Methods

Article	Citations
MFF-DTA: Multi-scale feature fusion for drug-target affinity prediction	204
Editorial Board	164
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies	98
Editorial Board	98
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features	95
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model	93
Microbiome metabolite quantification methods enabling insights into human health and disease	79
DMGL-MDA: A dual-modal graph learning method for microbe-drug association prediction	75
Predicting CircRNA disease associations using novel node classification and link prediction models on Graph Convolutional Networks	72
Additive manufacturing of bioactive glass biomaterials	69
Determining translocation orientations of nucleic acid helicases	66
SMAUG: Analyzing single-molecule tracks with nonparametric Bayesian statistics	62
Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes	59
Methods to investigate nucleosome structure and dynamics with single-molecule FRET	56
An overview of extracellular field potentials: Different potentiation and measurable components, interpretations, and hippocampal synaptic activity models	55
Advances in direct detection of lysine methylation and acetylation by nuclear magnetic resonance using 13C-enriched cofactors	55
An effective multi-task learning framework for drug repurposing based on graph representation learning	53
Software defined radio frequency sensing framework for intelligent monitoring of sleep apnea syndrome	51
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare	51
Retraction notice to “A methodological framework for rigorous systematic reviews: Tailoring comprehensive analyses to clinicians and healthcare professionals” [Methods 225 (2024) 38–43]	49
Editorial Board	48
Trends in deamidation across archaeological bones, ceramics and dental calculus	47
m6Am RNA modification detection by m6Am-seq	47
DeepSADPr: A hybrid-learning architecture for serine ADP-ribosylation site prediction	46
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome	46

Anle138b interaction in α-synuclein aggregates by dynamic nuclear polarization NMR	44
Interpretable thoracic pathologic prediction via learning group-disentangled representation	42
MDL-CPI: Multi-view deep learning model for compound-protein interaction prediction	42
Machine learning based identification of hub genes in renal clear cell carcinoma using multi-omics data	39
Method for the structural analysis of Twinkle mitochondrial DNA helicase by cryo-EM	39
Sleep Staging Framework with Physiologically Harmonized Sub-Networks	37
Engineered U1 snRNAs to modulate alternatively spliced exons	37
Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data	36
A mutual promotion encoder-decoder method for ultrasonic hydronephrosis diagnosis	36
Digital Intervention for behaviouR changE and Chronic disease prevenTION (DIRECTION): Study protocol for a randomized controlled trial of a web-based platform integrating nutrition, physical activity,	35
GNPI: Graph normalization to integrate phylogenetic information for metagenomic host phenotype prediction	35
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection	35
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data	33
SPIDE: A single cell potency inference method based on the local cell-specific network entropy	32
An integrated pipeline for high-throughput screening and profiling of spheroids using simple live image analysis of frame to frame variations	32
TopoStats – A program for automated tracing of biomolecules from AFM images	32
Design of a 1 × 4 micro-magnetic stimulation device and its targeted, coordinated regulation on LTP of Schaffer-CA1 in the hippocampus of rats	30
RDscan: Extracting RNA-disease relationship from the literature based on pre-training model	30
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites	29
Fluorescent human RPA to track assembly dynamics on DNA	28
m6Adecom: Analysis of m6A profile matrix based on graph regularized non-negative matrix factorization	28
Hydrogel-based hybrid membrane enhances in vitro ophthalmic drug evaluation in the OphthalMimic device	28
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics	28
Identification of potential pan-coronavirus therapies using a computational drug repurposing platform	28
Editorial: Artificial intelligence in drug discovery and development	28
m6A-Maize: Weakly supervised prediction of m6A-carrying transcripts and m6A-affecting mutations in maize (Zea mays)	27
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data	27
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells	27
Approaches for the sensitive detection of rare base and prime editing events	26
Does protein pretrained language model facilitate the prediction of protein–ligand interaction?	26
Stereological estimation of cardiomyocyte number and proliferation	26
On finding natural antibiotics based on TCM formulae	26
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer	26
A roadmap to cysteine specific labeling of membrane proteins for single-molecule photobleaching studies	26
Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies	23
Hutchinson-Gilford progeria syndrome: Rejuvenating old drugs to fight accelerated ageing	23
Bacterial flagellar motor as a multimodal biosensor	23
Editorial	23
