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[1]
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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, et al. 100 ancient genomes show repeated population turnovers in Neolithic
Denmark.
Nature, 625(7994):329--337, 2024.
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[2]
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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, et al. Population genomics of post-glacial western Eurasia.
Nature, 625(7994):301--311, 2024.
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[3]
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Nicola Alexandra Vogel, Joshua Daniel Rubin, Mikkel Swartz, Juliette Vlieghe,
Peter Wad Sackett, Anders Gorm Pedersen, Mikkel Winther Pedersen, and Gabriel Renaud.
euka: Robust tetrapodic and arthropodic taxa detection from modern
and ancient environmental DNA using pangenomic reference graphs.
Methods in Ecology and Evolution, 2023.
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[4]
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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, et al.
Ancient Clostridium DNA and variants of tetanus neurotoxins
associated with human archaeological remains.
Nature Communications, 14(1):5475, 2023.
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[5]
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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, et al.
The ancestry and geographical origins of St Helena's liberated
Africans.
The American Journal of Human Genetics, 110(9):1590--1599,
2023.
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[6]
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Joshua Daniel Rubin, Nicola Alexandra Vogel, Shyam Gopalakrishnan, Peter Wad
Sackett, and Gabriel Renaud. HaploCart: Human mtDNA haplogroup classification using a pangenomic
reference graph human mtDNA haplogroup inference.
PLOS Computational Biology, 19(6):e1011148, 2023.
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[7]
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Isabel Díaz-Pinés Cort, Joshua Daniel Rubin, Peter Wad Sackett, and
Gabriel Renaud. The Limits of Haplotype-Based Approaches: Exploring the
Applicability of the Li and Stephens Haplotype-Copying Model to Ancient
Samples.
bioRxiv, pages 2023--06, 2023.
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[8]
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Annette Lien, Leonardo Pestana Legori, Louis Kraft, Peter Wad Sackett, and
Gabriel Renaud. Benchmarking software tools for trimming adapters and merging
next-generation sequencing data for ancient DNA.
Frontiers in Bioinformatics, 3, 2023.
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[9]
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Nikolas Hallberg Thuesen, Michael Schantz Klausen, Shyam Gopalakrishnan, Thomas
Trolle, and Gabriel Renaud. Benchmarking freely available HLA typing algorithms across varying
genes, coverages and typing resolutions.
Frontiers in Immunology, 13:987655--987655, 2022.
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[10]
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Joshua D. Rubin, Nicola A. Vogel, Shyam Gopalakrishnan, Peter W. Sackett, and
Gabriel Renaud. HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic
Reference Graph.
bioRxiv, 2022.
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[11]
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Gabriel Renaud, Maibritt Nørgaard, Johan Lindberg, Henrik Grönberg, Bram De Laere, Jørgen Bjerggaard Jensen, Michael Borre, Claus Lindbjerg
Andersen, Karina Dalsgaard Sørensen, Lasse Maretty, et al.
Unsupervised detection of fragment length signatures of circulating
tumor DNA using non-negative matrix factorization.
eLife, 11:e71569, 2022.
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[12]
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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, 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, et al. Population Genomics of Stone Age Eurasia.
bioRxiv, 2022.
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[13]
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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, and Doxey Andrew C.
Ancient Clostridium DNA and variants of tetanus neurotoxins
associated with human archaeological remains.
bioRxiv, 2022.
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[14]
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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 de Barros Damgaard, Rui Martiniano, Gabriel Renaud, Claude Bhérer, J. Víctor Moreno-Mayar, et al.
Population genomics of the Viking world.
Nature, 585(7825):390--396, 2020.
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[15]
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J Víctor Moreno-Mayar, Thorfinn Sand Korneliussen, Jyoti Dalal, Gabriel Renaud, Anders Albrechtsen, Rasmus Nielsen, and Anna-Sapfo Malaspinas.
A likelihood method for estimating present-day human contamination in
ancient male samples using low-depth X-chromosome data.
Bioinformatics, 36(3):828--841, 2020.
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[16]
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Martin Sikora, Vladimir V Pitulko, Vitor C Sousa, Morten E Allentoft, Lasse
Vinner, Simon Rasmussen, Ashot Margaryan, Peter de Barros Damgaard, Constanza
de la Fuente, Gabriel Renaud, et al. The population history of northeastern siberia since the pleistocene.
