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Items: 29

1.

Back to the roots: Reducing evolutionary rate heterogeneity among sequences gives support for the early morphological hypothesis of the root of Siluriformes (Teleostei: Ostariophysi).

Rivera-Rivera CJ, Montoya-Burgos JI.

Mol Phylogenet Evol. 2018 Oct;127:272-279. doi: 10.1016/j.ympev.2018.06.004. Epub 2018 Jun 7.

PMID:
29885935
2.

Effect of hybridization with genome exclusion on extinction risk.

Quilodrán CS, Currat M, Montoya-Burgos JI.

Conserv Biol. 2018 Oct;32(5):1139-1149. doi: 10.1111/cobi.13120. Epub 2018 Jun 27.

PMID:
29691912
3.

Cryptic Biological Invasions: a General Model of Hybridization.

Quilodrán CS, Austerlitz F, Currat M, Montoya-Burgos JI.

Sci Rep. 2018 Feb 5;8(1):2414. doi: 10.1038/s41598-018-20543-6.

4.

Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish.

Jardim de Queiroz L, Torrente-Vilara G, Quilodran C, Rodrigues da Costa Doria C, Montoya-Burgos JI.

PLoS One. 2017 Dec 20;12(12):e0189349. doi: 10.1371/journal.pone.0189349. eCollection 2017.

5.

Trunk dental tissue evolved independently from underlying dermal bony plates but is associated with surface bones in living odontode-bearing catfish.

Rivera-Rivera CJ, Montoya-Burgos JI.

Proc Biol Sci. 2017 Oct 25;284(1865). pii: 20171831. doi: 10.1098/rspb.2017.1831.

6.

Risks associated with introduction of poeciliids for control of mosquito larvae: first record of the non-native Gambusia holbrooki in Argentina.

Cabrera MB, Bogan S, Posadas P, Somoza GM, Montoya-Burgos JI, Cardoso YP.

J Fish Biol. 2017 Aug;91(2):704-710. doi: 10.1111/jfb.13370. Epub 2017 Jul 10.

PMID:
28691205
7.

Positive selection on sperm ion channels in a brooding brittle star: consequence of life-history traits evolution.

Weber AA, Abi-Rached L, Galtier N, Bernard A, Montoya-Burgos JI, Chenuil A.

Mol Ecol. 2017 Jul;26(14):3744-3759. doi: 10.1111/mec.14024. Epub 2017 Feb 8.

PMID:
28099777
8.

LS³: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa.

Rivera-Rivera CJ, Montoya-Burgos JI.

Mol Biol Evol. 2016 Jun;33(6):1625-34. doi: 10.1093/molbev/msw043. Epub 2016 Feb 23.

9.

Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification.

Covain R, Fisch-Muller S, Oliveira C, Mol JH, Montoya-Burgos JI, Dray S.

Mol Phylogenet Evol. 2016 Jan;94(Pt B):492-517. doi: 10.1016/j.ympev.2015.10.018. Epub 2015 Oct 26.

PMID:
26516029
10.

Modelling interspecific hybridization with genome exclusion to identify conservation actions: the case of native and invasive Pelophylax waterfrogs.

Quilodrán CS, Montoya-Burgos JI, Currat M.

Evol Appl. 2015 Feb;8(2):199-210. doi: 10.1111/eva.12245. Epub 2015 Jan 28.

11.

A general model of distant hybridization reveals the conditions for extinction in Atlantic salmon and brown trout.

Quilodrán CS, Currat M, Montoya-Burgos JI.

PLoS One. 2014 Jul 8;9(7):e101736. doi: 10.1371/journal.pone.0101736. eCollection 2014.

12.

Patterns of positive selection and neutral evolution in the protein-coding genes of Tetraodon and Takifugu.

Montoya-Burgos JI.

PLoS One. 2011;6(9):e24800. doi: 10.1371/journal.pone.0024800. Epub 2011 Sep 13.

13.

Optimization of de novo transcriptome assembly from next-generation sequencing data.

Surget-Groba Y, Montoya-Burgos JI.

