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Items: 34

1.

Identifying loci under positive selection in complex population histories.

Refoyo-Martínez A, da Fonseca RR, Halldórsdóttir K, Árnason E, Mailund T, Racimo F.

Genome Res. 2019 Sep;29(9):1506-1520. doi: 10.1101/gr.246777.118. Epub 2019 Jul 30.

PMID:
31362936
2.

31° South: The physiology of adaptation to arid conditions in a passerine bird.

Ribeiro ÂM, Puetz L, Pattinson NB, Dalén L, Deng Y, Zhang G, da Fonseca RR, Smit B, Gilbert MTP.

Mol Ecol. 2019 Aug;28(16):3709-3721. doi: 10.1111/mec.15176. Epub 2019 Aug 6.

PMID:
31291502
3.

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits.

Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W, Su W, Liu G, Li Q, Fu W, Pan X, Liu C, Yang J, Zhang C, Yin Y, Wang Y, Zhao Y, Zhang C, Wang Z, Qin Y, Liu W, Wang B, Ren Y, Zhang R, Zeng Y, da Fonseca RR, Wei B, Li R, Wan W, Zhao R, Zhu W, Wang Y, Duan S, Gao Y, Zhang YE, Chen C, Hvilsom C, Epps CW, Chemnick LG, Dong Y, Mirarab S, Siegismund HR, Ryder OA, Gilbert MTP, Lewin HA, Zhang G, Heller R, Wang W.

Science. 2019 Jun 21;364(6446). pii: eaav6202. doi: 10.1126/science.aav6202.

PMID:
31221828
4.

Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle.

da Fonseca RR, Ureña I, Afonso S, Pires AE, Jørsboe E, Chikhi L, Ginja C.

BMC Genomics. 2019 May 3;20(1):334. doi: 10.1186/s12864-019-5685-2.

5.

Population genomic footprints of environmental pollution pressure in natural populations of the Mediterranean mussel.

Ribeiro ÂM, Canchaya CA, Penaloza F, Galindo J, da Fonseca RR.

Mar Genomics. 2019 Jun;45:11-15. doi: 10.1016/j.margen.2018.10.009. Epub 2018 Nov 14.

PMID:
30447893
6.

"Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus.

Machado AM, Tørresen OK, Kabeya N, Couto A, Petersen B, Felício M, Campos PF, Fonseca E, Bandarra N, Lopes-Marques M, Ferraz R, Ruivo R, Fonseca MM, Jentoft S, Monroig Ó, da Fonseca RR, C Castro LF.

Genes (Basel). 2018 Oct 9;9(10). pii: E485. doi: 10.3390/genes9100485.

7.

A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias.

Machado AM, Felício M, Fonseca E, da Fonseca RR, Castro LFC.

Data Brief. 2018 Mar 13;18:276-284. doi: 10.1016/j.dib.2018.03.013. eCollection 2018 Jun.

8.

Natural selection shaped the rise and fall of passenger pigeon genomic diversity.

Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill JA, Baker AJ, Demboski JR, Doll A, Da Fonseca RR, Fulton TL, Gilbert MTP, Heintzman PD, Letts B, McIntosh G, O'Connell BL, Peck M, Pipes ML, Rice ES, Santos KM, Sohrweide AG, Vohr SH, Corbett-Detig RB, Green RE, Shapiro B.

Science. 2017 Nov 17;358(6365):951-954. doi: 10.1126/science.aao0960.

PMID:
29146814
9.

Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution.

Tanner AR, Fuchs D, Winkelmann IE, Gilbert MT, Pankey MS, Ribeiro ÂM, Kocot KM, Halanych KM, Oakley TH, da Fonseca RR, Pisani D, Vinther J.

Proc Biol Sci. 2017 Mar 15;284(1850). pii: 20162818. doi: 10.1098/rspb.2016.2818.

10.

Marine genomics: News and views.

