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1.
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63 p, 25.7 MB |
A draft human pangenome reference
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Liao, Wen-Wei (Washington University School of Medicine) ;
Asri, Mobin (University of California) ;
Ebler, Jana (Heinrich Heine University) ;
Doerr, Daniel (Heinrich Heine University) ;
Haukness, Marina (University of California) ;
Hickey, Glenn (University of California) ;
Lu, Shuangjia (Yale University School of Medicine) ;
Lucas, Julian K. (University of California) ;
Monlong, Jean (University of California) ;
Abel, Haley J. (Washington University School of Medicine) ;
Buonaiuto, Silvia (Consiglio Nazionale delle Ricerche. Istituto di Genetica e Biofisica) ;
Chang, Xian H. (University of California) ;
Cheng, Haoyu (Harvard Medical School) ;
Chu, Justin (Dana-Farber Cancer Institute (Boston, Estats Units d'Amèrica)) ;
Colonna, Vincenza (University of Tennessee Health Science Center) ;
Eizenga, Jordan (University of California) ;
Feng, Xiaowen (Harvard Medical School) ;
Fischer, Christian (University of Tennessee Health Science Center) ;
Fulton, Robert S. (Washington University School of Medicine) ;
Garg, Shilpa (Technical University of Denmark) ;
Groza, Cristian (McGill University) ;
Guarracino, Andrea (Tecnopolo umano. Centro di ricerca sulla genomica) ;
Harvey, William T. (University of Washington School of Medicine) ;
Heumos, Simon (University of Tübingen) ;
Howe, Kerstin (Wellcome Trust Sanger Institute (Regne Unit)) ;
Jain, Miten (Northeastern University (USA)) ;
Lu, Tsung-Yu (University of Southern California) ;
Markello, Charles (University of California) ;
Martin, Fergal J. (Wellcome Genome Campus (UK)) ;
Mitchell, Matthew W. (Coriell Institute for Medical Research (USA)) ;
Munson, Katherine M. (University of Washington School of Medicine) ;
Mwaniki, Moses Njagi (Università di Pisa) ;
Novak, Adam M. (University of California) ;
Olsen, Hugh E. (University of California) ;
Pesout, Trevor (University of California) ;
Porubsky, David (University of Washington School of Medicine) ;
Prins, Pjotr (University of Tennessee Health Science Center) ;
Sibbesen, Jonas A. (University of Copenhagen) ;
Sirén, Jouni (University of California) ;
Tomlinson, Chad (Washington University School of Medicine) ;
Villani, Flavia (University of Tennessee Health Science Center) ;
Vollger, Mitchell R. (University of Washington School of Medicine) ;
Antonacci-Fulton, Lucinda L. (Washington University School of Medicine) ;
Baid, Gunjan (Google (USA)) ;
Baker, Carl A. (University of Washington School of Medicine) ;
Belyaeva, Anastasiya (Google (USA)) ;
Billis, Konstantinos (Wellcome Genome Campus (UK)) ;
Carroll, Andrew (Google (USA)) ;
Chang, Pi-Chuan (Google (USA)) ;
Cody, Sarah (Washington University School of Medicine) ;
Cook, Daniel E. (Google (USA)) ;
Cook-Deegan, Robert M. (Arizona State University) ;
Cornejo, Omar E. (University of California) ;
Diekhans, Mark (University of California) ;
Ebert, Peter (Heinrich Heine University) ;
Fairley, Susan (Wellcome Genome Campus (UK)) ;
Fedrigo, Olivier (The Rockefeller University) ;
Felsenfeld, Adam L. (National Institutes of Health (USA)) ;
Formenti, Giulio (The Rockefeller University) ;
Frankish, Adam (Wellcome Genome Campus (UK)) ;
Gao, Yan (The Children's Hospital of Philadelphia) ;
