Anna Sapfo Malaspinas

Publications | Mémoires et thèses

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47 publications

En préparation
 
Indigenous peoples in eastern Brazil: insights from 19<sup>th</sup> century genomes and metagenomes
Cruz Dávalos Diana Ivette, Arizmendi Cárdenas Yami Ommar, Bravo-Lopez Miriam Jetzabel, Neuenschwander Samuel, Reis Silvia, Bastos Murilo Q. R., Stenderup Jesper, Yediay Fulya Eylem, Villa-Islas Viridiana, Reyna-Blanco Carlos S. et al..
[DOI][serval:BIB_47F5B2CAEC7C]
 
Imputation of ancient genomes
Sousa da Mota Bárbara, Rubinacci Simone, Cruz Dávalos Diana Ivette, Amorim Carlos Eduardo G., Sikora Martin, Johannsen Niels N., Szmyt Marzena, Włodarczak Piotr, Szczepanek Anita, Przybyła Marcin M. et al..
[DOI][serval:BIB_AC8F25835B20]
2024
 
Towards predicting the geographical origin of ancient samples with metagenomic data.
Bozzi D., Neuenschwander S., Cruz Dávalos D.I., Sousa da Mota B., Schroeder H., Moreno-Mayar J.V., Allentoft M.E., Malaspinas A.S., 2024/09/18. Scientific reports, 14 (1) p. 21794. Peer-reviewed.
[DOI][Pmid][serval:BIB_4C67F4828BA4]
 
Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas.
Moreno-Mayar J.V., Sousa da Mota B., Higham T., Klemm S., Gorman Edmunds M., Stenderup J., Iraeta-Orbegozo M., Laborde V., Heyer E., Torres Hochstetter F. et al., 2024/09. Nature, 633 (8029) pp. 389-397. Peer-reviewed.
[DOI][Pmid][serval:BIB_AF80626A7AB8]
A resampling-based approach to share reference panels.
Cavinato T., Rubinacci S., Malaspinas A.S., Delaneau O., 2024/05. Nature computational science, 4 (5) pp. 360-366. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_981E899095A4]
Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA.
Garrido Marques A., Rubinacci S., Malaspinas A.S., Delaneau O., Sousa da Mota B., 2024/03/14. Scientific reports, 14 (1) p. 6227. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_6950F9B87B01]
2023
Imputation of ancient human genomes.
Sousa da Mota B., Rubinacci S., Cruz Dávalos D.I., G Amorim C.E., Sikora M., Johannsen N.N., Szmyt M.H., Włodarczak P., Szczepanek A., Przybyła M.M. et al., 2023/06/20. Nature communications, 14 (1) p. 3660. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6B67ECE9FE90]
 
Mapache: a flexible pipeline to map ancient DNA.
Neuenschwander S., Cruz Dávalos D.I., Anchieri L., Sousa da Mota B., Bozzi D., Rubinacci S., Delaneau O., Rasmussen S., Malaspinas A.S., 2023/02/03. Bioinformatics, 39 (2) pp. btad028. Peer-reviewed.
[DOI][Pmid][serval:BIB_B6D821D0E6BE]
2022
Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study.
Arizmendi Cárdenas Y.O., Neuenschwander S., Malaspinas A.S., 2022. PeerJ, 10 pp. e12784. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_F63ADE26A585]
2021
The genomic history of the Aegean palatial civilizations.
Clemente F., Unterländer M., Dolgova O., Amorim CEG, Coroado-Santos F., Neuenschwander S., Ganiatsou E., Cruz Dávalos D.I., Anchieri L., Michaud F. et al., 2021/05/13. Cell, 184 (10) pp. 2565-2586.e21. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_114B1DCAE1B5]
2020
Inference of natural selection from ancient DNA.
Dehasque M., Ávila-Arcos M.C., Díez-Del-Molino D., Fumagalli M., Guschanski K., Lorenzen E.D., Malaspinas A.S., Marques-Bonet T., Martin M.D., Murray GGR et al., 2020/04. Evolution letters, 4 (2) pp. 94-108. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D2F70344208C]
 
