Methods

Article	Citations
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	237
Editorial Board	113
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	109
Editorial Board	109
Interpretable thoracic pathologic prediction via learning group-disentangled representation	86
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	77
On finding natural antibiotics based on TCM formulae	76
Approaches for the sensitive detection of rare base and prime editing events	74
Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework	73
Predicting genes associated with ossification of the posterior longitudinal ligament using graph attention network	72
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	71
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	61
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm	61
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	60
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors	59
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	58
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	56
Editorial Board	54
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	54
An overview of extracellular field potentials: Different potentiation and measurable components, interpretations, and hippocampal synaptic activity models	52
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	51
Brain controllability and morphometry similarity of internet gaming addiction	51
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures	50
Editorial Board	48
Editorial Board	47

Trans ligation of RNAs to generate hybrid circular RNAs using highly efficient autocatalytic transcripts	47
Two minimally invasive strategies to implant guide cannulas for multiple injections in deep brain areas	46
Strategies for ocular drug delivery	45
MRDFF: A deep forest based framework for CT whole heart segmentation	43
Synthesis of carbon nanotubes using pre-sintered oil fly ash via a reproducible process with large-scale potential	42
MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models	41
Comprehensive evaluation of molecule property prediction with ChatGPT	41
Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets	38
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	37
DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions	37
Clinical analysis of eye movement-based data in the medical diagnosis of amblyopia	34
Non-canonical amino acids and protein dynamics	33
Atomic force microscope kymograph analysis: A case study of two membrane proteins	33
Isolation and culture of adult murine cardiac atrial and ventricular fibroblasts and myofibroblasts	32
Breaking barrier of binding buffer in colorimetric aptasensing of tetracycline in food fish using peroxidase mimic gold NanoZyme	31
The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years	31
MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction	31
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	30
Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues	30
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	30
Interpretable Multimodal Learning for Tumor Protein-Metal Binding: Progress, Challenges, and Perspectives	30
Pseudouridine RNA modification detection and quantification by RT-PCR	30
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis	28
Advanced glycation end products in musculoskeletal system and disorders	28
Development and validation of a stability-indicating HPLC method for assay of tonabersat in pharmaceutical formulations	28
Hybrid manifold-deep convolutional neural network for sleep staging	27
Editorial Board	27
Editorial Board	27
Multi-view contrastive clustering for cancer subtyping using fully and weakly paired multi-omics data	26
Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state	26
EpiHNet: Detecting epistasis by heterogeneous molecule network	26
Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination	26
Improving domain generalization performance for medical image segmentation via random feature augmentation	26
AntiT2DMP-Pred: Leveraging feature fusion and optimization for superior machine learning prediction of type 2 diabetes mellitus	25
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	25
Prediction of the transcription factor binding sites with meta-learning	25
Model-agnostic confidence measurement for aggregating multimodal ensemble models in automatic diagnostic systems	25
Guest Editor’s Introduction: Optical methods for characterisation of biomolecules	23
A heterogeneous graph transformer framework for accurate cancer driver gene prediction and downstream analysis	23
scGAAC: A graph attention autoencoder for clustering single-cell RNA-sequencing data	23
UGDAS: Unsupervised graph-network based denoiser for abstractive summarization in biomedical domain	22
MPFFPSDC: A multi-pooling feature fusion model for predicting synergistic drug combinations	22
Novel approaches to biomarker discover	22
MLFA-UNet: A multi-level feature assembly UNet for medical image segmentation	21
Measuring functional similarity of lncRNAs based on variable K-mer profiles of nucleotide sequences	21
Glaucoma screening using an attention-guided stereo ensemble network	20
Recent progress in the analysis of protein deamidation using mass spectrometry	20
A federated learning method for real-time emotion state classification from multi-modal streaming	20
A brief review of RNA modification related database resources	20
COVID-19 lesion detection and segmentation–A deep learning method	20

Steric trapping strategy for studying the folding of helical membrane proteins	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	19
Microproteins transitioning into a new Phase: Defining the undefined	19
Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects	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
Corrigendum to “Decoding selective auditory attention with EEG using a transformer model” [Methods 204 (2022) 410–417]	19
Baker’s yeast beta glucan supplementation was associated with an improved innate immune mRNA expression response after exercise	18
Exploring the artificial intelligence and machine learning models in the context of drug design difficulties and future potential for the pharmaceutical sectors	18