Garrison, Nanibaa' A. (University of California) ;
Giron, Carlos Garcia (Wellcome Genome Campus (UK)) ;
Green, Richard E. (Dovetail Genomics) ;
Haggerty, Leanne (Wellcome Genome Campus (UK)) ;
Hoekzema, Kendra (University of Washington School of Medicine) ;
Hourlier, Thibaut (Wellcome Genome Campus (UK)) ;
Ji, Hanlee P. (Stanford University School of Medicine) ;
Kenny, Eimear E. (Icahn School of Medicine at Mount Sinai) ;
Koenig, Barbara A. (University of California) ;
Kolesnikov, Alexey (Google (USA)) ;
Korbel, Jan O. (European Molecular Biology Laboratory) ;
Kordosky, Jennifer (University of Washington School of Medicine) ;
Koren, Sergey (National Institutes of Health (USA)) ;
Lee, HoJoon (Stanford University School of Medicine) ;
Lewis, Alexandra P. (University of Washington School of Medicine) ;
Magalhães, Hugo (Heinrich Heine University) ;
Marco-Sola, Santiago (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ;
Marijon, Pierre (Heinrich Heine University) ;
McCartney, Ann (National Institutes of Health (USA)) ;
McDaniel, Jennifer (National Institute of Standards and Technology (USA)) ;
Mountcastle, Jacquelyn (The Rockefeller University) ;
Nattestad, Maria (Google (USA)) ;
Nurk, Sergey (National Institutes of Health (USA)) ;
Olson, Nathan D. (National Institute of Standards and Technology (USA)) ;
Popejoy, Alice B. (University of California) ;
Puiu, Daniela (Johns Hopkins University) ;
Rautiainen, Mikko (National Institutes of Health (USA)) ;
Regier, Allison A. (Washington University School of Medicine) ;
Rhie, Arang (National Institutes of Health (USA)) ;
Sacco, Samuel (University of California) ;
Sanders, Ashley D. (Max Delbrück Center for Molecular Medicine in the Helmholtz Association) ;
Schneider, Valerie A. (National Institutes of Health (USA)) ;
Schultz, Baergen I. (National Institutes of Health (USA)) ;
Shafin, Kishwar (Google (USA)) ;
Smith, Michael W. (National Institutes of Health (USA)) ;
Sofia, Heidi J. (National Institutes of Health (USA)) ;
Abou Tayoun, Ahmad N. (Mohammed Bin Rashid University of Medicine and Health Sciences) ;
Thibaud-Nissen, Françoise (National Institutes of Health (USA)) ;
Tricomi, Francesca Floriana (Wellcome Genome Campus (UK)) ;
Wagner, Justin (National Institute of Standards and Technology (USA)) ;
Walenz, Brian (National Institutes of Health (USA)) ;
Wood, Jonathan M. D. (Wellcome Trust Sanger Institute (Regne Unit)) ;
Zimin, Aleksey V. (Johns Hopkins University) ;
Bourque, Guillaume (Kyoto University) ;
Chaisson, Mark (University of Southern California) ;
Flicek, Paul (Wellcome Genome Campus (UK)) ;
Phillippy, Adam M. (National Institutes of Health (USA)) ;
Zook, Justin M. (National Institute of Standards and Technology (USA)) ;
Eichler, Evan E. (Howard Hughes Medical Institute) ;
Haussler, David (Howard Hughes Medical Institute) ;
Wang, Ting (Washington University School of Medicine) ;
Jarvis, Erich (The Rockefeller University) ;
Miga, Karen H. (University of California) ;
Garrison, Erik (University of Tennessee Health Science Center) ;
Marschall, Tobias (Heinrich Heine University) ;
Hall, Ira M. (Yale University School of Medicine) ;
Li, Heng (Harvard Medical School) ;
Paten, Benedict (University of California)
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. [...]
2023 -  10.1038/s41586-023-05896-x
Nature, Vol. 617 (May 2023) , p. 312-324
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2.
