Methods

Article	Citations
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	244
Editorial Board	119
Editorial Board	116
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	112
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	92
Approaches for the sensitive detection of rare base and prime editing events	77
On finding natural antibiotics based on TCM formulae	77
Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework	76
Predicting genes associated with ossification of the posterior longitudinal ligament using graph attention network	74
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	73
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm	65
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	63
Editorial Board	62
An overview of extracellular field potentials: Different potentiation and measurable components, interpretations, and hippocampal synaptic activity models	61
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	60
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	56
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	56
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors	55
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	54
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	53
Interpretable thoracic pathologic prediction via learning group-disentangled representation	52
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures	48
Editorial Board	47
Editorial Board	47
Trans ligation of RNAs to generate hybrid circular RNAs using highly efficient autocatalytic transcripts	46

Two minimally invasive strategies to implant guide cannulas for multiple injections in deep brain areas	45
Strategies for ocular drug delivery	43
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	41
Synthesis of carbon nanotubes using pre-sintered oil fly ash via a reproducible process with large-scale potential	41
DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions	38
MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models	37
Comprehensive evaluation of molecule property prediction with ChatGPT	34
Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets	34
Pseudouridine RNA modification detection and quantification by RT-PCR	33
The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years	33
MRDFF: A deep forest based framework for CT whole heart segmentation	32
Clinical analysis of eye movement-based data in the medical diagnosis of amblyopia	32
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	32
Non-canonical amino acids and protein dynamics	31
Isolation and culture of adult murine cardiac atrial and ventricular fibroblasts and myofibroblasts	31
Atomic force microscope kymograph analysis: A case study of two membrane proteins	31
Breaking barrier of binding buffer in colorimetric aptasensing of tetracycline in food fish using peroxidase mimic gold NanoZyme	31
Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues	30
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis	28
Electrochemical assay for the quantification of anticancer drugs and their inhibition mechanism	28
MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction	28
Development and validation of a stability-indicating HPLC method for assay of tonabersat in pharmaceutical formulations	28
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	28
Advanced glycation end products in musculoskeletal system and disorders	27
Hybrid manifold-deep convolutional neural network for sleep staging	26
Editorial Board	26
Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state	26
Editorial Board	26
Improving domain generalization performance for medical image segmentation via random feature augmentation	25
Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination	25
Multi-view contrastive clustering for cancer subtyping using fully and weakly paired multi-omics data	25
COVID-19 lesion detection and segmentation–A deep learning method	25
EpiHNet: Detecting epistasis by heterogeneous molecule network	24
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
AntiT2DMP-Pred: Leveraging feature fusion and optimization for superior machine learning prediction of type 2 diabetes mellitus	23
scGAAC: A graph attention autoencoder for clustering single-cell RNA-sequencing data	22
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
MPFFPSDC: A multi-pooling feature fusion model for predicting synergistic drug combinations	21
A heterogeneous graph transformer framework for accurate cancer driver gene prediction and downstream analysis	21
UGDAS: Unsupervised graph-network based denoiser for abstractive summarization in biomedical domain	20
A brief review of RNA modification related database resources	20
Novel approaches to biomarker discover	20
Measuring functional similarity of lncRNAs based on variable K-mer profiles of nucleotide sequences	20
Glaucoma screening using an attention-guided stereo ensemble network	19
Corrigendum to “Decoding selective auditory attention with EEG using a transformer model” [Methods 204 (2022) 410–417]	19
Computational methods and strategies for combating COVID-19	19
Recent progress in the analysis of protein deamidation using mass spectrometry	19
A federated learning method for real-time emotion state classification from multi-modal streaming	19

Probing excited state 1Hα chemical shifts in intrinsically disordered proteins with a triple resonance-based CEST experiment: Application to a disorder-to-order switch	19
Characterization of targeted knock-in achieved via tandem paired nicking mediated by CRISPR/Cas9 nickases	19
MLFA-UNet: A multi-level feature assembly UNet for medical image segmentation	19
Steric trapping strategy for studying the folding of helical membrane proteins	19
Microproteins transitioning into a new Phase: Defining the undefined	18
Chromatin image-driven modelling	18
Biomedical event causal relation extraction with deep knowledge fusion and Roberta-based data augmentation	18
Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects	18
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	18
Inner leaflet cationic lipid increases nucleic acid loading independently of outer leaflet lipid charge in asymmetric liposomes	18
SGAE-MDA: Exploring the MiRNA-disease associations in herbal medicines based on semi-supervised graph autoencoder	18
Exploring the artificial intelligence and machine learning models in the context of drug design difficulties and future potential for the pharmaceutical sectors	18