Nature, 570(7760):182--188, 2019.
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[17]
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Xavier Mata, Gabriel Renaud, and Catherine Mollereau. The repertoire of family A-peptide GPCRs in archaic
hominins.
Peptides, 122:170154, 2019.
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[18]
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Gabriel Renaud, Kristian Hanghøj, Thorfinn Sand Korneliussen, Eske Willerslev, and Ludovic Orlando.
Joint Estimates of Heterozygosity and Runs of Homozygosity
for Modern and Ancient Samples.
Genetics, pages genetics--302057, 2019.
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[19]
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Kristian Hanghøj, Gabriel Renaud, Anders Albrechtsen, and Ludovic Orlando. DamMet: ancient methylome mapping accounting for errors, true
variants, and post-mortem DNA damage.
GigaScience, 8(4):giz025, 2019.
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[20]
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Gabriel Renaud, Mikkel Schubert, Susanna Sawyer, and Ludovic Orlando. Authentication and assessment of contamination in ancient DNA.
In Ancient DNA: Methods and Protocols, 2nd
Edition, pages 163--194. Humana Press, New York, NY, 2019.
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[21]
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Peter de Barros Damgaard, Nina Marchi, Simon Rasmussen, Michaël Peyrot,
Gabriel Renaud, Thorfinn Korneliussen, José Victor Moreno-Mayar, Mikkel Winther Pedersen, Amy Goldberg, Emma Usmanova, et al.
137 ancient human genomes from across the Eurasian steppes.
Nature, 557(7705):369--374, 2018.
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[22]
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Hannes Schroeder, Martin Sikora, Shyam Gopalakrishnan, Lara M Cassidy,
Pierpaolo Maisano Delser, Marcela Sandoval Velasco, Joshua G Schraiber, Simon
Rasmussen, Julian R Homburger, María C Ávila-Arcos, Morten E
Allentoft, J Víctor Moreno-Mayar, Gabriel Renaud, Alberto Gómez-Carballa, et al.
Origins and genetic legacies of the Caribbean Taino.
Proceedings of the National Academy of Sciences,
115(10):2341--2346, 2018.
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[23]
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Gabriel Renaud, Bent Petersen, Andaine Seguin-Orlando, Mads Frost Bertelsen, Andrew Waller, Richard Newton, Romain Paillot, Neil Bryant, Mark Vaudin,
Pablo Librado, et al.
Improved de novo genomic assembly for the domestic donkey.
Science Advances, 4(4):eaaq0392, 2018.
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[24]
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Gabriel Renaud. glactools: a command-line toolset for the management of genotype
likelihoods and allele counts.
Bioinformatics, 1:3, 2017.
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[25]
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Ana T Duggan, Alison JT Harris, Stephanie Marciniak, Ingeborg Marshall, Melanie
Kuch, Andrew Kitchen, Gabriel Renaud, John Southon, Ben Fuller, Janet Young, et al.
Genetic Discontinuity between the Maritime Archaic and
Beothuk Populations in Newfoundland, Canada.
Current Biology, 2017.
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[26]
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Martin Sikora, Andaine Seguin-Orlando, Vitor C. Sousa, Anders Albrechtsen,
Thorfinn Korneliussen, Amy Ko, Simon Rasmussen, Isabelle Dupanloup, Philip R
Nigst, Marjolein D Bosch, Gabriel Renaud, Morten E Allentoft, Ashot Margaryan, et al.
Ancient genomes show social and reproductive behaviour of early
Upper Paleolithic foragers.
Science, eaao1807, 2017.
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[27]
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Viviane Slon, Bence Viola, Gabriel Renaud, Marie-Theres Gansauge, Stefano Benazzi, Susanna Sawyer, Jean-Jacques Hublin, Michail V. Shunkov, Anatoly P.
Derevianko, Janet Kelso, Kay Prüfer, Matthias Meyer, and Svante
Pääbo.
A fourth Denisovan individual.
Science Advances, 3(7):e1700186, 2017.
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[28]
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Gabriel Renaud, Kristian Hanghøj, Eske Willerslev, and Ludovic Orlando. gargammel: a sequence simulator for ancient DNA.
