Mathieson Lab

Research

More information on Google Scholar.

2026

A reusable neural approach to recombination mapping for model and non-model species
A reusable neural approach to recombination mapping for model and non-model species
Kevin Korfmann, Neda Rahnamae, Sara Mathieson
openRxiv  ·  22 Aug 2026  ·  doi:10.64898/2026.08.20.746066
Popformer: Learning general signatures of positive selection with a self-supervised transformer
Popformer: Learning general signatures of positive selection with a self-supervised transformer
Leon Zong, Sorelle A. Friedler, Sara Mathieson
PLOS Computational Biology  ·  15 Jul 2026  ·  doi:10.1371/journal.pcbi.1014492
Fast pairwise coalescence enables gene-resolution scans for recent selection in diverse human populations
Fast pairwise coalescence enables gene-resolution scans for recent selection in diverse human populations
Kevin Korfmann, Sara Mathieson
openRxiv  ·  22 May 2026  ·  doi:10.64898/2026.05.21.726777
On the use of generative models for demographic inference in malaria vectors from genomic data
On the use of generative models for demographic inference in malaria vectors from genomic data
Amelia Adibe Eneli, Pui Chung Siu, Manolo F Perez, Austin Burt, Matteo Fumagalli, Sara Mathieson
G3: Genes, Genomes, Genetics  ·  14 May 2026  ·  doi:10.1093/g3journal/jkag114

2025

Interpreting Convolutional Neural Networks in Population Genetics
Interpreting Convolutional Neural Networks in Population Genetics
Huiting Xu, Leon Zong, Dylan D. Ray, Lei Lei, Daniel R. Schrider, Franz Baumdicker, Sara Mathieson
openRxiv  ·  09 Dec 2025  ·  doi:10.64898/2025.12.04.692404

2024

Identity-by-descent IBD segment outlier detection in endogamous populations using pedigree cohorts
Identity-by-descent (IBD) segment outlier detection in endogamous populations using pedigree cohorts
Shi Jie Samuel Tan, Huyen Trang Dang, Sarah Keim, Maja Bućan, Sara Mathieson
openRxiv  ·  09 Aug 2024  ·  doi:10.1101/2024.08.07.607051
Interpreting generative adversarial networks to infer natural selection from genetic data
Interpreting generative adversarial networks to infer natural selection from genetic data
Rebecca Riley, Iain Mathieson, Sara Mathieson
GENETICS  ·  22 Feb 2024  ·  doi:10.1093/genetics/iyae024

2023

The genomic footprint of social stratification in admixing American populations
The genomic footprint of social stratification in admixing American populations
Alex Mas-Sandoval, Sara Mathieson, Matteo Fumagalli
eLife  ·  01 Dec 2023  ·  doi:10.7554/eLife.84429

2021

Automatic inference of demographic parameters using generative adversarial networks
Automatic inference of demographic parameters using generative adversarial networks
Zhanpeng Wang, Jiaping Wang, Michael Kourakos, Nhung Hoang, Hyong Hark Lee, Iain Mathieson, Sara Mathieson
Molecular Ecology Resources  ·  03 May 2021  ·  doi:10.1111/1755-0998.13386
Ancestral haplotype reconstruction in endogamous populations using identity-by-descent
Ancestral haplotype reconstruction in endogamous populations using identity-by-descent
Kelly Finke, Michael Kourakos, Gabriela Brown, Huyen Trang Dang, Shi Jie Samuel Tan, …, Shweta Ramdas, Alejandro A. Schäffer, Rachel L. Kember, Maja Bućan, Sara Mathieson
PLOS Computational Biology  ·  26 Feb 2021  ·  doi:10.1371/journal.pcbi.1008638

2019

ImaGene: a convolutional neural network to quantify natural selection from genomic data
ImaGene: a convolutional neural network to quantify natural selection from genomic data
Luis Torada, Lucrezia Lorenzon, Alice Beddis, Ulas Isildak, Linda Pattini, Sara Mathieson, Matteo Fumagalli
BMC Bioinformatics  ·  01 Nov 2019  ·  doi:10.1186/s12859-019-2927-x

2018

A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks
Jeffrey Chan, Valerio Perrone, Jeffrey Spence, Paul Jenkins, Sara Mathieson, Yun Song
NeurIPS  ·  03 Dec 2018  ·  [no id info]
i FADS1 i and the Timing of Human Adaptation to Agriculture
FADS1 and the Timing of Human Adaptation to Agriculture
Sara Mathieson, Iain Mathieson
Molecular Biology and Evolution  ·  01 Oct 2018  ·  doi:10.1093/molbev/msy180

2016

Deep Learning for Population Genetic Inference
Deep Learning for Population Genetic Inference
Sara Sheehan, Yun S. Song
PLOS Computational Biology  ·  28 Mar 2016  ·  doi:10.1371/journal.pcbi.1004845

2014

Decoding Coalescent Hidden Markov Models in Linear Time
Decoding Coalescent Hidden Markov Models in Linear Time
Kelley Harris, Sara Sheehan, John A. Kamm, Yun S. Song
Lecture Notes in Computer Science  ·  01 Jan 2014  ·  doi:10.1007/978-3-319-05269-4_8

2013

Estimating Variable Effective Population Sizes from Multiple Genomes: A Sequentially Markov Conditional Sampling Distribution Approach
Estimating Variable Effective Population Sizes from Multiple Genomes: A Sequentially Markov Conditional Sampling Distribution Approach
Sara Sheehan, Kelley Harris, Yun S Song
Genetics  ·  01 Jul 2013  ·  doi:10.1534/genetics.112.149096

2012

Telescoper: i de novo i assembly of highly repetitive regions
Telescoper: de novo assembly of highly repetitive regions
Ma’ayan Bresler, Sara Sheehan, Andrew H. Chan, Yun S. Song
Bioinformatics  ·  03 Sep 2012  ·  doi:10.1093/bioinformatics/bts399