Ribeiro ÂM, Foote AD, Kupczok A, Frazão B, Limborg MT, Piñeiro R, Abalde S, Rocha S, da Fonseca RR.

Mar Genomics. 2017 Feb;31:1-8. doi: 10.1016/j.margen.2016.09.002. Epub 2016 Sep 17. Review.

PMID:
27650377
11.

Combined Transcriptomic and Proteomic Analysis of the Posterior Salivary Gland from the Southern Blue-Ringed Octopus and the Southern Sand Octopus.

Whitelaw BL, Strugnell JM, Faou P, da Fonseca RR, Hall NE, Norman M, Finn J, Cooke IR.

J Proteome Res. 2016 Sep 2;15(9):3284-97. doi: 10.1021/acs.jproteome.6b00452. Epub 2016 Aug 5.

PMID:
27427999
12.

Next-generation biology: Sequencing and data analysis approaches for non-model organisms.

da Fonseca RR, Albrechtsen A, Themudo GE, Ramos-Madrigal J, Sibbesen JA, Maretty L, Zepeda-Mendoza ML, Campos PF, Heller R, Pereira RJ.

Mar Genomics. 2016 Dec;30:3-13. doi: 10.1016/j.margen.2016.04.012. Epub 2016 May 13. Review.

13.

Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.).

Jacobsen MW, da Fonseca RR, Bernatchez L, Hansen MM.

Mol Phylogenet Evol. 2016 Feb;95:161-70. doi: 10.1016/j.ympev.2015.11.008. Epub 2015 Dec 2.

PMID:
26654959
14.

Proteomic profiling of gill GSTs in Mytilus galloprovincialis from the North of Portugal and Galicia evidences variations at protein isoform level with a possible relation with water quality.

Azevedo CC, Guzmán-Guillén R, Martins JC, Osório H, Vasconcelos V, da Fonseca RR, Campos A.

Mar Environ Res. 2015 Sep;110:152-61. doi: 10.1016/j.marenvres.2015.08.008. Epub 2015 Sep 2.

PMID:
26364681
15.

Shotgun analysis of the marine mussel Mytilus edulis hemolymph proteome and mapping the innate immunity elements.

Campos A, Apraiz I, da Fonseca RR, Cristobal S.

Proteomics. 2015 Dec;15(23-24):4021-9. doi: 10.1002/pmic.201500118. Epub 2015 Oct 13.

16.

A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis.

Ribeiro ÂM, Zepeda-Mendoza ML, Bertelsen MF, Kristensen AT, Jarvis ED, Gilbert MT, da Fonseca RR.

BMC Evol Biol. 2015 Jun 30;15:124. doi: 10.1186/s12862-015-0409-y.

17.

Phylogenomic analyses data of the avian phylogenomics project.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G; Avian Phylogenomics Consortium.

Gigascience. 2015 Feb 12;4:4. doi: 10.1186/s13742-014-0038-1. eCollection 2015.

18.

The origin and evolution of maize in the Southwestern United States.

da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C, Ávila-Arcos MC, Hufnagel DE, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, Nielsen R, Hufford MB, Albrechtsen A, Ross-Ibarra J, Gilbert MT.

Nat Plants. 2015 Jan 8;1:14003. doi: 10.1038/nplants.2014.3.

PMID:
27246050
19.

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G.

Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.

20.

Comparative genomics reveals insights into avian genome evolution and adaptation.

Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J.

Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11.

21.

DivA: detection of non-homologous and very divergent regions in protein sequence alignments.

Zepeda Mendoza ML, Nygaard S, da Fonseca RR.

BMC Res Notes. 2014 Nov 18;7:806. doi: 10.1186/1756-0500-7-806.

22.

The elusive nature of adaptive mitochondrial DNA evolution of an arctic lineage prone to frequent introgression.

Melo-Ferreira J, Vilela J, Fonseca MM, da Fonseca RR, Boursot P, Alves PC.

Genome Biol Evol. 2014 Apr;6(4):886-96. doi: 10.1093/gbe/evu059.

