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1.
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21 p, 11.5 MB |
Identification of constrained sequence elements across 239 primate genomes
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Kuderna, Lukas F. K. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Ulirsch, Jacob C. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Rashid, Sabrina (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Ameen, Mohamed (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Sundaram, Laksshman (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Hickey, Glenn (University of California. Santa Cruz Genomics Institute) ;
Cox, Anthony J. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Gao, Hong (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Kumar, Arvind (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Aguet, Francois (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Christmas, Matthew J. (Uppsala University. Department of Medical Biochemistry and Microbiology) ;
Clawson, Hiram (University of California. Santa Cruz Genomics Institute) ;
Haeussler, Maximilian (University of California. Santa Cruz Genomics Institu) ;
Janiak, Mareike C. (University of Salford. School of Science, Engineering and Environment) ;
Kuhlwilm, Martin (University of Vienna. Department of Evolutionary Anthropology) ;
Orkin, Joseph D. (Université de Montréal. Département d'Anthropologie) ;
Bataillon, Thomas (Aarhus University. Bioinformatics Research Centre) ;
Shivakumara Manu (Academy of Scientific and Innovative Research (Ghaziabad, Índia)) ;
Valenzuela, Alejandro (Institut de Biologia Evolutiva (Barcelona)) ;
Bergman, Juraj (Aarhus University. Bioinformatics Research Centre) ;
Rouselle, Marjolaine (Aarhus University. Bioinformatics Research Centre) ;
Silva, Felipe Ennes (Mamirauá Institute for Sustainable Development) ;
Agueda Calpena, Lidia (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
Blanc, Julie (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
Gut, Marta (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
de Vries, Dorien (University of Salford. School of Science, Engineering and Environment) ;
Goodhead, Ian (University of Salford. School of Science, Engineering and Environment) ;
Harris, R. Alan (Baylor College of Medicine. Department of Molecular and Human Genetics) ;
Raveendran, Muthuswamy (Baylor College of Medicine. Department of Molecular and Human Genetics) ;
Jensen, Axel (Uppsala University. Department of Ecology and Genetics) ;
Chuma, Idriss S. (Tanzania National Parks) ;
Horvath, Julie E. (University of North Carolina at Chapel Hill. Renaissance Computing Institute) ;
Hvilsom, Christina (Copenhagen Zoo) ;
Juan, David (Institut de Biologia Evolutiva (Barcelona)) ;
Frandsen, Peter (Copenhagen Zoo) ;
Schraiber, Joshua G. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
de Melo, Fabiano R. (Universidade Federal de Viçosa) ;
Bertuol, Fabrício (Universidade Federal do Amazonas. Departamento de Genética) ;
Byrne, Hazel (University of Utah. Department of Anthropology) ;
Sampaio, Iracilda (Universidade Federal do Pará (Brasil)) ;
Pires Farias, Izeni (Universidade Federal do Amazonas. Departamento de Genética) ;
Valsecchi, João (Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica-ComFauna) ;
Messias, Malu (Universidade Federal de Rondônia) ;
da Silva, Maria N. F. (Instituto Nacional de Pesquisas da Amazônia) ;
Trivedi, Mihir (Centre for Cellular and Molecular Biology (Hyderabad, Índia)) ;
Rossi, Rogerio (Universidade Federal do Mato Grosso. Instituto de Biociências) ;
Hrbek, Tomas (Trinity University. Department of Biology) ;
Andriaholinirina, Nicole (University of Mahajanga. Faculty of Science, Technology and Environment) ;
