AIMC Topic: Genome, Insect
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The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach.
Molecular ecology
Aug 26, 2024
This study explores the impact of positive selection on the genetic composition of a Drosophila serrata population in eastern Australia through a comprehensive analysis of 110 whole genome sequences. Utilizing an advanced deep learning algorithm (par...
Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive.
PloS one
Aug 11, 2021
Aging is universal, yet characterizing the molecular changes that occur in aging which lead to an increased risk for neurological disease remains a challenging problem. Aging affects the prefrontal cortex (PFC), which governs executive function, lear...
Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact.
Nature communications
Jun 8, 2021
Chromatin architecture plays an important role in gene regulation. Recent advances in super-resolution microscopy have made it possible to measure chromatin 3D structure and transcription in thousands of single cells. However, leveraging these comple...
Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs.
Scientific reports
Feb 11, 2020
Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational...
A Deep Learning Approach for Detecting Copy Number Variation in Next-Generation Sequencing Data.
G3 (Bethesda, Md.)
Nov 5, 2019
Copy number variants (CNV) are associated with phenotypic variation in several species. However, properly detecting changes in copy numbers of sequences remains a difficult problem, especially in lower quality or lower coverage next-generation sequen...
diploS/HIC: An Updated Approach to Classifying Selective Sweeps.
G3 (Bethesda, Md.)
May 31, 2018
Identifying selective sweeps in populations that have complex demographic histories remains a difficult problem in population genetics. We previously introduced a supervised machine learning approach, S/HIC, for finding both hard and soft selective s...
Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia.
PLoS genetics
Apr 23, 2018
Hybridization and gene flow between species appears to be common. Even though it is clear that hybridization is widespread across all surveyed taxonomic groups, the magnitude and consequences of introgression are still largely unknown. Thus it is cru...
A machine learning based framework to identify and classify long terminal repeat retrotransposons.
PLoS computational biology
Apr 23, 2018
Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. A...
Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster.
Genetics
May 27, 2016
Predicting individual quantitative trait phenotypes from high-resolution genomic polymorphism data is important for personalized medicine in humans, plant and animal breeding, and adaptive evolution. However, this is difficult for populations of unre...
Identifying targets of selection in mosaic genomes with machine learning: applications in Anopheles gambiae for detecting sites within locally adapted chromosomal inversions.
Molecular ecology
Apr 20, 2016
Chromosomal inversions are important structural changes that may facilitate divergent selection when they capture co-adaptive loci in the face of gene flow. However, identifying selection targets within inversions can be challenging. The high degrees...
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