Research

Our research interest is to computational methods applied to ancient DNA, sedimentary DNA, ancient microbes, low-coverage DNA, haplotypes and allele frequencies. We mostly use pangenomic graphs, Bayesian inference. We also collaborate closely with groups that produce empirical data.

Here are some publications from the group along with software that is being actively supported by the lab.

2024

Population genomics of post-glacial western Eurasia

Morten E. Allentoft, Martin Sikora, Anders Fischer, Karl-Göran Sjögren, Andrés Ingason, Ruairidh Macleod, Anders Rosengren, Bettina Schulz Paulsson, Marie Louise Schjellerup Jørkov, Maria Novosolov, Jesper Stenderup, T. Douglas Price, Morten Fischer Mortensen, Anne Birgitte Nielsen, Mikkel Ulfeldt Hede, Lasse Sørensen, Poul Otto Nielsen, Peter Rasmussen, Theis Zetner Trolle Jensen, Alba Refoyo-Martínez, Evan K. Irving-Pease, William Barrie, Alice Pearson, Bárbara Sousa da Mota, Fabrice Demeter, Rasmus A. Henriksen, Tharsika Vimala, Hugh McColl, Andrew Vaughn, Lasse Vinner, Gabriel Renaud, Aaron Stern, others

Nature · 18 Jan 2024

100 ancient genomes show repeated population turnovers in Neolithic Denmark

Morten E. Allentoft, Martin Sikora, Alba Refoyo-Martínez, Evan K. Irving-Pease, Anders Fischer, William Barrie, Andrés Ingason, Jesper Stenderup, Karl-Göran Sjögren, Alice Pearson, Bárbara Sousa da Mota, Bettina Schulz Paulsson, Alma Halgren, Ruairidh Macleod, Marie Louise Schjellerup Jørkov, Fabrice Demeter, Lasse Sørensen, Poul Otto Nielsen, Rasmus A. Henriksen, Tharsika Vimala, Hugh McColl, Ashot Margaryan, Melissa Ilardo, Andrew Vaughn, Morten Fischer Mortensen, Anne Birgitte Nielsen, Mikkel Ulfeldt Hede, Niels Nørkjær Johannsen, Peter Rasmussen, Lasse Vinner, Gabriel Renaud, Aaron Stern, others

Nature · 18 Jan 2024

2023

Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA

Annette Lien, Leonardo Pestana Legori, Louis Kraft, Peter Wad Sackett, Gabriel Renaud

Frontiers in Bioinformatics · 07 Dec 2023

The ancestry and geographical origins of St Helena's liberated Africans

Marcela Sandoval-Velasco, Anuradha Jagadeesan, Jazmín Ramos-Madrigal, María C Ávila-Arcos, Cesar A Fortes-Lima, Judy Watson, Erna Johannesdóttir, Diana I Cruz-Dávalos, Shyam Gopalakrishnan, J Víctor Moreno-Mayar, others

The American Journal of Human Genetics · 05 Nov 2023

euka: Robust tetrapodic and arthropodic taxa detection from modern and ancient environmental DNA using pangenomic reference graphs

Nicola Alexandra Vogel, Joshua Daniel Rubin, Mikkel Swartz, Juliette Vlieghe, Peter Wad Sackett, Anders Gorm Pedersen, Mikkel Winther Pedersen, Gabriel Renaud

Methods in Ecology and Evolution · 23 Sep 2023

Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains

Harold P Hodgins, Pengsheng Chen, Briallen Lobb, Xin Wei, Benjamin JM Tremblay, Michael J Mansfield, Victoria CY Lee, Pyung-Gang Lee, Jeffrey Coffin, Ana T Duggan, others

Nature Communications · 06 Sep 2023

The Limits of Haplotype-Based Approaches: Exploring the Applicability of the Li and Stephens Haplotype-Copying Model to Ancient Samples

Isabel Díaz-Pinés Cort, Joshua Daniel Rubin, Peter Wad Sackett, Gabriel Renaud

bioRxiv · 24 Jun 2023

HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph human mtDNA haplogroup inference

Joshua Daniel Rubin, Nicola Alexandra Vogel, Shyam Gopalakrishnan, Peter Wad Sackett, Gabriel Renaud

PLOS Computational Biology · 07 Jun 2023

2022

Unsupervised detection of fragment length signatures of circulating tumor DNA using non-negative matrix factorization

Gabriel Renaud, Maibritt Nørgaard, Johan Lindberg, Henrik Grönberg, Bram De Laere, Jørgen Bjerggaard Jensen, Michael Borre, Claus Lindbjerg Andersen, Karina Dalsgaard Sørensen, Lasse Maretty, and others

eLife · 27 Jul 2022

Population Genomics of Stone Age Eurasia

Morten E. Allentoft, Martin Sikora, Alba Refoyo-Martı́nez, Evan K. Irving-Pease, Anders Fischer, William Barrie, Andrés Ingason, Jesper Stenderup, Karl-Göran Sjögren, Alice Pearson, Barbara Mota, Bettina Schulz Paulsson, Alma Halgren, Ruairidh Macleod, Marie Louise Schjellerup Jørkov, Fabrice Demeter, Maria Novosolov, Lasse Sørensen, Poul-Otto Nielsen, Rasmus H.A. Henriksen, Tharsika Vimala, Hugh McColl, Ashot Margaryan, Melissa Ilardo, Andrew Vaughn, Morten Fischer Mortensen, Anne Birgitte Nielsen, Mikkel Ulfeldt Hede, Peter Rasmussen, Lasse Vinner, Gabriel Renaud, Aaron Stern, and others

bioRxiv · 05 May 2022

Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions

Nikolas Hallberg Thuesen, Michael Schantz Klausen, Shyam Gopalakrishnan, Thomas Trolle, Gabriel Renaud

Frontiers in Immunology · 08 Nov 2022

Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains

Harold P Hodgins, Pengsheng Chen, Briallen Lobb, Benjamin JM Tremblay, Michael J Mansfield, Victoria CY Lee, Pyung-Gang Lee, Jeffrey Coffin, Xin Wei, Ana T Duggan, Alexis E Dolphin, Gabriel Renaud, Min Dong, Doxey Andrew C

bioRxiv · 30 Jun 2022

2020

Population genomics of the Viking world

Ashot Margaryan, Daniel J Lawson, Martin Sikora, Fernando Racimo, Simon Rasmussen, Ida Moltke, Lara M Cassidy, Emil Jørsboe, Andrés Ingason, Mikkel W Pedersen, Thorfinn Korneliussen, Helene Wilhelmson, Magdalena Buś, Peter Barros Damgaard, Rui Martiniano, Gabriel Renaud, Claude Bhérer, J. Vı́ctor Moreno-Mayar, and others

Nature · 16 Sep 2020