Bioinformatics, 33(4):577--579, 2016.
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[29]
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Swapan Mallick, Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, Fernando
Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon,
Pontus Skoglund, Iosif Lazaridis, Sriram Sankararaman, Qiaomei Fu, Nadin
Rohland, Gabriel Renaud, Yaniv Erlich, Carla Gallo, et al. The Simons Genome Diversity Project: 300 genomes from 142
diverse populations.
Nature, 538(7624):201--206, 2016.
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[30]
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Gabriel Renaud*, Fernando Racimo*, and Montgomery Slatkin. Joint estimation of contamination, error and demography for nuclear
DNA from ancient humans.
PLoS Genetics, 12(4):e1005972, 2016.
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[31]
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Cosimo Posth, Gabriel Renaud, Alissa Mittnik, Dorothée G Drucker, Hélène Rougier, Christophe Cupillard, et al.
Pleistocene Mitochondrial Genomes Suggest a Single Major
Dispersal of Non-Africans and a Late Glacial Population
Turnover in Europe.
Current Biology, 26(6):827--833, 2016.
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[32]
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Gabriel Renaud, Viviane Slon, Ana T. Duggan, and Janet Kelso. Schmutzi: estimation of contamination and endogenous mitochondrial
consensus calling for ancient DNA.
Genome Biology, 16:224, 2015.
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[33]
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Gabriel Renaud*, Susanna Sawyer*, Bence Viola, Jean-Jacques Hublin, Marie Theres-Gansauge, Michail Shunkovc, Anatoly Dereviankoc, Kay Pruefer, Janet
Kelso, and Svante Pääbo.
Nuclear and mitochondrial DNA sequences from two Denisovan
individuals.
Proceedings of the National Academy of Sciences,
112(51):15696--15700, Dec 2015.
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[34]
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Diana Le Duc, Gabriel Renaud, Arunkumar Krishnan, Markus Sällman Almén, Leon Huynen, Sonja J. Prohaska, Matthias Ongyerth, Bárbara D. Bitarello,
Helgi B. Schiöth, Michael Hofreiter, Peter F. Stadler, Kay Prüfer,
David Lambert, Janet Kelso, and Torsten Schöneberg.
Kiwi genome provides insights into nocturnal adaptation.
Genome Biology, 16:147, 2015.
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[35]
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Gabriel Renaud, Udo Stenzel, Tomislav Maricic, Victor Wiebe, and Janet Kelso. deML: robust demultiplexing of Illumina sequences using a
likelihood-based approach.
Bioinformatics, 31(5):770--772, Mar 2015.
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[36]
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Gabriel Renaud*, Matthew C LaFave*, Jin Liang, Tyra G Wolfsberg, and Shawn M Burgess.
trieFinder: an efficient program for annotating Digital Gene
Expression (DGE) tags.
BMC Bioinformatics, 15(1):329, 2014.
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[37]
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Gabriel Renaud, Udo Stenzel, and Janet Kelso. leeHom: adaptor trimming and merging for Illumina sequencing
reads.
Nucleic Acids Research, 42(18):e141, Oct 2014.
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[38]
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Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Karola Kirsanow, Peter H Sudmant, Joshua G Schraiber, Sergi
Castellano, Mark Lipson, et al.
Ancient human genomes suggest three ancestral populations for
present-day Europeans.
Nature, 513(7518):409--413, Sep 2014.
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[39]
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Sebastian Lippold, Hongyang Xu, Albert Ko, Mingkun Li, Gabriel Renaud, Anne Butthof, Roland Schröder, Mark Stoneking, et al.
Human paternal and maternal demographic histories: insights from
high-resolution Y chromosome and mtDNA sequences.
Investigative Genetics, 5:13, 2014.
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[40]
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Gabriel Renaud, Martin Kircher, Udo Stenzel, and Janet Kelso. freeIbis: an efficient basecaller with calibrated quality scores
for Illumina sequencers.
Bioinformatics, 29(9):1208--1209, May 2013.