Rabarivola, Clément J. (University of Mahajanga. Faculty of Science, Technology and Environment) ;
Zaramody, Alphonse (University of Mahajanga. Faculty of Science, Technology and Environment) ;
Jolly, Clifford J. (New York University .Department of Anthropology) ;
Phillips-Conroy, Jane (Washington University School of Medicine in St Louis. Department of Neuroscience) ;
Wilkerson, Gregory (MD Anderson Cancer Center. Keeling Center for Comparative Medicine and Research) ;
Abbee, C. (MD Anderson Cancer Center. Keeling Center for Comparative Medicine and Research) ;
Simmons, Joe H. (MD Anderson Cancer Center. Keeling Center for Comparative Medicine and Research) ;
Fernandez-Duque, Eduardo (Yale University. Department of Anthropology) ;
Kanthaswamy, Sree (University of California. California National Primate Research Center) ;
Shiferaw, Fekadu (The Carter Center Ethiopia) ;
Wu, Dong-Dong (Chinese Academy of Sciences. Kunming Institute of Zoology. State Key Laboratory of Genetic Resources and Evolution) ;
Zhou, Long (Zhejiang University School of Medicine. Center for Evolutionary and Organismal Biology) ;
Shao, Yong (Chinese Academy of Sciences. Kunming Institute of Zoology. State Key Laboratory of Genetic Resources and Evolution) ;
Zhang, Guojie (Zhejiang University Medical Center) ;
Keyyu, Julius D. (Tanzania Wildlife Research Institute) ;
Knauf, Sascha (Justus Liebig University. Faculty of Veterinary Medicine) ;
Le, Minh D. (Vietnam National University. Department of Environmental Ecology) ;
Lizano, Esther (Institut Català de Paleontologia Miquel Crusafont) ;
Merker, Stefan epartment of Environmental Ecology (State Museum of Natural History Stuttgart. Department of Zoology) ;
Navarro, Arcadi, 1969- (Institut de Biologia Evolutiva (Barcelona)) ;
Nadler, Tilo (Cuc Phuong Commune) ;
Khor, Chiea Chuen (Genome Institute of Singapore) ;
Lee, Jessica (Mandai Nature) ;
Tan, Patrick (Duke-NUS Medical School) ;
Lim, Weng Khong (SingHealth Duke-NUS Genomic Medicine Centre) ;
Kitchener, Andrew C. (School of Geosciences) ;
Zinner, Dietmar (Leibniz ScienceCampus Primate Cognition) ;
Gut, Ivo (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
Melin, Amanda D. (University of Calgary. Alberta Children's Hospital Research Institute) ;
Guschanski, Katerina (University of Edinburgh. School of Biological Sciences) ;
Schierup, Mikkel Heide (Aarhus University. Bioinformatics Research Centre) ;
Beck, Robin (University of Salford. School of Science, Engineering and Environment) ;
Karakikes, Ioannis (Stanford University. Department of Cardiothoracic Surgery) ;
Wang, Kevin C. (Veterans Affairs Palo Alto Healthcare System) ;
Umapathy, Govindhaswamy (Centre for Cellular and Molecular Biology (Hyderabad, Índia)) ;
Roos, Christian (Leibniz Institute for Primate Research. German Primate Center) ;
Boubli, Jean (University of Salford. School of Science, Engineering and Environment) ;
Siepel, Adam (Simons Center for Quantitative Biology. Cold Spring Harbor Laboratory) ;
Kundaje, Anshul (Stanford University. Department of Genetics) ;
Paten, Benedict (University of California. Santa Cruz Genomics Institute) ;
Lindblad-Toh, Kerstin (Uppsala University. Department of Medical Biochemistry and Microbiology) ;
Rogers, Jeffrey (Baylor College of Medicine. Department of Molecular and Human Genetics) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Farh, Kyle Kai-How (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units))
Noncoding DNA is central to our understanding of human gene regulation and complex diseases and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome. [...]
2023 -  10.1038/s41586-023-06798-8
Nature, Published online nov. 2023
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2.
