Methods

Article	Citations
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	144
Editorial Board	113
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	108
Editorial Board	90
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	82
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors	81
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	78
Interpretable thoracic pathologic prediction via learning group-disentangled representation	77
Predicting genes associated with ossification of the posterior longitudinal ligament using graph attention network	71
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	71
Precision mapping of NF-κB-DNA binding: high-resolution insights via dynamic UV-laser footprinting	65
An overview of extracellular field potentials: Different potentiation and measurable components, interpretations, and hippocampal synaptic activity models	63
On finding natural antibiotics based on TCM formulae	60
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	58
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	56
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	56
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	55
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm	53
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	48
Strategies for ocular drug delivery	47
Non-canonical amino acids and protein dynamics	47
Two minimally invasive strategies to implant guide cannulas for multiple injections in deep brain areas	44
Atomic force microscope kymograph analysis: A case study of two membrane proteins	43
Isolation and culture of adult murine cardiac atrial and ventricular fibroblasts and myofibroblasts	41
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures	41

MRDFF: A deep forest based framework for CT whole heart segmentation	39
Clinical analysis of eye movement-based data in the medical diagnosis of amblyopia	39
Unravelling cell heterogeneity and gene regulation mechanisms in multiple myeloma through single-cell RNA-seq	38
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis	37
Pseudouridine RNA modification detection and quantification by RT-PCR	35
Electrochemical assay for the quantification of anticancer drugs and their inhibition mechanism	34
Interpretable multimodal learning for tumor protein-metal binding: Progress, challenges, and perspectives	33
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	33
Advancing antisense oligonucleotide delivery through click chemistry based chemical conjugation with designed short non-cationic peptides for Duchenne muscular dystrophy	33
Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues	32
Viral-mediated fluorescent labelling of activated hippocampal memory engrams to study epigenetic dynamics associated with gene expression	32
Comprehensive evaluation of molecule property prediction with ChatGPT	31
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	31
DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions	31
The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years	31
MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models	30
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	30
Breaking barrier of binding buffer in colorimetric aptasensing of tetracycline in food fish using peroxidase mimic gold NanoZyme	29
Development and validation of a stability-indicating HPLC method for assay of tonabersat in pharmaceutical formulations	29
Advanced glycation end products in musculoskeletal system and disorders	29
MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction	28
Editorial Board	27
scGAAC: A graph attention autoencoder for clustering single-cell RNA-sequencing data	27
Prediction of the transcription factor binding sites with meta-learning	26
Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination	26
AntiT2DMP-Pred: Leveraging feature fusion and optimization for superior machine learning prediction of type 2 diabetes mellitus	25
Syntenins at the crossroads of host–virus interactions	25
Guest Editor’s Introduction: Optical methods for characterisation of biomolecules	24
Measuring functional similarity of lncRNAs based on variable K-mer profiles of nucleotide sequences	24
Editorial Board	24
Characterization of targeted knock-in achieved via tandem paired nicking mediated by CRISPR/Cas9 nickases	23
Materials-Based spatiotemporal analysis of microbial responses to glyphosate in Winogradsky columns	23
Hybrid manifold-deep convolutional neural network for sleep staging	23
COVID-19 lesion detection and segmentation–A deep learning method	23
A heterogeneous graph transformer framework for accurate cancer driver gene prediction and downstream analysis	23
Novel approaches to biomarker discover	23
Multi-view contrastive clustering for cancer subtyping using fully and weakly paired multi-omics data	22
Validation of combo ichroma as a reliable concentration-based alternative for AST and ALT measurement in liver disease monitoring	22
Glaucoma screening using an attention-guided stereo ensemble 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 brief review of RNA modification related database resources	22
Model-agnostic confidence measurement for aggregating multimodal ensemble models in automatic diagnostic systems	21
MPFFPSDC: A multi-pooling feature fusion model for predicting synergistic drug combinations	21
A federated learning method for real-time emotion state classification from multi-modal streaming	21
Improving domain generalization performance for medical image segmentation via random feature augmentation	21