23.

Cephalopod genomics: A plan of strategies and organization.

Albertin CB, Bonnaud L, Brown CT, Crookes-Goodson WJ, da Fonseca RR, Di Cristo C, Dilkes BP, Edsinger-Gonzales E, Freeman RM Jr, Hanlon RT, Koenig KM, Lindgren AR, Martindale MQ, Minx P, Moroz LL, Nödl MT, Nyholm SV, Ogura A, Pungor JR, Rosenthal JJ, Schwarz EM, Shigeno S, Strugnell JM, Wollesen T, Zhang G, Ragsdale CW.

Stand Genomic Sci. 2012 Oct 10;7(1):175-88. doi: 10.4056/sigs.3136559. Epub 2012 Sep 26.

24.

Adaptive evolution of the Retinoid X receptor in vertebrates.

Philip S, Castro LF, da Fonseca RR, Reis-Henriques MA, Vasconcelos V, Santos MM, Antunes A.

Genomics. 2012 Feb;99(2):81-9. doi: 10.1016/j.ygeno.2011.12.001. Epub 2011 Dec 14.

25.

IMPACT: integrated multiprogram platform for analyses in ConTest.

Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A.

J Hered. 2011 May-Jun;102(3):366-9. doi: 10.1093/jhered/esr003. Epub 2011 Mar 16.

PMID:
21414966
26.

Amino acid patterns around disulfide bonds.

Marques JR, da Fonseca RR, Drury B, Melo A.

Int J Mol Sci. 2010 Nov 18;11(11):4673-86. doi: 10.3390/ijms11114673.

27.

Conformational characterization of disulfide bonds: a tool for protein classification.

Marques JR, da Fonseca RR, Drury B, Melo A.

J Theor Biol. 2010 Dec 7;267(3):388-95. doi: 10.1016/j.jtbi.2010.09.012. Epub 2010 Sep 16.

PMID:
20851707
28.

Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases.

da Fonseca RR, Johnson WE, O'Brien SJ, Vasconcelos V, Antunes A.

BMC Evol Biol. 2010 Sep 15;10:281. doi: 10.1186/1471-2148-10-281.

29.

Positive selection on the killer whale mitogenome.

Foote AD, Morin PA, Durban JW, Pitman RL, Wade P, Willerslev E, Gilbert MT, da Fonseca RR.

Biol Lett. 2011 Feb 23;7(1):116-8. doi: 10.1098/rsbl.2010.0638. Epub 2010 Sep 1.

30.

Positive selection on apoptosis related genes.

da Fonseca RR, Kosiol C, Vinar T, Siepel A, Nielsen R.

FEBS Lett. 2010 Feb 5;584(3):469-76. doi: 10.1016/j.febslet.2009.12.022. Epub 2009 Dec 22. Review.

31.

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution.

Willerslev E, Gilbert MT, Binladen J, Ho SY, Campos PF, Ratan A, Tomsho LP, da Fonseca RR, Sher A, Kuznetsova TV, Nowak-Kemp M, Roth TL, Miller W, Schuster SC.

BMC Evol Biol. 2009 May 11;9:95. doi: 10.1186/1471-2148-9-95.

32.

Patterns of positive selection in six Mammalian genomes.

Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A.

PLoS Genet. 2008 Aug 1;4(8):e1000144. doi: 10.1371/journal.pgen.1000144.

33.

The adaptive evolution of the mammalian mitochondrial genome.

da Fonseca RR, Johnson WE, O'Brien SJ, Ramos MJ, Antunes A.

BMC Genomics. 2008 Mar 4;9:119. doi: 10.1186/1471-2164-9-119.

34.

Structural divergence and adaptive evolution in mammalian cytochromes P450 2C.

da Fonseca RR, Antunes A, Melo A, Ramos MJ.

Gene. 2007 Jan 31;387(1-2):58-66. Epub 2006 Sep 1.

PMID:
17045425

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