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Detecting epistasis via Markov bases.
Published in:
Journal of Algebraic Statistics, 2011, v. 2, n. 1, p. 36, doi. 10.18409/jas.v2i1.27
By:
- Malaspinas, Anna-Sapfo;
- Uhler, Caroline
Publication type:
Article
Estimating Allele Age and Selection Coefficient from Time-Serial Data.
Published in:
Genetics, 2012, v. 192, n. 2, p. 599, doi. 10.1534/genetics.112.140939
By:
- Malaspinas, Anna-Sapfo;
- Malaspinas, Orestis;
- Evans, Steven N.;
- Slatkin, Montgomery
Publication type:
Article
Mapache: a flexible pipeline to map ancient DNA.
Published in:
Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad028
By:
- Neuenschwander, Samuel;
- Dávalos, Diana I Cruz;
- Anchieri, Lucas;
- Mota, Bárbara Sousa da;
- Bozzi, Davide;
- Rubinacci, Simone;
- Delaneau, Olivier;
- Rasmussen, Simon;
- Malaspinas, Anna-Sapfo
Publication type:
Article
Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective.
Published in:
Molecular Ecology, 2016, v. 25, n. 1, p. 24, doi. 10.1111/mec.13492
By:
- Malaspinas, Anna‐Sapfo
Publication type:
Article
Imputation of ancient human genomes.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-39202-0
By:
- Sousa da Mota, Bárbara;
- Rubinacci, Simone;
- Cruz Dávalos, Diana Ivette;
- G. Amorim, Carlos Eduardo;
- Sikora, Martin;
- Johannsen, Niels N.;
- Szmyt, Marzena H.;
- Włodarczak, Piotr;
- Szczepanek, Anita;
- Przybyła, Marcin M.;
- Schroeder, Hannes;
- Allentoft, Morten E.;
- Willerslev, Eske;
- Malaspinas, Anna-Sapfo;
- Delaneau, Olivier
Publication type:
Article
Parametric Analysis of Alignment and Phylogenetic Uncertainty.
Published in:
Bulletin of Mathematical Biology, 2011, v. 73, n. 4, p. 795, doi. 10.1007/s11538-010-9610-8
By:
- Malaspinas, Anna-Sapfo;
- Eriksson, Nicholas;
- Huggins, Peter
Publication type:
Article
Towards predicting the geographical origin of ancient samples with metagenomic data.
Published in:
Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-023-40246-x
By:
- Bozzi, Davide;
- Neuenschwander, Samuel;
- Cruz Dávalos, Diana Ivette;
- Sousa da Mota, Bárbara;
- Schroeder, Hannes;
- Moreno-Mayar, J. Víctor;
- Allentoft, Morten E.;
- Malaspinas, Anna-Sapfo
Publication type:
Article
Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity.
Published in:
Molecular Biology & Evolution, 2012, v. 29, n. 10, p. 2987, doi. 10.1093/molbev/mss117
By:
- Yang, Melinda A.;
- Malaspinas, Anna-Sapfo;
- Durand, Eric Y.;
- Slatkin, Montgomery
Publication type:
Article
Inference of natural selection from ancient DNA.
Published in:
Evolution Letters, 2020, v. 4, n. 2, p. 94, doi. 10.1002/evl3.165
By:
- Dehasque, Marianne;
- Ávila‐Arcos, María C.;
- Díez‐del‐Molino, David;
- Fumagalli, Matteo;
- Guschanski, Katerina;
- Lorenzen, Eline D.;
- Malaspinas, Anna‐Sapfo;
- Marques‐Bonet, Tomas;
- Martin, Michael D.;
- Murray, Gemma G. R.;
- Papadopulos, Alexander S. T.;
- Therkildsen, Nina Overgaard;
- Wegmann, Daniel;
- Dalén, Love;
- Foote, Andrew D.
Publication type:
Article
Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as Outgroup.
Published in:
PLoS Biology, 2007, v. 5, n. 8, p. 1663, doi. 10.1371/journal.pbio.0050207
By:
- Rohland, Nadin;
- Malaspinas, Anna-Sapfo;
- Pollack, Joshua L.;
- Slatkin, Montgomery;
- Matheus, Paul;
- Hofreiter, Michael
Publication type:
Article
Population genomics of Bronze Age Eurasia.
Published in:
Nature, 2015, v. 522, n. 7555, p. 167, doi. 10.1038/nature14507
By:
- Allentoft, Morten E.;
- Sikora, Martin;
- Sjögren, Karl-Göran;
- Rasmussen, Simon;
- Rasmussen, Morten;
- Stenderup, Jesper;
- Damgaard, Peter B.;
- Schroeder, Hannes;
- Ahlström, Torbjörn;
- Vinner, Lasse;
- Malaspinas, Anna-Sapfo;
- Margaryan, Ashot;
- Higham, Tom;
- Chivall, David;
- Lynnerup, Niels;
- Harvig, Lise;
- Baron, Justyna;
- Casa, Philippe Della;
- Dąbrowski, Paweł;
- Duffy, Paul R.
Publication type:
Article
The genome of a Late Pleistocene human from a Clovis burial site in western Montana.