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11 p, 2.4 MB |
Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability : the case of Malassezia
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Christinaki, Anastasia C. (Westerdijk Fungal Biodiversity Institute) ;
Theelen, Bart (Westerdijk Fungal Biodiversity Institute) ;
Zania, Alkmini (Westerdijk Fungal Biodiversity Institute) ;
Coutinho, Selene Dall' Acqua (Paulista University. Laboratory of Molecular and Cellular Biology) ;
Cabañes Sáenz, Francisco Javier (Universitat Autònoma de Barcelona. Departament de Sanitat i d'Anatomia Animals) ;
Boekhout, Teun (King Saud University. College of Science) ;
Kouvelis, Vassili N. (National and Kapodistrian University of Athens. Department of Biology)
Mitogenomes are essential due to their contribution to cell respiration. Recently they have also been implicated in fungal pathogenicity mechanisms. Members of the basidiomycetous yeast genus Malassezia are an important fungal component of the human skin microbiome, linked to various skin diseases, bloodstream infections, and they are increasingly implicated in gut diseases and certain cancers. [...]
2023 - 10.1038/s41598-023-33486-4
Scientific reports, Vol. 13 (april 2023)
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3.
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11 p, 1.4 MB |
Microchromosomes are building blocks of bird, reptile, and mammal chromosomes
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Waters, Paul D. (UNSW Sydney. School of Biotechnology and Biomolecular Science) ;
Patel, Hardip R. (Australian National University. The John Curtin School of Medical Research) ;
Ruiz-Herrera Moreno, Aurora (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Álvarez-González, Lucía (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Lister, Nicholas C. (UNSW Sydney. School of Biotechnology and Biomolecular Science) ;
Simakov, Oleg (University of Vienna. Department of Neurosciences and Developmental Biology) ;
Ezaz, Tariq (University of Canberra. Institute for Applied Ecology) ;
Kaur, Parwinder (The University of Western Australia. UWA School of Agriculture and Environment) ;
Frere, Celine (University of the Sunshine Coast (Australia)) ;
Grutzner, Frank (University of Adelaide. School of Biological Sciences (Australia)) ;
Georges, Arthur (University of Canberra. Institute for Applied Ecology) ;
Marshall Graves, Jennifer A. (La Trobe University. School of Life Sciences (Australia))
Microchromosomes, once considered unimportant shreds of the chicken genome, are gene-rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole-genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds, and mammals. [...]
2021 - 10.1073/pnas.2112494118
Proceedings of the National Academy of Sciences of the United States of America, Vol. 118, Issue 45 (November 2021) , art. e2112494118
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4.
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32 p, 22.5 MB |
Towards complete and error-free genome assemblies of all vertebrate species
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Rhie, Arang (National Institutes of Health. National Human Genome Research Institute (USA)) ;
McCarthy, Shane A. (University of Cambridge. Department of Genetics (UK)) ;
Fedrigo, Olivier (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Damas, Joana (University of California Davis. The Genome Center (USA)) ;
Formenti, Giulio (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Koren, Sergey (National Institutes of Health. National Human Genome Research Institute (USA)) ;
Uliano da Silva, Marcela (Leibniz Institute for Zoo and Wildlife Research. Department of Evolutionary Genetics (Germany)) ;
Chow, William (Wellcome Trust Sanger Institute (Regne Unit)) ;
Fungtammasan, Arkarachai (DNAnexus Inc. (USA)) ;
Kim, Juwan (Seoul National University. Interdisciplinary Program in Bioinformatics (Republic of Korea)) ;
Lee, Chul (Seoul National University. Interdisciplinary Program in Bioinformatics (Republic of Korea)) ;
