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Items: 13

1.

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

Renaud G, Hanghøj K, Korneliussen TS, Willerslev E, Orlando L.

Genetics. 2019 Jul;212(3):587-614. doi: 10.1534/genetics.119.302057. Epub 2019 May 14.

2.

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.

Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, Bayarsaikhan J, Benecke N, Bernáldez-Sánchez E, Berrocal-Rangel L, Biglari F, Boessenkool S, Boldgiv B, Brem G, Brown D, Burger J, Crubézy E, Daugnora L, Davoudi H, de Barros Damgaard P, de Los Ángeles de Chorro Y de Villa-Ceballos M, Deschler-Erb S, Detry C, Dill N, do Mar Oom M, Dohr A, Ellingvåg S, Erdenebaatar D, Fathi H, Felkel S, Fernández-Rodríguez C, García-Viñas E, Germonpré M, Granado JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM, Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Monchalov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, Pitulko V, Pitskhelauri K, Pruvost M, Rajic Sikanjic P, Rapan Papeša A, Roslyakova N, Sardari A, Sauer E, Schafberg R, Scheu A, Schibler J, Schlumbaum A, Serrand N, Serres-Armero A, Shapiro B, Sheikhi Seno S, Shevnina I, Shidrang S, Southon J, Star B, Sykes N, Taheri K, Taylor W, Teegen WR, Trbojević Vukičević T, Trixl S, Tumen D, Undrakhbold S, Usmanova E, Vahdati A, Valenzuela-Lamas S, Viegas C, Wallner B, Weinstock J, Zaibert V, Clavel B, Lepetz S, Mashkour M, Helgason A, Stefánsson K, Barrey E, Willerslev E, Outram AK, Librado P, Orlando L.

Cell. 2019 May 30;177(6):1419-1435.e31. doi: 10.1016/j.cell.2019.03.049. Epub 2019 May 2.

3.

Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding.

Hanghøj K, Moltke I, Andersen PA, Manica A, Korneliussen TS.

Gigascience. 2019 May 1;8(5). pii: giz034. doi: 10.1093/gigascience/giz034.

4.

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

Hanghøj K, Renaud G, Albrechtsen A, Orlando L.

Gigascience. 2019 Apr 1;8(4). pii: giz025. doi: 10.1093/gigascience/giz025.

5.

Ancient genomes revisit the ancestry of domestic and Przewalski's horses.

Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P, Mittnik A, Mohaseb AF, Davoudi H, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Crubézy E, Benecke N, Olsen S, Brown D, Anthony D, Massy K, Pitulko V, Kasparov A, Brem G, Hofreiter M, Mukhtarova G, Baimukhanov N, Lõugas L, Onar V, Stockhammer PW, Krause J, Boldgiv B, Undrakhbold S, Erdenebaatar D, Lepetz S, Mashkour M, Ludwig A, Wallner B, Merz V, Merz I, Zaibert V, Willerslev E, Librado P, Outram AK, Orlando L.

Science. 2018 Apr 6;360(6384):111-114. doi: 10.1126/science.aao3297. Epub 2018 Feb 22.

PMID:
29472442
6.

fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample.

Jørsboe E, Hanghøj K, Albrechtsen A.

Bioinformatics. 2017 Oct 1;33(19):3148-3150. doi: 10.1093/bioinformatics/btx474.

PMID:
28957500
7.

Clonal yeast biofilms can reap competitive advantages through cell differentiation without being obligatorily multicellular.

Regenberg B, Hanghøj KE, Andersen KS, Boomsma JJ.

Proc Biol Sci. 2016 Nov 16;283(1842). pii: 20161303.

8.

gargammel: a sequence simulator for ancient DNA.

Renaud G, Hanghøj K, Willerslev E, Orlando L.

Bioinformatics. 2017 Feb 15;33(4):577-579. doi: 10.1093/bioinformatics/btw670.

9.

Combining bleach and mild predigestion improves ancient DNA recovery from bones.

Boessenkool S, Hanghøj K, Nistelberger HM, Der Sarkissian C, Gondek AT, Orlando L, Barrett JH, Star B.

Mol Ecol Resour. 2017 Jul;17(4):742-751. doi: 10.1111/1755-0998.12623. Epub 2016 Dec 15.

PMID:
27790833
10.

The Evolutionary Origin and Genetic Makeup of Domestic Horses.

Librado P, Fages A, Gaunitz C, Leonardi M, Wagner S, Khan N, Hanghøj K, Alquraishi SA, Alfarhan AH, Al-Rasheid KA, Der Sarkissian C, Schubert M, Orlando L.

Genetics. 2016 Oct;204(2):423-434. Review.

11.

Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.

Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L.

Mol Biol Evol. 2016 Dec;33(12):3284-3298. Epub 2016 Sep 13.

12.

metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data.

Louvel G, Der Sarkissian C, Hanghøj K, Orlando L.

Mol Ecol Resour. 2016 Nov;16(6):1415-1427. doi: 10.1111/1755-0998.12546. Epub 2016 Jun 22.

PMID:
27238636
13.

Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing.

Gamba C, Hanghøj K, Gaunitz C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Bradley DG, Orlando L.

Mol Ecol Resour. 2016 Mar;16(2):459-69. doi: 10.1111/1755-0998.12470. Epub 2015 Oct 15.

PMID:
26401836

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