AIMC Topic: Gene Expression Regulation, Developmental

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Codon bias and gene ontology in holometabolous and hemimetabolous insects.

Journal of experimental zoology. Part B, Molecular and developmental evolution Oct 26, 2015
The relationship between preferred codon use (PCU), developmental mode, and gene ontology (GO) was investigated in a sample of nine insect species with sequenced genomes. These species were selected to represent two distinct modes of insect developme...
Phylogeny Base Composition Insect Proteins Metamorphosis, Biological Genome, Insect Sequence Analysis, DNA Animals Gene Expression Regulation, Developmental Gene Ontology Insecta Codon
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Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach.

BMC genomics Sep 15, 2015
BACKGROUND: Assembly and function of neuronal synapses require the coordinated expression of a yet undetermined set of genes. Although roughly a thousand genes are expected to be important for this function in Drosophila melanogaster, just a few hund...
Transcriptome Algorithms Datasets as Topic Computational Biology Models, Biological Animals Organ Specificity Rats Drosophila Gene Expression Profiling Synapses Gene Expression Regulation, Developmental Humans Machine Learning
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Deep convolutional neural networks for annotating gene expression patterns in the mouse brain.

BMC bioinformatics May 7, 2015
BACKGROUND: Profiling gene expression in brain structures at various spatial and temporal scales is essential to understanding how genes regulate the development of brain structures. The Allen Developing Mouse Brain Atlas provides high-resolution 3-D...
In Situ Hybridization Neural Networks, Computer Brain Mice Animals Molecular Sequence Annotation Pattern Recognition, Automated Gene Expression Profiling Gene Expression Regulation, Developmental Image Processing, Computer-Assisted
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The potential of AOP networks for reproductive and developmental toxicity assay development.

Reproductive toxicology (Elmsford, N.Y.) Apr 15, 2015
Historically, the prediction of reproductive and developmental toxicity has largely relied on the use of animals. The adverse outcome pathway (AOP) framework forms a basis for the development of new non-animal test methods. It also provides biologica...
Gene Regulatory Networks Female Gene Expression Regulation, Developmental Signal Transduction Animals Animal Testing Alternatives Humans Models, Biological Risk Assessment Computer Simulation Systems Integration Embryonic Development Knowledge Bases Fetal Development Pregnancy Toxicity Tests Reproduction
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The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model.

Nucleic acids research Jul 22, 2024
Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) and cis-regulatory elements (CREs). The uneven distribution of TF binding sites across the genome poses challenges in understanding how this distr...
Mice Chickens Transcription Factors Machine Learning Animals Cattle Binding Sites Gene Expression Regulation, Developmental Chromatin Oryzias Evolution, Molecular Embryonic Development Promoter Regions, Genetic Humans
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Uncovering tissue-specific binding features from differential deep learning.

Nucleic acids research Mar 18, 2020
Transcription factors (TFs) can bind DNA in a cooperative manner, enabling a mutual increase in occupancy. Through this type of interaction, alternative binding sites can be preferentially bound in different tissues to regulate tissue-specific expres...
Protein Binding Mice Computational Biology Models, Genetic Animals Deep Learning Embryo, Mammalian Organ Specificity Protein Isoforms Binding Sites Myeloid Ecotropic Viral Integration Site 1 Protein Poisson Distribution Chromatin Immunoprecipitation Homeodomain Proteins RNA Branchial Region Gene Expression Regulation, Developmental High-Throughput Nucleotide Sequencing
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Challenges and Opportunities for Increasing the Knowledge Base Related to Drug Biotransformation and Pharmacokinetics during Growth and Development.

Drug metabolism and disposition: the biological fate of chemicals Jul 1, 2016
It is generally acknowledged that there is a need and role for informative pharmacokinetic models to improve predictions and simulation as well as individualization of drug therapy in pediatric populations of different ages and developmental stages. ...
Child Development Enzymes Gene Expression Regulation, Developmental Pharmacokinetics Membrane Transport Proteins Gene Expression Regulation, Enzymologic Adolescent Development Child, Preschool Child Aging Age Factors Humans Infant Computer Simulation Knowledge Bases Adolescent Infant, Newborn Biotransformation Pharmaceutical Preparations Models, Biological
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