This page contains papers from the Nielsen Lab starting in 2020. For earlier papers, please see Google Scholar.

2023

Bayesian inference of admixture graphs on Native American and Arctic populations

Nielsen and Vaughn et al. 2023. PLOS Genetics.

2022

SCONCE2: jointly inferring single cell copy number profles and tumor evolutionary distances

Hui and Nielsen 2022. BMC Bioinformatics.

Overcoming Language Barriers in Academia: Machine Translation Tools and a Vision for a Multilingual Future

Steigerwald et al. 2022. BioScience.

Population Genomics of Variegated Toad-Headed Lizard Phrynocephalus versicolor and Its Adaptation to the Colorful Sand of the Gobi Desert

Jin and Aguilar-Gómez et al. 2022. Genome Biology and Evolution.

Evaluation of methods for estimating coalescence times using ancestral recombination graphs

Brandt et al. 2022. Genetics.

SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing

Hui and Nielsen 2022. Bioinformatics.

2021

AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees

Pipes and Nielsen 2021. Bioinformatics.

Detecting selection in multiple populations by modelling ancestral admixture components

Cheng et al. 2021. Molecular Biology and Evolution.

Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

Ai et al. 2021. GigaScience.

The distribution of waiting distances in ancestral recombination graphs

Deng, Song, and Nielsen. 2021. Theoretical Population Biology.

The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans

Zhang et al. 2021. PNAS.

Investigate the origins of COVID-19

Bloom et al. 2021. Science.

Inferring adaptive introgression using hidden Markov models

Svedberg et al. 2021. Molecular Biology and Evolution.

Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation

Rocha et al. 2021. Trends in Ecology and Evolution.

Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny

Pipes et al. 2021. Molecular Biology and Evolution.

The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity

Meyer et al. 2021. California Agriculture.

Disentangling selection on genetically correlated polygenic traits via whole-genome genealogies

Stern et al. 2021. AJHG.

Synonymous mutations and the molecular evolution of SARS-Cov-2 origins

Wang, Pipes, and Nielsen. 2021. Virus Evolution.

The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system

Stuckert et al. 2021. Molecular Ecology.

2020

The genetic architecture of sporadic and multiple consecutive miscarriage

Laisk et al. 2020. Nature Communications.

Divergence, gene flow, and the origin of leapfrog geographic distributions: The history of colour pattern variation in Phyllobates poison‐dart frogs

Márquez et al. 2020. Molecular Ecology.

On the distribution of tract lengths during adaptive introgression

Shchur et al. 2020. G3: Genes, Genomes, Genetics.

Population genomics of the Viking world

Margaryan et al. 2020. Nature.

Inferring the ancestry of parents and grandparents from genetic data

Pei et al. 2020. PLoS Computational Biology.

Massive haplotypes underlie ecotypic differentiation in sunflowers

Todesco et al. 2020. Nature.

VolcanoFinder: genomic scans for adaptive introgression

Setter et al. 2020. PLoS Genetics.

Phenotypic convergence is not mirrored at the protein level in a lizard adaptive radiation

Corbett-Detig et al. 2020. Molecular Biology and Evolution.

Ancient hybridization with an unknown population facilitated high-altitude adaptation of canids

Wang et al. 2020. Molecular Biology and Evolution.

A Bayesian framework for inferring the influence of sequence context on point mutations

Ling et al. 2020. Molecular Biology and Evolution.

No statistical evidence for an effect of CCR5-Δ 32 on lifespan in the UK Biobank cohort

Maier et al. 2020. Nature Medicine.

A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data

Moreno-Mayar et al. 2020. Bioinformatics.

Pronounced somatic bottleneck in mitochondrial DNA of human hair

Barrett et al. 2020. Philosophical Transactions of the Royal Society B.

A draft genome sequence of the elusive giant squid, Architeuthis dux

Da Fonseca et al. 2020. GigaScience.