Ko, Byung June (Seoul National University. Department of Agricultural Biotechnology (Republic of Korea)) ;
Chaisson, Mark (University of Southern California (USA)) ;
Gedman, Gregory L. (The Rockefeller University. Laboratory of Neurogenetics of Language (USA)) ;
Cantin, Lindsey J. (The Rockefeller University. Laboratory of Neurogenetics of Language (USA)) ;
Thibaud-Nissen, Françoise (National Library of Medicine. National Center for Biotechnology Information (USA)) ;
Haggerty, Leanne (European Bioinformatics Institute. European Molecular Biology Laboratory (UK)) ;
Bista, Iliana (University of Cambridge. Department of Genetics (UK)) ;
Smith, Michelle (Wellcome Trust Sanger Institute (Regne Unit)) ;
Haase, Bettina (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Mountcastle, Jacquelyn (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Winkler, Sylke (Max Planck Institute of Molecular Cell Biology and Genetics (Germany)) ;
Paez, Sadye (The Rockefeller University. Vertebrate Genome Lab (USA)) ;
Howard, Jason (Novogene (USA)) ;
Vernes, Sonja C. (Donders Institute for Brain, Cognition and Behaviour (The Netherlands)) ;
Lama, Tanya M. (University of Massachusetts. Cooperative Fish and Wildlife Research Unit (USA)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Warren, Wesley (University of Missouri. Bond Life Sciences Center (USA)) ;
Balakrishnan, Christopher N. (East Carolina University. Department of Biology (USA)) ;
Burt, Dave (University of Queensland. UQ Genomics (Australia)) ;
George, Julia M. (Clemson University. Department of Biological Sciences (USA)) ;
Biegler, Matthew T. (The Rockefeller University. Laboratory of Neurogenetics of Language (USA)) ;
Iorns, David (The Genetic Rescue Foundation (New Zealand)) ;
Digby, Andrew (Kākāpō Recovery, Department of Conservation (New Zealand)) ;
Eason, Daryl (Kākāpō Recovery, Department of Conservation (New Zealand)) ;
Robertson, Bruce (University of Otago. Department of Zoology (New Zealand)) ;
Edwards, Taylor (University of Arizona Genetics Core (USA)) ;
Wilkinson, Mark (Natural History Museum. Department of Life Sciences (UK)) ;
Turner, George (Bangor University. School of Natural Sciences (UK)) ;
Meyer, Axel (University of Konstanz. Department of Biology (Germany)) ;
Kautt, Andreas F. (University of Konstanz. Department of Biology (Germany)) ;
Franchini, Paolo (University of Konstanz. Department of Biology (Germany)) ;
Detrich III, H. William (Northeastern University Marine Science Center. Department of Marine and Environmental Sciences (USA)) ;
Svardal, Hannes (University of Antwerp. Department of Biology (Belgium)) ;
Wagner, Maximilian (Karl-Franzens University of Graz. Institute of Biology (Austria)) ;
Naylor, Gavin J. P. (University of Florida. Florida Museum of Natural History (USA)) ;
Pippel, Martin (Max Planck Institute of Molecular Cell Biology and Genetics (Germany)) ;
Malinsky, Milan (University of Basel. Zoological Institute (Switzerland)) ;
Mooney, Mark (Tag.bio (USA)) ;
Simbirsky, Maria (DNAnexus Inc. (USA)) ;
Hannigan, Brett T. (DNAnexus Inc. (USA)) ;
Pesout, Trevor (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Houck, Marlys (San Diego Zoo Global (USA)) ;
Misuraca, Ann (San Diego Zoo Global (USA)) ;
Kingan, Sarah B. (Pacific Biosciences (USA)) ;
Hall, Richard (Pacific Biosciences (USA)) ;
Kronenberg, Zev (Pacific Biosciences (USA)) ;
Sović, Ivan (Pacific Biosciences (USA)) ;
Dunn, Christopher (Pacific Biosciences (USA)) ;
Ning, Zemin (Wellcome Trust Sanger Institute (Regne Unit)) ;
Hastie, Alex (Bionano Genomics (USA)) ;
Lee, Joyce (Bionano Genomics (USA)) ;
Selvaraj, Siddarth (Arima Genomics (USA)) ;
Green, Richard E. (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Putnam, Nicholas H. (Independent Researcher. Santa Cruz (USA)) ;
Gut, Ivo (Centro Nacional de Análisis Genómico. Instituto de Ciencia y Tecnología de Barcelona) ;
Ghurye, Jay (University of Maryland College Park. Department of Computer Science (USA)) ;
Garrison, Erik (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Sims, Ying (Wellcome Trust Sanger Institute (Regne Unit)) ;
Collins, Joanna (Wellcome Trust Sanger Institute (Regne Unit)) ;