A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data.
Moreno-Mayar J.V., Korneliussen T.S., Dalal J., Renaud G., Albrechtsen A., Nielsen R., Malaspinas A.S., 2020/02/01. Bioinformatics, 36 (3) pp. 828-841. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1A2FB983348E]
2019
 
An Ancient Genome from the Indus Valley Civilization.
Raghavan M., Schroeder H., Malaspinas A.S., 2019/10/17. Cell, 179 (3) pp. 586-588. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B12841BECB56]
A likelihood method for estimating present-day human contamination in ancient DNA samples using low-depth haploid chromosome data
Moreno-Mayar J. Víctor, Korneliussen Thorfinn Sand, Albrechtsen Anders, Dalal Jyoti, Renaud Gabriel, Nielsen Rasmus, Malaspinas Anna-Sapfo, 2019/05..
[URN][DOI][serval:BIB_84C6FA3621CE]
2018
 
Early human dispersals within the Americas.
Moreno-Mayar J.V., Vinner L., de Barros Damgaard P., de la Fuente C., Chan J., Spence J.P., Allentoft M.E., Vimala T., Racimo F., Pinotti T. et al., 2018/12/07. Science, 362 (6419) pp. eaav2621. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_62FDEB830CCD]
In-solution Y-chromosome capture-enrichment on ancient DNA libraries.
Cruz-Dávalos D.I., Nieves-Colón M.A., Sockell A., Poznik G.D., Schroeder H., Stone A.C., Bustamante C.D., Malaspinas A.S., Ávila-Arcos M.C., 2018/08/14. BMC genomics, 19 (1) p. 608. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2A08928BDEB8]
 
Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans.
Moreno-Mayar J.V., Potter B.A., Vinner L., Steinrücken M., Rasmussen S., Terhorst J., Kamm J.A., Albrechtsen A., Malaspinas A.S., Sikora M. et al., 2018/01/11. Nature, 553 (7687) pp. 203-207. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A71C9F6D2CEC]
Ancient nuclear genomes enable repatriation of Indigenous human remains.
Wright J.L., Wasef S., Heupink T.H., Westaway M.C., Rasmussen S., Pardoe C., Fourmile G.G., Young M., Johnson T., Slade J. et al., 2018. Science Advances, 4 (12) pp. eaau5064. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_30B5C29E67D9]
Decline of genetic diversity in ancient domestic stallions in Europe.
Wutke S., Sandoval-Castellanos E., Benecke N., Döhle H.J., Friederich S., Gonzalez J., Hofreiter M., Lõugas L., Magnell O., Malaspinas A.S. et al., 2018. Science Advances, 4 (4) pp. eaap9691. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BD64E7EF0115]
Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia.
de la Fuente C., Ávila-Arcos M.C., Galimany J., Carpenter M.L., Homburger J.R., Blanco A., Contreras P., Cruz Dávalos D., Reyes O., San Roman M. et al., 2018. Proceedings of the National Academy of Sciences of the United States of America, 115 (17) pp. E4006-E4012. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_603BEE9432CE]
Human bony labyrinth is an indicator of population history and dispersal from Africa.
Ponce de León M.S., Koesbardiati T., Weissmann J.D., Milella M., Reyna-Blanco C.S., Suwa G., Kondo O., Malaspinas A.S., White T.D., Zollikofer CPE, 2018. Proceedings of the National Academy of Sciences of the United States of America, 115 (16) pp. 4128-4133. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_00B4361FE936]
 
The prehistoric peopling of Southeast Asia.
McColl H., Racimo F., Vinner L., Demeter F., Gakuhari T., Moreno-Mayar J.V., van Driem G., Gram Wilken U., Seguin-Orlando A., de la Fuente Castro C. et al., 2018. Science, 361 (6397) pp. 88-92. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_69332F683F70]
2017
 
