Publications by authors named "Juan I Montoya-Burgos"

29Publications

Projecting introgression from domestic cats into European wildcats in the Swiss Jura.

Evol Appl 2020 Sep 5;13(8):2101-2112. Epub 2020 May 5.

Department of Genetics and Evolution - Anthropology Unit Laboratory of Anthropology Genetics and Peopling History University of Geneva Geneva Switzerland.

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http://dx.doi.org/10.1111/eva.12968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7463310PMC
September 2020

Harmonizing hybridization dissonance in conservation.

Commun Biol 2020 Jul 21;3(1):391. Epub 2020 Jul 21.

Laboratory of Anthropology, Genetics and Peopling History, Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.

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http://dx.doi.org/10.1038/s42003-020-1116-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7374702PMC
July 2020

LS: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference.

BMC Bioinformatics 2019 Aug 13;20(1):420. Epub 2019 Aug 13.

Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland.

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http://dx.doi.org/10.1186/s12859-019-3020-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6693147PMC
August 2019

An integrated approach clarifies the cryptic diversity in Hypostomus Lacépède 1803 from the Lower La Plata Basin.

An Acad Bras Cienc 2019 25;91(2):e20180131. Epub 2019 Apr 25.

Département de Génétique et Évolution, Université de Genève, 30 quai Ernest Ansermet, 1211, Genève 4, Switzerland.

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http://dx.doi.org/10.1590/0001-3765201920180131DOI Listing
June 2019

Hybridization and introgression during density-dependent range expansion: European wildcats as a case study.

Evolution 2019 04 6;73(4):750-761. Epub 2019 Mar 6.

Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.

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http://dx.doi.org/10.1111/evo.13704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594108PMC
April 2019

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

Mol Phylogenet Evol 2018 10 7;127:272-279. Epub 2018 Jun 7.

Department of Genetics and Evolution, University of Geneva, Switzerland; Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2018.06.004DOI Listing
October 2018

Effect of hybridization with genome exclusion on extinction risk.

Conserv Biol 2018 10 27;32(5):1139-1149. Epub 2018 Jun 27.

Laboratory of Vertebrate Evolution, Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland.

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http://dx.doi.org/10.1111/cobi.13120DOI Listing
October 2018

Cryptic Biological Invasions: a General Model of Hybridization.

Sci Rep 2018 02 5;8(1):2414. Epub 2018 Feb 5.

Laboratory of vertebrate evolution, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.

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http://dx.doi.org/10.1038/s41598-018-20543-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799175PMC
February 2018

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

Mol Biol Evol 2016 06 23;33(6):1625-34. Epub 2016 Feb 23.

Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland

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http://dx.doi.org/10.1093/molbev/msw043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868118PMC
June 2016

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

Mol Phylogenet Evol 2016 Jan 26;94(Pt B):492-517. Epub 2015 Oct 26.

Université de Lyon, F-69000 Lyon, France; Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2015.10.018DOI Listing
January 2016

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

Evol Appl 2015 Feb 28;8(2):199-210. Epub 2015 Jan 28.

Laboratory of anthropology, genetics and peopling history, Anthropology Unit, Department of Genetics and Evolution, University of Geneva Geneva, Switzerland.

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http://dx.doi.org/10.1111/eva.12245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319866PMC
February 2015

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

PLoS One 2014 8;9(7):e101736. Epub 2014 Jul 8.

Laboratory of molecular phylogeny and evolution in vertebrates, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0101736PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086968PMC
March 2015

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

PLoS One 2011 13;6(9):e24800. Epub 2011 Sep 13.

Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024800PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3172292PMC
February 2012

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

Genome Res 2010 Oct 6;20(10):1432-40. Epub 2010 Aug 6.

Department of Zoology and Animal Biology, University of Geneva, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1101/gr.103846.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945192PMC
October 2010

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

Nature 2010 Mar;464(7285):99-103

National Research Center Frontiers in Genetics, Department of Zoology and Animal Biology, University of Geneva, Sciences III, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1038/nature08789DOI Listing
March 2010

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

BMC Genomics 2010 Feb 22;11:126. Epub 2010 Feb 22.

Department of Zoology and Animal Biology, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1186/1471-2164-11-126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838844PMC
February 2010

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

Genome Res 2009 Apr 18;19(4):602-10. Epub 2009 Feb 18.

National Research Center "Frontiers in Genetics," Department of Zoology and Animal Biology, University of Geneva, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1101/gr.087932.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665779PMC
April 2009

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

Mol Ecol 2009 Mar;18(5):947-64

Department of Zoology and Animal Biology, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1111/j.1365-294X.2008.04068.xDOI Listing
March 2009

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

Mol Phylogenet Evol 2008 Nov 29;49(2):606-17. Epub 2008 Aug 29.

Departamento de Morfologia, Universidade Estadual Paulista Júlio de Mesquita Filho, Instituto de Biociências, Laboratório de Biologia e Genética de Peixes, Rubião Junior 18618000, Botucatu, SP, Brazil.

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http://dx.doi.org/10.1016/j.ympev.2008.08.013DOI Listing
November 2008

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

Mol Phylogenet Evol 2008 Mar 25;46(3):986-1002. Epub 2007 Dec 25.

Département d'herpétologie et d'ichtyologie, Muséum d'histoire naturelle, 1 route de Malagnou, C.P. 6434, CH-1211 Genève 6, Switzerland.

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http://dx.doi.org/10.1016/j.ympev.2007.12.015DOI Listing
March 2008

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

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

Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva, Switzerland.

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http://dx.doi.org/10.1073/pnas.0705658104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2154450PMC
December 2007

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

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

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

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

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://mendel.stanford.edu/sidowlab/pdfs/2007EncodeGR.pdf
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http://www.genome.org/cgi/doi/10.1101/gr.6034307
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http://dx.doi.org/10.1101/gr.6034307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
June 2007

Divergent evolution among teleost V1r receptor genes.

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

Department of Zoology and Animal Biology, University of Geneva, Geneva, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000379PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1849887PMC
April 2007

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

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

Department of Zoology and Animal Biology, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1016/j.ympev.2005.04.028DOI Listing
January 2006