Pelan, Sarah (Wellcome Trust Sanger Institute (Regne Unit)) ;
Torrance, James (Wellcome Trust Sanger Institute (Regne Unit)) ;
Tracey, Alan (Wellcome Trust Sanger Institute (Regne Unit)) ;
Wood, Jonathan (Wellcome Trust Sanger Institute (Regne Unit)) ;
Dagnew, Robel E. (University of Southern California (USA)) ;
Guan, Dengfeng (Harbin Institute of Technology. Center for Bioinformatics. School of Computer Science and Technology (China)) ;
London, Sarah E. (University of Chicago. Institute for Mind and Biology. Department of Psychology (USA)) ;
Clayton, David F. (Clemson University. Department of Genetics and Biochemistry (USA)) ;
Mello, Claudio V. (Oregon Health and Science University. Department of Behavioral Neuroscience (USA)) ;
Friedrich, Samantha R. (Oregon Health and Science University. Department of Behavioral Neuroscience (USA)) ;
Lovell, Peter V. (Oregon Health and Science University. Department of Behavioral Neuroscience (USA)) ;
Osipova, Ekaterina (Max Planck Institute for the Physics of Complex Systems (Germany)) ;
Al-Ajli, Farooq O. (Monash University Malaysia. Tropical Medicine and Biology Multidisciplinary Platform (Malaysia)) ;
Secomandi, Simona (University of Milan. Department of Biosciences (Italy)) ;
Kim, Heebal (Seoul National University. Interdisciplinary Program in Bioinformatics (Republic of Korea)) ;
Theofanopoulou, Constantina (The Rockefeller University. Laboratory of Neurogenetics of Language (USA)) ;
Hiller, Michael (Goethe-University. Faculty of Biosciences (Germany)) ;
Zhou, Yang (BGI-Shenzhen (China)) ;
Harris, Robert S. (Pennsylvania State University. Department of Biology (USA)) ;
Makova, Kateryna D. (Pennsylvania State University. Department of Biology (USA)) ;
Medvedev, Paul (Pennsylvania State University. Center for Medical Genomics (USA)) ;
Hoffman, Jinna (National Library of Medicine. National Center for Biotechnology Information (USA)) ;
Masterson, Patrick (National Library of Medicine. National Center for Biotechnology Information (USA)) ;
Clark, Karen (National Library of Medicine. National Center for Biotechnology Information (USA)) ;
Martin, Fergal J. (European Bioinformatics Institute. European Molecular Biology Laboratory (UK)) ;
Howe, Kevin (European Bioinformatics Institute. European Molecular Biology Laboratory (UK)) ;
Flicek, Paul (European Bioinformatics Institute. European Molecular Biology Laboratory (UK)) ;
Walenz, Brian P. (National Institutes of Health. National Human Genome Research Institute (USA)) ;
Kwak, Woori (eGnome, Inc. (Republic of Korea)) ;
Clawson, Hiram (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Diekhans, Mark (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Nassar, Luis (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Paten, Benedict (University of California. UC Santa Cruz Genomics Institute (USA)) ;
Kraus, Robert H. S. (Max Planck Institute of Animal Behavior. Department of Migration (Germany)) ;
Crawford, Andrew J. (Universidad de los Andes. Department of Biological Sciences (Colombia)) ;
Gilbert, M. Thomas P. (University of Copenhagen. The GLOBE Institute. Center for Evolutionary Hologenomics (Denmark)) ;
Zhang, Guojie (Chinese Academy of Sciences. Center for Excellence in Animal Evolution and Genetics (China)) ;
Venkatesh, Byrappa (A*STAR. Institute of Molecular and Cell Biology (Singapore)) ;
Murphy, Robert W. (Royal Ontario Museum. Centre for Biodiversity (Canada)) ;
Koepfli, Klaus-Peter (Smithsonian Conservation Biology Institute) ;
Shapiro, Beth (Howard Hughes Medical Institute (USA)) ;
Johnson, Warren E. (Smithsonian Conservation Biology Institute) ;
Di Palma, Federica (University of East Anglia. Earlham Institute. Department of Biological Sciences (UK)) ;
Teeling, Emma C. (University College Dublin. School of Biology and Environmental Science (Ireland)) ;
Warnow, Tandy (The University of Illinois at Urbana-Champaign. Department of Computer Science (USA)) ;
Graves, Jennifer Marshall (La Trobe University. School of Life Science (Australia)) ;
Ryder, Oliver A. (University of California San Diego. Department of Evolution, Behavior, and Ecology (USA)) ;