UGDAS: Unsupervised graph-network based denoiser for abstractive summarization in biomedical domain	21
Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state	21
MLFA-UNet: A multi-level feature assembly UNet for medical image segmentation	21
Identification of immunoregulatory peptides from gut microbiota modulating Epstein-Barr virus-induced gene 3 (EBI3) using a novel specific AlphaLISA™ assay	21
HI-CeFSpot: High-throughput Immune Cell FluoroSpot assay	20

Scale-adjusted distance transform and its applications to segmentation of multimodal images	20
Gold nanoparticles for salivary-based sensors: A review	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
Identification of DNase I hypersensitive sites in the human genome by multiple sequence descriptors	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	19
Biomedical event causal relation extraction with deep knowledge fusion and Roberta-based data augmentation	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
Corrigendum to “Decoding selective auditory attention with EEG using a transformer model” [Methods 204 (2022) 410–417]	19
Steric trapping strategy for studying the folding of helical membrane proteins	19
Microproteins transitioning into a new Phase: Defining the undefined	18
MDM2/p53-based live-cell quantitative FRET imaging for apoptosis drug discovery	18
Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects	18
Baker’s yeast beta glucan supplementation was associated with an improved innate immune mRNA expression response after exercise	18
Editorial Board	18
Chromatin image-driven modelling	17
Deciphering cellular heterogeneity: Breakthroughs and prospects of single-cell-level SERS analysis in precision medicine	17
Editorial Board	17
SGAE-MDA: Exploring the MiRNA-disease associations in herbal medicines based on semi-supervised graph autoencoder	17
Exploring the artificial intelligence and machine learning models in the context of drug design difficulties and future potential for the pharmaceutical sectors	17
CSSEC: An adaptive approach integrating consensus and specific self-expressive coefficients for multi-omics cancer subtyping	17
Modeling repeated self-reported outcome data: A continuous-time longitudinal Item Response Theory model	17
The semisynthesis of site-specifically modified histones and histone-based probes of chromatin-modifying enzymes	17
Deep learning based method for predicting DNA N6-methyladenosine sites	17
A dual-function fluorescence 'turn-on' probe that allows Zn (II) bioimaging and quantification of water in the organic solvent	16
Detection and quantification of nanoparticle-induced intracellular ROS in live cells by laser scanning confocal microscopy	16
ZeRPI: A graph neural network model for zero-shot prediction of RNA-protein interactions	16
Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme	16
Meta-IL4: An ensemble learning approach for IL-4-inducing peptide prediction	16
A compact and interpretable convolutional neural network for cross-subject driver drowsiness detection from single-channel EEG	16
Convolutional autoencoder based on latent subspace projection for anomaly detection	16
Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts	16
DRCNNTLe: A deep recurrent convolutional neural network with transfer learning through pre-trained embeddings for automated ICD coding	16
Hybrid multimodal fusion for graph learning in disease prediction	16
Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing	16
A comprehensive preanalytical protocol for fresh solid tumor biospecimens	16
CLCAP: Contrastive learning improves antigenicity prediction for influenza A virus using convolutional neural networks	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
Single molecule methods for studying CRISPR Cas9-induced DNA unwinding	16
Assessing the role of intrinsic disorder in RNA-binding protein function: hnRNP K as a case study	16
Authentication of Panax notoginseng with high-efficiency Proofman-LMTIA technology	16
The prognostic value of machine learning techniques versus cox regression model for head and neck cancer	16
Editorial Board	15
In silico identification of Histone Deacetylase inhibitors using Streamlined Masked Transformer-based Pretrained features	15
Graph matching survey for medical imaging: On the way to deep learning	15
HistoSPACE: Histology-inspired spatial transcriptome prediction and characterization engine	15
Kinetics measurements of G-quadruplex binding and unfolding by helicases	15
Predicting miRNA-lncRNA interactions on plant datasets based on bipartite network embedding method	15
Unveiling the pathogenicity of allosteric protein mutations via multifaceted feature ensembling	15
Smartphone-based low-cost and rapid quantitative detection of urinary creatinine with the Tyndall effect	15
Identification of adaptor proteins by incorporating deep learning and PSSM profiles	15
Editorial Board	15
dsRNAPredictor-II: An improved predictor of identifying dsRNA and its silencing efficiency for Tribolium castaneum based on sequence length distribution	15
A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis	14
Towards transparent and interpretable screening: multi-biofluid FTIR spectroscopy with LLM-Augmented explainability for pancreatic cancer detection	14
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	14
Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET	14
Atrial-specific hiPSC-derived cardiomyocytes in drug discovery and disease modeling	14
Editorial Board	14
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer	14
