Methods

Article	Citations
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	222
Editorial Board	106
Editorial Board	103
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	102
Interpretable thoracic pathologic prediction via learning group-disentangled representation	84
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	76
On finding natural antibiotics based on TCM formulae	75
Approaches for the sensitive detection of rare base and prime editing events	72
Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework	69
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	69
Targeted mutagenesis in human iPSCs using CRISPR genome-editing tools	61
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	58
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm	57
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	57
Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies	55
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	55
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	51
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	51
Brain controllability and morphometry similarity of internet gaming addiction	50
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	49
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors	49
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures	48
Editorial Board	47
Editorial Board	46
Trans ligation of RNAs to generate hybrid circular RNAs using highly efficient autocatalytic transcripts	45

Two minimally invasive strategies to implant guide cannulas for multiple injections in deep brain areas	41
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae	41
Strategies for ocular drug delivery	41
Pseudouridine RNA modification detection and quantification by RT-PCR	40
Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues	40
Clinical analysis of eye movement-based data in the medical diagnosis of amblyopia	38
MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models	38
Atomic force microscope kymograph analysis: A case study of two membrane proteins	36
Non-canonical amino acids and protein dynamics	36
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	33
Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets	33
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis	32
Isolation and culture of adult murine cardiac atrial and ventricular fibroblasts and myofibroblasts	32
Advanced glycation end products in musculoskeletal system and disorders	31
MRDFF: A deep forest based framework for CT whole heart segmentation	31
Synthetic PPR proteins as tools for sequence-specific targeting of RNA	31
Synthesis of carbon nanotubes using pre-sintered oil fly ash via a reproducible process with large-scale potential	30
Comprehensive evaluation of molecule property prediction with ChatGPT	30
MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction	30
Development and validation of a stability-indicating HPLC method for assay of tonabersat in pharmaceutical formulations	29
The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years	29
DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions	29
Hybrid manifold-deep convolutional neural network for sleep staging	28
COVID-19 lesion detection and segmentation–A deep learning method	28
Editorial Board	28
Editorial Board	27
MLFA-UNet: A multi-level feature assembly UNet for medical image segmentation	27
Recent progress in the analysis of protein deamidation using mass spectrometry	26
Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state	26
Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination	25
Improving domain generalization performance for medical image segmentation via random feature augmentation	25
EpiHNet: Detecting epistasis by heterogeneous molecule network	24
Multi-view contrastive clustering for cancer subtyping using fully and weakly paired multi-omics data	24
Prediction of the transcription factor binding sites with meta-learning	23
Guest Editor’s Introduction: Optical methods for characterisation of biomolecules	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	23
Model-agnostic confidence measurement for aggregating multimodal ensemble models in automatic diagnostic systems	23
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	23
Novel approaches to biomarker discover	22
A heterogeneous graph transformer framework for accurate cancer driver gene prediction and downstream analysis	22
MPFFPSDC: A multi-pooling feature fusion model for predicting synergistic drug combinations	22
UGDAS: Unsupervised graph-network based denoiser for abstractive summarization in biomedical domain	22
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
Measuring functional similarity of lncRNAs based on variable K-mer profiles of nucleotide sequences	21
A brief review of RNA modification related database resources	21
Corrigendum to “Decoding selective auditory attention with EEG using a transformer model” [Methods 204 (2022) 410–417]	20
Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects	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
Inner leaflet cationic lipid increases nucleic acid loading independently of outer leaflet lipid charge in asymmetric liposomes	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
Steric trapping strategy for studying the folding of helical membrane proteins	19
Identifying and ranking potential cancer drivers using representation learning on attributed network	18
Statistical methods for comparing test positivity rates between countries: Which method should be used and why?	18
Exploring the artificial intelligence and machine learning models in the context of drug design difficulties and future potential for the pharmaceutical sectors	18
Chromatin image-driven modelling	18
DRCNNTLe: A deep recurrent convolutional neural network with transfer learning through pre-trained embeddings for automated ICD coding	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	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
Biomedical event causal relation extraction with deep knowledge fusion and Roberta-based data augmentation	18
