54
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	50
Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework	50
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	48
Targeted mutagenesis in human iPSCs using CRISPR genome-editing tools	47
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	47
Comprehensive evaluation of molecule property prediction with ChatGPT	46
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures	46
Editorial Board	46
Editorial Board	45

MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models	41
Development and validation of a stability-indicating HPLC method for assay of tonabersat in pharmaceutical formulations	40
Synthesis of carbon nanotubes using pre-sintered oil fly ash via a reproducible process with large-scale potential	40
Trans ligation of RNAs to generate hybrid circular RNAs using highly efficient autocatalytic transcripts	40
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	38
Non-canonical amino acids and protein dynamics	37
Clinical analysis of eye movement-based data in the medical diagnosis of amblyopia	37
Pseudouridine RNA modification detection and quantification by RT-PCR	37
MRDFF: A deep forest based framework for CT whole heart segmentation	36
The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years	36
Atomic force microscope kymograph analysis: A case study of two membrane proteins	33
MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction	33
Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets	32
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	32
Isolation and culture of adult murine cardiac atrial and ventricular fibroblasts and myofibroblasts	31
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis	30
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	30
Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues	28
Editorial Board	28
DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions	28
COVID-19 lesion detection and segmentation–A deep learning method	28
Advanced glycation end products in musculoskeletal system and disorders	28
Hybrid manifold-deep convolutional neural network for sleep staging	27
Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state	27
A federated learning method for real-time emotion state classification from multi-modal streaming	27
Recent progress in the analysis of protein deamidation using mass spectrometry	27
Measuring functional similarity of lncRNAs based on variable K-mer profiles of nucleotide sequences	26
Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination	26
Glaucoma screening using an attention-guided stereo ensemble network	26
MLFA-UNet: A multi-level feature assembly UNet for medical image segmentation	26
Improving domain generalization performance for medical image segmentation via random feature augmentation	25
Multi-view contrastive clustering for cancer subtyping using fully and weakly paired multi-omics data	24
A brief review of RNA modification related database resources	24
Discover novel disease-associated genes based on regulatory networks of long-range chromatin interactions	24
AntiT2DMP-Pred: Leveraging feature fusion and optimization for superior machine learning prediction of type 2 diabetes mellitus	23
Prediction of the transcription factor binding sites with meta-learning	23
Model-agnostic confidence measurement for aggregating multimodal ensemble models in automatic diagnostic systems	23
EpiHNet: Detecting epistasis by heterogeneous molecule network	23
Guest Editor’s Introduction: Optical methods for characterisation of biomolecules	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
scGAAC: A graph attention autoencoder for clustering single-cell RNA-sequencing data	22
MPFFPSDC: A multi-pooling feature fusion model for predicting synergistic drug combinations	21
Novel approaches to biomarker discover	21
UGDAS: Unsupervised graph-network based denoiser for abstractive summarization in biomedical domain	21
A heterogeneous graph transformer framework for accurate cancer driver gene prediction and downstream analysis	21
Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects	20
Baker’s yeast beta glucan supplementation was associated with an improved innate immune mRNA expression response after exercise	20
Computational methods and strategies for combating COVID-19	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
Microproteins transitioning into a new Phase: Defining the undefined	20

Corrigendum to “Decoding selective auditory attention with EEG using a transformer model” [Methods 204 (2022) 410–417]	20
Steric trapping strategy for studying the folding of helical membrane proteins	19
Modeling repeated self-reported outcome data: A continuous-time longitudinal Item Response Theory model	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
SGAE-MDA: Exploring the MiRNA-disease associations in herbal medicines based on semi-supervised graph autoencoder	18
Chromatin image-driven modelling	18
Identification of DNase I hypersensitive sites in the human genome by multiple sequence descriptors	18
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
Identifying and ranking potential cancer drivers using representation learning on attributed network	18
Universal Southern blot protocol with cold or radioactive probes for the validation of alleles obtained by homologous recombination	17
Hybrid multimodal fusion for graph learning in disease prediction	17
The semisynthesis of site-specifically modified histones and histone-based probes of chromatin-modifying enzymes	17
Detection and quantification of nanoparticle-induced intracellular ROS in live cells by laser scanning confocal microscopy	17
DRCNNTLe: A deep recurrent convolutional neural network with transfer learning through pre-trained embeddings for automated ICD coding	17
Convolutional autoencoder based on latent subspace projection for anomaly detection	17
Deep learning based method for predicting DNA N6-methyladenosine sites	17
