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Items: 19

1.

Gene Fusions derived by transcriptional readthrough are Driven by Segmental Duplication in Human.

Am M, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez J, Prado-Martinez J, Creevey CJ, Aspden JL, McInerney JO, Marques-Bonet T, Mj O.

Genome Biol Evol. 2019 Aug 10. pii: evz163. doi: 10.1093/gbe/evz163. [Epub ahead of print]

PMID:
31400206
2.

Response to Giem.

Haber M, Doumet-Serhal C, Scheib C, Xue Y, Danecek P, Mezzavilla M, Youhanna S, Martiniano R, Prado-Martinez J, Szpak M, Matisoo-Smith E, Schutkowski H, Mikulski R, Zalloua P, Kivisild T, Tyler-Smith C.

Am J Hum Genet. 2018 Feb 1;102(2):331. doi: 10.1016/j.ajhg.2018.01.002. No abstract available.

3.

Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species.

Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M, Desai T, Groves C, Pybus M, Sonay TB, Roos C, Lameira AR, Wich SA, Askew J, Davila-Ross M, Fredriksson G, de Valles G, Casals F, Prado-Martinez J, Goossens B, Verschoor EJ, Warren KS, Singleton I, Marques DA, Pamungkas J, Perwitasari-Farajallah D, Rianti P, Tuuga A, Gut IG, Gut M, Orozco-terWengel P, van Schaik CP, Bertranpetit J, Anisimova M, Scally A, Marques-Bonet T, Meijaard E, Krützen M.

Curr Biol. 2017 Nov 20;27(22):3576-3577. doi: 10.1016/j.cub.2017.11.020. No abstract available.

4.

Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species.

Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M, Desai T, Groves C, Pybus M, Sonay TB, Roos C, Lameira AR, Wich SA, Askew J, Davila-Ross M, Fredriksson G, de Valles G, Casals F, Prado-Martinez J, Goossens B, Verschoor EJ, Warren KS, Singleton I, Marques DA, Pamungkas J, Perwitasari-Farajallah D, Rianti P, Tuuga A, Gut IG, Gut M, Orozco-terWengel P, van Schaik CP, Bertranpetit J, Anisimova M, Scally A, Marques-Bonet T, Meijaard E, Krützen M.

Curr Biol. 2017 Nov 20;27(22):3487-3498.e10. doi: 10.1016/j.cub.2017.09.047. Epub 2017 Nov 2. Erratum in: Curr Biol. 2017 Nov 20;27(22):3576-3577.

5.

Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences.

Haber M, Doumet-Serhal C, Scheib C, Xue Y, Danecek P, Mezzavilla M, Youhanna S, Martiniano R, Prado-Martinez J, Szpak M, Matisoo-Smith E, Schutkowski H, Mikulski R, Zalloua P, Kivisild T, Tyler-Smith C.

Am J Hum Genet. 2017 Aug 3;101(2):274-282. doi: 10.1016/j.ajhg.2017.06.013. Epub 2017 Jul 27.

6.

Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations.

Haber M, Mezzavilla M, Bergström A, Prado-Martinez J, Hallast P, Saif-Ali R, Al-Habori M, Dedoussis G, Zeggini E, Blue-Smith J, Wells RS, Xue Y, Zalloua PA, Tyler-Smith C.

Am J Hum Genet. 2016 Dec 1;99(6):1316-1324. doi: 10.1016/j.ajhg.2016.10.012. Epub 2016 Nov 23.

7.

Chimpanzee genomic diversity reveals ancient admixture with bonobos.

de Manuel M, Kuhlwilm M, Frandsen P, Sousa VC, Desai T, Prado-Martinez J, Hernandez-Rodriguez J, Dupanloup I, Lao O, Hallast P, Schmidt JM, Heredia-Genestar JM, Benazzo A, Barbujani G, Peter BM, Kuderna LF, Casals F, Angedakin S, Arandjelovic M, Boesch C, Kühl H, Vigilant L, Langergraber K, Novembre J, Gut M, Gut I, Navarro A, Carlsen F, Andrés AM, Siegismund HR, Scally A, Excoffier L, Tyler-Smith C, Castellano S, Xue Y, Hvilsom C, Marques-Bonet T.

Science. 2016 Oct 28;354(6311):477-481. Epub 2016 Oct 27.

8.

Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.