Targeted mutagenesis in human iPSCs using CRISPR genome-editing tools	22
m6Acancer-Net: Identification of m6A-mediated cancer driver genes from gene-site heterogeneous network	22
Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework	22
Movement recognition via channel-activation-wise sEMG attention	21
Introduction of mutations in plants with prime editing	21
Advances in base editing with an emphasis on an AAV-based strategy	21
Multi-targeting approach for nsp3, nsp9, nsp12 and nsp15 proteins of SARS-CoV-2 by Diosmin as illustrated by molecular docking and molecular dynamics simulation methodologies	21
Methods to study circRNA-protein interactions	21
Machine learning for the analysis of multi-omics data	21
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors	21
A method for assaying DNA flexibility	20
Brain controllability and morphometry similarity of internet gaming addiction	20

Learning from imbalanced COVID-19 chest X-ray (CXR) medical imaging data	20
Using Drosophila to uncover molecular and physiological functions of circRNAs	19
WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction	19
Pan-methylarginine antibody generation using PEG linked GAR motifs as antigens	19
Explore drug-like space with deep generative models	19
The platform development, adherence and efficacy to a digital Brief therapy for insomnia (dBTI) during the COVID-19 pandemic	19
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment	19
Editorial Board	18
Editorial Board	18
WITHDRAWN: Deep networks and network representation in bioinformatics	18
Local augmented graph neural network for multi-omics cancer prognosis prediction and analysis	18
Methods special issue: DNA and RNA helicases	18
Design in biology and rational design in vaccinology: A conceptual analysis	17
Point-of-care image-based quantitative urinalysis with commercial reagent strips: Design and clinical evaluation	17
Predicting Drug-drug Interaction with Graph Mutual Interaction Attention Mechanism	17
Editorial Board	17
Disease biomarker identification based on sample network optimization	17
Special issue Methods: Nano-/bio-interface and biomedical applications	17
Editorial Board	17
Toward drug-miRNA resistance association prediction by positional encoding graph neural network and multi-channel neural network	17
Split light up aptamers as a probing tool for nucleic acids	17
Editorial Board	16
Editorial Board	16
Test positivity – Evaluation of a new metric to assess epidemic dispersal mediated by non-symptomatic cases	16
Methods for preparation of nanoconstructs	16
Editorial Board	16
Methods for circular RNAs	16
Editorial Board	16
Deep Learning in Bioinformatics and Biomedicine	16
Prediction of YY1 loop anchor based on multi-omics features	16
A novel deep learning identifier for promoters and their strength using heterogeneous features	16
PDSM-LGCN: Prediction of drug sensitivity associated microRNAs via light graph convolution neural network	15
Methods special issue: Recent advancement on fluorescent chemosensing and bioimaging	15
An aggregation-induced emission-based ratiometric fluorescent chemosensor for Hg(II) and its application in Caenorhabditis elegans imaging	15
SiBERT: A Siamese-based BERT network for Chinese medical entities alignment	15
Editorial Board	15
scSSA: A clustering method for single cell RNA-seq data based on semi-supervised autoencoder	15
Fluorescent turn-on sensing of albumin proteins (BSA and ovalbumin) using vitamin B6 cofactor derived Schiff base	15
Current methodologies in studying chromatin and gene expression	15
Advanced deep learning approaches enable high-throughput biological and biomedicine data analysis	14
DNMG: Deep molecular generative model by fusion of 3D information for de novo drug design	14
Therapeutic approaches for SARS-CoV-2 infection	14
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin	14
Systems dynamics and the uncertainties of diagnostics, testing and contact tracing for COVID-19	14
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations	14
PhosBERT: A self-supervised learning model for identifying phosphorylation sites in SARS-CoV-2-infected human cells	14
NMR-based isotope editing, chemoselection and isotopomer distribution analysis in stable isotope resolved metabolomics	14
Development of europium(III) complex functionalized silica nanoprobe for luminescence detection of tetracycline	14
A new lysosome-targeted fluorescent probe for hydrogen peroxide based on a benzothiazole derivative	14
Functional imaging using radiomic features in assessment of lymphoma	13
Triplex digital PCR assays for the quantification of intact proviral HIV-1 DNA	13
Editorial for methods special issue: Big data in digital health: methods, analysis and prospects	13
SpaInGNN: Enhanced clustering and integration of spatial transcriptomics based on refined graph neural networks	13
MVCLST: A spatial transcriptome data analysis pipeline for cell type classification based on multi-view comparative learning	13
Deep6mAPred: A CNN and Bi-LSTM-based deep learning method for predicting DNA N6-methyladenosine sites across plant species	13
A fitness training optimization system based on heart rate prediction under different activities	12
Intervening on psychopathology networks: Evaluating intervention targets through simulations	12
