Gabriel Renaud

Gabriel Renaud

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Gabriel Renaud

Gabriel Renaud

Publications by authors named "Gabriel Renaud"

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Authentication and Assessment of Contamination in Ancient DNA.

Methods Mol Biol 2019 ;1963:163-194

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark.

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http://dx.doi.org/10.1007/978-1-4939-9176-1_17DOI Listing
September 2019

The repertoire of family A-peptide GPCRs in archaic hominins.

Peptides 2019 Sep 24:170154. Epub 2019 Sep 24.

Laboratoire Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France. Electronic address:

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http://dx.doi.org/10.1016/j.peptides.2019.170154DOI Listing
September 2019

Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.

Genetics 2019 07 14;212(3):587-614. Epub 2019 May 14.

Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark.

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http://dx.doi.org/10.1534/genetics.119.302057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6614887PMC
July 2019

DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage.

Gigascience 2019 04;8(4)

Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark.

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http://dx.doi.org/10.1093/gigascience/giz025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474913PMC
April 2019

Author Correction: 137 ancient human genomes from across the Eurasian steppes.

Nature 2018 11;563(7729):E16

Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41586-018-0488-1DOI Listing
November 2018

137 ancient human genomes from across the Eurasian steppes.

Nature 2018 05 9;557(7705):369-374. Epub 2018 May 9.

Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

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http://www.nature.com/articles/s41586-018-0094-2
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http://dx.doi.org/10.1038/s41586-018-0094-2DOI Listing
May 2018

glactools: a command-line toolset for the management of genotype likelihoods and allele counts.

Authors:
Gabriel Renaud

Bioinformatics 2018 04;34(8):1398-1400

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx749DOI Listing
April 2018

Genetic Discontinuity between the Maritime Archaic and Beothuk Populations in Newfoundland, Canada.

Curr Biol 2017 Oct 12;27(20):3149-3156.e11. Epub 2017 Oct 12.

McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Humans & the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2017.08.053DOI Listing
October 2017

A fourth Denisovan individual.

Sci Adv 2017 07 7;3(7):e1700186. Epub 2017 Jul 7.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

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http://dx.doi.org/10.1126/sciadv.1700186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501502PMC
July 2017

gargammel: a sequence simulator for ancient DNA.

Bioinformatics 2017 02;33(4):577-579

Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btw670DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408798PMC
February 2017

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Nature 2016 Oct 21;538(7624):201-206. Epub 2016 Sep 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature18964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161557PMC
October 2016

Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans.

PLoS Genet 2016 Apr 6;12(4):e1005972. Epub 2016 Apr 6.

Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822957PMC
April 2016

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe.

Curr Biol 2016 Mar 4;26(6):827-33. Epub 2016 Feb 4.

Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Rümelinstraße 23, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72072 Tübingen, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09609822160008
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http://dx.doi.org/10.1016/j.cub.2016.01.037DOI Listing
March 2016

Nuclear and mitochondrial DNA sequences from two Denisovan individuals.

Proc Natl Acad Sci U S A 2015 Dec 16;112(51):15696-700. Epub 2015 Nov 16.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany;

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http://dx.doi.org/10.1073/pnas.1519905112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697428PMC
December 2015

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach.

Bioinformatics 2015 Mar 30;31(5):770-2. Epub 2014 Oct 30.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony D-04103, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btu719DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341068PMC
March 2015

leeHom: adaptor trimming and merging for Illumina sequencing reads.

Nucleic Acids Res 2014 Oct 6;42(18):e141. Epub 2014 Aug 6.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany

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http://academic.oup.com/nar/article/42/18/e141/2434537/leeHo
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http://dx.doi.org/10.1093/nar/gku699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191382PMC
October 2014

trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags.

BMC Bioinformatics 2014 Oct 13;15:329. Epub 2014 Oct 13.

Translational and Functional Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-8004, USA.

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http://dx.doi.org/10.1186/1471-2105-15-329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287429PMC
October 2014

Ancient human genomes suggest three ancestral populations for present-day Europeans.

Authors:
Iosif Lazaridis Nick Patterson Alissa Mittnik Gabriel Renaud Swapan Mallick Karola Kirsanow Peter H Sudmant Joshua G Schraiber Sergi Castellano Mark Lipson Bonnie Berger Christos Economou Ruth Bollongino Qiaomei Fu Kirsten I Bos Susanne Nordenfelt Heng Li Cesare de Filippo Kay Prüfer Susanna Sawyer Cosimo Posth Wolfgang Haak Fredrik Hallgren Elin Fornander Nadin Rohland Dominique Delsate Michael Francken Jean-Michel Guinet Joachim Wahl George Ayodo Hamza A Babiker Graciela Bailliet Elena Balanovska Oleg Balanovsky Ramiro Barrantes Gabriel Bedoya Haim Ben-Ami Judit Bene Fouad Berrada Claudio M Bravi Francesca Brisighelli George B J Busby Francesco Cali Mikhail Churnosov David E C Cole Daniel Corach Larissa Damba George van Driem Stanislav Dryomov Jean-Michel Dugoujon Sardana A Fedorova Irene Gallego Romero Marina Gubina Michael Hammer Brenna M Henn Tor Hervig Ugur Hodoglugil Aashish R Jha Sena Karachanak-Yankova Rita Khusainova Elza Khusnutdinova Rick Kittles Toomas Kivisild William Klitz Vaidutis Kučinskas Alena Kushniarevich Leila Laredj Sergey Litvinov Theologos Loukidis Robert W Mahley Béla Melegh Ene Metspalu Julio Molina Joanna Mountain Klemetti Näkkäläjärvi Desislava Nesheva Thomas Nyambo Ludmila Osipova Jüri Parik Fedor Platonov Olga Posukh Valentino Romano Francisco Rothhammer Igor Rudan Ruslan Ruizbakiev Hovhannes Sahakyan Antti Sajantila Antonio Salas Elena B Starikovskaya Ayele Tarekegn Draga Toncheva Shahlo Turdikulova Ingrida Uktveryte Olga Utevska René Vasquez Mercedes Villena Mikhail Voevoda Cheryl A Winkler Levon Yepiskoposyan Pierre Zalloua Tatijana Zemunik Alan Cooper Cristian Capelli Mark G Thomas Andres Ruiz-Linares Sarah A Tishkoff Lalji Singh Kumarasamy Thangaraj Richard Villems David Comas Rem Sukernik Mait Metspalu Matthias Meyer Evan E Eichler Joachim Burger Montgomery Slatkin Svante Pääbo Janet Kelso David Reich Johannes Krause

