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Genome-Wide Prediction of Disease Resistance Gene Analogs in Flax
Flax (Linum usitatissimum L.) is an important crop as the sources of fiber and seed oil. Annually, various pathogens cause significant loss to flax...
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Spatial Gene Expression Prediction from Histology Images with STco
In recent years, the rapid development of spatial transcriptome technology has fundamentally transformed our understanding of gene expression...
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MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge
Messenger RNA (mRNA) has an essential role in the protein production process. Predicting mRNA expression levels accurately is crucial for...
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Identification of gene-level methylation for disease prediction
DNA methylation is an epigenetic alteration that plays a fundamental part in governing gene regulatory processes. The DNA methylation mechanism...
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A gene signature linked to fibroblast differentiation for prognostic prediction of mesothelioma
BackgroundMalignant mesothelioma is a type of infrequent tumor that is substantially related to asbestos exposure and has a terrible prognosis. We...
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SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images
Cancer is one of the leading causes of deaths worldwide. Survival analysis and prediction of cancer patients is of great significance for their...
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Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies
Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield,...
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Comparing methods for drug–gene interaction prediction on the biomedical literature knowledge graph: performance versus explainability
This paper applies different link prediction methods on a knowledge graph generated from biomedical literature, with the aim to compare their ability...
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ENGEP: advancing spatial transcriptomics with accurate unmeasured gene expression prediction
Imaging-based spatial transcriptomics techniques provide valuable spatial and gene expression information at single-cell resolution. However, their...
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A gene mutation-based risk model for prognostic prediction in liver metastases
BackgroundLiver metastasis is the major challenge in the treatment for malignant tumors. Genomic profiling is increasingly used in the diagnosis,...
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FragGeneScanRs: faster gene prediction for short reads
BackgroundFragGeneScan is currently the most accurate and popular tool for gene prediction in short and error-prone reads, but its execution speed is...
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Prediction of lung cancer using gene expression and deep learning with KL divergence gene selection
BackgroundLung cancer is one of the cancers with the highest mortality rate in China. With the rapid development of high-throughput sequencing...
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Genomic prediction of zinc-biofortification potential in rice gene bank accessions
Key messageA genomic prediction model successfully predicted grain Zn concentrations in 3000 gene bank accessions and this was verified...
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Integrating temporal single-cell gene expression modalities for trajectory inference and disease prediction
BackgroundCurrent methods for analyzing single-cell datasets have relied primarily on static gene expression measurements to characterize the...
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Development of a 32-gene signature using machine learning for accurate prediction of inflammatory bowel disease
Inflammatory bowel disease (IBD) is a chronic inflammatory condition caused by multiple genetic and environmental factors. Numerous genes are...
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Development and validation of an RBP gene signature for prognosis prediction in colorectal cancer based on WGCNA
BackgroundRNA binding proteins (RBPs) have been implicated in oncogenesis and progression in various cancers. However, the potential value of RBPs as...
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Bioinformatics Methods for Prediction of Gene Families Encoding Extracellular Peptides
Genes encoding small secreted peptides are widely distributed among plant genomes but their detection and annotation remains challenging. The...
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Exploration and validation of a combined Hypoxia and m6A/m5C/m1A regulated gene signature for prognosis prediction of liver cancer
BackgroundIt is widely acknowledged that hypoxia and m6A/m5C/m1A RNA modifications promote the occurrence and development of tumors by regulating the...
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Assessment of deep learning and transfer learning for cancer prediction based on gene expression data
BackgroundMachine learning is now a standard tool for cancer prediction based on gene expression data. However, deep learning is still new for this...
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SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment
Topological network alignment aims to align two networks node-wise in order to maximize the observed common connection (edge) topology between them....
