AIMC Topic: Transcriptome

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Machine Learning and Network Analyses Reveal Disease Subtypes of Pancreatic Cancer and their Molecular Characteristics.

Scientific reports Jan 27, 2020
Given that the biological processes governing the oncogenesis of pancreatic cancers could present useful therapeutic targets, there is a pressing need to molecularly distinguish between different clinically relevant pancreatic cancer subtypes. To add...
Cell Line, Tumor RNA-Seq RNA, Messenger Proteome Machine Learning Biomarkers, Tumor Transcriptome Exome Sequencing Transcription, Genetic DNA Methylation MicroRNAs Pancreatic Neoplasms Humans
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Genome-scale transcriptional dynamics and environmental biosensing.

Proceedings of the National Academy of Sciences of the United States of America Jan 23, 2020
Genome-scale technologies have enabled mapping of the complex molecular networks that govern cellular behavior. An emerging theme in the analyses of these networks is that cells use many layers of regulatory feedback to constantly assess and precisel...
Machine Learning Gene Expression Profiling High-Throughput Screening Assays Genes, Bacterial Promoter Regions, Genetic Environmental Monitoring Metals, Heavy Escherichia coli Microfluidic Analytical Techniques Transcriptome Databases, Genetic Biosensing Techniques Equipment Design Genomics
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Identification and transfer of spatial transcriptomics signatures for cancer diagnosis.

Breast cancer research : BCR Jan 13, 2020
BACKGROUND: Distinguishing ductal carcinoma in situ (DCIS) from invasive ductal carcinoma (IDC) regions in clinical biopsies constitutes a diagnostic challenge. Spatial transcriptomics (ST) is an in situ capturing method, which allows quantification ...
Transcriptome ROC Curve Carcinoma, Intraductal, Noninfiltrating Spatial Analysis Female Breast Neoplasms Biomarkers, Tumor Humans Carcinoma, Ductal, Breast Machine Learning Molecular Typing
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Machine Learning Supports Long Noncoding RNAs as Expression Markers for Endometrial Carcinoma.

BioMed research international Jan 10, 2020
Uterine corpus endometrial carcinoma (UCEC) is the second most common type of gynecological tumor. Several research studies have recently shown the potential of different ncRNAs as biomarkers for prognostics and diagnosis in different types of cancer...
Transcriptome ROC Curve Gene Regulatory Networks Endometrial Neoplasms Databases, Genetic RNA, Long Noncoding Female Biomarkers, Tumor Gene Expression Profiling Humans Machine Learning
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De novo generation of hit-like molecules from gene expression signatures using artificial intelligence.

Nature communications Jan 3, 2020
Finding new molecules with a desired biological activity is an extremely difficult task. In this context, artificial intelligence and generative models have been used for molecular de novo design and compound optimization. Herein, we report a generat...
Artificial Intelligence Drug Design Transcriptome Pharmaceutical Preparations Neural Networks, Computer
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Using transfer learning from prior reference knowledge to improve the clustering of single-cell RNA-Seq data.

Scientific reports Dec 30, 2019
In many research areas scientists are interested in clustering objects within small datasets while making use of prior knowledge from large reference datasets. We propose a method to apply the machine learning concept of transfer learning to unsuperv...
Computational Biology Sequence Analysis, RNA Cluster Analysis Humans Reproducibility of Results High-Throughput Nucleotide Sequencing Machine Learning Gene Expression Profiling Transcriptome Algorithms ROC Curve Single-Cell Analysis
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Joint learning improves protein abundance prediction in cancers.

BMC biology Dec 23, 2019
BACKGROUND: The classic central dogma in biology is the information flow from DNA to mRNA to protein, yet complicated regulatory mechanisms underlying protein translation often lead to weak correlations between mRNA and protein abundances. This is pa...
Ovarian Neoplasms Breast Neoplasms Humans Transcriptome Machine Learning Proteomics Female Proteome
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StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis.

BMC genomics Dec 20, 2019
BACKGROUND: Recently, a number of studies have been conducted to investigate how plants respond to stress at the cellular molecular level by measuring gene expression profiles over time. As a result, a set of time-series gene expression data for the ...
Genetic Association Studies Computational Biology Models, Biological Arabidopsis Stress, Physiological Genes, Plant Phenotype Gene Expression Profiling Transcriptome Neural Networks, Computer Machine Learning
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Transcriptome analysis and identification of genes associated with chicken sperm storage duration.

Poultry science Dec 13, 2019
The sperm storage tubules located in the mucosal folds of the uterovaginal junction (UVJ) are the primary site of sperm storage in chicken hens after natural mating or artificial insemination (AI). The short-term sperm storage (24 h after mating or A...
Avian Proteins Transcriptome Animals Insemination, Artificial Chickens Male Spermatozoa Gene Expression Profiling
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Discovery and annotation of novel microRNAs in the porcine genome by using a semi-supervised transductive learning approach.

Genomics Dec 6, 2019
Despite the broad variety of available microRNA (miRNA) prediction tools, their application to the discovery and annotation of novel miRNA genes in domestic species is still limited. In this study we designed a comprehensive pipeline (eMIRNA) for miR...
Sequence Homology, Nucleic Acid Machine Learning Muscle, Skeletal Genetic Loci Molecular Sequence Annotation Algorithms Nucleotide Motifs Sus scrofa RNA-Seq Animals Genome RNA Precursors Genomics Transcriptome Liver MicroRNAs
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