Nature 2014 Sep;513(7518):409-13

1] Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany. [2] Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany. [3] Max Planck Institut für Geschichte und Naturwissenschaften, Jena 07745, Germany.

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https://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_fil
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http://biorxiv.org/content/biorxiv/early/2013/12/23/001552.f
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http://www.geo.uni-tuebingen.de/fileadmin/website/arbeitsber
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http://www.nature.com/doifinder/10.1038/nature13673
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http://dx.doi.org/10.1038/nature13673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574PMC
September 2014

Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences.

Investig Genet 2014 24;5:13. Epub 2014 Sep 24.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany.

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http://dx.doi.org/10.1186/2041-2223-5-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174254PMC
September 2014

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers.

Bioinformatics 2013 May 6;29(9):1208-9. Epub 2013 Mar 6.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btt117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634191PMC
May 2013

The stat3/socs3a pathway is a key regulator of hair cell regeneration in zebrafish. [corrected].

J Neurosci 2012 Aug;32(31):10662-73

Genome Technology Branch, and Inherited Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1523/JNEUROSCI.5785-10.2012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427933PMC
August 2012

Segtor: rapid annotation of genomic coordinates and single nucleotide variations using segment trees.

PLoS One 2011 1;6(11):e26715. Epub 2011 Nov 1.

Bioinformatics Unit, Clinical Research Coordination, Instituto Nacional de Cancer-INCA, Centro, Rio de Janeiro, Brazil.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026715PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206052PMC
March 2012

Identical sequence patterns in the ends of exons and introns of human protein-coding genes.

Comput Biol Chem 2012 Feb 12;36:55-61. Epub 2012 Jan 12.

Bioinformatics Unit, Clinical Research Coordination, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37 - CEP 20231-050, Rio de Janeiro, RJ, Brazil.

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http://dx.doi.org/10.1016/j.compbiolchem.2012.01.002DOI Listing
February 2012

Challenges in the use of NG2 antigen as a marker to predict MLL rearrangements in multi-center studies.

Leuk Res 2011 Aug 27;35(8):1001-7. Epub 2011 Mar 27.

Pediatric Hematology and Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.

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http://linkinghub.elsevier.com/retrieve/pii/S014521261100122
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http://dx.doi.org/10.1016/j.leukres.2011.03.006DOI Listing
August 2011

Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees.

BMC Bioinformatics 2009 Mar 5;10:77. Epub 2009 Mar 5.

Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA.

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http://www.biomedcentral.com/1471-2105/10/77
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http://dx.doi.org/10.1186/1471-2105-10-77DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660304PMC
March 2009

Bioinformatic flowchart and database to investigate the origins and diversity of clan AA peptidases.

Biol Direct 2009 Jan 27;4. Epub 2009 Jan 27.

Institut Cavanilles de Biodiversitat i Biología Evolutiva, Universitat de València, Paterna, Valencia, Spain.

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http://dx.doi.org/10.1186/1745-6150-4-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642776PMC
January 2009

Reduced genotoxicity of avian sarcoma leukosis virus vectors in rhesus long-term repopulating cells compared to standard murine retrovirus vectors.

Mol Ther 2008 Sep 24;16(9):1617-23. Epub 2008 Jun 24.

Molecular Hematopoiesis Section, Hematology Branch, National Heart, Lung, Blood Institute, National Institute of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1038/mt.2008.135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561952PMC
September 2008

Identification of neural crest and glial enhancers at the mouse Sox10 locus through transgenesis in zebrafish.

PLoS Genet 2008 Sep 5;4(9):e1000174. Epub 2008 Sep 5.

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

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https://dx.plos.org/10.1371/journal.pgen.1000174
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http://dx.doi.org/10.1371/journal.pgen.1000174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518861PMC
September 2008

A diversity profile of the human skin microbiota.

Genome Res 2008 Jul 23;18(7):1043-50. Epub 2008 May 23.

Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1101/gr.075549.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493393PMC
July 2008

DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.

Nat Methods 2006 Jul;3(7):503-9

National Human Genome Research Institute, National Institutes of Health, Building 31, Room 4B09, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1038/nmeth888DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2698431PMC
July 2006