AIMC Topic: Gene Expression Regulation, Developmental
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The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis.
Developmental cell
Jan 15, 2025
The 5' UTRs of mRNAs are critical for translation regulation during development, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massivel...
Identification of Key Genes in Fetal Gut Development at Single-Cell Level by Exploiting Machine Learning Techniques.
Proteomics
Sep 26, 2024
The study of fetal gut development is critical due to its substantial influence on immediate neonatal and long-term adult health. Current research largely focuses on microbiome colonization, gut immunity, and barrier function, alongside the impact of...
Predictive biomarkers for embryotoxicity: a machine learning approach to mitigating multicollinearity in RNA-Seq.
Archives of toxicology
Sep 6, 2024
Multicollinearity, characterized by significant co-expression patterns among genes, often occurs in high-throughput expression data, potentially impacting the predictive model's reliability. This study examined multicollinearity among closely related...
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...
Transcriptome
Genome-Wide Association Study
Protein Interaction Maps
Gene Regulatory Networks
Female
Male
Neoplasms
Multigene Family
Genome, Human
Tissue Distribution
Gene Expression Regulation, Developmental
Genetic Association Studies
Computational Biology
Models, Genetic
Transcription Factors
Humans
Machine Learning
Software
Machine learning-assisted high-content analysis of pluripotent stem cell-derived embryos in vitro.
Stem cell reports
Apr 22, 2021
Stem cell-based embryo models by cultured pluripotent and extra-embryonic lineage stem cells are novel platforms to model early postimplantation development. We showed that induced pluripotent stem cells (iPSCs) could form ITS (iPSCs and trophectoder...
Prediction of future gene expression profile by analyzing its past variation pattern.
Gene expression patterns : GEP
Jan 12, 2021
A number of initial Hematopoietic Stem Cells (HSC) are considered in a container that are able to divide into HSCs or differentiate into various types of descendant cells. In this paper, a method is designed to predict an approximate gene expression ...
GOATOOLS: A Python library for Gene Ontology analyses.
Scientific reports
Jul 18, 2018
The biological interpretation of gene lists with interesting shared properties, such as up- or down-regulation in a particular experiment, is typically accomplished using gene ontology enrichment analysis tools. Given a list of genes, a gene ontology...
Accurate identification of RNA editing sites from primitive sequence with deep neural networks.
Scientific reports
Apr 16, 2018
RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, tim...
McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.
Genome biology
Oct 26, 2017
Transcriptional enhancers regulate spatio-temporal gene expression. While genomic assays can identify putative enhancers en masse, assigning target genes is a complex challenge. We devised a machine learning approach, McEnhancer, which links target g...
Transcriptomes of lineage-specific Drosophila neuroblasts profiled by genetic targeting and robotic sorting.
Development (Cambridge, England)
Dec 23, 2015
A brain consists of numerous distinct neurons arising from a limited number of progenitors, called neuroblasts in Drosophila. Each neuroblast produces a specific neuronal lineage. To unravel the transcriptional networks that underlie the development ...
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