Genome Res. 2010 Oct;20(10):1432-40. doi: 10.1101/gr.103846.109. Epub 2010 Aug 6.

14.

Changes in Hox genes' structure and function during the evolution of the squamate body plan.

Di-Poï N, Montoya-Burgos JI, Miller H, Pourquié O, Milinkovitch MC, Duboule D.

Nature. 2010 Mar 4;464(7285):99-103. doi: 10.1038/nature08789.

PMID:
20203609
15.

Transcriptome screen for fast evolving genes by Inter-Specific Selective Hybridization (ISSH).

Montoya-Burgos JI, Foulon A, Bahechar I.

BMC Genomics. 2010 Feb 22;11:126. doi: 10.1186/1471-2164-11-126.

16.

Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard.

Di-Poï N, Montoya-Burgos JI, Duboule D.

Genome Res. 2009 Apr;19(4):602-10. doi: 10.1101/gr.087932.108. Epub 2009 Feb 18.

17.

Unexpected diversity in the catfish Pseudancistrus brevispinis reveals dispersal routes in a Neotropical center of endemism: the Guyanas Region.

Cardoso YP, Montoya-Burgos JI.

Mol Ecol. 2009 Mar;18(5):947-64. doi: 10.1111/j.1365-294X.2008.04068.x.

PMID:
19207251
18.

Molecular systematic and historical biogeography of the armored Neotropical catfishes Hypoptopomatinae and Neoplecostominae (Siluriformes: Loricariidae).

Chiachio MC, Oliveira C, Montoya-Burgos JI.

Mol Phylogenet Evol. 2008 Nov;49(2):606-17. doi: 10.1016/j.ympev.2008.08.013. Epub 2008 Aug 29.

PMID:
18793736
19.

Assessing phylogenetic dependence of morphological traits using co-inertia prior to investigate character evolution in Loricariinae catfishes.

Covain R, Dray S, Fisch-Muller S, Montoya-Burgos JI.

Mol Phylogenet Evol. 2008 Mar;46(3):986-1002. doi: 10.1016/j.ympev.2007.12.015. Epub 2007 Dec 25. Erratum in: Mol Phylogenet Evol. 2010 May;55(2):751.

PMID:
18272407
20.

Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements.

Nikolaev SI, Montoya-Burgos JI, Popadin K, Parand L, Margulies EH; National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program, Antonarakis SE.

Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20443-8. Epub 2007 Dec 11.

21.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

22.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A.

Genome Res. 2007 Jun;17(6):760-74.

23.

Divergent evolution among teleost V1r receptor genes.

Pfister P, Randall J, Montoya-Burgos JI, Rodriguez I.

PLoS One. 2007 Apr 18;2(4):e379.

24.

Early history of mammals is elucidated with the ENCODE multiple species sequencing data.

Nikolaev S, Montoya-Burgos JI, Margulies EH; NISC Comparative Sequencing Program, Rougemont J, Nyffeler B, Antonarakis SE.

PLoS Genet. 2007 Jan 5;3(1):e2.

25.

Molecular phylogeny, evolutionary rates, and divergence timing of the symbiotic dinoflagellate genus Symbiodinium.

Pochon X, Montoya-Burgos JI, Stadelmann B, Pawlowski J.

Mol Phylogenet Evol. 2006 Jan;38(1):20-30. Epub 2005 Jun 22.

PMID:
15978847
27.

Recombination explains isochores in mammalian genomes.

Montoya-Burgos JI, Boursot P, Galtier N.

Trends Genet. 2003 Mar;19(3):128-30. Review.

PMID:
12615004
28.

Mycobacterium doricum sp. nov.

Tortoli E, Piersimoni C, Kroppenstedt RM, Montoya-Burgos JI, Reischl U, Giacometti A, Emler S.

Int J Syst Evol Microbiol. 2001 Nov;51(Pt 6):2007-12.

PMID:
11760941
29.

Origin of the Mesozoa inferred from 18S rRNA gene sequences.

Pawlowski J, Montoya-Burgos JI, Fahrni JF, Wüest J, Zaninetti L.

Mol Biol Evol. 1996 Oct;13(8):1128-32.

PMID:
8865666

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