Baker’s yeast beta glucan supplementation was associated with an improved innate immune mRNA expression response after exercise	18
Modeling repeated self-reported outcome data: A continuous-time longitudinal Item Response Theory model	18
Identification of DNase I hypersensitive sites in the human genome by multiple sequence descriptors	18
Convolutional autoencoder based on latent subspace projection for anomaly detection	17
The semisynthesis of site-specifically modified histones and histone-based probes of chromatin-modifying enzymes	17
DRCNNTLe: A deep recurrent convolutional neural network with transfer learning through pre-trained embeddings for automated ICD coding	17
Editorial Board	17
Statistical methods for comparing test positivity rates between countries: Which method should be used and why?	17
Deep learning based method for predicting DNA N6-methyladenosine sites	17
Meta-IL4: An ensemble learning approach for IL-4-inducing peptide prediction	16
Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins	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
CSSEC: An adaptive approach integrating consensus and specific self-expressive coefficients for multi-omics cancer subtyping	16
Hybrid multimodal fusion for graph learning in disease prediction	16
Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme	15
Assessing the role of intrinsic disorder in RNA-binding protein function: hnRNP K as a case study	15
ZeRPI: A graph neural network model for zero-shot prediction of RNA-protein interactions	15
Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing	15
The prognostic value of machine learning techniques versus cox regression model for head and neck cancer	15
Single molecule methods for studying CRISPR Cas9-induced DNA unwinding	15
Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts	15
Detection and quantification of nanoparticle-induced intracellular ROS in live cells by laser scanning confocal microscopy	15
A dual-function fluorescence 'turn-on' probe that allows Zn (II) bioimaging and quantification of water in the organic solvent	14
A comprehensive preanalytical protocol for fresh solid tumor biospecimens	14
Editorial Board	14
Predicting miRNA-lncRNA interactions on plant datasets based on bipartite network embedding method	14
Methods for preparation of niosomes: A focus on thin-film hydration method	14
Identification of adaptor proteins by incorporating deep learning and PSSM profiles	14
In silico identification of Histone Deacetylase inhibitors using Streamlined Masked Transformer-based Pretrained features	14
Editorial Board	14
A compact and interpretable convolutional neural network for cross-subject driver drowsiness detection from single-channel EEG	14
Graph matching survey for medical imaging: On the way to deep learning	14
dsRNAPredictor-II: An improved predictor of identifying dsRNA and its silencing efficiency for Tribolium castaneum based on sequence length distribution	14
Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET	14
Smartphone-based low-cost and rapid quantitative detection of urinary creatinine with the Tyndall effect	13
Kinetics measurements of G-quadruplex binding and unfolding by helicases	13
Atrial-specific hiPSC-derived cardiomyocytes in drug discovery and disease modeling	13
Integrating a multi-omics strategy framework to screen potential targets in cognitive impairment-related epilepsy	13
A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis	13
Signal and noise in circRNA translation	13
Latest progress in the study of nanoparticle-based delivery of the CRISPR/Cas9 system	13
Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields	13
m5c-iDeep: 5-Methylcytosine sites identification through deep learning	13
HistoSPACE: Histology-inspired spatial transcriptome prediction and characterization engine	13
MTGNN: Multi-Task Graph Neural Network based few-shot learning for disease similarity measurement	13
Editorial Board	13
Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes	12
Editorial Board	12
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	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
Bacterial flagellar motor as a multimodal biosensor	12
Resources for computational prediction of intrinsic disorder in proteins	12
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications	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
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer	12
Introduction of mutations in plants with prime editing	12
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	12
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	12
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	12
Editorial Board	12
Design of a 1 × 4 micro-magnetic stimulation device and its targeted, coordinated regulation on LTP of Schaffer-CA1 in the hippocampus of rats	12
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies	12
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	12
Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data	12
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	12

Methods to study circRNA-protein interactions	12
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph	11
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome	11
Novel, standardized sample collection from the brain-nose interface	11
Editorial Board	11
Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors	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
Enhancing RNA Delivery: Practical insights into NeoLNPTM transfection reagent	11
Efficient experimental method for purifying allergens from aqueous extracts	11
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	11
Study of circular RNA translation using reporter systems in living cells	11
Hexagonal image segmentation on spatially resolved transcriptomics	11
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	11
Publisher’s note	10
NGOME-Lite: Proteome-wide prediction of spontaneous protein deamidation highlights differences between taxa	10
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy	10
Guitar2: An improved version of the Guitar for sketching the transcriptomic view of RNA-related biological features	10
Prediction of drug-induced hepatotoxicity based on histopathological whole slide images	10
Integrated analyses of prognostic and immunotherapeutic significance of EZH2 in uveal melanoma	10
Machine learning aided single cell image analysis improves understanding of morphometric heterogeneity of human mesenchymal stem cells	10