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[41]
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Sergi Castellano, Genís Parra, Federico A Sánchez-Quinto, Fernando
Racimo, Martin Kuhlwilm, Martin Kircher, Susanna Sawyer, Qiaomei Fu, Anja
Heinze, Birgit Nickel, Jesse Dabney, Michael Siebauer, Louise White,
Hernán A Burbano, Gabriel Renaud, Udo Stenzel, Carles Lalueza-Fox, et al. Patterns of coding variation in the complete exomes of three
Neandertals.
Proceedings of the National Academy of Sciences,
111(18):6666--6671, 2014.
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[42]
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Kay Prüfer, Fernando Racimo, Nick Patterson, Flora Jay, Sriram
Sankararaman, Susanna Sawyer, Anja Heinze, Gabriel Renaud, Peter H Sudmant, Cesare de Filippo, et al.
The complete genome sequence of a Neanderthal from the Altai
Mountains.
Nature, 505(7481):43--49, 2014.
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[43]
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Daphne W Bell, Nilabja Sikdar, Kyoo-young Lee, Jessica C Price, Raghunath
Chatterjee, Hee-Dong Park, Jennifer Fox, Masamichi Ishiai, Meghan L Rudd,
Lana M Pollock, Sarah K Fogoros, Hassan Mohamed, Christin L Hanigan, Suiyuan
Zhang, Pedro Cruz, Gabriel Renaud, Nancy F Hansen, et al. Predisposition to cancer caused by genetic and functional defects
of mammalian Atad5.
PLoS Genetics, 7(8):e1002245, 2011.
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[44]
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Jin Liang, Gabriel Renaud, and Shawn M Burgess. Sequencing-based expression profiling in Zebrafish.
Methods in Cell Biology, 104:379, 2011.
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[45]
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Jin Liang, Dongmei Wang, Gabriel Renaud, Tyra G Wolfsberg, Alexander F Wilson, and Shawn M Burgess.
The stat3/socs3a pathway is a key regulator of hair cell
regeneration in zebrafish.
The Journal of Neuroscience, 32(31):10662--10673, Aug
2012.
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[46]
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Fabricio F Costa, Jared M Bischof, Elio F Vanin, Rishi R Lulla, Simone T
Sredni, Veena Rajaram, Min Wang, Gabriel Renaud, Fabio Passetti, Tadanori Tomita, et al.
Identification of differentially expressed microRNAs and
other non-coding RNAs in ependymomas.
Cancer Research, 72(8 Supplement):198--198, 2012.
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[47]
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Raphael Tavares, Gabriel Renaud, Paulo Sergio Lopes Oliveira, Carlos G Ferreira, Emmanuel Dias-Neto, and Fabio Passetti.
Identical sequence patterns in the ends of exons and introns of
human protein-coding genes.
Computational Biology and Chemistry, 36:55--61, 2012.
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[48]
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Mariana Emerenciano, Gabriel Renaud, Mariana Sant'Ana, Caroline Barbieri, Fabio Passetti, Maria S Pombo-de Oliveira, and Brazilian Collaborative Study Group
of Infant Acute Leukemia.
Challenges in the use of NG2 antigen as a marker to predict
MLL rearrangements in multi-center studies.
Leukemia Research, 35(8):1001--1007, 2011.
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[49]
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Gabriel Renaud, Pedro Neves, Edson Luiz Folador, Carlos Gil Ferreira, and Fabio Passetti.
Segtor: rapid annotation of genomic coordinates and single
nucleotide variations using segment trees.
PLOS ONE, 6(11):e26715, 2011.
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[50]
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Donna M Toleno, Gabriel Renaud, Tyra G Wolfsberg, Munirul Islam, Derek E Wildman, Kimberly D Siegmund, and Joseph G Hacia.
Development and evaluation of new mask protocols for gene
expression profiling in humans and chimpanzees.
BMC Bioinformatics, 10(1):77, 2009.
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[51]
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Stacie K Loftus, Anthony Antonellis, Ivana Matera, Gabriel Renaud, Laura L Baxter, Duncan Reid, Tyra G Wolfsberg, Yidong Chen, ChenWei Wang, Megana K
Prasad, et al.
Gpnmb is a melanoblast-expressed, MITF-dependent gene.
Pigment Cell & Melanoma Research, 22(1):99--110, 2009.