Madjedbebe and genomic histories of Aboriginal Australia
Dortch J., Malaspinas A.S., 2017. Australian Archaeology, 83 (3) pp. 174-177. Peer-reviewed.
[DOI][WoS][serval:BIB_2065B92AC73D]
2016
 
Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective
Malaspinas Anna-Sapfo, 2016/01. Mol Ecol, 25 (1) pp. 24-41.
[DOI][serval:BIB_28CB9756DB87]
2015
 
Genomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan Maanasa, Steinrücken Matthias, Harris Kelley, Schiffels Stephan, Rasmussen Simon, DeGiorgio Michael, Albrechtsen Anders, Valdiosera Cristina, Ávila-Arcos María C., Malaspinas Anna-Sapfo et al., 2015/08. Science, 349 (6250) pp. aab3884.
[DOI][Pmid][serval:BIB_18D191F10C63]
 
Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries
Ávila-Arcos María C., Sandoval-Velasco Marcela, Schroeder Hannes, Carpenter Meredith L., Malaspinas Anna-Sapfo, Wales Nathan, Peñaloza Fernando, Bustamante Carlos D., Gilbert M. Thomas P., 2015/06. Methods in Ecology and Evolution, 6 (6) pp. 725-734.
[DOI][serval:BIB_A6BC97E41AC6]
 
Population genomics of Bronze Age Eurasia
Allentoft Morten E., Sikora Martin, Sjögren Karl-Göran, Rasmussen Simon, Rasmussen Morten, Stenderup Jesper, Damgaard Peter B., Schroeder Hannes, Ahlström Torbjörn, Vinner Lasse et al., 2015/06. Nature, 522 (7555) pp. 167-172.
[DOI][serval:BIB_A38C679AC39B]
 
Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean.
Schroeder H., Ávila-Arcos M.C., Malaspinas A.S., Poznik G.D., Sandoval-Velasco M., Carpenter M.L., Moreno-Mayar J.V., Sikora M., Johnson P.L., Allentoft M.E. et al., 2015/03/24. Proceedings of the National Academy of Sciences of the United States of America, 112 (12) pp. 3669-3673. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_41B4BBA8A768]
2014
 
Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years.
Seguin-Orlando A., Korneliussen T.S., Sikora M., Malaspinas A.S., Manica A., Moltke I., Albrechtsen A., Ko A., Margaryan A., Moiseyev V. et al., 2014/11/28. Science, 346 (6213) pp. 1113-1118. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AE125FE0BDAC]
 
Genome-wide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans.
Moreno-Mayar J.V., Rasmussen S., Seguin-Orlando A., Rasmussen M., Liang M., Flåm S.T., Lie B.A., Gilfillan G.D., Nielsen R., Thorsby E. et al., 2014/11/03. Current biology, 24 (21) pp. 2518-2525. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_736E7E1162C7]
 
Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil.
Malaspinas A.S., Lao O., Schroeder H., Rasmussen M., Raghavan M., Moltke I., Campos P.F., Sagredo F.S., Rasmussen S., Gonçalves V.F. et al., 2014/11/03. Current biology, 24 (21) pp. R1035-7. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A15E08285B66]
 
bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).
Malaspinas A.S., Tange O., Moreno-Mayar J.V., Rasmussen M., DeGiorgio M., Wang Y., Valdiosera C.E., Politis G., Willerslev E., Nielsen R., 2014/10/15. Bioinformatics, 30 (20) pp. 2962-2964. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_699EFB431D16]
 
The genetic prehistory of the New World Arctic.
Raghavan M., DeGiorgio M., Albrechtsen A., Moltke I., Skoglund P., Korneliussen T.S., Grønnow B., Appelt M., Gulløv H.C., Friesen T.M. et al., 2014/08/29. Science, 345 (6200) p. 1255832. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F3774809A509]
 