Haussler, David (University of California Santa Cruz. Department of Ecology and Evolutionary Biology (USA)) ;
O'Brien, Stephen J. (ITMO University. Laboratory of Genomics Diversity-Center for Computer Technologies (Russian Federation)) ;
Korlach, Jonas (Pacific Biosciences (USA)) ;
Lewin, Harris A. (University of California Davis. John Muir Institute for the Environment (USA)) ;
Howe, Kerstin (Wellcome Trust Sanger Institute (Regne Unit)) ;
Myers, Eugene W. (Max Planck Institute of Molecular Cell Biology and Genetics (Germany)) ;
Durbin, Richard (University of Cambridge. Department of Genetics (UK)) ;
Phillippy, Adam M. (National Institutes of Health. National Human Genome Research Institute (USA)) ;
Jarvis, Erich (The Rockefeller University. Vertebrate Genome Lab (USA))
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species 1, 2, 3, 4. [...]
2021 - 10.1038/s41586-021-03451-0
Nature, Vol. 592 (April 2021) , p. 737-746
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5.
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6.
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14 p, 1.8 MB |
Evolutionary and functional impact of common polymorphic inversions in the human genome
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Giner-Delgado, Carla (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Villatoro, Sergi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Lerga Jaso, Jon (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Gayà Vidal, Magdalena (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Oliva Pavia, Meritxell (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Castellano Esteve, David (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pantano, Lorena (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Bitarello, Bárbara D. (Max-Planck-Institut für Evolutionäre Anthropologie) ;
Izquierdo Fontanills, David (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Noguera, Isaac (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Olalde, Iñigo (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Delprat Obeaga, Alejandra (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Blancher, Antoine (Centre de Physiopathologie Toulouse-Purpan) ;
Lalueza-Fox, Carles (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Esko, Tõnu (Estonian Genome Center) ;
O'Reilly, Paul F. (King's College London. Institute of Psychiatry, Psychology & Neuroscience) ;
Andrés, Aida M. (Max-Planck-Institut für Evolutionäre Anthropologie) ;
Ferretti, Luca (University of Oxford. Big Data Institute) ;
Puig Font, Marta (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Cáceres Aguilar, Mario (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Inversions are one type of structural variants linked to phenotypic differences and adaptation in multiple organisms. However, there is still very little information about polymorphic inversions in the human genome due to the difficulty of their detection. [...]
2019 - 10.1038/s41467-019-12173-x
Nature communications, Vol. 10 (2019) , art. 4222
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7.
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6 p, 700.6 KB |
IMKT : the integrative McDonald and Kreitman test
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Murga-Moreno, Jesus (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Coronado-Zamora, Marta (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Hervás Fernández, Sergi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Casillas Viladerrams, Sònia (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
The McDonald and Kreitman test (MKT) is one of the most powerful and widely used methods to detect and quantify recurrent natural selection using DNA sequence data. Here we present iMKT (acronym for integrative McDonald and Kreitman test), a novel web-based service performing four distinct MKT types. [...]
2019 - 10.1093/nar/gkz372
Nucleic acids research, Vol. 47, issue W1 (Jan. 2019) , p. W283-W288
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8.
