Methods

Article	Citations
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	262
Predicting genes associated with ossification of the posterior longitudinal ligament using graph attention network	137
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	130
Interpretable thoracic pathologic prediction via learning group-disentangled representation	129
Editorial Board	103
An overview of extracellular field potentials: Different potentiation and measurable components, interpretations, and hippocampal synaptic activity models	88
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	85
Editorial Board	82
Editorial Board	82
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	80
On finding natural antibiotics based on TCM formulae	78
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors	69
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm	68
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	68
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	65
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	61
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	60
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	60
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	59
Non-canonical amino acids and protein dynamics	55
Strategies for ocular drug delivery	54
Isolation and culture of adult murine cardiac atrial and ventricular fibroblasts and myofibroblasts	52
Breaking barrier of binding buffer in colorimetric aptasensing of tetracycline in food fish using peroxidase mimic gold NanoZyme	50
Two minimally invasive strategies to implant guide cannulas for multiple injections in deep brain areas	48
Electrochemical assay for the quantification of anticancer drugs and their inhibition mechanism	47

Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets	46
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	45
Editorial Board	39
Trans ligation of RNAs to generate hybrid circular RNAs using highly efficient autocatalytic transcripts	38
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures	38
Synthesis of carbon nanotubes using pre-sintered oil fly ash via a reproducible process with large-scale potential	37
Interpretable multimodal learning for tumor protein-metal binding: Progress, challenges, and perspectives	36
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	36
Clinical analysis of eye movement-based data in the medical diagnosis of amblyopia	36
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	36
The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years	36
Comprehensive evaluation of molecule property prediction with ChatGPT	35
Development and validation of a stability-indicating HPLC method for assay of tonabersat in pharmaceutical formulations	35
Advancing antisense oligonucleotide delivery through click chemistry based chemical conjugation with designed short non-cationic peptides for Duchenne muscular dystrophy	34
DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions	32
Atomic force microscope kymograph analysis: A case study of two membrane proteins	32
MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction	31
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis	31
MRDFF: A deep forest based framework for CT whole heart segmentation	31
Pseudouridine RNA modification detection and quantification by RT-PCR	30
Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues	29
Advanced glycation end products in musculoskeletal system and disorders	29
MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models	29
Editorial Board	28
Validation of combo ichroma as a reliable concentration-based alternative for AST and ALT measurement in liver disease monitoring	28
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
Measuring functional similarity of lncRNAs based on variable K-mer profiles of nucleotide sequences	27
Model-agnostic confidence measurement for aggregating multimodal ensemble models in automatic diagnostic systems	26
Guest Editor’s Introduction: Optical methods for characterisation of biomolecules	26
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	26
A brief review of RNA modification related database resources	26
AntiT2DMP-Pred: Leveraging feature fusion and optimization for superior machine learning prediction of type 2 diabetes mellitus	24
Novel approaches to biomarker discover	24
Prediction of the transcription factor binding sites with meta-learning	23
UGDAS: Unsupervised graph-network based denoiser for abstractive summarization in biomedical domain	23
Editorial Board	23
Hybrid manifold-deep convolutional neural network for sleep staging	23
Characterization of targeted knock-in achieved via tandem paired nicking mediated by CRISPR/Cas9 nickases	22
A heterogeneous graph transformer framework for accurate cancer driver gene prediction and downstream analysis	22
Improving domain generalization performance for medical image segmentation via random feature augmentation	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
Multi-view contrastive clustering for cancer subtyping using fully and weakly paired multi-omics data	21
A federated learning method for real-time emotion state classification from multi-modal streaming	21
Glaucoma screening using an attention-guided stereo ensemble network	21
EpiHNet: Detecting epistasis by heterogeneous molecule network	21
Identification of immunoregulatory peptides from gut microbiota modulating Epstein-Barr virus-induced gene 3 (EBI3) using a novel specific AlphaLISA™ assay	21
MPFFPSDC: A multi-pooling feature fusion model for predicting synergistic drug combinations	20
Microproteins transitioning into a new Phase: Defining the undefined	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
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	20
Recent progress in the analysis of protein deamidation using mass spectrometry	20
Computational methods and strategies for combating COVID-19	20
Chromatin image-driven modelling	20
Baker’s yeast beta glucan supplementation was associated with an improved innate immune mRNA expression response after exercise	19
Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects	19
Corrigendum to “Decoding selective auditory attention with EEG using a transformer model” [Methods 204 (2022) 410–417]	19
SGAE-MDA: Exploring the MiRNA-disease associations in herbal medicines based on semi-supervised graph autoencoder	19
Modeling repeated self-reported outcome data: A continuous-time longitudinal Item Response Theory model	19
Deciphering cellular heterogeneity: Breakthroughs and prospects of single-cell-level SERS analysis in precision medicine	19
Biomedical event causal relation extraction with deep knowledge fusion and Roberta-based data augmentation	19
Steric trapping strategy for studying the folding of helical membrane proteins	18
Exploring the artificial intelligence and machine learning models in the context of drug design difficulties and future potential for the pharmaceutical sectors	18
Inner leaflet cationic lipid increases nucleic acid loading independently of outer leaflet lipid charge in asymmetric liposomes	18
Deep learning based method for predicting DNA N6-methyladenosine sites	18
HI-CeFSpot: High-throughput Immune Cell FluoroSpot assay	18
Identification of DNase I hypersensitive sites in the human genome by multiple sequence descriptors	18
Single molecule methods for studying CRISPR Cas9-induced DNA unwinding	17
Editorial Board	17
Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing	17
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
Assessing the role of intrinsic disorder in RNA-binding protein function: hnRNP K as a case study	17
CSSEC: An adaptive approach integrating consensus and specific self-expressive coefficients for multi-omics cancer subtyping	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
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
Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme	16
Authentication of Panax notoginseng with high-efficiency Proofman-LMTIA technology	16
CLCAP: Contrastive learning improves antigenicity prediction for influenza A virus using convolutional neural networks	16
A dual-function fluorescence 'turn-on' probe that allows Zn (II) bioimaging and quantification of water in the organic solvent	16
Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts	16
A compact and interpretable convolutional neural network for cross-subject driver drowsiness detection from single-channel EEG	16
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
In silico identification of Histone Deacetylase inhibitors using Streamlined Masked Transformer-based Pretrained features	15
The prognostic value of machine learning techniques versus cox regression model for head and neck cancer	15
Methods for preparation of niosomes: A focus on thin-film hydration method	15
Kinetics measurements of G-quadruplex binding and unfolding by helicases	15
DRCNNTLe: A deep recurrent convolutional neural network with transfer learning through pre-trained embeddings for automated ICD coding	15
Meta-IL4: An ensemble learning approach for IL-4-inducing peptide prediction	15
Identification of adaptor proteins by incorporating deep learning and PSSM profiles	15
Graph matching survey for medical imaging: On the way to deep learning	14
Editorial Board	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
m5c-iDeep: 5-Methylcytosine sites identification through deep learning	14
Unveiling the pathogenicity of allosteric protein mutations via multifaceted feature ensembling	14
Editorial Board	14
Predicting miRNA-lncRNA interactions on plant datasets based on bipartite network embedding method	14
A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis	14
HistoSPACE: Histology-inspired spatial transcriptome prediction and characterization engine	14
MTGNN: Multi-Task Graph Neural Network based few-shot learning for disease similarity measurement	14
Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields	14
Atrial-specific hiPSC-derived cardiomyocytes in drug discovery and disease modeling	14
Signal and noise in circRNA translation	14
Smartphone-based low-cost and rapid quantitative detection of urinary creatinine with the Tyndall effect	14
Editorial Board	14
An effective multi-task learning framework for drug repurposing based on graph representation learning	13
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer	13
Integrating a multi-omics strategy framework to screen potential targets in cognitive impairment-related epilepsy	13
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications	13
Editorial Board	13
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	13
Methods to study circRNA-protein interactions	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
PCR-generated DNA templates enable efficient, rapid, and cost-effective mRNA synthesis	13
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	13
Current methodologies in studying chromatin and gene expression	13
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	13
Resources for computational prediction of intrinsic disorder in proteins	12
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	12
Novel, standardized sample collection from the brain-nose interface	12
Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review	12
Study of circular RNA translation using reporter systems in living cells	12
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies	12
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	12
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	12

Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	12
Low friction hydrogel with diclofenac eluting ability for dry eye therapeutic contact lenses	12
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data	12
Editorial Board	12
Primary sequence-assisted prediction of m6A RNA methylation sites 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
Efficient experimental method for purifying allergens from aqueous extracts	12
Isothermal titration calorimetry and surface plasmon resonance methods to probe protein–protein interactions	12
Enhancing RNA Delivery: Practical insights into NeoLNPTM transfection reagent	11
Temperature-jump microscopy and interaction of Hsp70 heat shock protein with a client protein in vivo	11
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph	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
Optimized CUT&Tag enables robust epigenome profiling in Schizosaccharomyces pombe	11
Hexagonal image segmentation on spatially resolved transcriptomics	11
Coffee – a ubiquitous substitute for uranyl acetate in staining of biological ultrathin sections for electron microscopy studies	11
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome	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
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy	11
Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors	11
Editorial Board	11
NGOME-Lite: Proteome-wide prediction of spontaneous protein deamidation highlights differences between taxa	10
Triazole-linked amidopyrene-tagged fluorometric probe for Au3+ ions and pH control aggregation-induced emission	10
Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms	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
Corrigendum to “Smart biomaterials: From 3D printing to 4D bioprinting” [Methods 205 (2022) 191–199]	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
Publisher’s note	10
Prediction of coronary heart disease based on combined reinforcement multitask progressive time-series networks	10
DNA building blocks for AFM tip functionalization: An easy, fast and stable strategy	10
Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq	10
Integrated analyses of prognostic and immunotherapeutic significance of EZH2 in uveal melanoma	10
Editorial Board	10
Exploring drug-target interaction prediction on cold-start scenarios via meta-learning-based graph transformer	10
Multimodal contrastive representation learning for drug-target binding affinity prediction	10
Fragile methods, fractured trust: rethinking scientific responsibility	10
High resolution imaging of viruses: Scanning probe microscopy and related techniques	10
GCHN-DTI: Predicting drug-target interactions by graph convolution on heterogeneous networks	10
Guitar2: An improved version of the Guitar for sketching the transcriptomic view of RNA-related biological features	10
Editorial Board	10