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Items: 26

1.

Detecting signatures of positive selection along defined branches of a population tree using LSD.

Librado P, Orlando L.

Mol Biol Evol. 2018 Mar 29. doi: 10.1093/molbev/msy053. [Epub ahead of print]

PMID:
29617830
2.

Convergent genomic signatures of domestication in sheep and goats.

Alberto FJ, Boyer F, Orozco-terWengel P, Streeter I, Servin B, de Villemereuil P, Benjelloun B, Librado P, Biscarini F, Colli L, Barbato M, Zamani W, Alberti A, Engelen S, Stella A, Joost S, Ajmone-Marsan P, Negrini R, Orlando L, Rezaei HR, Naderi S, Clarke L, Flicek P, Wincker P, Coissac E, Kijas J, Tosser-Klopp G, Chikhi A, Bruford MW, Taberlet P, Pompanon F.

Nat Commun. 2018 Mar 6;9(1):813. doi: 10.1038/s41467-018-03206-y.

3.

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
4.

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.

Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A.

Mol Biol Evol. 2017 Dec 1;34(12):3299-3302. doi: 10.1093/molbev/msx248.

PMID:
29029172
5.

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory.

Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang TH, Farr KM, Fujita T, Hiwatashi Y, Hoshi Y, Imai T, Kasahara M, Librado P, Mao L, Mori H, Nishiyama T, Nozawa M, Pálfalvi G, Pollard ST, Rozas J, Sánchez-Gracia A, Sankoff D, Shibata TF, Shigenobu S, Sumikawa N, Uzawa T, Xie M, Zheng C, Pollock DD, Albert VA, Li S, Hasebe M.

Nat Ecol Evol. 2017 Feb 6;1(3):59. doi: 10.1038/s41559-016-0059.

PMID:
28812732
6.

Ancient genomic changes associated with domestication of the horse.

Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L.

Science. 2017 Apr 28;356(6336):442-445. doi: 10.1126/science.aam5298.

PMID:
28450643
7.

Evolutionary Patterns and Processes: Lessons from Ancient DNA.

Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Gamba C, Willerslev E, Orlando L.

Syst Biol. 2017 Jan 1;66(1):e1-e29. doi: 10.1093/sysbio/syw059. Review. Erratum in: Syst Biol. 2017 Jul 1;66(4):660.

8.

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.

9.

Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family in Drosophila.

Clifton BD, Librado P, Yeh SD, Solares ES, Real DA, Jayasekera SU, Zhang W, Shi M, Park RV, Magie RD, Ma HC, Xia XQ, Marco A, Rozas J, Ranz JM.

Mol Biol Evol. 2017 Jan;34(1):51-65. doi: 10.1093/molbev/msw212. Epub 2016 Oct 3.

10.

Experimental conditions improving in-solution target enrichment for ancient DNA.

Cruz-Dávalos DI, Llamas B, Gaunitz C, Fages A, Gamba C, Soubrier J, Librado P, Seguin-Orlando A, Pruvost M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Scheu A, Beneke N, Ludwig A, Cooper A, Willerslev E, Orlando L.

Mol Ecol Resour. 2017 May;17(3):508-522. doi: 10.1111/1755-0998.12595. Epub 2016 Sep 18.

PMID:
27566552
11.
12.

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.

Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, Boulygina E, Tsygankova S, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Sicheritz-Ponten T, Popov R, Grigoriev S, Alekseev AN, Rubin EM, McCue M, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J, Prokhortchouk E, Orlando L.

Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):E6889-97. doi: 10.1073/pnas.1513696112. Epub 2015 Nov 23.

13.

Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila.

Calvo-Martín JM, Librado P, Aguadé M, Papaceit M, Segarra C.

Heredity (Edinb). 2016 Feb;116(2):213-23. doi: 10.1038/hdy.2015.91. Epub 2015 Oct 21.

14.

Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.

Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jónsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A, Magnussen K, Fages A, Gamba C, Lorente-Galdos B, Polani S, Steiner C, Neuditschko M, Jagannathan V, Feh C, Greenblatt CL, Ludwig A, Abramson NI, Zimmermann W, Schafberg R, Tikhonov A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder S, Leeb T, Slatkin M, Orlando L.

Curr Biol. 2015 Oct 5;25(19):2577-83. doi: 10.1016/j.cub.2015.08.032. Epub 2015 Sep 24.

15.

Assessing associations between the AURKA-HMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers.

Blanco I, Kuchenbaecker K, Cuadras D, Wang X, Barrowdale D, de Garibay GR, Librado P, Sánchez-Gracia A, Rozas J, Bonifaci N, McGuffog L, Pankratz VS, Islam A, Mateo F, Berenguer A, Petit A, Català I, Brunet J, Feliubadaló L, Tornero E, Benítez J, Osorio A, Ramón y Cajal T, Nevanlinna H, Aittomäki K, Arun BK, Toland AE, Karlan BY, Walsh C, Lester J, Greene MH, Mai PL, Nussbaum RL, Andrulis IL, Domchek SM, Nathanson KL, Rebbeck TR, Barkardottir RB, Jakubowska A, Lubinski J, Durda K, Jaworska-Bieniek K, Claes K, Van Maerken T, Díez O, Hansen TV, Jønson L, Gerdes AM, Ejlertsen B, de la Hoya M, Caldés T, Dunning AM, Oliver C, Fineberg E, Cook M, Peock S, McCann E, Murray A, Jacobs C, Pichert G, Lalloo F, Chu C, Dorkins H, Paterson J, Ong KR, Teixeira MR; Teixeira, Hogervorst FB, van der Hout AH, Seynaeve C, van der Luijt RB, Ligtenberg MJ, Devilee P, Wijnen JT, Rookus MA, Meijers-Heijboer HE, Blok MJ, van den Ouweland AM, Aalfs CM, Rodriguez GC, Phillips KA, Piedmonte M, Nerenstone SR, Bae-Jump VL, O'Malley DM, Ratner ES, Schmutzler RK, Wappenschmidt B, Rhiem K, Engel C, Meindl A, Ditsch N, Arnold N, Plendl HJ, Niederacher D, Sutter C, Wang-Gohrke S, Steinemann D, Preisler-Adams S, Kast K, Varon-Mateeva R, Gehrig A, Bojesen A, Pedersen IS, Sunde L, Jensen UB, Thomassen M, Kruse TA, Foretova L, Peterlongo P, Bernard L, Peissel B, Scuvera G, Manoukian S, Radice P, Ottini L, Montagna M, Agata S, Maugard C, Simard J, Soucy P, Berger A, Fink-Retter A, Singer CF, Rappaport C, Geschwantler-Kaulich D, Tea MK, Pfeiler G; BCFR, John EM, Miron A, Neuhausen SL, Terry MB, Chung WK, Daly MB, Goldgar DE, Janavicius R, Dorfling CM, van Rensburg EJ, Fostira F, Konstantopoulou I, Garber J, Godwin AK, Olah E, Narod SA, Rennert G, Paluch SS, Laitman Y, Friedman E; SWE-BRCA, Liljegren A, Rantala J, Stenmark-Askmalm M, Loman N, Imyanitov EN, Hamann U; kConFab Investigators, Spurdle AB, Healey S, Weitzel JN, Herzog J, Margileth D, Gorrini C, Esteller M, Gómez A, Sayols S, Vidal E, Heyn H; GEMO, Stoppa-Lyonnet D, Léoné M, Barjhoux L, Fassy-Colcombet M, de Pauw A, Lasset C, Ferrer SF, Castera L, Berthet P, Cornelis F, Bignon YJ, Damiola F, Mazoyer S, Sinilnikova OM, Maxwell CA, Vijai J, Robson M, Kauff N, Corines MJ, Villano D, Cunningham J, Lee A, Lindor N, Lázaro C, Easton DF, Offit K, Chenevix-Trench G, Couch FJ, Antoniou AC, Pujana MA.