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[52]
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Tiffany C Scharschmidt, Karin List, Elizabeth A Grice, Roman Szabo, Gabriel Renaud, Chyi-Chia R Lee, Tyra G Wolfsberg, Thomas H Bugge, and Julia A Segre.
Matriptase-deficient mice exhibit ichthyotic skin with a selective
shift in skin microbiota.
Journal of Investigative Dermatology, 129(10):2435--2442,
2009.
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[53]
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Yoo-Jin Kim, Yoon-Sang Kim, Andre Larochelle, Gabriel Renaud, Tyra G Wolfsberg, Rima Adler, Robert E Donahue, Peiman Hematti, Bum-Kee Hong, Jean Roayaei,
et al.
Sustained high-level polyclonal hematopoietic marking and transgene
expression 4 years after autologous transplantation of rhesus macaques with
SIV lentiviral vector--transduced CD34+ cells.
Blood, 113(22):5434--5443, 2009.
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[54]
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Elizabeth A Grice, Heidi H Kong, Gabriel Renaud, Alice C Young, Gerard G Bouffard, Robert W Blakesley, Tyra G Wolfsberg, Maria L Turner, and Julia A
Segre.
A diversity profile of the human skin microbiota.
Genome Research, 18(7):1043--1050, 2008.
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[55]
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Brian L Pike, Timothy C Greiner, Xiaoming Wang, Dennis D Weisenburger, Ya-Hsuan
Hsu, Gabriel Renaud, Tyra G Wolfsberg, Myungjin Kim, Daniel J Weisenberger, Kimberly D Siegmund, et al.
DNA methylation profiles in diffuse large B-cell lymphoma and
their relationship to gene expression status.
Leukemia, 22(5):1035--1043, 2008.
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[56]
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Anthony Antonellis, Jimmy L Huynh, Shih-Queen Lee-Lin, Ryan M Vinton, Gabriel Renaud, Stacie K Loftus, Gene Elliot, Tyra G Wolfsberg, Eric D Green,
Andrew S McCallion, et al.
Identification of neural crest and glial enhancers at the mouse
Sox10 locus through transgenesis in zebrafish.
PLoS Genetics, 4(9):e1000174, 2008.
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[57]
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FA Grice, HH Kong, G Renaud, AC Young, N. Program, GG Bouffard, RW Blakesley,
TG Wolfsberg, ML Tumer, and JA Segre.
Genomic analysis of the cutaneous skin microflora.
In Journal of Investigative Dermatology, volume 128,
pages S121--S121. Nature Publishing Group, 2008.
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[58]
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Jingqiong Hu, Gabriel Renaud, Theotonius Golmes, Andrea Ferris, Paul C Hendrie, Robert E Donahue, Stephen H Hughes, Tyra G Wolfsberg, David W Russell, and
Cynthia E Dunbar.
Reduced genotoxicity of avian sarcoma leukosis virus vectors in
rhesus long-term repopulating cells compared to standard murine retrovirus
vectors.
Molecular Therapy, 16(9):1617--1623, 2008.
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[59]
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Jingqiong Hu, Theotonius Gomes, Andrea Ferris, Gabriel Renaud, Paul C Hendrie, Allen E Krouse, Robert E Donahue, Tyra G Wolfsberg, Stephen H Hughes, David W
Russell, et al.
Distinctive integration profile of avian sarcoma leukosis virus
vectors in rhesus long-term repopulating cells.
Blood, 110(11):66A--66A, 2007.
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[60]
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Gregory E Crawford, Sean Davis, Peter C Scacheri, Gabriel Renaud, Mohamad J Halawi, Michael R Erdos, Roland Green, Paul S Meltzer, Tyra G Wolfsberg, and
Francis S Collins.
DNase-chip: a high-resolution method to identify DNase I
hypersensitive sites using tiled microarrays.
Nature Methods, 3(7):503--509, 2006.
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[61]
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Gabriel Renaud. Protein Secondary Structure Prediction using
inter-residue contacts.
Master's thesis, University of Waterloo, 2005.
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[62]
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Gabriel Renaud. Bayesian maximum a posteriori algorithms for modern and
ancient DNA sequencing.
PhD thesis, Max Planck Institute for Evolutionary
Anthropology/Leipzig University, 1 2016.
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