Statistical methods for comparing test positivity rates between countries: Which method should be used and why?	17
Editorial Board	17
Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme	17
A compact and interpretable convolutional neural network for cross-subject driver drowsiness detection from single-channel EEG	16
Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins	16
CSSEC: An adaptive approach integrating consensus and specific self-expressive coefficients for multi-omics cancer subtyping	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
A dual-function fluorescence 'turn-on' probe that allows Zn (II) bioimaging and quantification of water in the organic solvent	16
Assessing the role of intrinsic disorder in RNA-binding protein function: hnRNP K as a case study	16
The prognostic value of machine learning techniques versus cox regression model for head and neck cancer	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
CLCAP: Contrastive learning improves antigenicity prediction for influenza A virus using convolutional neural networks	16
ZeRPI: A graph neural network model for zero-shot prediction of RNA-protein interactions	16
Single molecule methods for studying CRISPR Cas9-induced DNA unwinding	16
Methods for preparation of niosomes: A focus on thin-film hydration method	16
Atrial-specific hiPSC-derived cardiomyocytes in drug discovery and disease modeling	15
MTGNN: Multi-Task Graph Neural Network based few-shot learning for disease similarity measurement	15
Meta-IL4: An ensemble learning approach for IL-4-inducing peptide prediction	15
Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields	15
Kinetics measurements of G-quadruplex binding and unfolding by helicases	15
Graph matching survey for medical imaging: On the way to deep learning	15
A comprehensive preanalytical protocol for fresh solid tumor biospecimens	15
Identification of adaptor proteins by incorporating deep learning and PSSM profiles	15
Predicting miRNA-lncRNA interactions on plant datasets based on bipartite network embedding method	15
A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis	14
Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET	14
Editorial Board	13
Latest progress in the study of nanoparticle-based delivery of the CRISPR/Cas9 system	13
Smartphone-based low-cost and rapid quantitative detection of urinary creatinine with the Tyndall effect	13
Editorial Board	13
Editorial Board	13
Signal and noise in circRNA translation	13
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	13
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications	13
dsRNAPredictor-II: An improved predictor of identifying dsRNA and its silencing efficiency for Tribolium castaneum based on sequence length distribution	13
In silico identification of Histone Deacetylase inhibitors using Streamlined Masked Transformer-based Pretrained features	13
m5c-iDeep: 5-Methylcytosine sites identification through deep learning	13
Methods to study circRNA-protein interactions	13
HistoSPACE: Histology-inspired spatial transcriptome prediction and characterization engine	13
Resources for computational prediction of intrinsic disorder in proteins	12
Editorial Board	12
Introduction of mutations in plants with prime editing	12
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	12
Integrating a multi-omics strategy framework to screen potential targets in cognitive impairment-related epilepsy	12
Editorial Board	12
Stereological estimation of cardiomyocyte number and proliferation	12
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	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
Current methodologies in studying chromatin and gene expression	12
Machine learning for the analysis of multi-omics data	12
Efficient experimental method for purifying allergens from aqueous extracts	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
Bacterial flagellar motor as a multimodal biosensor	11
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data	11
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	11
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	11
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	11
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies	11
A fluorescence turn “on-off” imaging probe for sequential detection of Al3+ and L-Cysteine in HeLa cells	11
Editorial Board	11

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
Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes	11
Novel, standardized sample collection from the brain-nose interface	10
Multiple analyte profiling (MAP) index as a powerful diagnostic and therapeutic monitoring tool	10
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome	10
Study of circular RNA translation using reporter systems in living cells	10
Isothermal titration calorimetry and surface plasmon resonance methods to probe protein–protein interactions	10
Editorial Board	10
Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review	10
Model-based autoencoders for imputing discrete single-cell RNA-seq data	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
Low friction hydrogel with diclofenac eluting ability for dry eye therapeutic contact lenses	10
Integrating multi-omics data by learning modality invariant representations for improved prediction of overall survival of cancer	10
Publisher’s note	10
Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors	10
Efficient allele conversion in mouse zygotes and primary cells based on electroporation of Cre protein	10
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph	10
TPQCI: A topology potential-based method to quantify functional influence of copy number variations	10
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy	10
Editorial Board	10
Hexagonal image segmentation on spatially resolved transcriptomics	10
Temperature-jump microscopy and interaction of Hsp70 heat shock protein with a client protein in vivo	9