PLoS One. 2015 Apr 1;10(4):e0120020. doi: 10.1371/journal.pone.0120020. eCollection 2015.

16.

High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba.

Carretero-Paulet L, Librado P, Chang TH, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA.

Mol Biol Evol. 2015 May;32(5):1284-95. doi: 10.1093/molbev/msv020. Epub 2015 Jan 31.

PMID:
25637935
17.

Streptococcus gallolyticus subsp. gallolyticus from human and animal origins: genetic diversity, antimicrobial susceptibility, and characterization of a vancomycin-resistant calf isolate carrying a vanA-Tn1546-like element.

Romero-Hernández B, Tedim AP, Sánchez-Herrero JF, Librado P, Rozas J, Muñoz G, Baquero F, Cantón R, Del Campo R.

Antimicrob Agents Chemother. 2015 Apr;59(4):2006-15. doi: 10.1128/AAC.04083-14. Epub 2015 Jan 20.

18.

Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba.

Carretero-Paulet L, Chang TH, Librado P, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA.

Genome Biol Evol. 2015 Jan 9;7(2):444-56. doi: 10.1093/gbe/evu288.

19.

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.

Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P.

Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.

20.

Mycobacterial phylogenomics: an enhanced method for gene turnover analysis reveals uneven levels of gene gain and loss among species and gene families.

Librado P, Vieira FG, Sánchez-Gracia A, Kolokotronis SO, Rozas J.

Genome Biol Evol. 2014 Jun 5;6(6):1454-65. doi: 10.1093/gbe/evu117.

21.

Uncovering the functional constraints underlying the genomic organization of the odorant-binding protein genes.

Librado P, Rozas J.

Genome Biol Evol. 2013;5(11):2096-108. doi: 10.1093/gbe/evt158.

22.

The Drosophila melanogaster Genetic Reference Panel.

Mackay TF, Richards S, Stone EA, Barbadilla A, Ayroles JF, Zhu D, Casillas S, Han Y, Magwire MM, Cridland JM, Richardson MF, Anholt RR, Barrón M, Bess C, Blankenburg KP, Carbone MA, Castellano D, Chaboub L, Duncan L, Harris Z, Javaid M, Jayaseelan JC, Jhangiani SN, Jordan KW, Lara F, Lawrence F, Lee SL, Librado P, Linheiro RS, Lyman RF, Mackey AJ, Munidasa M, Muzny DM, Nazareth L, Newsham I, Perales L, Pu LL, Qu C, Ràmia M, Reid JG, Rollmann SM, Rozas J, Saada N, Turlapati L, Worley KC, Wu YQ, Yamamoto A, Zhu Y, Bergman CM, Thornton KR, Mittelman D, Gibbs RA.

Nature. 2012 Feb 8;482(7384):173-8. doi: 10.1038/nature10811.

23.

Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition.

Yeh SD, Do T, Chan C, Cordova A, Carranza F, Yamamoto EA, Abbassi M, Gandasetiawan KA, Librado P, Damia E, Dimitri P, Rozas J, Hartl DL, Roote J, Ranz JM.

Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2043-8. doi: 10.1073/pnas.1121327109. Epub 2012 Jan 23.

24.

PopDrowser: the Population Drosophila Browser.

Ràmia M, Librado P, Casillas S, Rozas J, Barbadilla A.

Bioinformatics. 2012 Feb 15;28(4):595-6. doi: 10.1093/bioinformatics/btr691. Epub 2011 Dec 15.

PMID:
22180410
25.

BadiRate: estimating family turnover rates by likelihood-based methods.

Librado P, Vieira FG, Rozas J.

Bioinformatics. 2012 Jan 15;28(2):279-81. doi: 10.1093/bioinformatics/btr623. Epub 2011 Nov 10.

26.

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.

Librado P, Rozas J.

Bioinformatics. 2009 Jun 1;25(11):1451-2. doi: 10.1093/bioinformatics/btp187. Epub 2009 Apr 3.

PMID:
19346325

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