TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting von Rivas-González, Iker, Schierup, Mikkel H, Wakeley, John, Hobolth, Asger

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RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters von Preker, Pascal, Nielsen, Jesper, Kammler, Susanne, Lykke-Andersen, Søren, Christensen, Marianne S, Mapendano, Christophe K, Schierup, Mikkel H, Jensen, Torben Heick

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Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change von Bergman, Juraj, Pedersen, Rasmus Ø., Lundgren, Erick J., Lemoine, Rhys T., Monsarrat, Sophie, Pearce, Elena A., Schierup, Mikkel H., Svenning, Jens-Christian

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Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence von Dutheil, Julien Y, Munch, Kasper, Nam, Kiwoong, Mailund, Thomas, Schierup, Mikkel H

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Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection von Hobolth, Asger, Dutheil, Julien Y, Hawks, John, Schierup, Mikkel H, Mailund, Thomas

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Repeated adaptive introgression at a gene under multiallelic balancing selection von Castric, Vincent, Bechsgaard, Jesper, Schierup, Mikkel H, Vekemans, Xavier

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Single-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus von Frank, Manuel, Fechete, Lavinia Ioana, Tedeschi, Francesca, Nadzieja, Marcin, Nørgaard, Malita Malou Malekzadeh, Montiel, Jesus, Andersen, Kasper Røjkjær, Schierup, Mikkel H., Reid, Dugald, Andersen, Stig Uggerhøj

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Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model von Hobolth, Asger, Christensen, Ole F, Mailund, Thomas, Schierup, Mikkel H

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SOAPindel: efficient identification of indels from short paired reads von Li, Shengting, Li, Ruiqiang, Li, Heng, Lu, Jianliang, Li, Yingrui, Bolund, Lars, Schierup, Mikkel H, Wang, Jun

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Characterizing the evolution and phenotypic impact of ampliconic Y chromosome regions von Lucotte, Elise A., Guðmundsdóttir, Valdís Björt, Jensen, Jacob M., Skov, Laurits, Macià, Moisès Coll, Almstrup, Kristian, Schierup, Mikkel H., Helgason, Agnar, Stefansson, Kari

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Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck von Guo, Ya-Long, Bechsgaard, Jesper S, Slotte, Tanja, Neuffer, Barbara, Lascoux, Martin, Weigel, Detlef, Schierup, Mikkel H

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Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola von Stukenbrock, Eva H, Jørgensen, Frank G, Zala, Marcello, Hansen, Troels T, McDonald, Bruce A, Schierup, Mikkel H

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A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species von Mailund, Thomas, Halager, Anders E, Westergaard, Michael, Dutheil, Julien Y, Munch, Kasper, Andersen, Lars N, Lunter, Gerton, Prüfer, Kay, Scally, Aylwyn, Hobolth, Asger, Schierup, Mikkel H

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Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity von Athanasiadis, Georgios, Cheng, Jade Y, Vilhjálmsson, Bjarni J, Jørgensen, Frank G, Als, Thomas D, Le Hellard, Stephanie, Espeseth, Thomas, Sullivan, Patrick F, Hultman, Christina M, Kjærgaard, Peter C, Schierup, Mikkel H, Mailund, Thomas

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Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model von Mailund, Thomas, Dutheil, Julien Y, Hobolth, Asger, Lunter, Gerton, Schierup, Mikkel H

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The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates von Bergeron, Lucie A, Besenbacher, Søren, Turner, Tychele, Versoza, Cyril J, Wang, Richard J, Price, Alivia Lee, Armstrong, Ellie, Riera, Meritxell, Carlson, Jedidiah, Chen, Hwei-Yen, Hahn, Matthew W, Harris, Kelley, Kleppe, April Snøfrid, López-Nandam, Elora H, Moorjani, Priya, Pfeifer, Susanne P, Tiley, George P, Yoder, Anne D, Zhang, Guojie, Schierup, Mikkel H

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Consequences of Recombination on Traditional Phylogenetic Analysis von Schierup, Mikkel H, Hein, Jotun

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Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach von Dutheil, Julien Y, Ganapathy, Ganesh, Hobolth, Asger, Mailund, Thomas, Uyenoyama, Marcy K, Schierup, Mikkel H

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Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing von Wernersson, Rasmus, Schierup, Mikkel H, Jørgensen, Frank G, Gorodkin, Jan, Panitz, Frank, Staerfeldt, Hans-Henrik, Christensen, Ole F, Mailund, Thomas, Hornshøj, Henrik, Klein, Ami, Wang, Jun, Liu, Bin, Hu, Songnian, Dong, Wei, Li, Wei, Wong, Gane K S, Yu, Jun, Wang, Jian, Bendixen, Christian, Fredholm, Merete, Brunak, Søren, Yang, Huanming, Bolund, Lars

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Assembly and analysis of 100 full MHC haplotypes from the Danish population von Jensen, Jacob M, Villesen, Palle, Friborg, Rune M, Mailund, Thomas, Besenbacher, Søren, Schierup, Mikkel H

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