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50 p, 7.5 MB |
Pseudomonas fitomaticsae sp. nov., isolated at Marimurtra Botanical Garden in Blanes, Catalonia, Spain
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Atanasov, Kostadin E. (Centre de Recerca en Agrigenòmica) ;
Miñana-Galbis, David (Universitat de Barcelona. Departament de Biologia, Sanitat i Medi Ambient) ;
Cornadó, Deborah (Leitat Technological Center (Terrassa)) ;
Serpico, Annabel (Leitat Technological Center (Terrassa)) ;
Sánchez, Guiomar (Leitat Technological Center (Terrassa)) ;
Bosch, Montserrat (Leitat Technological Center (Terrassa)) ;
Ferrer, Albert (Centre de Recerca en Agrigenòmica) ;
Altabella Artigas, Teresa (Centre de Recerca en Agrigenòmica)
In the framework of the research project called fitomatics, we have isolated and characterized a bacterial plant-endophyte from the rhizomes of Iris germanica, hereafter referred to as strain FIT81. The bacterium is Gram negative, rod-shaped with lophotrichous flagella, and catalase-and oxidase-positive. [...]
2022 - 10.1099/IJSEM.0.005557
International Journal of Systematic and Evolutionary Microbiology, Vol. 72, Issue 10 (October 2022) , art. 5557
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3.
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15 p, 5.0 MB |
3D chromatin remodelling in the germ line modulates genome evolutionary plasticity
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Álvarez-González, Lucía (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Burden, Frances (University of Kent. School of Bioscience) ;
Doddamani, Dadakhalandar (University of Kent. School of Bioscience) ;
Malinverni, Roberto (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Leach, Emma (University of Kent. School of Bioscience) ;
Marín-García, Cristina (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Marin Gual, Laia (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Gubern Burset, Albert (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Vara González, Covadonga (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Paytuví-Gallart, Andreu (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Buschbeck, Marcus (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ellis, Peter J. I. (University of Kent. School of Bioscience) ;
Farré, Marta (University of Kent. School of Bioscience) ;
Ruiz-Herrera Moreno, Aurora (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Chromosome folding has profound impacts on gene regulation, whose evolutionary consequences are far from being understood. Here we explore the relationship between 3D chromatin remodelling in mouse germ cells and evolutionary changes in genome structure. [...]
2022 - 10.1038/s41467-022-30296-6
Nature communications, Vol. 13 (May 2022) , art. 2608
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4.
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13 p, 3.0 MB |
Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
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Serres-Armero, Aitor (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Davis, Brian W. (Texas A&M University. Department of Veterinary Integrative Biosciences) ;
Povolotskaya, Inna S. (Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University) ;
Morcillo-Suarez, Carlos (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Plassais, Jocelyn (National Institutes of Health. Cancer Genetics and Comparative Genomics Branch) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Ostrander, Elaine A. (National Institutes of Health. Cancer Genetics and Comparative Genomics Branch) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. [...]
2021 - 10.1101/gr.266049.120
Genome research, Vol. 31 (May 2021) , p. 762-774
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5.
