Rute R Fonseca

Rute R da Fonseca

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Rute R Fonseca

Rute R da Fonseca

Publications by authors named "Rute R da Fonseca"

35Publications

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1PubMed Central Citations

Identifying loci under positive selection in complex population histories.

Genome Res 2019 09 30;29(9):1506-1520. Epub 2019 Jul 30.

Lundbeck GeoGenetics Centre, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1350, Denmark.

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http://dx.doi.org/10.1101/gr.246777.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724678PMC
September 2019

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

Mol Ecol 2019 Aug 6;28(16):3709-3721. Epub 2019 Aug 6.

Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1111/mec.15176DOI Listing
August 2019

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

Mar Genomics 2019 Jun 14;45:11-15. Epub 2018 Nov 14.

CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.margen.2018.10.009DOI Listing
June 2019

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

BMC Genomics 2019 May 3;20(1):334. Epub 2019 May 3.

CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.

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http://dx.doi.org/10.1186/s12864-019-5685-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500009PMC
May 2019

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

Data Brief 2018 Jun 13;18:276-284. Epub 2018 Mar 13.

CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal.

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http://dx.doi.org/10.1016/j.dib.2018.03.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996228PMC
June 2018

Marine genomics: News and views.

Mar Genomics 2017 Feb 17;31:1-8. Epub 2016 Sep 17.

The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.margen.2016.09.002DOI Listing
February 2017

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

Mar Genomics 2016 Dec 13;30:3-13. Epub 2016 May 13.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1016/j.margen.2016.04.012DOI Listing
December 2016

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

J Proteome Res 2016 09 5;15(9):3284-97. Epub 2016 Aug 5.

Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University , Melbourne, Victoria 3086, Australia.

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http://dx.doi.org/10.1021/acs.jproteome.6b00452DOI Listing
September 2016

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.).

Mol Phylogenet Evol 2016 Feb 2;95:161-70. Epub 2015 Dec 2.

Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1016/j.ympev.2015.11.008DOI Listing
February 2016

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

Proteomics 2015 Dec 13;15(23-24):4021-9. Epub 2015 Oct 13.

Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.

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http://dx.doi.org/10.1002/pmic.201500118DOI Listing
December 2015

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

BMC Evol Biol 2015 Jun 30;15:124. Epub 2015 Jun 30.

Interdisciplinary Centre of Marine and Environmental Research-CIIMAR/CIMAR, University of Porto, Rua dos Bragas 289, 4050-123, Porto, Portugal.

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http://dx.doi.org/10.1186/s12862-015-0409-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486697PMC
June 2015

Comparative genomics reveals insights into avian genome evolution and adaptation.

Science 2014 Dec 11;346(6215):1311-20. Epub 2014 Dec 11.

China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Department of Medicine, University of Hong Kong, Hong Kong.

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http://jarvislab.net/wp-content/uploads/2014/12/Science-2014
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http://www.sciencemag.org/cgi/doi/10.1126/science.1251385
Publisher Site
http://dx.doi.org/10.1126/science.1251385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390078PMC
December 2014

