Methods

Papers
(The TQCC of Methods is 10. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-06-01 to 2025-06-01.)
ArticleCitations
Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations222
Editorial Board106
Editorial Board103
FedMCC: Federated multi-center clustering algorithm to improve privacy healthcare102
Interpretable thoracic pathologic prediction via learning group-disentangled representation84
RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data76
On finding natural antibiotics based on TCM formulae75
Approaches for the sensitive detection of rare base and prime editing events72
Pyrogallol-based dipodal optical probe as new smart analytical tool for sustainable detection of cobalt in biosystem69
Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework69
Targeted mutagenesis in human iPSCs using CRISPR genome-editing tools61
Multi-omics data integration and drug screening of AML cancer using Generative Adversarial Network58
LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin57
Development of novel digital PCR assays for the rapid quantification of Gram-negative bacteria biomarkers using RUCS algorithm57
Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints55
Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies55
Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection51
A transformer-based multi-features fusion model for prediction of conversion in mild cognitive impairment51
Brain controllability and morphometry similarity of internet gaming addiction50
Automatic ICD-10-CM coding via Lambda-Scaled attention based deep learning model49
In vivo detection of GPCR-dependent signaling using fiber photometry and FRET-based biosensors49
PIF – A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures48
Editorial Board47
Editorial Board46
Trans ligation of RNAs to generate hybrid circular RNAs using highly efficient autocatalytic transcripts45
Strategies for ocular drug delivery41
Two minimally invasive strategies to implant guide cannulas for multiple injections in deep brain areas41
iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae41
Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues40
Pseudouridine RNA modification detection and quantification by RT-PCR40
Clinical analysis of eye movement-based data in the medical diagnosis of amblyopia38
MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models38
Non-canonical amino acids and protein dynamics36
Atomic force microscope kymograph analysis: A case study of two membrane proteins36
Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets33
MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation33
Comparing performance of iterative and non-iterative algorithms on various feature schemes for arrhythmia analysis32
Isolation and culture of adult murine cardiac atrial and ventricular fibroblasts and myofibroblasts32
Synthetic PPR proteins as tools for sequence-specific targeting of RNA31
Advanced glycation end products in musculoskeletal system and disorders31
MRDFF: A deep forest based framework for CT whole heart segmentation31
MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction30
Synthesis of carbon nanotubes using pre-sintered oil fly ash via a reproducible process with large-scale potential30
Comprehensive evaluation of molecule property prediction with ChatGPT30
DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions29
Development and validation of a stability-indicating HPLC method for assay of tonabersat in pharmaceutical formulations29
The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years29
Editorial Board28
Hybrid manifold-deep convolutional neural network for sleep staging28
COVID-19 lesion detection and segmentation–A deep learning method28
MLFA-UNet: A multi-level feature assembly UNet for medical image segmentation27
Editorial Board27
Recent progress in the analysis of protein deamidation using mass spectrometry26
Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state26
Improving domain generalization performance for medical image segmentation via random feature augmentation25
Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination25
EpiHNet: Detecting epistasis by heterogeneous molecule network24
Multi-view contrastive clustering for cancer subtyping using fully and weakly paired multi-omics data24
Model-agnostic confidence measurement for aggregating multimodal ensemble models in automatic diagnostic systems23
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 disease23
Prediction of the transcription factor binding sites with meta-learning23
Guest Editor’s Introduction: Optical methods for characterisation of biomolecules23
AntiT2DMP-Pred: Leveraging feature fusion and optimization for superior machine learning prediction of type 2 diabetes mellitus23
scGAAC: A graph attention autoencoder for clustering single-cell RNA-sequencing data23
MPFFPSDC: A multi-pooling feature fusion model for predicting synergistic drug combinations22
UGDAS: Unsupervised graph-network based denoiser for abstractive summarization in biomedical domain22
Novel approaches to biomarker discover22
A heterogeneous graph transformer framework for accurate cancer driver gene prediction and downstream analysis22