Published in:
Nature, 2014, v. 506, n. 7487, p. 225, doi. 10.1038/nature13025
By:
- Rasmussen, Morten;
- Anzick, Sarah L.;
- Waters, Michael R.;
- Skoglund, Pontus;
- DeGiorgio, Michael;
- Stafford, Thomas W.;
- Rasmussen, Simon;
- Moltke, Ida;
- Albrechtsen, Anders;
- Doyle, Shane M.;
- Poznik, G. David;
- Gudmundsdottir, Valborg;
- Yadav, Rachita;
- Malaspinas, Anna-Sapfo;
- V, Samuel Stockton White;
- Allentoft, Morten E.;
- Cornejo, Omar E.;
- Tambets, Kristiina;
- Eriksson, Anders;
- Heintzman, Peter D.
Publication type:
Article
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
Published in:
Nature, 2013, v. 499, n. 7456, p. 74, doi. 10.1038/nature12323
By:
- Orlando, Ludovic;
- Ginolhac, Aurélien;
- Zhang, Guojie;
- Froese, Duane;
- Albrechtsen, Anders;
- Stiller, Mathias;
- Schubert, Mikkel;
- Cappellini, Enrico;
- Petersen, Bent;
- Moltke, Ida;
- Johnson, Philip L. F.;
- Fumagalli, Matteo;
- Vilstrup, Julia T.;
- Raghavan, Maanasa;
- Korneliussen, Thorfinn;
- Malaspinas, Anna-Sapfo;
- Vogt, Josef;
- Szklarczyk, Damian;
- Kelstrup, Christian D.;
- Vinther, Jakob
Publication type:
Article
Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study.
Published in:
PeerJ, 2022, p. 1, doi. 10.7717/peerj.12784
By:
- Cárdenas, Yami Ommar Arizmendi;
- Neuenschwander, Samuel;
- Malaspinas, Anna-Sapfo
Publication type:
Article
In-solution Y-chromosome capture-enrichment on ancient DNA libraries.
Published in:
BMC Genomics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12864-018-4945-x
By:
- Cruz-Dávalos, Diana I.;
- Nieves-Colón, María A.;
- Sockell, Alexandra;
- Poznik, G. David;
- Schroeder, Hannes;
- Stone, Anne C.;
- Bustamante, Carlos D.;
- Malaspinas, Anna-Sapfo;
- Ávila-Arcos, María C.
Publication type:
Article
Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective.
Published in:
PLoS Genetics, 2014, v. 10, n. 2, p. 1, doi. 10.1371/journal.pgen.1004185
By:
- Foll, Matthieu;
- Poh, Yu-Ping;
- Renzette, Nicholas;
- Ferrer-Admetlla, Anna;
- Bank, Claudia;
- Shim, Hyunjin;
- Malaspinas, Anna-Sapfo;
- Ewing, Gregory;
- Liu, Ping;
- Wegmann, Daniel;
- Caffrey, Daniel R.;
- Zeldovich, Konstantin B.;
- Bolon, Daniel N.;
- Wang, Jennifer P.;
- Kowalik, Timothy F.;
- Schiffer, Celia A.;
- Finberg, Robert W.;
- Jensen, Jeffrey D.
Publication type:
Article
Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary.
Published in:
BMC Evolutionary Biology, 2008, v. 8, p. 1, doi. 10.1186/1471-2148-8-220
By:
- Krause, Johannes;
- Unger, Tina;
- Noçon, Aline;
- Malaspinas, Anna-Sapfo;
- Kolokotronis, Sergios-Orestis;
- Stiller, Mathias;
- Soibelzon, Leopoldo;
- Spriggs, Helen;
- Dear, Paul H.;
- Briggs, Adrian W.;
- Bray, Sarah C. E.;
- O'Brien, Stephen J.;
- Rabeder, Gernot;
- Matheus, Paul;
- Cooper, Alan;
- Slatkin, Montgomery;
- Pääbo, Svante;
- Hofreiter, Michael
Publication type:
Article
A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data.
Published in:
Bioinformatics, 2020, v. 36, n. 3, p. 828, doi. 10.1093/bioinformatics/btz660
By:
- Moreno-Mayar, J Víctor;
- Korneliussen, Thorfinn Sand;
- Dalal, Jyoti;
- Renaud, Gabriel;
- Albrechtsen, Anders;
- Nielsen, Rasmus;
- Malaspinas, Anna-Sapfo
Publication type:
Article
bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).
Published in:
Bioinformatics, 2014, v. 30, n. 20, p. 2962, doi. 10.1093/bioinformatics/btu410
By:
- Malaspinas, Anna-Sapfo;
- Tange, Ole;
- Moreno-Mayar, José Víctor;
- Rasmussen, Morten;
- DeGiorgio, Michael;
- Wang, Yong;
- Valdiosera, Cristina E.;
- Politis, Gustavo;
- Willerslev, Eske;
- Nielsen, Rasmus
Publication type:
Article
Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA.
Published in:
Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-56584-3
By:
- Garrido Marques, Antonio;
- Rubinacci, Simone;
- Malaspinas, Anna-Sapfo;
- Delaneau, Olivier;
- Sousa da Mota, Bárbara
Publication type:
Article
Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries.
Published in:
Methods in Ecology & Evolution, 2015, v. 6, n. 6, p. 725, doi. 10.1111/2041-210X.12353
By:
- 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.;
- Bunce, Michael
Publication type:
Article

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