Editorial Board	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
Temperature-jump microscopy and interaction of Hsp70 heat shock protein with a client protein in vivo	10
LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm	10
DNA building blocks for AFM tip functionalization: An easy, fast and stable strategy	10
MSO-GP: 3-D segmentation of large and complex conjoined tree structures	10
Editorial Board	10
Low friction hydrogel with diclofenac eluting ability for dry eye therapeutic contact lenses	10
Exploring drug-target interaction prediction on cold-start scenarios via meta-learning-based graph transformer	10
Prediction of coronary heart disease based on combined reinforcement multitask progressive time-series networks	10
Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms	10
Optimizing Retinal Imaging: Evaluation of ultrasmall TiO2 nanoparticle- fluorescein conjugates for improved Fundus Fluorescein Angiography	9
Editorial	9
Dimensional emotion recognition from camera-based PRV features	9
Copper catalyzed cycloaddition for the synthesis of non isomerisable 2′ and 3′-regioisomers of arg-tRNAarg	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
Triazole-linked amidopyrene-tagged fluorometric probe for Au3+ ions and pH control aggregation-induced emission	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
Multimodal contrastive representation learning for drug-target binding affinity prediction	9
Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays	9
A posterior probability based Bayesian method for single-cell RNA-seq data imputation	9
Fluorescence-based ratiometric sensors as emerging tools for CN− detection: Chemical structures, sensing mechanisms and applications	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
High resolution imaging of viruses: Scanning probe microscopy and related techniques	9
GCHN-DTI: Predicting drug-target interactions by graph convolution on heterogeneous networks	9
RLDOCK method for predicting RNA-small molecule binding modes	9
Fluorescent molecular probes for imaging and detection of oxidases and peroxidases in biological samples	9
Trans-m5C: A transformer-based model for predicting 5-methylcytosine (m5C) sites	9
SGMFQP: An ontology-based Swine Gut Microbiota Federated Query Platform	9
Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq	9
AntiMF: A deep learning framework for predicting anticancer peptides based on multi-view feature extraction	9
LiteMamba-Bound: A lightweight Mamba-based model with boundary-aware and normalized active contour loss for skin lesion segmentation	9
Corrigendum to “Smart biomaterials: From 3D printing to 4D bioprinting” [Methods 205 (2022) 191–199]	9
DNA base order parameter determination without influence of chemical exchange	8
StackDPPIV: A novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides	8
Adversarial learning for semi-supervised pediatric sleep staging with single-EEG channel	8
DBPboost:A method of classification of DNA-binding proteins based on improved differential evolution algorithm and feature extraction	8
Guide to studying intrinsically disordered proteins by high-speed atomic force microscopy	8
Advances in machine learning for epigenetics and biomedical applications	8
Optimising multiplex immunofluorescence staining for characterising the tumour immune micro-environment	8
Multitask learning model for predicting non-coding RNA-disease associations: Incorporating local and global context	8
Generation of site-specifically labelled fluorescent human XPA to investigate DNA binding dynamics during nucleotide excision repair	8
The design and synthesis of circular RNAs	8
Surface-enhanced Raman scattering (SERS) technology: Emerging applications in cancer imaging and precision medicine	8
Rapid in vitro and computer-aided method for assessing synergistic interactions between NSAIDs and analgesics	8
CRISPR-Cas systems for diagnosing infectious diseases	8
Weighted hypergraph learning and adaptive inductive matrix completion for SARS-CoV-2 drug repositioning	8
Development and validation of a machine learning model for predicting drug-drug interactions with oral diabetes medications	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
Evaluation of unitary conductance of gap junction channels based on stationary fluctuation analysis	8
RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features	8
Challenges, optimization strategies, and future horizons of advanced deep learning approaches for brain lesion segmentation	8
Progression and application of CRISPR-Cas genomic editors	8
Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13	8
Machine learning algorithms for prediction of entrapment efficiency in nanomaterials	8
Artificial intelligence and computer-aided drug discovery: Methods development and application	8
Measuring hypertrophy in neonatal rat primary cardiomyocytes and human iPSC-derived cardiomyocytes	8
CRISPR-ENHANCE: An enhanced nucleic acid detection platform using Cas12a	8
A domain-label-guided translation model for molecular optimization	8
Biochemical analysis of DNA synthesis blockage by G-quadruplex structure and bypass facilitated by a G4-resolving helicase	8
Applicability analysis of immunotherapy for lung cancer patients based on deep learning	8
Immunological methods for the determination of AGE-RAGE axis generated glutathionylated and carbonylated proteins as oxidative stress markers	8
Site-specific incorporation of biophysical probes into NF-ĸB with non-canonical amino acids	8
Editorial Board	8
What’s the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry	8
Design and characterization of hollow microneedles for localized intrascleral drug delivery of ocular formulations	7
Learning from imbalanced COVID-19 chest X-ray (CXR) medical imaging data	7
Systems dynamics and the uncertainties of diagnostics, testing and contact tracing for COVID-19	7
PENet: Prior evidence deep neural network for bladder cancer staging	7
PDSM-LGCN: Prediction of drug sensitivity associated microRNAs via light graph convolution neural network	7
A hierarchical three-step superpixels and deep learning framework for skin lesion classification	7
Predicting CircRNA disease associations using novel node classification and link prediction models on Graph Convolutional Networks	7
Anle138b interaction in α-synuclein aggregates by dynamic nuclear polarization NMR	7
Deep Learning in Bioinformatics and Biomedicine	7