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10 p, 3.7 MB |
PopHumanScan : the online catalog of human genome adaptation
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Murga-Moreno, Jesus (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Coronado-Zamora, Marta (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Bodelon de Frutos, Alejandra (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Casillas Viladerrams, Sònia (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Since the migrations that led humans to colonize Earth, our species has faced frequent adaptive challenges that have left signatures in the landscape of genetic variation and that we can identify in our today-s genomes. [...]
2019 - 10.1093/nar/gky959
Nucleic acids research, Vol. 47, issue D1 (Jan 2019) , p. D1080-D1089
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9.
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21 p, 1.7 MB |
Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects
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Karageorgiou, Charikleia (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Gámez Visairas, Víctor (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Tarrío, Rosa (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Rodríguez-Trelles, Francisco (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Background: Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, together with the available wealth of genetic marker information, to assemble and annotate a high-quality nuclear and complete mitochondrial genome for the species. [...]
2019 - 10.1186/s12864-019-5590-8
BMC genomics, Vol. 20 (March 2019) , art. 223
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10.
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27 p, 2.2 MB |
Novel polyomaviruses in mammals from multiple orders and reassessment of polyomavirus evolution and taxonomy
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Ehlers, Bernhard (Robert Koch Institute. Division 12 Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients) ;
Anoh, A. E. (Université Alassane Ouattara. Centre de Recherche pour le Développement) ;
Salem, N. B. (Robert Koch Institute. Division 12 Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients) ;
Broll, S. (Robert Koch Institute. Division 12 Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients) ;
Couacy-Hymann, E. (Laboratoire National d'Appui Au Développement Agricole. Laboratoire Central de Pathologie Animale) ;
Fischer, D. (Robert Koch Institute. Division 12 Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients) ;
Gedvilaite, A. (Institute of Biotechnology. Vilnius University) ;
Ingenhütt, N. (Robert Koch Institute. Division 12 Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients) ;
Liebmann, S. (Robert Koch Institute. Division 12 Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients) ;
Martin, Maite (Institut de Recerca i Tecnologia Agroalimentàries. Centre de Recerca en Sanitat Animal) ;
Mossoun, A. (Laboratoire National d'Appui Au Développement Agricole. Laboratoire Central de Pathologie Animale) ;
Mugisha, L. (Makerere University. College of Veterinary Medicine. Animal Resources and Biosecurity (COVAB)) ;
Muyembe-Tamfum, J. J. (Institut National de Recherche Bio-Médicale) ;
Pauly, M. (Robert Koch Institute. Epidemiology of Highly Pathogenic Microorganisms) ;
De Val, B. P. (Institut de Recerca i Tecnologia Agroalimentàries. Centre de Recerca en Sanitat Animal) ;
Preugschas, H. (Robert Koch Institute. Division 12 Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients) ;
Richter, D. (Technische Universität Braunschweig) ;
Schubert, G. (Robert Koch Institute. Epidemiology of Highly Pathogenic Microorganisms) ;
Szentiks, C. A. (Leibniz Institute for Zoo and Wildlife Research (IZW)) ;
Teichmann, T. (Robert Koch Institute. Division 12 Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients) ;
Walter, C. (Robert Koch Institute. Division 12 Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients) ;
Ulrich, R. G. (Partner Site Hamburg-Lübeck-Borstel-Insel Riems. German Center for Infection Research (DZIF)) ;
Wiersma, L. (Robert Koch Institute. Epidemiology of Highly Pathogenic Microorganisms) ;
Leendertz, F. H. (Robert Koch Institute. Epidemiology of Highly Pathogenic Microorganisms) ;
Calvignac-Spencer, S. (Robert Koch Institute. Viral Evolution)
As the phylogenetic organization of mammalian polyomaviruses is complex and currently incompletely resolved, we aimed at a deeper insight into their evolution by identifying polyomaviruses in host orders and families that have either rarely or not been studied. [...]
2019 - 10.3390/v11100930
Viruses, Vol. 11 Núm. 10 (october 2019) , p. 930
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