Aarhus University Seal / Aarhus Universitets segl

Jade Yu Cheng

  1. 2020
  2. Published

    Ancestral population genomics with Jocx, a coalescent hidden markov model. / Cheng, Jade Yu; Mailund, Thomas.

    Statistical population genomics. ed. / Julien Y. Dutheil. New York : Humana Press, 2020. p. 167-189 (Methods in Molecular Biology, Vol. 2090).

    Research output: Contribution to book/anthology/report/proceedingBook chapterResearchpeer-review

  3. 2019
  4. Published

    Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry. / Walker, Jerilyn A.; Jordan, Vallmer E.; Storer, Jessica M.; Steely, Cody J.; Gonzalez-Quiroga, Paulina; Beckstrom, Thomas O.; Rewerts, Lydia C.; St. Romain, Corey P.; Rockwell, Catherine E.; Rogers, Jeffrey; Jolly, Clifford J.; Konkel, Miriam K.; The Baboon Genome Analysis Consortium; Batzer, Mark A.

    In: Mobile DNA, Vol. 10, No. 1, 46, 26.11.2019.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  5. Published

    The comparative genomics and complex population history of Papio baboons. / Rogers, Jeffrey; Raveendran, Muthuswamy; Alan Harris, R.; Mailund, Thomas; Leppälä, Kalle; Athanasiadis, Georgios; Schierup, Mikkel Heide; Cheng, Jade; Munch, Kasper; Walker, Jerilyn A.; Konkel, Miriam K.; Jordan, Vallmer; Steely, Cody J.; Beckstrom, Thomas O.; Bergey, Christina; Burrell, Andrew; Schrempf, Dominik; Noll, Angela; Kothe, Maximillian; Kopp, Gisela H.; Liu, Yue; Murali, Shwetha; Billis, Konstantinos; Martin, Fergal J.; Muffato, Matthieu; Cox, Laura; Else, James; Disotell, Todd; Muzny, Donna M.; Phillips-Conroy, Jane; Aken, Bronwen; Eichler, Evan E.; Marques-Bonet, Tomas; Kosiol, Carolin; Batzer, Mark A.; Hahn, Matthew W.; Tung, Jenny; Zinner, Dietmar; Roos, Christian; Jolly, Clifford J.; Gibbs, Richard A.; Worley, Kim C.; Baboon Genome Analysis Consortium.

    In: Science Advances, Vol. 5, No. 1, 6947, 30.01.2019.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  6. 2018
  7. Published

    A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms. / Jordan, Vallmer E.; Walker, Jerilyn A.; Beckstrom, Thomas O.; Steely, Cody J.; McDaniel, Cullen L.; St Romain, Corey P.; The Baboon Genome Analysis Consortium; Worley, Kim C.; Phillips-Conroy, Jane; Jolly, Clifford J.; Rogers, Jeffrey; Konkel, Miriam K.; Batzer, Mark A.

    In: Mobile DNA, Vol. 9, No. 1, 13, 05.04.2018.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  8. Published

    Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis. / The Baboon Genome Analysis Consortium.

    In: Mobile DNA, Vol. 9, No. 1, 10, 19.03.2018.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  9. 2017
  10. Published

    Alu insertion polymorphisms as evidence for population structure in baboons. / The Baboon Genome Analysis Consortium.

    In: Genome Biology and Evolution, Vol. 9, No. 9, 01.09.2017, p. 2418-2427.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  11. Published

    Fast admixture analysis and population tree estimation for SNP and NGS data. / Cheng, Jade Yu; Mailund, Thomas; Nielsen, Rasmus.

    In: Bioinformatics (Online), Vol. 33, No. 14, 15.07.2017, p. 2148–2155.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  12. Published

    Papio baboon species indicative Alu elements. / The Baboon Genome Analysis Consortium.

