Publications by authors named "Guillaume Achaz"

39Publications

ASAP: Assemble Species by Automatic Partitioning.

Mol Ecol Resour 2020 Oct 15. Epub 2020 Oct 15.

Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 26, 75005, Paris, France.

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http://dx.doi.org/10.1111/1755-0998.13281DOI Listing
October 2020

No HIV-1 molecular evolution on long-term antiretroviral therapy initiated during primary HIV-1 infection.

AIDS 2020 Oct;34(12):1745-1753

Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de Virologie.

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http://dx.doi.org/10.1097/QAD.0000000000002629DOI Listing
October 2020

The genomic view of diversification.

J Evol Biol 2020 Jul 11. Epub 2020 Jul 11.

Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.

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http://dx.doi.org/10.1111/jeb.13677DOI Listing
July 2020

Testing for population decline using maximal linkage disequilibrium blocks.

Theor Popul Biol 2020 Aug 9;134:171-181. Epub 2020 Apr 9.

Atelier de Bioinformatique, UMR 7205 ISYEB, Sorbonne Université, CNRS, EPHE, Muséum National d'Histoire Naturelle, Paris, France; SMILE (Stochastic Models for the Inference of Life Evolution), UMR 7241 CIRB, Collège de France, CNRS, INSERM, PSL Research University, Paris, France.

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http://dx.doi.org/10.1016/j.tpb.2020.03.004DOI Listing
August 2020

Correction: The landscape of epilepsy-related GATOR1 variants.

Genet Med 2019 Aug;21(8):1896

Sorbonne Université, UPMC Univ Paris 06, UMR S 1127, F-75013 Paris, France.

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http://dx.doi.org/10.1038/s41436-018-0325-9DOI Listing
August 2019

Correction to: The landscape of epilepsy-related GATOR1 variants.

Genet Med 2019 Jul;21(7):1671

Sorbonne Université, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.

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http://dx.doi.org/10.1038/s41436-018-0284-1DOI Listing
July 2019

The landscape of epilepsy-related GATOR1 variants.

Genet Med 2019 02 10;21(2):398-408. Epub 2018 Aug 10.

Sorbonne Université, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.

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http://www.nature.com/articles/s41436-018-0060-2
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http://dx.doi.org/10.1038/s41436-018-0060-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6292495PMC
February 2019

Evolutionary constraints in fitness landscapes.

Heredity (Edinb) 2018 11 11;121(5):466-481. Epub 2018 Jul 11.

Institut de Systématique Evolution, Biodiversité, ISYEB, UMR 7205 CNRS MNHN UPMC EPHE, Paris, France.

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http://dx.doi.org/10.1038/s41437-018-0110-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180097PMC
November 2018

The neutral frequency spectrum of linked sites.

Theor Popul Biol 2018 09 28;123:70-79. Epub 2018 Jun 28.

Institut de Systématique, Evolution, Biodiversité, UMR 7205, MNHN and Centre Interdisciplinaire de Recherche en Biologie, UMR 7241, Collége de France, Paris, France.

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https://linkinghub.elsevier.com/retrieve/pii/S00405809173013
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http://dx.doi.org/10.1016/j.tpb.2018.06.001DOI Listing
September 2018

Clinical and genetic study of Tunisian families with genetic generalized epilepsy: contribution of CACNA1H and MAST4 genes.

Neurogenetics 2018 08 12;19(3):165-178. Epub 2018 Jun 12.

UPMC Univ Paris 06, Inserm, CNRS, APHP, Institut du Cerveau et la Moelle (ICM), Hôpital Pitié-Salpêtrière, Sorbonne Universités, Paris, France.

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http://dx.doi.org/10.1007/s10048-018-0550-zDOI Listing
August 2018

A Molecular Portrait of De Novo Genes in Yeasts.

Mol Biol Evol 2018 03;35(3):631-645

Atelier de BioInformatique, ISyEB UMR7205 Muséum National d'Histoire Naturelle, Paris, France.

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http://dx.doi.org/10.1093/molbev/msx315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850487PMC
March 2018

Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography.

Genetics 2018 01 10;208(1):323-338. Epub 2017 Nov 10.

School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

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http://dx.doi.org/10.1534/genetics.117.300499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753866PMC
January 2018

Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests.

Genetics 2017 09 5;207(1):229-240. Epub 2017 Jul 5.

Centre for Research in Agricultural Genomics (CRAG), Bellaterra, 08290 Barcelona, Spain.

