Visualitza per autoria "Kuderna, Lukas, 1989-"

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  • A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)
    Kuderna, Lukas, 1989-; Laayouni, Hafid, 1968-; García Pérez, Raquel, 1989-; Povolotskaya, Inna, 1986-; Serres Armero, Aitor, 1992-; Gómez Garrido, Jèssica; Alioto, Tyler; Navarro i Cuartiellas, Arcadi, 1969-; Bertranpetit, Jaume, 1952-; Marquès i Bonet, Tomàs, 1975- (Oxford University Press, 2017)
    The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high-quality reference genome assembly; however, as with most mammalian genomes, the current ...
  • A comparative genomics multitool for scientific discovery and conservation
    Zoonomia Consortium; Serres Armero, Aitor, 1992-; Juan, David; Kuderna, Lukas, 1989-; Marquès i Bonet, Tomàs, 1975- (Nature Research, 2020)
    The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe ...
  • A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)
    Palmada Flores, Marc; Orkin, Joseph D.; Haase, Bettina; Mountcastle, Jacquelyn; Bertelsen, Mads F.; Fedrigo, Olivier; Kuderna, Lukas, 1989-; Jarvis, Erich D.; Marquès i Bonet, Tomàs, 1975- (Oxford University Press, 2022)
    Background: The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in ...
  • Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum
    Boubli, Jean P.; Ruiz-Gartzia, Irune; Kuderna, Lukas, 1989-; Marquès i Bonet, Tomàs, 1975-; Roos, Christian (Science Press, 2021)
    The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo ...
  • Application of genome assembly methods to human and non-human primate genomics
    Kuderna, Lukas, 1989- (Universitat Pompeu Fabra, 2020-02-14)
    Genomic analyses are at the center of contemporary biology. These studies heavily rely on reference genome assemblies, yet those are typically highly fragmented. Having accurate representations of complex genomes, or parts ...
  • Arctic-adapted dogs emerged at the Pleistocene-Holocene transition
    Sinding, Mikkel Holger S.; Kuderna, Lukas, 1989-; Marquès i Bonet, Tomàs, 1975-; Gilbert, M Thomas (American Association for the Advancement of Science (AAAS), 2020)
    Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal ...
  • Chimpanzee genomic diversity reveals ancient admixture with bonobos
    de Manuel, Marc; Kuhlwilm, Martin; Sousa, Victor C.; Prado Martínez, Javier, 1987-; Hernández Rodríguez, Jéssica, 1983-; Dupanloup, Isabelle; Lao Grueso, Oscar, 1976-; Heredia Genestar, José María, 1985-; Kuderna, Lukas, 1989-; Casals López, Ferran; Angedakin, Samuel; Arandjelovic, Mimi; Boesch, Christophe; Kühl, Hjalmar S.; Vigilant, Linda; Navarro i Cuartiellas, Arcadi, 1969-; Excoffier, Laurent; Marquès i Bonet, Tomàs, 1975- (American Association for the Advancement of Science (AAAS), 2016)
    Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that ...
  • Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly
    Warren, Wesley C.; García Pérez, Raquel, 1989-; Xu, Sen; Lampert, Kathrin P.; Chapolin, Domitille; Stöck, Matthias; Loewe, Laurence; Lu, Yuan; Kuderna, Lukas, 1989-; Minx, Patrick; Montague, Michael J.; Tomlinson, Chad; Hillier, LeDeana W.; Murphy, Daniel N.; Wang, John; Wang, Zhongwei; Macias Garcia, Constantino; Thomas, Gregg C. W.; Volff, Jean-Nicolas; Farias, Fabiana; Aken, Bronwen; Walter, Ronald B.; Pruitt, Kim D.; Marquès i Bonet, Tomàs, 1975-; Hahn, Matthew W.; Kneitz, Susanne; Lynch, Michael; Schartl, Manfred (Nature Publishing Group, 2018)
    The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual ...
  • Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
    Mak, Sarah Siu Tze; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger S.; Kuderna, Lukas, 1989-; Zhang, Wenwei; Fu, Shujin; Vieira, Filipe Garrett; Germonpré, Mietje; Bocherens, Hervé; Fedorov, Sergey E.; Petersen, Bent; Sicheritz-Ponten, Thomas; Marquès i Bonet, Tomàs, 1975-; Zhang, Guojie; Jiang, Hui; Gilbert, M Thomas (Oxford University Press, 2017)
    Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant ...
  • Complex evolutionary history with extensive ancestral gene flow in an African primate radiation
    Jensen, Axel; Swift, Frances; de Vries, Dorien; Beck, Robin M. D.; Kuderna, Lukas, 1989-; Knauf, Sascha; Chuma, Idrissa S.; Keyyu, Julius D.; Kitchener, Andrew C.; Farh, Kyle; Rogers, Jeffrey; Marquès i Bonet, Tomàs, 1975-; Detwiler, Kate M.; Roos, Christian; Guschanski, Katerina (Oxford University Press, 2023)
    Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons ...
  • Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual
    Kuderna, Lukas, 1989-; Solís Moruno, Manuel, 1993-; Batlle Masó, Laura, 1993-; Julià, Eva; Lizano González, Esther, 1974-; Anglada Busquets, Roger; Ramírez Bautista, Eva; Bote, Alex; Tormo, Marc; Marquès i Bonet, Tomàs, 1975-; Fornas Carreño, Oscar; Casals López, Ferran (Frontiers Media, 2020)
    Sorting of individual chromosomes by Flow Cytometry (flow-sorting) is an enrichment method to potentially simplify genome assembly by isolating chromosomes from the context of the genome. We have recently developed a ...