Baker’s yeast beta glucan supplementation was associated with an improved innate immune mRNA expression response after exercise	18
Editorial Board	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
Detection and quantification of nanoparticle-induced intracellular ROS in live cells by laser scanning confocal microscopy	17
Universal Southern blot protocol with cold or radioactive probes for the validation of alleles obtained by homologous recombination	17
CSSEC: An adaptive approach integrating consensus and specific self-expressive coefficients for multi-omics cancer subtyping	17
Deep learning based method for predicting DNA N6-methyladenosine sites	17
Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing	17
CLCAP: Contrastive learning improves antigenicity prediction for influenza A virus using convolutional neural networks	17
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
Single molecule methods for studying CRISPR Cas9-induced DNA unwinding	16
Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins	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
ZeRPI: A graph neural network model for zero-shot prediction of RNA-protein interactions	16
A compact and interpretable convolutional neural network for cross-subject driver drowsiness detection from single-channel EEG	16
Kinetics measurements of G-quadruplex binding and unfolding by helicases	15
Hybrid multimodal fusion for graph learning in disease prediction	15
Graph matching survey for medical imaging: On the way to deep learning	15
Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts	15
dsRNAPredictor-II: An improved predictor of identifying dsRNA and its silencing efficiency for Tribolium castaneum based on sequence length distribution	15
Methods for preparation of niosomes: A focus on thin-film hydration method	15
Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields	15
Identification of adaptor proteins by incorporating deep learning and PSSM profiles	15
Editorial Board	15
A dual-function fluorescence 'turn-on' probe that allows Zn (II) bioimaging and quantification of water in the organic solvent	15
A comprehensive preanalytical protocol for fresh solid tumor biospecimens	15
Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET	15
Editorial Board	14
Smartphone-based low-cost and rapid quantitative detection of urinary creatinine with the Tyndall effect	14
In silico identification of Histone Deacetylase inhibitors using Streamlined Masked Transformer-based Pretrained features	14
Signal and noise in circRNA translation	14
Latest progress in the study of nanoparticle-based delivery of the CRISPR/Cas9 system	14
A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis	14
Atrial-specific hiPSC-derived cardiomyocytes in drug discovery and disease modeling	13
HistoSPACE: Histology-inspired spatial transcriptome prediction and characterization engine	13
Editorial Board	13
An effective multi-task learning framework for drug repurposing based on graph representation learning	13
Predicting miRNA-lncRNA interactions on plant datasets based on bipartite network embedding method	13
m5c-iDeep: 5-Methylcytosine sites identification through deep learning	13
Resources for computational prediction of intrinsic disorder in proteins	13
Editorial Board	13
MTGNN: Multi-Task Graph Neural Network based few-shot learning for disease similarity measurement	13
Methods to study circRNA-protein interactions	13
Integrating a multi-omics strategy framework to screen potential targets in cognitive impairment-related epilepsy	13
Editorial Board	13
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	12
Current methodologies in studying chromatin and gene expression	12
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	12
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies	12
Introduction of mutations in plants with prime editing	12
Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data	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
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer	12
Stereological estimation of cardiomyocyte number and proliferation	12
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	11
A fluorescence turn “on-off” imaging probe for sequential detection of Al3+ and L-Cysteine in HeLa cells	11
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications	11
Editorial Board	11
Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review	11
TPQCI: A topology potential-based method to quantify functional influence of copy number variations	11
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome	11
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data	11

HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	11
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	11
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	11
Efficient allele conversion in mouse zygotes and primary cells based on electroporation of Cre protein	11
Model-based autoencoders for imputing discrete single-cell RNA-seq data	11
Efficient experimental method for purifying allergens from aqueous extracts	11
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	11
Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes	11
Bacterial flagellar motor as a multimodal biosensor	11
Novel, standardized sample collection from the brain-nose interface	11
Multiple analyte profiling (MAP) index as a powerful diagnostic and therapeutic monitoring tool	11
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph	11
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
Editorial Board	10
Hexagonal image segmentation on spatially resolved transcriptomics	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
MSO-GP: 3-D segmentation of large and complex conjoined tree structures	10
Integrated analyses of prognostic and immunotherapeutic significance of EZH2 in uveal melanoma	10
Corrigendum to “Smart biomaterials: From 3D printing to 4D bioprinting” [Methods 205 (2022) 191–199]	10
NGOME-Lite: Proteome-wide prediction of spontaneous protein deamidation highlights differences between taxa	10
