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Ion entropy and accurate entropy-based FDR estimation in metabolomics.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae056
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Structure prediction of linear and cyclic peptides using CABS-flex.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae003
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Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbad508
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RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae064
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Cracking the black box of deep sequence-based protein–protein interaction prediction.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae076
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Translational bioinformatics and data science for biomarker discovery in mental health: an analytical review.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae098
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Should we really use graph neural networks for transcriptomic prediction?
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae027
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Benchmarking enrichment analysis methods with the disease pathway network.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae069
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Deqformer: high-definition and scalable deep learning probe design method.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae007
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Deeply integrating latent consistent representations in high-noise multi-omics data for cancer subtyping.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae061
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The rise of taxon-specific epitope predictors.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae092
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scMLC: an accurate and robust multiplex community detection method for single-cell multi-omics data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae101
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ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae024
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ChIP-GPT: a managed large language model for robust data extraction from biomedical database records.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbad535
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Exploring miRNA–target gene pair detection in disease with coRmiT.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae060
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Multiscale topology in interactomic network: from transcriptome to antiaddiction drug repurposing.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae054
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scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae096
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eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae034
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SuperCUT, an unsupervised multimodal image registration with deep learning for biomedical microscopy.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae029
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MyoV: a deep learning-based tool for the automated quantification of muscle fibers.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbad528
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Likelihood-based feature representation learning combined with neighborhood information for predicting circRNA–miRNA associations.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae020
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Biolinguistic graph fusion model for circRNA–miRNA association prediction.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae058
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From G1 to M: a comparative study of methods for identifying cell cycle phases.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbad517
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SynergyX: a multi-modality mutual attention network for interpretable drug synergy prediction.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae015
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scCorrector: a robust method for integrating multi-study single-cell data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbad525
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Comparative analysis of models in predicting the effects of SNPs on TF-DNA binding using large-scale in vitro and in vivo data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae110
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Standigm ASK™: knowledge graph and artificial intelligence platform applied to target discovery in idiopathic pulmonary fibrosis.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae035
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MRSL: a causal network pruning algorithm based on GWAS summary data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae086
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Effective multi-modal clustering method via skip aggregation network for parallel scRNA-seq and scATAC-seq data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae102
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Dual-channel hypergraph convolutional network for predicting herb–disease associations.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae067
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Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae016
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Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer's disease.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbad526
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Single-residue linear and conformational B cell epitopes prediction using random and ESM-2 based projections.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae084
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FEOpti-ACVP: identification of novel anti-coronavirus peptide sequences based on feature engineering and optimization.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae037
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epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbad521
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Integrative open workflow for confident annotation and molecular networking of metabolomics MS<sup>E</sup>/DIA data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae013
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PANCDR: precise medicine prediction using an adversarial network for cancer drug response.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae088
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DDK-Linker: a network-based strategy identifies disease signals by linking high-throughput omics datasets to disease knowledge.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae111
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Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae002
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GPCR-IPL score: multilevel featurization of GPCR–ligand interaction patterns and prediction of ligand functions from selectivity to biased activation.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae105
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GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbad529
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Partial order relation–based gene ontology embedding improves protein function prediction.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae077
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A kinetic model for solving a combination optimization problem in ab-initio Cryo-EM 3D reconstruction.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbad473
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Chromosome structure modeling tools and their evaluation in bacteria.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae044
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High-dimensional generalized median adaptive lasso with application to omics data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae059
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Challenges in distinguishing functional proteins from polyproteins in databases: implications for drug discovery.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae012
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Deep reinforcement learning identifies personalized intermittent androgen deprivation therapy for prostate cancer.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae071
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Interpretable feature extraction and dimensionality reduction in ESM2 for protein localization prediction.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbad534
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New techniques to identify the tissue of origin for cancer of unknown primary in the era of precision medicine: progress and challenges.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae028
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Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing.
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- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae001
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