Resources for computational prediction of intrinsic disorder in proteins	12
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints	12
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem	12
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties	12
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm	12
Minimal invasive fluorescence methods to quantify advanced glycation end products (AGEs) in skin and plasma of humans	12
A hierarchical three-step superpixels and deep learning framework for skin lesion classification	12
A fluorescence turn “on-off” imaging probe for sequential detection of Al3+ and L-Cysteine in HeLa cells	12
An interpretable deep learning model for classifying adaptor protein complexes from sequence information	12
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network	12
Design and characterization of hollow microneedles for localized intrascleral drug delivery of ocular formulations	12
Heterogeneous graph attention networks for drug virus association prediction	12
MultiscaleDTA: A multiscale-based method with a self-attention mechanism for drug-target binding affinity prediction	12
DNA shape features improve prediction of CRISPR/Cas9 activity	12
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods	11
Subject matching for cross-subject EEG-based recognition of driver states related to situation awareness	11
Single-cell RNA-seq data analysis based on directed graph neural network	11
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications	11
Emulation of Quantitative Systems Pharmacology models to accelerate virtual population inference in immuno-oncology	11
Prediction and interpretation of cancer survival using graph convolution neural networks	11
Radiomics for precision medicine: Current challenges, future prospects, and the proposal of a new framework	11
In vitro production and multiplex quantification of 2′,3′-cyclic phosphate-containing 5′-tRNA half molecules	11
Clinical analysis of eye movement-based data in the medical diagnosis of amblyopia	10

DAMS-Net: Dual attention and multi-scale information fusion network for 12-lead ECG classification	10
Non-canonical amino acids and protein dynamics	10
Efficient experimental method for purifying allergens from aqueous extracts	10
A heat diffusion multilayer network approach for the identification of functional biomarkers in rumen methane emissions	10
Editorial Board	10
Recent developments for the analysis of latent constructs using measurement scales in health research	10
Identification of drug-side effect association via correntropy-loss based matrix factorization with neural tangent kernel	10
A transferability-guided protein-ligand interaction prediction method	10
Latest trends & strategies in ocular drug delivery	10
Editorial Board	10
Editorial Board	10
Utilization of passive visual perception task in detecting patients with major depressive disorder for active health	10
Nucleic acid sample preparation techniques for bead-based suspension arrays	10
Comprehensive evaluation of molecule property prediction with ChatGPT	10
MPEMDA: A multi-similarity integration approach with pre-completion and error correction for predicting microbe-drug associations	10
PENet: Prior evidence deep neural network for bladder cancer staging	10
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures	10
Editorial Board	10
Detection and Segmentation of Breast Masses Based on Multi-Layer Feature Fusion	10
Atomic force microscope kymograph analysis: A case study of two membrane proteins	9
Editorial Board	9
Bioinformatics resources for understanding RNA modifications	9
Machine learning methods for bio-medical image and signal processing: Recent advances	9
Naphthalimide-based new architecture for fluorescence turn-on sensing of Cu2+ and colorimetric detection of F-/CN–	9
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome	9
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation	9
CHiTA: A scarless high-throughput pipeline for characterization of ribozymes	9
Sizing, stabilising, and cloning repeat-expansions for gene targeting constructs	9
Measuring occupancies of the nucleosome and nucleosome-interacting factors in vivo in Saccharomyces cerevisiae genome-wide	9
Editorial Board	9
Site-specific protein conjugates incorporating Para-Azido-L-Phenylalanine for cellular and in vivo imaging	9
Identifying and characterizing virus-encoded circular RNAs	9
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis	9
Enhancing Arabidopsis thaliana ubiquitination site prediction through knowledge distillation and natural language processing	9
N-GlycoPred: A hybrid deep learning model for accurate identification of N-glycosylation sites	9
Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review	9
Furan-based (photo)oxidation reactions and their application in nucleic acid and protein targeting	9
COVID-19 related interdisciplinary methods: Preventing errors and detecting research opportunities	9
Determination of rate constants for conformational changes of RNA helicases by single-molecule FRET TIRF microscopy	9
Multi-sample dual-decoder graph autoencoder	9
Ensemble learning models that predict surface protein abundance from single-cell multimodal omics data	9
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	9