A brief review of RNA modification related database resources21
A federated learning method for real-time emotion state classification from multi-modal streaming21
Glaucoma screening using an attention-guided stereo ensemble network21
Measuring functional similarity of lncRNAs based on variable K-mer profiles of nucleotide sequences21
Probing excited state 1Hα chemical shifts in intrinsically disordered proteins with a triple resonance-based CEST experiment: Application to a disorder-to-order switch20
Microproteins transitioning into a new Phase: Defining the undefined20
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 effects20
Computational methods and strategies for combating COVID-1920
Steric trapping strategy for studying the folding of helical membrane proteins19
Inner leaflet cationic lipid increases nucleic acid loading independently of outer leaflet lipid charge in asymmetric liposomes19
SGAE-MDA: Exploring the MiRNA-disease associations in herbal medicines based on semi-supervised graph autoencoder19
Modeling repeated self-reported outcome data: A continuous-time longitudinal Item Response Theory model19
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 study18
Biomedical event causal relation extraction with deep knowledge fusion and Roberta-based data augmentation18
Baker’s yeast beta glucan supplementation was associated with an improved innate immune mRNA expression response after exercise18
Exploring the artificial intelligence and machine learning models in the context of drug design difficulties and future potential for the pharmaceutical sectors18
Identifying and ranking potential cancer drivers using representation learning on attributed network18
Statistical methods for comparing test positivity rates between countries: Which method should be used and why?18
Chromatin image-driven modelling18
DRCNNTLe: A deep recurrent convolutional neural network with transfer learning through pre-trained embeddings for automated ICD coding18
Identification of DNase I hypersensitive sites in the human genome by multiple sequence descriptors18
Convolutional autoencoder based on latent subspace projection for anomaly detection18
Editorial Board17
The semisynthesis of site-specifically modified histones and histone-based probes of chromatin-modifying enzymes17
Assessing the role of intrinsic disorder in RNA-binding protein function: hnRNP K as a case study17
Detection and quantification of nanoparticle-induced intracellular ROS in live cells by laser scanning confocal microscopy17
Universal Southern blot protocol with cold or radioactive probes for the validation of alleles obtained by homologous recombination17
CSSEC: An adaptive approach integrating consensus and specific self-expressive coefficients for multi-omics cancer subtyping17
Deep learning based method for predicting DNA N6-methyladenosine sites17
Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing17
CLCAP: Contrastive learning improves antigenicity prediction for influenza A virus using convolutional neural networks17
Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme16
Meta-IL4: An ensemble learning approach for IL-4-inducing peptide prediction16
Single molecule methods for studying CRISPR Cas9-induced DNA unwinding16
Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins16
The prognostic value of machine learning techniques versus cox regression model for head and neck cancer16
A novel carboxyl polymer-modified upconversion luminescent nanoprobe for detection of prostate-specific antigen in the clinical gray zonebase by flow immunoassay strip16
ZeRPI: A graph neural network model for zero-shot prediction of RNA-protein interactions16
A compact and interpretable convolutional neural network for cross-subject driver drowsiness detection from single-channel EEG16
A dual-function fluorescence 'turn-on' probe that allows Zn (II) bioimaging and quantification of water in the organic solvent15
A comprehensive preanalytical protocol for fresh solid tumor biospecimens15
Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET15
Kinetics measurements of G-quadruplex binding and unfolding by helicases15
Hybrid multimodal fusion for graph learning in disease prediction15
Graph matching survey for medical imaging: On the way to deep learning15
Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts15
dsRNAPredictor-II: An improved predictor of identifying dsRNA and its silencing efficiency for Tribolium castaneum based on sequence length distribution15
Methods for preparation of niosomes: A focus on thin-film hydration method15
Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields15
Identification of adaptor proteins by incorporating deep learning and PSSM profiles15
Editorial Board15
A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis14
Editorial Board14
Smartphone-based low-cost and rapid quantitative detection of urinary creatinine with the Tyndall effect14
In silico identification of Histone Deacetylase inhibitors using Streamlined Masked Transformer-based Pretrained features14
Signal and noise in circRNA translation14
Latest progress in the study of nanoparticle-based delivery of the CRISPR/Cas9 system14