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)	9
Corrigendum to “Smart biomaterials: From 3D printing to 4D bioprinting” [Methods 205 (2022) 191–199]	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
Machine learning aided single cell image analysis improves understanding of morphometric heterogeneity of human mesenchymal stem cells	9
Prediction of drug-induced hepatotoxicity based on histopathological whole slide images	9
Prediction of coronary heart disease based on combined reinforcement multitask progressive time-series networks	9
CRISPR-mediated knock-in in the mouse embryo using long single stranded DNA donors synthesised by biotinylated PCR	9
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
Exploring drug-target interaction prediction on cold-start scenarios via meta-learning-based graph transformer	9
High resolution imaging of viruses: Scanning probe microscopy and related techniques	9
Integrated analyses of prognostic and immunotherapeutic significance of EZH2 in uveal melanoma	9
DNA building blocks for AFM tip functionalization: An easy, fast and stable strategy	9
GCHN-DTI: Predicting drug-target interactions by graph convolution on heterogeneous networks	9
Triazole-linked amidopyrene-tagged fluorometric probe for Au3+ ions and pH control aggregation-induced emission	9
Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq	9
Guitar2: An improved version of the Guitar for sketching the transcriptomic view of RNA-related biological features	9
LiteMamba-Bound: A lightweight Mamba-based model with boundary-aware and normalized active contour loss for skin lesion segmentation	9
NGOME-Lite: Proteome-wide prediction of spontaneous protein deamidation highlights differences between taxa	9
RLDOCK method for predicting RNA-small molecule binding modes	9
MSO-GP: 3-D segmentation of large and complex conjoined tree structures	9
LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm	9
Copper catalyzed cycloaddition for the synthesis of non isomerisable 2′ and 3′-regioisomers of arg-tRNAarg	9
Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms	9
Immunological methods for the determination of AGE-RAGE axis generated glutathionylated and carbonylated proteins as oxidative stress markers	8
CRISPR-Cas systems for diagnosing infectious diseases	8
Progression and application of CRISPR-Cas genomic editors	8
Generation of site-specifically labelled fluorescent human XPA to investigate DNA binding dynamics during nucleotide excision repair	8
Editorial	8
Dimensional emotion recognition from camera-based PRV features	8
Fluorescent molecular probes for imaging and detection of oxidases and peroxidases in biological samples	8
AntiMF: A deep learning framework for predicting anticancer peptides based on multi-view feature extraction	8
A posterior probability based Bayesian method for single-cell RNA-seq data imputation	8
Site-specific incorporation of biophysical probes into NF-ĸB with non-canonical amino acids	8
StackDPPIV: A novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides	8
RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features	8
DNA base order parameter determination without influence of chemical exchange	8
Artificial intelligence and computer-aided drug discovery: Methods development and application	8
A 3D polydimethylsiloxane microhourglass-shaped channel array made by reflowing photoresist structures for engineering a blood capillary network	8
What’s the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry	8
Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13	8
Multimodal contrastive representation learning for drug-target binding affinity prediction	8
Optimizing Retinal Imaging: Evaluation of ultrasmall TiO2 nanoparticle- fluorescein conjugates for improved Fundus Fluorescein Angiography	8
The design and synthesis of circular RNAs	8
Challenges, optimization strategies, and future horizons of advanced deep learning approaches for brain lesion segmentation	8
Optimising multiplex immunofluorescence staining for characterising the tumour immune micro-environment	8
A multi-objective optimization method for identification of module biomarkers for disease diagnosis	8
Editorial Board	8
Trans-m5C: A transformer-based model for predicting 5-methylcytosine (m5C) sites	8
Prediction of drug response in multilayer networks based on fusion of multiomics data	8
Machine learning algorithms for prediction of entrapment efficiency in nanomaterials	8
Fluorescence-based ratiometric sensors as emerging tools for CN− detection: Chemical structures, sensing mechanisms and applications	8
Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays	8
SGMFQP: An ontology-based Swine Gut Microbiota Federated Query Platform	8
PhosBERT: A self-supervised learning model for identifying phosphorylation sites in SARS-CoV-2-infected human cells	7
Methods for circular RNAs	7
Split light up aptamers as a probing tool for nucleic acids	7
Learning from imbalanced COVID-19 chest X-ray (CXR) medical imaging data	7
WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction	7
Hydrogel-based hybrid membrane enhances in vitro ophthalmic drug evaluation in the OphthalMimic device	7
Editorial for methods special issue: Big data in digital health: methods, analysis and prospects	7
Design and characterization of hollow microneedles for localized intrascleral drug delivery of ocular formulations	7
Special issue Methods: Nano-/bio-interface and biomedical applications	7
Editorial	7
Does protein pretrained language model facilitate the prediction of protein–ligand interaction?	7
Methods special issue: DNA and RNA helicases	7
Deep Learning in Bioinformatics and Biomedicine	7
Comprehensive method for isolation and functional characterization of bacterial vesicles from human biological samples	7
Editorial Board	7
Editorial Board	7
Methods for preparation of nanoconstructs	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
DNA shape features improve prediction of CRISPR/Cas9 activity	7