    In: Genome Biology and Evolution, Vol. 9, No. 6, 01.06.2017, p. 1788-1796.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  13. 2016
  14. Published

    Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. / Abascal, Federico; Corvelo, André; Cruz, Fernando; Villanueva-Cañas, José L; Vlasova, Anna; Marcet-Houben, Marina; Martínez-Cruz, Begoña; Cheng, Jade Yu; Prieto, Pablo; Quesada, Víctor; Quilez, Javier; Li, Gang; García, Francisca; Rubio-Camarillo, Miriam; Frias, Leonor; Ribeca, Paolo; Capella-Gutiérrez, Salvador; Rodríguez, José M; Câmara, Francisco; Lowy, Ernesto; Cozzuto, Luca; Erb, Ionas; Tress, Michael L; Rodriguez-Ales, Jose L; Ruiz-Orera, Jorge; Reverter, Ferran; Casas-Marce, Mireia; Soriano, Laura; Arango, Javier R; Derdak, Sophia; Galán, Beatriz; Blanc, Julie; Gut, Marta; Lorente-Galdos, Belen; Andrés-Nieto, Marta; López-Otín, Carlos; Valencia, Alfonso; Gut, Ivo; García, José L; Guigó, Roderic; Murphy, William J; Ruiz-Herrera, Aurora; Marques-Bonet, Tomas; Roma, Guglielmo; Notredame, Cedric; Mailund, Thomas; Albà, M Mar; Gabaldón, Toni; Alioto, Tyler; Godoy, José A.

    In: Genome Biology (Online), Vol. 17, No. 1, 14.12.2016, p. 251.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  15. Published

    Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity. / 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.

    In: Genetics, Vol. 204, No. 2, 17.08.2016, p. 711-722.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  16. Published

    Learning with Admixture: Modeling, Optimization, and Applications in Population Genetics. / Cheng, Jade Yu.

    2016. 201 p.

    Research output: Book/anthology/dissertation/reportPh.D. thesis

  17. Published

    A genomic history of Aboriginal Australia. / Malaspinas, Anna-Sapfo; Westaway, Michael C; Muller, Craig; Sousa, Vitor C; Lao, Oscar; Alves, Isabel; Athanasiadis, Georgios; Cheng, Jade Y; Crawford, Jacob E; Heupink, Tim H; Macholdt, Enrico; Peischl, Stephan; Schiffels, Stephan; Subramanian, Sankar; Wright, Joanne L; Albrechtsen, Anders; Barbieri, Chiara; Dupanloup, Isabelle; Eriksson, Anders; Margaryan, Ashot; Moltke, Ida; Pugach, Irina; Korneliussen, Thorfinn S; Levkivskyi, Ivan P; Moreno-Mayar, J Víctor; Ni, Shengyu; Racimo, Fernando; Sikora, Martin; Xue, Yali; Aghakhanian, Farhang A; Brucato, Nicolas; Brunak, Søren; Campos, Paula F; Clark, Warren; Ellingvåg, Sturla; Fourmile, Gudjugudju; Gerbault, Pascale; Injie, Darren; Koki, George; Leavesley, Matthew; Logan, Betty; Lynch, Aubrey; Matisoo-Smith, Elizabeth A; McAllister, Peter J; Mentzer, Alexander J; Metspalu, Mait; Migliano, Andrea B; Murgha, Les; Phipps, Maude E; Pomat, William; Reynolds, Doc; Ricaut, Francois-Xavier; Siba, Peter; Thomas, Mark G; Wales, Thomas; Wall, Colleen Ma'run; Oppenheimer, Stephen J; Tyler-Smith, Chris; Durbin, Richard; Dortch, Joe; Manica, Andrea; Schierup, Mikkel H; Foley, Robert A; Lahr, Marta Mirazón; Bowern, Claire; Wall, Jeffrey D; Mailund, Thomas; Stoneking, Mark; Sandhu, Manjinder S; Excoffier, Laurent; Lambert, David M; Willerslev, Eske.

    In: Nature, Vol. 538, No. 7624, 2016, p. 207-214.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  18. Published

    Spitting for Science : Danish High School Students Commit to a Large-Scale Self-Reported Genetic Study. / Athanasiadis, Georgios; Jorgensen, Frank G.; Cheng, Jade Y.; Kjaergaard, Peter C.; Schierup, Mikkel H.; Mailund, Thomas.

    In: P L o S One, Vol. 11, No. 8, e0161822, 2016.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  19. 2015
  20. Published

    Ancestral population genomics using coalescence hidden Markov models and heuristic optimisation algorithms. / Cheng, Jade Yu; Mailund, Thomas.

    In: Computational Biology and Chemistry, Vol. 57, 08.2015, p. 80-92.

    Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review