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

Authors:
Erich D Jarvis Siavash Mirarab Andre J Aberer Bo Li Peter Houde Cai Li Simon Y W Ho Brant C Faircloth Benoit Nabholz Jason T Howard Alexander Suh Claudia C Weber Rute R da Fonseca Jianwen Li Fang Zhang Hui Li Long Zhou Nitish Narula Liang Liu Ganesh Ganapathy Bastien Boussau Md Shamsuzzoha Bayzid Volodymyr Zavidovych Sankar Subramanian Toni Gabaldón Salvador Capella-Gutiérrez Jaime Huerta-Cepas Bhanu Rekepalli Kasper Munch Mikkel Schierup Bent Lindow Wesley C Warren David Ray Richard E Green Michael W Bruford Xiangjiang Zhan Andrew Dixon Shengbin Li Ning Li Yinhua Huang Elizabeth P Derryberry Mads Frost Bertelsen Frederick H Sheldon Robb T Brumfield Claudio V Mello Peter V Lovell Morgan Wirthlin Maria Paula Cruz Schneider Francisco Prosdocimi José Alfredo Samaniego Amhed Missael Vargas Velazquez Alonzo Alfaro-Núñez Paula F Campos Bent Petersen Thomas Sicheritz-Ponten An Pas Tom Bailey Paul Scofield Michael Bunce David M Lambert Qi Zhou Polina Perelman Amy C Driskell Beth Shapiro Zijun Xiong Yongli Zeng Shiping Liu Zhenyu Li Binghang Liu Kui Wu Jin Xiao Xiong Yinqi Qiuemei Zheng Yong Zhang Huanming Yang Jian Wang Linnea Smeds Frank E Rheindt Michael Braun Jon Fjeldsa Ludovic Orlando F Keith Barker Knud Andreas Jønsson Warren Johnson Klaus-Peter Koepfli Stephen O'Brien David Haussler Oliver A Ryder Carsten Rahbek Eske Willerslev Gary R Graves Travis C Glenn John McCormack Dave Burt Hans Ellegren Per Alström Scott V Edwards Alexandros Stamatakis David P Mindell Joel Cracraft Edward L Braun Tandy Warnow Wang Jun M Thomas P Gilbert Guojie Zhang

Science 2014 Dec;346(6215):1320-31

China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.1253451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904PMC
December 2014

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

BMC Res Notes 2014 Nov 18;7:806. Epub 2014 Nov 18.

Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1756-0500-7-806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4240845PMC
November 2014

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

Genome Biol Evol 2014 Apr;6(4):886-96

CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal.

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http://dx.doi.org/10.1093/gbe/evu059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4007550PMC
April 2014

Adaptive evolution of the Retinoid X receptor in vertebrates.

Genomics 2012 Feb 14;99(2):81-9. Epub 2011 Dec 14.

CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal.

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http://dx.doi.org/10.1016/j.ygeno.2011.12.001DOI Listing
February 2012

IMPACT: integrated multiprogram platform for analyses in ConTest.

J Hered 2011 May-Jun;102(3):366-9. Epub 2011 Mar 16.

CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal.

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http://dx.doi.org/10.1093/jhered/esr003DOI Listing
July 2011

Positive selection on the killer whale mitogenome.

Biol Lett 2011 Feb 1;7(1):116-8. Epub 2010 Sep 1.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350 Copenhagen, Denmark.

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http://dx.doi.org/10.1098/rsbl.2010.0638DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030902PMC
February 2011

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

J Theor Biol 2010 Dec 16;267(3):388-95. Epub 2010 Sep 16.

REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal.

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http://dx.doi.org/10.1016/j.jtbi.2010.09.012DOI Listing
December 2010

Amino acid patterns around disulfide bonds.

Int J Mol Sci 2010 Nov 18;11(11):4673-86. Epub 2010 Nov 18.

REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal; E-Mail:

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http://dx.doi.org/10.3390/ijms11114673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000107PMC
November 2010

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

BMC Evol Biol 2010 Sep 15;10:281. Epub 2010 Sep 15.

CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, Porto, Portugal.

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http://dx.doi.org/10.1186/1471-2148-10-281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955027PMC
September 2010

Positive selection on apoptosis related genes.

FEBS Lett 2010 Feb 22;584(3):469-76. Epub 2009 Dec 22.

Department of Integrative Biology, UC-Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.febslet.2009.12.022DOI Listing
February 2010

Patterns of positive selection in six Mammalian genomes.

PLoS Genet 2008 Aug 1;4(8):e1000144. Epub 2008 Aug 1.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483296PMC
August 2008

The adaptive evolution of the mammalian mitochondrial genome.

BMC Genomics 2008 Mar 4;9:119. Epub 2008 Mar 4.

REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
Publisher Site
http://dx.doi.org/10.1186/1471-2164-9-119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375446PMC
March 2008

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

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

REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.

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http://dx.doi.org/10.1016/j.gene.2006.08.017DOI Listing
January 2007