m5c-iDeep: 5-Methylcytosine sites identification through deep learning	14
Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields	14
Current methodologies in studying chromatin and gene expression	14
Editorial Board	14
An effective multi-task learning framework for drug repurposing based on graph representation learning	13
Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data	13
PCR-generated DNA templates enable efficient, rapid, and cost-effective mRNA synthesis	13
A fluorescence turn “on-off” imaging probe for sequential detection of Al3+ and L-Cysteine in HeLa cells	13
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	13
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	13
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	13
Editorial Board	13
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	13
Resources for computational prediction of intrinsic disorder in proteins	13
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	13
Integrating a multi-omics strategy framework to screen potential targets in cognitive impairment-related epilepsy	13
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies	13
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data	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
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications	13

Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	13
Natural language processing	13
Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review	12
Coffee – a ubiquitous substitute for uranyl acetate in staining of biological ultrathin sections for electron microscopy studies	12
3D printing of calcium doped Isomalt via custom-made Extruder: Facile approach for creating blood vascular like networks within tissue mimicking hydrogel matrix	12
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome	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
Novel, standardized sample collection from the brain-nose interface	12
Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors	12
Hexagonal image segmentation on spatially resolved transcriptomics	12
Low friction hydrogel with diclofenac eluting ability for dry eye therapeutic contact lenses	12
Enhancing RNA Delivery: Practical insights into NeoLNPTM transfection reagent	11
Editorial Board	11
Publisher’s note	11
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph	11
Navigating the frontier of human microglia isolation—standardization and translational insight	11
Machine learning aided single cell image analysis improves understanding of morphometric heterogeneity of human mesenchymal stem cells	11
Editorial Board	11
Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq	11
Optimized CUT&Tag enables robust epigenome profiling in Schizosaccharomyces pombe	11
Efficient experimental method for purifying allergens from aqueous extracts	11
Integrated analyses of prognostic and immunotherapeutic significance of EZH2 in uveal melanoma	11
Prediction of drug-induced hepatotoxicity based on histopathological whole slide images	11
LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm	11
Imaging flow cytometry reveals LPS-induced changes to intracellular intensity and distribution of α-synuclein in a TLR4-dependent manner in STC-1 cells	11
Temperature-jump microscopy and interaction of Hsp70 heat shock protein with a client protein in vivo	11
Clinical assessment of the diagnostic performance of the LIAISON® Legionella urinary antigen assay	11
Isothermal titration calorimetry and surface plasmon resonance methods to probe protein–protein interactions	11
Sensitive and specific detection of ctDNA using Copper-Free click chemistry and magnetic bead Technology	10
Corrigendum to “Smart biomaterials: From 3D printing to 4D bioprinting” [Methods 205 (2022) 191–199]	10
GCHN-DTI: Predicting drug-target interactions by graph convolution on heterogeneous networks	10
LiteMamba-Bound: A lightweight Mamba-based model with boundary-aware and normalized active contour loss for skin lesion segmentation	10
DNA-regulated structural engineering of metal nanomaterials: A strategy for advanced optical biosensing	10
Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13	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
MSO-GP: 3-D segmentation of large and complex conjoined tree structures	10
Guitar2: An improved version of the Guitar for sketching the transcriptomic view of RNA-related biological features	10
AntiMF: A deep learning framework for predicting anticancer peptides based on multi-view feature extraction	10
Multimodal contrastive representation learning for drug-target binding affinity prediction	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	10
Dimensional emotion recognition from camera-based PRV features	10
Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays	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
Copper catalyzed cycloaddition for the synthesis of non isomerisable 2′ and 3′-regioisomers of arg-tRNAarg	10
Fragile methods, fractured trust: rethinking scientific responsibility	10
Exploring drug-target interaction prediction on cold-start scenarios via meta-learning-based graph transformer	10
Trans-m5C: A transformer-based model for predicting 5-methylcytosine (m5C) sites	10
Fluorescent molecular probes for imaging and detection of oxidases and peroxidases in biological samples	10
Fluorescence-based ratiometric sensors as emerging tools for CN− detection: Chemical structures, sensing mechanisms and applications	10
Triazole-linked amidopyrene-tagged fluorometric probe for Au3+ ions and pH control aggregation-induced emission	10