Exploring drug-target interaction prediction on cold-start scenarios via meta-learning-based graph transformer	10
Publisher’s note	10
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy	10
Low friction hydrogel with diclofenac eluting ability for dry eye therapeutic contact lenses	10
GCHN-DTI: Predicting drug-target interactions by graph convolution on heterogeneous networks	10
LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm	10
RLDOCK method for predicting RNA-small molecule binding modes	10
Machine learning aided single cell image analysis improves understanding of morphometric heterogeneity of human mesenchymal stem cells	10
Prediction of drug-induced hepatotoxicity based on histopathological whole slide images	10
Editorial Board	10
Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors	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
LiteMamba-Bound: A lightweight Mamba-based model with boundary-aware and normalized active contour loss for skin lesion segmentation	10
Guitar2: An improved version of the Guitar for sketching the transcriptomic view of RNA-related biological features	10
What’s the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry	9
High resolution imaging of viruses: Scanning probe microscopy and related techniques	9
Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq	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
AntiMF: A deep learning framework for predicting anticancer peptides based on multi-view feature extraction	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
Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13	9
Dimensional emotion recognition from camera-based PRV features	9
Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms	9
CRISPR-mediated knock-in in the mouse embryo using long single stranded DNA donors synthesised by biotinylated PCR	9
Copper catalyzed cycloaddition for the synthesis of non isomerisable 2′ and 3′-regioisomers of arg-tRNAarg	9
Fluorescence-based ratiometric sensors as emerging tools for CN− detection: Chemical structures, sensing mechanisms and applications	9
Optimizing Retinal Imaging: Evaluation of ultrasmall TiO2 nanoparticle- fluorescein conjugates for improved Fundus Fluorescein Angiography	9
Trans-m5C: A transformer-based model for predicting 5-methylcytosine (m5C) sites	9
Prediction of coronary heart disease based on combined reinforcement multitask progressive time-series networks	9
Multimodal contrastive representation learning for drug-target binding affinity prediction	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
Fluorescent molecular probes for imaging and detection of oxidases and peroxidases in biological samples	9
DNA base order parameter determination without influence of chemical exchange	8
A 3D polydimethylsiloxane microhourglass-shaped channel array made by reflowing photoresist structures for engineering a blood capillary network	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
Biochemical analysis of DNA synthesis blockage by G-quadruplex structure and bypass facilitated by a G4-resolving helicase	8
CRISPR-Cas systems for diagnosing infectious diseases	8
Site-specific incorporation of biophysical probes into NF-ĸB with non-canonical amino acids	8
Artificial intelligence and computer-aided drug discovery: Methods development and application	8
SGMFQP: An ontology-based Swine Gut Microbiota Federated Query Platform	8
A posterior probability based Bayesian method for single-cell RNA-seq data imputation	8
Prediction of drug response in multilayer networks based on fusion of multiomics data	8
RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features	8
Methods of genome engineering and model validation	8
Evaluation of unitary conductance of gap junction channels based on stationary fluctuation analysis	8
StackDPPIV: A novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides	8
Advances in machine learning for epigenetics and biomedical applications	8
A multi-objective optimization method for identification of module biomarkers for disease diagnosis	8
Editorial Board	8
Machine learning algorithms for prediction of entrapment efficiency in nanomaterials	8
Editorial	8
Generation of site-specifically labelled fluorescent human XPA to investigate DNA binding dynamics during nucleotide excision repair	8
Immunological methods for the determination of AGE-RAGE axis generated glutathionylated and carbonylated proteins as oxidative stress markers	8
A domain-label-guided translation model for molecular optimization	8
Guide to studying intrinsically disordered proteins by high-speed atomic force microscopy	8
Optimising multiplex immunofluorescence staining for characterising the tumour immune micro-environment	8
Progression and application of CRISPR-Cas genomic editors	8
The design and synthesis of circular RNAs	8
Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays	8
Movement recognition via channel-activation-wise sEMG attention	7
Systems dynamics and the uncertainties of diagnostics, testing and contact tracing for COVID-19	7
DNA shape features improve prediction of CRISPR/Cas9 activity	7
Learning from imbalanced COVID-19 chest X-ray (CXR) medical imaging data	7
Deep Learning in Bioinformatics and Biomedicine	7
PDSM-LGCN: Prediction of drug sensitivity associated microRNAs via light graph convolution neural network	7
Does protein pretrained language model facilitate the prediction of protein–ligand interaction?	7
Hydrogel-based hybrid membrane enhances in vitro ophthalmic drug evaluation in the OphthalMimic device	7
Editorial	7
Predicting CircRNA disease associations using novel node classification and link prediction models on Graph Convolutional Networks	7
RDscan: Extracting RNA-disease relationship from the literature based on pre-training model	7
Design and characterization of hollow microneedles for localized intrascleral drug delivery of ocular formulations	7
Anle138b interaction in α-synuclein aggregates by dynamic nuclear polarization NMR	7