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http://dx.doi.org/10.1534/genetics.116.188763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5586374PMC
September 2017

Accuracy of Demographic Inferences from the Site Frequency Spectrum: The Case of the Yoruba Population.

Genetics 2017 05 24;206(1):439-449. Epub 2017 Mar 24.

Atelier de Bioinformatique, UMR 7205 ISyEB, MNHN-UPMC-CNRS-EPHE, Muséum National d'Histoire Naturelle, 75005 Paris, France.

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http://dx.doi.org/10.1534/genetics.116.192708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5419487PMC
May 2017

Testing for Independence between Evolutionary Processes.

Syst Biol 2016 Sep 21;65(5):812-23. Epub 2016 May 21.

UMR7138 "Evolution Paris-Seine" UPMC-CNRS Bât A, 4ème étage, porte 414, Case 5 7 quai Saint Bernard, 75252 Paris Cedex 05; Atelier de BioInformatique - MNHN Boite Courier 50 Batiment 139 - RdC 45 rue Buffon, 75005 Paris; Smile "Stochastic Models for the Inference of Life Evolution" Center for Interdisciplinary Research in Biology Collège de France 11, place Marcelin Berthelot 75231 Paris Cedex 05;

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http://dx.doi.org/10.1093/sysbio/syw004DOI Listing
September 2016

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

Mol Biol Evol 2016 07 1;33(7):1711-25. Epub 2016 Mar 1.

Institut Pasteur, Microbial Evolutionary Genomics, Paris, France CNRS, UMR3525, Paris, France

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http://dx.doi.org/10.1093/molbev/msw048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915353PMC
July 2016

Measuring epistasis in fitness landscapes: The correlation of fitness effects of mutations.

J Theor Biol 2016 May 20;396:132-43. Epub 2016 Feb 20.

Evolution Paris-Seine (UMR 7138) and Atelier de Bio-Informatique, UPMC, Paris, France; SMILE, CIRB (UMR 7241), Collège de France, Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2016.01.037DOI Listing
May 2016

Mutational pattern of a sample from a critical branching population.

J Math Biol 2016 09 9;73(3):627-64. Epub 2016 Jan 9.

Laboratoire de Probabilités et Modèles Aléatoires, UMR 7599 CNRS and UPMC Univ Paris 06, Paris, France.

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http://dx.doi.org/10.1007/s00285-015-0964-2DOI Listing
September 2016

MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads.

Mol Ecol Resour 2016 03 14;16(2):524-33. Epub 2015 Oct 14.

UPMC Univ Paris 06, Institut de Biologie Paris-Seine, Evolution Paris-Seine (UMR 7138), Team 'Eucaryotic Genome Evolution' Université Pierre et Marie Curie, Sorbonne Universités, Bat A Et 4 7, quai St Bernard, F-75005, Paris, France.

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http://dx.doi.org/10.1111/1755-0998.12467DOI Listing
March 2016

Mass extinction in poorly known taxa.

Proc Natl Acad Sci U S A 2015 Jun 8;112(25):7761-6. Epub 2015 Jun 8.

UMR 7204, Département Ecologie et Gestion de la Biodiversité, Muséum National d'Histoire Naturelle, 75231 Paris Cedex 05, France.

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http://dx.doi.org/10.1073/pnas.1502350112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4485135PMC
June 2015

Properties of selected mutations and genotypic landscapes under Fisher's geometric model.

Evolution 2014 Dec 17;68(12):3537-54. Epub 2014 Nov 17.

Bioinformatics Research Centre, University of Aarhus, 8000C, Aarhus, Denmark.

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http://dx.doi.org/10.1111/evo.12545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326662PMC
December 2014

The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing.

Adv Exp Med Biol 2014 ;781:211-31

UMR7148 and Atelier de Bioinformatique, UPMC, Paris, France.

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http://dx.doi.org/10.1007/978-94-007-7347-9_11DOI Listing
April 2014

Mutations of DEPDC5 cause autosomal dominant focal epilepsies.

Nat Genet 2013 May 31;45(5):552-5. Epub 2013 Mar 31.

Institut National de la Santé et de la Recherche Médicale (INSERM) U975, Institut du Cerveau et de la Moelle Epinière (ICM), Hôpital Pitié-Salpêtrière, Paris, France.

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http://dx.doi.org/10.1038/ng.2601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010101PMC
May 2013

Evolution of coding microsatellites in primate genomes.