The genome of a Late Pleistocene human from a Clovis burial site in western Montana.
Rasmussen M., Anzick S.L., Waters M.R., Skoglund P., DeGiorgio M., Stafford T.W., Rasmussen S., Moltke I., Albrechtsen A., Doyle S.M. et al., 2014/02/13. Nature, 506 (7487) pp. 225-229. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_17FF5CAC485C]
Influenza virus drug resistance: a time-sampled population genetics perspective.
Foll M., Poh Y.P., Renzette N., Ferrer-Admetlla A., Bank C., Shim H., Malaspinas A.S., Ewing G., Liu P., Wegmann D. et al., 2014/02. PLoS genetics, 10 (2) pp. e1004185. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0719718A8EE7]
2013
 
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
Orlando L., Ginolhac A., Zhang G., Froese D., Albrechtsen A., Stiller M., Schubert M., Cappellini E., Petersen B., Moltke I. et al., 2013/07/04. Nature, 499 (7456) pp. 74-78. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_08402CD29297]
 
Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil.
Gonçalves V.F., Stenderup J., Rodrigues-Carvalho C., Silva H.P., Gonçalves-Dornelas H., Líryo A., Kivisild T., Malaspinas A.S., Campos P.F., Rasmussen M. et al., 2013/04/16. Proceedings of the National Academy of Sciences of the United States of America, 110 (16) pp. 6465-6469. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_2203A17F2571]
2012
 
Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity.
Yang M.A., Malaspinas A.S., Durand E.Y., Slatkin M., 2012/10. Molecular biology and evolution, 29 (10) pp. 2987-2995. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6371D82CEC00]
 
Estimating allele age and selection coefficient from time-serial data.
Malaspinas A.S., Malaspinas O., Evans S.N., Slatkin M., 2012/10. Genetics, 192 (2) pp. 599-607. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A517FCA505D9]
2011
 
Match probabilities in a finite, subdivided population.
Malaspinas A.S., Slatkin M., Song Y.S., 2011/05. Theoretical population biology, 79 (3) pp. 55-63. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A616746D45F9]
 
Detecting epistasis via Markov bases
Malaspinas Anna-Sapfo, Uhler Caroline, 2011/04/30. Journal of Algebraic Statistics, 2 (1).
[DOI][serval:BIB_01518DC3CB93]
 
Parametric analysis of alignment and phylogenetic uncertainty.
Malaspinas A.S., Eriksson N., Huggins P., 2011/04. Bulletin of mathematical biology, 73 (4) pp. 795-810. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_19338F8E10EF]
2010
 
A draft sequence of the Neandertal genome.
Green R.E., Krause J., Briggs A.W., Maricic T., Stenzel U., Kircher M., Patterson N., Li H., Zhai W., Fritz M.H. et al., 2010/05/07. Science, 328 (5979) pp. 710-722. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_119A573C3F63]
2009
 
Coat color variation at the beginning of horse domestication.
Ludwig A., Pruvost M., Reissmann M., Benecke N., Brockmann G.A., Castaños P., Cieslak M., Lippold S., Llorente L., Malaspinas A.S. et al., 2009/04/24. Science, 324 (5926) p. 485. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_92304A60CB7B]
2008
 
A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing.
Green R.E., Malaspinas A.S., Krause J., Briggs A.W., Johnson P.L., Uhler C., Meyer M., Good J.M., Maricic T., Stenzel U. et al., 2008/08/08. Cell, 134 (3) pp. 416-426. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0FA7872A1B4E]
 
Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary.
Krause J., Unger T., Noçon A., Malaspinas A.S., Kolokotronis S.O., Stiller M., Soibelzon L., Spriggs H., Dear P.H., Briggs A.W. et al., 2008/07/28. BMC evolutionary biology, 8 p. 220. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_04BDC6EBD06E]
2007
 
Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as Outgroup
Rohland Nadin, Malaspinas Anna-Sapfo, Pollack Joshua L, Slatkin Montgomery, Matheus Paul, Hofreiter Michael, 2007/07. PLoS Biology, 5 (8) pp. e207.
[DOI][serval:BIB_C68A41AC66EC]
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