  • Genomic legacy of the African cheetah, Acinonyx jubatus
    Dobrynin, Pavel; Liu, Shiping; Tamazian, Gaik; Xiong, Zijun; Yurchenko, Andrey A.; Krasheninnikova, Ksenia; Kliver, Sergey; Schmidt-Küntzel, Anne; Koepfli, Klaus-Peter; Johnson, Warren; Kuderna, Lukas, 1989-; García Pérez, Raquel, 1989-; de Manuel, Marc; Godinez, Ricardo; Komissarov, Aleksey; Makunin, Alexey; Brukhin, Vladimir; Qiu, Weilin; Zhou, Long; Li, Fang; Yi, Jian; Driscoll, Carlos; Antunes, Agostinho; Oleksyk, Taras K.; Eizirik, Eduardo; Perelman, Polina; Roelke, Melody; Wildt, David; Diekhans, Mark; Marquès i Bonet, Tomàs, 1975-; Marker, Laurie; Bhak, Jong; Wang, Jun; Zhang, Guojie; O'Brien, Stephen J. (BioMed Central, 2015)
    BACKGROUND: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS: Here the genome sequence of wild-born African cheetahs ...
  • Genomic legacy of the African cheetah, Acinonyx jubatus
    Dobrynin, Pavel; Kuderna, Lukas, 1989-; García Pérez, Raquel, 1989-; de Manuel, Marc; Marquès i Bonet, Tomàs, 1975-; O’Brien, Stephen J. (BioMed Central, 2015)
    BACKGROUND: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS: Here the genome sequence of wild-born African cheetahs ...
  • Giant tortoise genomes provide insights into longevity and age-related disease
    Quesada, Víctor; Kuderna, Lukas, 1989-; Marquès i Bonet, Tomàs, 1975-; López Otín, Carlos (Nature Research, 2019)
    Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on ...
  • Identification of constrained sequence elements across 239 primate genomes
    Kuderna, Lukas, 1989-; Valenzuela, Alejandro; Navarro i Cuartiellas, Arcadi, 1969-; Marquès i Bonet, Tomàs, 1975-; Kai-How Farh, Kyle (Nature Research, 2023)
    Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in ...
  • Insights from the rescue and breeding management of Cuvier’s gazelle (Gazella cuvieri) through whole-genome sequencing
    Alvarez-Estape, Marina; Fontseré Alemany, Clàudia, 1992-; Serres Armero, Aitor, 1992-; Kuderna, Lukas, 1989-; Dobrynin, Pavel; Guidara, Héla; Pukazhenthi, Budhan S.; Koepfli, Klaus-Peter; Marquès i Bonet, Tomàs, 1975-; Moreno, Eulalia; Lizano González, Esther, 1974- (Wiley, 2022)
    Captive breeding programmes represent the most intensive type of ex situ population management for threatened species. One example is the Cuvier’s gazelle programme that started in 1975 with only four founding individuals, ...
  • Interspecific gene flow shaped the evolution of the genus canis
    Gopalakrishnan, Shyam; Montero, Marc de Manuel; Kuderna, Lukas, 1989-; Serres Armero, Aitor, 1992-; González-Basallote, Víctor Manuel; Marquès i Bonet, Tomàs, 1975-; Gilbert, M Thomas (Elsevier, 2018)
    The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1-6]. We assembled ...
  • Return to the sea, get huge, beat cancer: an analysis of cetacean genomes including an asssembly for the humpback whale (megaptera novaeangliae)
    Tollis, Marc; Robbins, Jooke; Webb, Andrew E.; Kuderna, Lukas, 1989-; Caulin, Aleah F.; Garcia, Jacinda D.; Bèrubè, Martine; Pourmand, Nader; Marquès i Bonet, Tomàs, 1975-; O'Connell, Mary J.; Palsbøll, Per J.; Maley, Carlo C. (Oxford University Press, 2019)
    Cetaceans are a clade of highly specialized aquatic mammals that include the largest animals that have ever lived. The largest whales can have ∼1,000× more cells than a human, with long lifespans, leaving them theoretically ...
  • Selective single molecule sequencing and assembly of a human Y chromosome of African origin
    Kuderna, Lukas, 1989-; Lizano González, Esther, 1974-; Julià, Eva; Gómez Garrido, Jèssica; Serres Armero, Aitor, 1992-; Kuhlwilm, Martin; Alandes, Regina Antoni; Alvarez-Estape, Marina; Juan, David; Simon, Heath; Alioto, Tyler; Gut, Marta; Gut, Ivo Glynne; Schierup, Mikkel H.; Fornas Carreño, Oscar; Marquès i Bonet, Tomàs, 1975- (Nature Research, 2019)
    Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have their Y chromosome properly ...
  • Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing
    Serres Armero, Aitor, 1992-; Povolotskaya, Inna, 1986-; Quilez Oliete, Javier; Ramírez, Oscar; Santpere Baró, Gabriel, 1981-; Kuderna, Lukas, 1989-; Hernández Rodríguez, Jéssica, 1983-; Fernández Callejo, Marcos; Gómez Sánchez, Daniel; Freedman, Adam H.; Fan, Zhenxin; Novembre, John; Navarro i Cuartiellas, Arcadi, 1969-; Boyko, Adam; Wayne, Robert K.; Vilà, Carles; Lorente-Galdós, Belén, 1981-; Marquès i Bonet, Tomàs, 1975- (BioMed Central, 2017)
    BACKGROUND: Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites ...

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