Genome Biol Evol 2013 ;5(2):283-95

UMR 7138, Systématique, Adaptation, Evolution (UPMC, CNRS, MNHN, IRD), Paris, France.

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http://dx.doi.org/10.1093/gbe/evt003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590770PMC
September 2013

Characterization of the meiosis-specific recombinase Dmc1 of pneumocystis.

J Infect Dis 2010 Dec 4;202(12):1920-9. Epub 2010 Nov 4.

Critical Care Medicine Department, National Institutes of Health (NIH) Clinical Center, National Institutes of Allergy and Infectious Diseases, USA.

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http://dx.doi.org/10.1086/657414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058675PMC
December 2010

Frequency spectrum neutrality tests: one for all and all for one.

Authors:
Guillaume Achaz

Genetics 2009 Sep 22;183(1):249-58. Epub 2009 Jun 22.

Systématique, Adaptation et Evolution (UMR 7138) and Atelier de Bioinformatique, Université Pierre et Marie Curie-Paris VI, Centre National de la Recherche Scientifique, Museum National d'Histoire Naturelle, Institut de Recherche pour le Développment, 75005 Paris, France.

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http://dx.doi.org/10.1534/genetics.109.104042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746149PMC
September 2009

A novel heuristic for local multiple alignment of interspersed DNA repeats.

IEEE/ACM Trans Comput Biol Bioinform 2009 Apr-Jun;6(2):180-9

Institut Pasteur, CNRS and UPMC University, Paris, France.

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http://dx.doi.org/10.1109/TCBB.2009.9DOI Listing
August 2009

Hypermutability of genes in Homo sapiens due to the hosting of long mono-SSR.

Mol Biol Evol 2009 Jan 8;26(1):111-21. Epub 2008 Oct 8.

Université Pierre et Marie Curie-Paris 6, Unité Mixte de recherche 7592, Institut Jacques Monod, Paris, France.

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http://dx.doi.org/10.1093/molbev/msn230DOI Listing
January 2009

Variation in the major surface glycoprotein genes in Pneumocystis jirovecii.

J Infect Dis 2008 Sep;198(5):741-9

Critical Care Medicine Department, National Institutes of Health Clinical Center, National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1086/590433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561252PMC
September 2008

Testing for neutrality in samples with sequencing errors.

Authors:
Guillaume Achaz

Genetics 2008 Jul 18;179(3):1409-24. Epub 2008 Jun 18.

Systématique, Adaptation et Evolution (UMR 7138) and Atelier de Bioinformatique, Université Pierre et Marie Curie-Paris VI, 75005 Paris, France.

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http://dx.doi.org/10.1534/genetics.107.082198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475743PMC
July 2008

Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum.

Appl Environ Microbiol 2008 Jun 18;74(12):3702-9. Epub 2008 Apr 18.

INRA, Mathématique Informatique et Génome UR1077, F-78350 Jouy-en-Josas, France.

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http://dx.doi.org/10.1128/AEM.00244-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2446562PMC
June 2008

Novel insights into RNAi off-target effects using C. elegans paralogs.

BMC Genomics 2007 Apr 19;8:106. Epub 2007 Apr 19.

Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-8-106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868761PMC
April 2007

Repseek, a tool to retrieve approximate repeats from large DNA sequences.

Bioinformatics 2007 Jan 11;23(1):119-21. Epub 2006 Oct 11.

Atelier de Bioinformatique, Université Pierre et Marie Curie-Paris 6 12, rue Cuvier, 75005 Paris, France.

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http://dx.doi.org/10.1093/bioinformatics/btl519DOI Listing
January 2007

cis-Regulatory and protein evolution in orthologous and duplicate genes.

Genome Res 2004 Aug 15;14(8):1530-6. Epub 2004 Jul 15.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138 USA.

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http://dx.doi.org/10.1101/gr.2662504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC509261PMC
August 2004

HIV-1 compartmentalization in diverse leukocyte populations during antiretroviral therapy.

J Leukoc Biol 2004 Sep 24;76(3):562-70. Epub 2004 Jun 24.

Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Darcy Road, Westmead, Sydney NSW 2145, Australia.

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http://dx.doi.org/10.1189/jlb.0404234DOI Listing
September 2004

Associations between inverted repeats and the structural evolution of bacterial genomes.

Genetics 2003 Aug;164(4):1279-89

Structure et Dynamique des Génomes, Institut Jacques Monod, 75251 Paris, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462642PMC
August 2003