Lobon I, Tucci S, de Manuel M, Ghirotto S, Benazzo A, Prado-Martinez J, Lorente-Galdos B, Nam K, Dabad M, Hernandez-Rodriguez J, Comas D, Navarro A, Schierup MH, Andres AM, Barbujani G, Hvilsom C, Marques-Bonet T.

Genome Biol Evol. 2016 Jul 3;8(6):2020-30. doi: 10.1093/gbe/evw124.

9.

Genetic Load of Loss-of-Function Polymorphic Variants in Great Apes.

de Valles-Ibáñez G, Hernandez-Rodriguez J, Prado-Martinez J, Luisi P, Marquès-Bonet T, Casals F.

Genome Biol Evol. 2016 Mar 26;8(3):871-7. doi: 10.1093/gbe/evw040.

10.

Ancient gene flow from early modern humans into Eastern Neanderthals.

Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Marques-Bonet T, Andrés AM, Viola B, Pääbo S, Meyer M, Siepel A, Castellano S.

Nature. 2016 Feb 25;530(7591):429-33. doi: 10.1038/nature16544. Epub 2016 Feb 17.

11.

The interplay between DNA methylation and sequence divergence in recent human evolution.

Hernando-Herraez I, Heyn H, Fernandez-Callejo M, Vidal E, Fernandez-Bellon H, Prado-Martinez J, Sharp AJ, Esteller M, Marques-Bonet T.

Nucleic Acids Res. 2015 Sep 30;43(17):8204-14. doi: 10.1093/nar/gkv693. Epub 2015 Jul 13.

12.

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding.

Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q, Szpak M, Frandsen P, Chen Y, Yngvadottir B, Cooper DN, de Manuel M, Hernandez-Rodriguez J, Lobon I, Siegismund HR, Pagani L, Quail MA, Hvilsom C, Mudakikwa A, Eichler EE, Cranfield MR, Marques-Bonet T, Tyler-Smith C, Scally A.

Science. 2015 Apr 10;348(6231):242-245. doi: 10.1126/science.aaa3952. Epub 2015 Apr 9.

13.

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.

Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CW, DeGiorgio M, Prado-Martinez J, Rodríguez JA, Rasmussen S, Quilez J, Ramírez O, Marigorta UM, Fernández-Callejo M, Prada ME, Encinas JM, Nielsen R, Netea MG, Novembre J, Sturm RA, Sabeti P, Marquès-Bonet T, Navarro A, Willerslev E, Lalueza-Fox C.

Nature. 2014 Mar 13;507(7491):225-8. doi: 10.1038/nature12960. Epub 2014 Jan 26.

14.

Dynamics of DNA methylation in recent human and great ape evolution.

Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, Hvilsom C, Navarro A, Esteller M, Sharp AJ, Marques-Bonet T.

PLoS Genet. 2013;9(9):e1003763. doi: 10.1371/journal.pgen.1003763. Epub 2013 Sep 5.

15.

Rates and patterns of great ape retrotransposition.

Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C; Great Ape Genome Project, Marques-Bonet T, Ventura M, Batzer MA, Eichler EE.

Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13457-62. doi: 10.1073/pnas.1310914110. Epub 2013 Jul 24.

16.

Evolution and diversity of copy number variation in the great ape lineage.

Sudmant PH, Huddleston J, Catacchio CR, Malig M, Hillier LW, Baker C, Mohajeri K, Kondova I, Bontrop RE, Persengiev S, Antonacci F, Ventura M, Prado-Martinez J; Great Ape Genome Project, Marques-Bonet T, Eichler EE.

Genome Res. 2013 Sep;23(9):1373-82. doi: 10.1101/gr.158543.113. Epub 2013 Jul 3.

17.

Great ape genetic diversity and population history.

Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T.

Nature. 2013 Jul 25;499(7459):471-5. doi: 10.1038/nature12228. Epub 2013 Jul 3.

18.

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild.

Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, de la Calle-Mustienes E, Casillas S, Rubio-Acero R, Melé M, Engelken J, Caceres M, Gomez-Skarmeta JL, Gut M, Bertranpetit J, Gut IG, Abello T, Eichler EE, Mingarro I, Lalueza-Fox C, Navarro A, Marques-Bonet T.

BMC Genomics. 2013 May 31;14:363. doi: 10.1186/1471-2164-14-363.

19.

Insights into hominid evolution from the gorilla genome sequence.

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R.

Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.

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