SGAE-MDA: Exploring the MiRNA-disease associations in herbal medicines based on semi-supervised graph autoencoder	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
DRCNNTLe: A deep recurrent convolutional neural network with transfer learning through pre-trained embeddings for automated ICD coding	18
Identifying and ranking potential cancer drivers using representation learning on attributed network	18
Identification of DNase I hypersensitive sites in the human genome by multiple sequence descriptors	18
Chromatin image-driven modelling	18
Convolutional autoencoder based on latent subspace projection for anomaly detection	18
Statistical methods for comparing test positivity rates between countries: Which method should be used and why?	18
Biomedical event causal relation extraction with deep knowledge fusion and Roberta-based data augmentation	18
Modeling repeated self-reported outcome data: A continuous-time longitudinal Item Response Theory model	18
Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts	17
The semisynthesis of site-specifically modified histones and histone-based probes of chromatin-modifying enzymes	17
A dual-function fluorescence 'turn-on' probe that allows Zn (II) bioimaging and quantification of water in the organic solvent	17
Editorial Board	17
CLCAP: Contrastive learning improves antigenicity prediction for influenza A virus using convolutional neural networks	17
The prognostic value of machine learning techniques versus cox regression model for head and neck cancer	17
Deep learning based method for predicting DNA N6-methyladenosine sites	17
CSSEC: An adaptive approach integrating consensus and specific self-expressive coefficients for multi-omics cancer subtyping	16
Meta-IL4: An ensemble learning approach for IL-4-inducing peptide prediction	16
Methods for preparation of niosomes: A focus on thin-film hydration method	16
A compact and interpretable convolutional neural network for cross-subject driver drowsiness detection from single-channel EEG	16
Detection and quantification of nanoparticle-induced intracellular ROS in live cells by laser scanning confocal microscopy	16
Hybrid multimodal fusion for graph learning in disease prediction	16
Single molecule methods for studying CRISPR Cas9-induced DNA unwinding	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
Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins	16
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
Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing	15
Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme	15
ZeRPI: A graph neural network model for zero-shot prediction of RNA-protein interactions	15
A comprehensive preanalytical protocol for fresh solid tumor biospecimens	15
Editorial Board	14
Signal and noise in circRNA translation	14
m5c-iDeep: 5-Methylcytosine sites identification through deep learning	14
A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis	14
Identification of adaptor proteins by incorporating deep learning and PSSM profiles	14
Editorial Board	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
dsRNAPredictor-II: An improved predictor of identifying dsRNA and its silencing efficiency for Tribolium castaneum based on sequence length distribution	14
In silico identification of Histone Deacetylase inhibitors using Streamlined Masked Transformer-based Pretrained features	14
Kinetics measurements of G-quadruplex binding and unfolding by helicases	14
HistoSPACE: Histology-inspired spatial transcriptome prediction and characterization engine	14
Editorial Board	13
Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields	13
Atrial-specific hiPSC-derived cardiomyocytes in drug discovery and disease modeling	13
An effective multi-task learning framework for drug repurposing based on graph representation learning	13
Smartphone-based low-cost and rapid quantitative detection of urinary creatinine with the Tyndall effect	13
Editorial Board	13
Editorial Board	13
Latest progress in the study of nanoparticle-based delivery of the CRISPR/Cas9 system	13
MTGNN: Multi-Task Graph Neural Network based few-shot learning for disease similarity measurement	13
Integrating a multi-omics strategy framework to screen potential targets in cognitive impairment-related epilepsy	13
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data	12
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	12
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer	12
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	12
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	12
Resources for computational prediction of intrinsic disorder in proteins	12
Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes	12
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies	12
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications	12
A fluorescence turn “on-off” imaging probe for sequential detection of Al3+ and L-Cysteine in HeLa cells	12
Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data	12
Methods to study circRNA-protein interactions	12
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	12
Introduction of mutations in plants with prime editing	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
Current methodologies in studying chromatin and gene expression	12
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	12

Bacterial flagellar motor as a multimodal biosensor	12
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	12
Model-based autoencoders for imputing discrete single-cell RNA-seq data	11
Isothermal titration calorimetry and surface plasmon resonance methods to probe protein–protein interactions	11
Efficient experimental method for purifying allergens from aqueous extracts	11
TPQCI: A topology potential-based method to quantify functional influence of copy number variations	11
Editorial Board	11
Low friction hydrogel with diclofenac eluting ability for dry eye therapeutic contact lenses	11
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy	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
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph	11
Hexagonal image segmentation on spatially resolved transcriptomics	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
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
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	11
Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review	11
Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors	11
Study of circular RNA translation using reporter systems in living cells	11
Editorial Board	10
Exploring drug-target interaction prediction on cold-start scenarios via meta-learning-based graph transformer	10
Editorial Board	10
Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq	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
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
High resolution imaging of viruses: Scanning probe microscopy and related techniques	10
Prediction of drug-induced hepatotoxicity based on histopathological whole slide images	10
Publisher’s note	10
AntiMF: A deep learning framework for predicting anticancer peptides based on multi-view feature extraction	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
Copper catalyzed cycloaddition for the synthesis of non isomerisable 2′ and 3′-regioisomers of arg-tRNAarg	10
Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms	10
Temperature-jump microscopy and interaction of Hsp70 heat shock protein with a client protein in vivo	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
LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm	10
NGOME-Lite: Proteome-wide prediction of spontaneous protein deamidation highlights differences between taxa	10
Integrated analyses of prognostic and immunotherapeutic significance of EZH2 in uveal melanoma	10
LiteMamba-Bound: A lightweight Mamba-based model with boundary-aware and normalized active contour loss for skin lesion segmentation	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
Fluorescent molecular probes for imaging and detection of oxidases and peroxidases in biological samples	9
Editorial	9
Dimensional emotion recognition from camera-based PRV features	9
Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays	9
Optimizing Retinal Imaging: Evaluation of ultrasmall TiO2 nanoparticle- fluorescein conjugates for improved Fundus Fluorescein Angiography	9
RLDOCK method for predicting RNA-small molecule binding modes	9
Guitar2: An improved version of the Guitar for sketching the transcriptomic view of RNA-related biological features	9
Prediction of drug response in multilayer networks based on fusion of multiomics data	9
A posterior probability based Bayesian method for single-cell RNA-seq data imputation	9
Machine learning algorithms for prediction of entrapment efficiency in nanomaterials	9
Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13	9
Multimodal contrastive representation learning for drug-target binding affinity prediction	9
Triazole-linked amidopyrene-tagged fluorometric probe for Au3+ ions and pH control aggregation-induced emission	9
GCHN-DTI: Predicting drug-target interactions by graph convolution on heterogeneous networks	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
What’s the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry	9
Machine learning aided single cell image analysis improves understanding of morphometric heterogeneity of human mesenchymal stem cells	9
Fluorescence-based ratiometric sensors as emerging tools for CN− detection: Chemical structures, sensing mechanisms and applications	9
The design and synthesis of circular RNAs	8
A multi-objective optimization method for identification of module biomarkers for disease diagnosis	8
CRISPR-Cas systems for diagnosing infectious diseases	8
Optimising multiplex immunofluorescence staining for characterising the tumour immune micro-environment	8
Prediction of drug protein interactions based on variable scale characteristic pyramid convolution network	8
Adversarial learning for semi-supervised pediatric sleep staging with single-EEG channel	8
Development and validation of a machine learning model for predicting drug-drug interactions with oral diabetes medications	8
Guide to studying intrinsically disordered proteins by high-speed atomic force microscopy	8
StackDPPIV: A novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides	8
Challenges, optimization strategies, and future horizons of advanced deep learning approaches for brain lesion segmentation	8
Generation of site-specifically labelled fluorescent human XPA to investigate DNA binding dynamics during nucleotide excision repair	8
Progression and application of CRISPR-Cas genomic editors	8
Artificial intelligence and computer-aided drug discovery: Methods development and application	8
Biochemical analysis of DNA synthesis blockage by G-quadruplex structure and bypass facilitated by a G4-resolving helicase	8
Measuring hypertrophy in neonatal rat primary cardiomyocytes and human iPSC-derived cardiomyocytes	8
Weighted hypergraph learning and adaptive inductive matrix completion for SARS-CoV-2 drug repositioning	8
Applicability analysis of immunotherapy for lung cancer patients based on deep learning	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
RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features	8
Immunological methods for the determination of AGE-RAGE axis generated glutathionylated and carbonylated proteins as oxidative stress markers	8
DNA base order parameter determination without influence of chemical exchange	8
Editorial Board	8
Advances in machine learning for epigenetics and biomedical applications	8
Evaluation of unitary conductance of gap junction channels based on stationary fluctuation analysis	8
A domain-label-guided translation model for molecular optimization	8
CRISPR-ENHANCE: An enhanced nucleic acid detection platform using Cas12a	8
DBPboost:A method of classification of DNA-binding proteins based on improved differential evolution algorithm and feature extraction	8
Ultrasensitive detection and quantification of viral nucleic acids with Raindance droplet digital PCR (ddPCR)	8
Site-specific incorporation of biophysical probes into NF-ĸB with non-canonical amino acids	8
Multitask learning model for predicting non-coding RNA-disease associations: Incorporating local and global context	8
TopoStats – A program for automated tracing of biomolecules from AFM images	7
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
Editorial Board	7
Predicting CircRNA disease associations using novel node classification and link prediction models on Graph Convolutional Networks	7