AIMC Topic: Transcriptome

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SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells.

Genome biology Aug 10, 2021
Single-cell RNA-seq (scRNA-seq) profiles gene expression with high resolution. Here, we develop a stepwise computational method-called SCAPTURE to identify, evaluate, and quantify cleavage and polyadenylation sites (PASs) from 3' tag-based scRNA-seq....
Sequence Analysis, RNA Polyadenylation Humans COVID-19 Transcriptome Deep Learning SARS-CoV-2 Single-Cell Analysis Sensitivity and Specificity RNA-Seq
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Using a machine learning approach to identify key prognostic molecules for esophageal squamous cell carcinoma.

BMC cancer Aug 9, 2021
BACKGROUND: A plethora of prognostic biomarkers for esophageal squamous cell carcinoma (ESCC) that have hitherto been reported are challenged with low reproducibility due to high molecular heterogeneity of ESCC. The purpose of this study was to ident...
Algorithms Prognosis Reproducibility of Results Biomarkers, Tumor Humans Machine Learning Esophageal Squamous Cell Carcinoma Gene Expression Profiling Transcriptome Computational Biology Kaplan-Meier Estimate
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CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis.

BMC bioinformatics Aug 9, 2021
BACKGROUND: The rise of spatial transcriptomics technologies is leading to new insights about how gene regulation happens in a spatial context. Determining which genes are expressed in similar spatial patterns can reveal gene regulatory relationships...
Neural Networks, Computer Transcriptome Cluster Analysis Spatial Analysis
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Semi-Supervised Topological Analysis for Elucidating Hidden Structures in High-Dimensional Transcriptome Datasets.

IEEE/ACM transactions on computational biology and bioinformatics Aug 6, 2021
Topological data analysis (TDA) is a powerful method for reducing data dimensionality, mining underlying data relationships, and intuitively representing the data structure. The Mapper algorithm is one such tool that projects high-dimensional data to...
Humans Algorithms Computational Biology Databases, Genetic Ovarian Neoplasms Supervised Machine Learning Data Mining Computer Simulation Female Gene Expression Profiling Transcriptome
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Discriminant Projection Shared Dictionary Learning for Classification of Tumors Using Gene Expression Data.

IEEE/ACM transactions on computational biology and bioinformatics Aug 6, 2021
With a variety of tumor subtypes, personalized treatments need to identify the subtype of a tumor as accurately as possible. The development of DNA microarrays provides an opportunity to predict tumor classification. One strategy is to use gene expre...
Gene Expression Profiling Transcriptome Computational Biology Databases, Genetic Humans Machine Learning Algorithms Neoplasms
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Identification of Tissue of Origin and Guided Therapeutic Applications in Cancers of Unknown Primary Using Deep Learning and RNA Sequencing (TransCUPtomics).

The Journal of molecular diagnostics : JMD Jul 26, 2021
Cancers of unknown primary (CUP) are metastatic cancers for which the primary tumor is not found despite thorough diagnostic investigations. Multiple molecular assays have been proposed to identify the tissue of origin (TOO) and inform clinical care;...
Aged, 80 and over Adult Biomarkers, Tumor Male Middle Aged Transcriptome Deep Learning RNA-Seq Prospective Studies Retrospective Studies Female Aged Humans Data Accuracy Neoplasms, Unknown Primary Gene Fusion
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Accurate prediction of breast cancer survival through coherent voting networks with gene expression profiling.

Scientific reports Jul 19, 2021
For a patient affected by breast cancer, after tumor removal, it is necessary to decide which adjuvant therapy is able to prevent tumor relapse and formation of metastases. A prediction of the outcome of adjuvant therapy tailored for the patient is h...
Neoplasm Recurrence, Local Survival Analysis Microarray Analysis Female Chemotherapy, Adjuvant Breast Neoplasms Neural Networks, Computer Biomarkers, Tumor Artificial Intelligence Gene Expression Profiling Machine Learning Gene Expression Regulation, Neoplastic Prognosis Predictive Value of Tests Transcriptome Humans Mastectomy Gene Regulatory Networks
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Prioritizing and characterizing functionally relevant genes across human tissues.

PLoS computational biology Jul 16, 2021
Knowledge of genes that are critical to a tissue's function remains difficult to ascertain and presents a major bottleneck toward a mechanistic understanding of genotype-phenotype links. Here, we present the first machine learning model-FUGUE-combini...
Tissue Distribution Gene Expression Regulation, Developmental Models, Genetic Transcription Factors Multigene Family Genome, Human Male Neoplasms Transcriptome Genome-Wide Association Study Protein Interaction Maps Gene Regulatory Networks Genetic Association Studies Computational Biology Humans Machine Learning Software Female
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An Unbiased Machine Learning Exploration Reveals Gene Sets Predictive of Allograft Tolerance After Kidney Transplantation.

Frontiers in immunology Jul 8, 2021
Efforts at finding potential biomarkers of tolerance after kidney transplantation have been hindered by limited sample size, as well as the complicated mechanisms underlying tolerance and the potential risk of rejection after immunosuppressant withdr...
Oligonucleotide Array Sequence Analysis Time Factors Graft Survival Transplantation Tolerance Risk Factors Humans Treatment Outcome Risk Assessment Immunosuppressive Agents Machine Learning Databases, Genetic Gene Expression Profiling Kidney Transplantation Predictive Value of Tests Transcriptome Clinical Decision-Making Graft Rejection Patient Selection
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Dual-Organ Transcriptomic Analysis of Rainbow Trout Infected With Through Co-Expression and Machine Learning.

Frontiers in immunology Jul 8, 2021
is a major pathogen that causes a high mortality rate in trout farms. However, systemic responses to the pathogen and its interactions with multiple organs during the course of infection have not been well described. In this study, dual-organ transc...
Transcriptome Oncorhynchus mykiss RNA-Seq Ciliophora Infections Machine Learning Gene Regulatory Networks Hymenostomatida Virulence Animals Signal Transduction Gene Expression Regulation Host-Pathogen Interactions Gills Immunity, Innate Head Kidney Fish Diseases Liver Virulence Factors
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