Atrial-specific hiPSC-derived cardiomyocytes in drug discovery and disease modeling13
HistoSPACE: Histology-inspired spatial transcriptome prediction and characterization engine13
Editorial Board13
An effective multi-task learning framework for drug repurposing based on graph representation learning13
Predicting miRNA-lncRNA interactions on plant datasets based on bipartite network embedding method13
m5c-iDeep: 5-Methylcytosine sites identification through deep learning13
Resources for computational prediction of intrinsic disorder in proteins13
Editorial Board13
MTGNN: Multi-Task Graph Neural Network based few-shot learning for disease similarity measurement13
Methods to study circRNA-protein interactions13
Integrating a multi-omics strategy framework to screen potential targets in cognitive impairment-related epilepsy13
Editorial Board13
SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer12
Stereological estimation of cardiomyocyte number and proliferation12
Carbon dots fluorescence can be used to distinguish isobaric peptide and to monitor protein oligomerization dynamics12
Current methodologies in studying chromatin and gene expression12
Mouse4mC-BGRU: Deep learning for predicting DNA N4-methylcytosine sites in mouse genome12
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies12
Introduction of mutations in plants with prime editing12
Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data12
Design of a 1 × 4 micro-magnetic stimulation device and its targeted, coordinated regulation on LTP of Schaffer-CA1 in the hippocampus of rats12
Multiple analyte profiling (MAP) index as a powerful diagnostic and therapeutic monitoring tool11
DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph11
Accurate contactless sleep apnea detection framework with signal processing and machine learning methods11
A fluorescence turn “on-off” imaging probe for sequential detection of Al3+ and L-Cysteine in HeLa cells11
Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications11
Editorial Board11
Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review11
TPQCI: A topology potential-based method to quantify functional influence of copy number variations11
GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome11
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data11
HPE-GCN: Predicting efficacy of tonic formulae via graph convolutional networks integrating traditionally defined herbal properties11
KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites11
APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features11
Efficient allele conversion in mouse zygotes and primary cells based on electroporation of Cre protein11
Model-based autoencoders for imputing discrete single-cell RNA-seq data11
Efficient experimental method for purifying allergens from aqueous extracts11
Near-infrared fluorescent probe based on rhodamine derivative for detection of NADH in live cells11
Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes11
Bacterial flagellar motor as a multimodal biosensor11
Novel, standardized sample collection from the brain-nose interface11
Guitar2: An improved version of the Guitar for sketching the transcriptomic view of RNA-related biological features10
Publisher’s note10
Temperature-jump microscopy and interaction of Hsp70 heat shock protein with a client protein in vivo10
Facile green synthesis of ZnO-RGO nanocomposites with enhanced anticancer efficacy10
DNA building blocks for AFM tip functionalization: An easy, fast and stable strategy10
Low friction hydrogel with diclofenac eluting ability for dry eye therapeutic contact lenses10
GCHN-DTI: Predicting drug-target interactions by graph convolution on heterogeneous networks10
LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm10
Corrigendum to “Smart biomaterials: From 3D printing to 4D bioprinting” [Methods 205 (2022) 191–199]10
Editorial Board10
NGOME-Lite: Proteome-wide prediction of spontaneous protein deamidation highlights differences between taxa10
Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors10
Exploring drug-target interaction prediction on cold-start scenarios via meta-learning-based graph transformer10
Study of circular RNA translation using reporter systems in living cells10
Isothermal titration calorimetry and surface plasmon resonance methods to probe protein–protein interactions10
LiteMamba-Bound: A lightweight Mamba-based model with boundary-aware and normalized active contour loss for skin lesion segmentation10
RLDOCK method for predicting RNA-small molecule binding modes10
Editorial Board10
Machine learning aided single cell image analysis improves understanding of morphometric heterogeneity of human mesenchymal stem cells10
Hexagonal image segmentation on spatially resolved transcriptomics10
Prediction of drug-induced hepatotoxicity based on histopathological whole slide images10
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 samples10
MSO-GP: 3-D segmentation of large and complex conjoined tree structures10
Integrated analyses of prognostic and immunotherapeutic significance of EZH2 in uveal melanoma10
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