AIMC Topic: RNA, Messenger

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A classification model for lncRNA and mRNA based on k-mers and a convolutional neural network.

BMC bioinformatics Sep 13, 2019
BACKGROUND: Long-chain non-coding RNA (lncRNA) is closely related to many biological activities. Since its sequence structure is similar to that of messenger RNA (mRNA), it is difficult to distinguish between the two based only on sequence biometrics...
Mice RNA, Messenger Chickens RNA, Long Noncoding Humans Neural Networks, Computer Animals
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Robotic platform for microinjection into single cells in brain tissue.

EMBO reports Aug 30, 2019
Microinjection into single cells in brain tissue is a powerful technique to study and manipulate neural stem cells. However, such microinjection requires expertise and is a low-throughput process. We developed the "Autoinjector", a robot that utilize...
Brain Cell Communication Neurogenesis Animals Automation Microinjections Humans Single-Cell Analysis Cell Lineage Mice, Inbred C57BL Neural Stem Cells Image Processing, Computer-Assisted Telencephalon Robotics RNA, Messenger
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Gene Ontology and Expression Studies of Strigolactone Analogues on a Hepatocellular Carcinoma Cell Line.

Analytical cellular pathology (Amsterdam) Aug 4, 2019
Human hepatocellular carcinoma (HCC) is the most common and recurrent type of primary adult liver cancer without any effective therapy. Plant-derived compounds acting as anticancer agents can induce apoptosis by targeting several signaling pathways. ...
Lactones RNA, Messenger Gene Ontology Humans Gene Expression Regulation, Neoplastic Down-Regulation Liver Neoplasms Hep G2 Cells Up-Regulation Carcinoma, Hepatocellular
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Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data.

BMC bioinformatics Jul 8, 2019
BACKGROUND: Unsupervised machine learning methods (deep learning) have shown their usefulness with noisy single cell mRNA-sequencing data (scRNA-seq), where the models generalize well, despite the zero-inflation of the data. A class of neural network...
Neural Networks, Computer Gene Expression Profiling Cluster Analysis Unsupervised Machine Learning Single-Cell Analysis RNA, Messenger Sequence Analysis, RNA
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A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation.

Cell Jun 6, 2019
Alternative polyadenylation (APA) is a major driver of transcriptome diversity in human cells. Here, we use deep learning to predict APA from DNA sequence alone. We trained our model (APARENT, APA REgression NeT) on isoform expression data from over ...
Gene Expression Synthetic Biology HEK293 Cells RNA, Messenger Models, Genetic Databases, Genetic 3' Untranslated Regions RNA Cleavage Base Sequence Mutagenesis Polyadenylation Deep Learning RNA-Seq Humans Transcriptome
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Robust identification of molecular phenotypes using semi-supervised learning.

BMC bioinformatics May 28, 2019
BACKGROUND: Modern molecular profiling techniques are yielding vast amounts of data from patient samples that could be utilized with machine learning methods to provide important biological insights and improvements in patient outcomes. Unsupervised ...
Humans Gene Expression Regulation, Neoplastic Lymphoma Supervised Machine Learning Chemotherapy, Adjuvant Female Disease-Free Survival Algorithms Breast Neoplasms Databases as Topic Phenotype RNA, Messenger Prognosis
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Recognition of 3'-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models.

Scientific reports May 10, 2019
The role of 3'-end stem-loops in retrotransposition was experimentally demonstrated for transposons of various species, where LINE-SINE retrotransposons share the same 3'-end sequences, containing a stem-loop. We have discovered that 62-68% of proces...
Genome, Human Pseudogenes 3' Untranslated Regions Long Interspersed Nucleotide Elements Humans Alu Elements Area Under Curve Machine Learning ROC Curve RNA, Messenger
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Predicting miRNA-lncRNA interactions and recognizing their regulatory roles in stress response of plants.

Mathematical biosciences Apr 26, 2019
It has been found that each non-coding RNA (ncRNA) can act not only through its target gene, but also interact with each other to act on biological traits, and this interaction is more common. Many studies focus mainly on the analysis of microRNA(miR...
Stress, Physiological Arabidopsis RNA, Plant Models, Genetic Support Vector Machine MicroRNAs Gene Regulatory Networks RNA, Long Noncoding RNA, Messenger
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Prediction of Long Non-Coding RNAs Based on Deep Learning.

Genes Apr 3, 2019
With the rapid development of high-throughput sequencing technology, a large number of transcript sequences have been discovered, and how to identify long non-coding RNAs (lncRNAs) from transcripts is a challenging task. The identification and inclus...
Genetic Predisposition to Disease Computational Biology RNA, Messenger High-Throughput Nucleotide Sequencing Models, Genetic RNA, Long Noncoding Humans Algorithms Deep Learning
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RNA sequencing and swarm intelligence-enhanced classification algorithm development for blood-based disease diagnostics using spliced blood platelet RNA.

Nature protocols Mar 20, 2019
Blood-based diagnostics tests, using individual or panels of biomarkers, may revolutionize disease diagnostics and enable minimally invasive therapy monitoring. However, selection of the most relevant biomarkers from liquid biosources remains an imme...
Biomarkers High-Throughput Nucleotide Sequencing Computational Biology Blood Platelets DNA, Complementary Humans RNA, Messenger Sequence Analysis, RNA Support Vector Machine RNA Splicing
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