Deep learning as a tool for ecology and evolution

ML Borowiec, RB Dikow, PB Frandsen… - Methods in Ecology …, 2022 - Wiley Online Library
Deep learning is driving recent advances behind many everyday technologies, including
speech and image recognition, natural language processing and autonomous driving. It is …

Harnessing deep learning for population genetic inference

X Huang, A Rymbekova, O Dolgova, O Lao… - Nature Reviews …, 2024 - nature.com
In population genetics, the emergence of large-scale genomic data for various species and
populations has provided new opportunities to understand the evolutionary forces that drive …

Neural ADMIXTURE for rapid genomic clustering

A Dominguez Mantes, D Mas Montserrat… - Nature computational …, 2023 - nature.com
Characterizing the genetic structure of large cohorts has become increasingly important as
genetic studies extend to massive, increasingly diverse biobanks. Popular methods …

SALAI-Net: species-agnostic local ancestry inference network

B Oriol Sabat, D Mas Montserrat, X Giro-i-Nieto… - …, 2022 - academic.oup.com
Motivation Local ancestry inference (LAI) is the high resolution prediction of ancestry labels
along a DNA sequence. LAI is important in the study of human history and migrations, and it …

Inference of coalescence times and variant ages using convolutional neural networks

J Nait Saada, Z Tsangalidou, M Stricker… - Molecular Biology …, 2023 - academic.oup.com
Accurate inference of the time to the most recent common ancestor (TMRCA) between pairs
of individuals and of the age of genomic variants is key in several population genetic …

High resolution ancestry deconvolution for next generation genomic data

H Hilmarsson, AS Kumar, R Rastogi, CD Bustamante… - bioRxiv, 2021 - biorxiv.org
As genome-wide association studies and genetic risk prediction models are extended to
globally diverse and admixed cohorts, ancestry deconvolution has become an increasingly …

Predicting dog phenotypes from genotypes

ER Bartusiak, M Barrabés… - 2022 44th Annual …, 2022 - ieeexplore.ieee.org
We analyze dog genotypes (ie, positions of dog DNA sequences that often vary between
different dogs) in order to predict the corresponding phenotypes (ie, unique observed …

Deep variational autoencoders for population genetics

M Geleta, DM Montserrat, X Giro-i-Nieto, AG Ioannidis - biorxiv, 2023 - biorxiv.org
Motivation Modern biobanks provide numerous high-resolution genomic sequences of
diverse populations. These datasets enable a better understanding of genotype-phenotype …

AncestryGrapher toolkit: Python command-line pipelines to visualize global-and local-ancestry inferences from the RFMIX version 2 software

A Lisi, MC Campbell - Bioinformatics, 2024 - academic.oup.com
Admixture is a fundamental process that has shaped levels and patterns of genetic variation
in human populations. RFMIX version 2 (RFMIX2) utilizes a robust modeling approach to …

Neural admixture: rapid population clustering with autoencoders

AD Mantes, DM Montserrat, CD Bustamante… - bioRxiv, 2021 - biorxiv.org
Characterizing the genetic substructure of large cohorts has become increasingly important
as genetic association and prediction studies are extended to massive, increasingly diverse …