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8 p, 1.3 MB |
Standards recommendations for the Earth BioGenome Project
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Lawniczak, Mara K. N. (Wellcome Sanger Institute (Cambridge)) ;
Durbin, Richard (University of Cambridge. Department of Genetics) ;
Flicek, Paul (Wellcome Sanger Institute (Cambridge)) ;
Lindblad-Toh, Kerstin (Uppsala University. Department of Medical Biochemistry & Microbiology) ;
Wei, Xiaofeng (China National GeneBank) ;
Archibald, John M. (Dalhousie University. Department of Biochemistry & Molecular Biology) ;
Baker, William J.. (Royal Botanic Gardens. Department of Accelerated Taxonomy) ;
Belov, Katherine (University of Sydney. School of Life and Environmental Sciences) ;
Blaxter, Mark (Wellcome Sanger Institute (Cambridge)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Childers, Anna K. (US Department of Agriculture. Beltsville Agricultural Research Center) ;
Coddington, Jonathan A. (Smithsonian Institution. National Museum of Natural History) ;
Crandall, Keith A. (George Washington University. Department of Biostatistics & Bioinformatics) ;
Crawford, Andrew J. (Universidad de los Andes. Department of Biological Sciences (Colombia)) ;
Davey, Robert P. (Norwich Research Park. Earlham Institute (UK)) ;
Di Palma, Federica (Genome British Columbia (Vancouver)) ;
Fang, Qi (BGI-Shenzhen (China)) ;
Haerty, Wilfried (Norwich Research Park. Earlham Institute (UK)) ;
Hall, Neil (Norwich Research Park. Earlham Institute (UK)) ;
Hoff, Katharina (University of Greifswald. Center for Functional Genomics of Microbes) ;
Howe, Kerstin (Wellcome Sanger Institute (Cambridge)) ;
Jarvis, Erich (The Rockefeller University. Vertebrate Genomes Laboratory (USA)) ;
Johnson, Warren E. (Smithsonian Conservation Biology Institute) ;
Johnson, Rebecca (Smithsonian Institution. National Museum of Natural History) ;
Kersey, Paul J. (European Bioinformatics Institute. European Molecular Biology Laboratory (UK)) ;
Liu, Xin (China National GeneBank) ;
Lopez, Jose V. (Nova Southeastern University. Guy Harvey Oceanographic Center) ;
Myers, Eugene W. (Max Planck Institute of Molecular Cell Biology and Genetics (Germany)) ;
Vinnere Pettersson, Olga (Uppsala University. Science for Life Laboratory) ;
Phillippy, Adam M. (National Institutes of Health. National Human Genome Research Institute (USA)) ;
Poelchau, Monica (United States. Department of Agriculture. Agricultural Research Service) ;
Pruitt, Kim D. (National Library of Medicine. National Center for Biotechnology Information (USA)) ;
Rhie, Arang (National Institutes of Health. National Human Genome Research Institute (USA)) ;
Castilla-Rubio, Juan Carlos (Spacetime Ventures (Brazil)) ;
Sahu, Sunil Kumar (China National GeneBank) ;
Salmon, Nicholas A. (Wellcome Sanger Institute (Cambridge)) ;
Soltis, Pamela (University of Florida. Florida Museum of Natural History) ;
Swarbreck, David (Norwich Research Park. Earlham Institute (UK)) ;
Thibaud-Nissen, Françoise (National Library of Medicine. National Center for Biotechnology Information (USA)) ;
Wang, Sibo (China National GeneBank) ;
Wegrzyn, Jill (University of Connecticut. Department of Ecology and Evolutionary Biology) ;
Zhang, Guojie (China National GeneBank) ;
Zhang, He (BGI-Shenzhen (China)) ;
Lewin, Harris A. (University of California Davis. Department of Evolution and Ecology (USA)) ;
Richards, Stephen (University of California Davis. Genome Center)
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. [...]
2022 - 10.1073/pnas.2115639118
Proceedings of the National Academy of Sciences of the United States of America, Vol. 119, Num. 4 (January 2022) , art. e2115639118
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6.
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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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7.
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14 p, 2.0 MB |
Changes in long-range rDNA-genomic interactions associate with altered RNA polymerase II gene programs during malignant transformation
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Diesch, Jeannine (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Bywater, M. J. (QIMR Berghofer Medical Research Institute (Brisbane, Austràlia)) ;
Sanij, E. (Department of Pathology. University of Melbourne) ;
Cameron, D. P. (Sir Peter MacCallum Department of Oncology. University of Melbourne) ;
Schierding, W. (Liggins Institute. The University of Auckland) ;
Brajanovski, N. (Cancer Research Division. Peter MacCallum Cancer Centre) ;
Son, J. (Sir Peter MacCallum Department of Oncology. University of Melbourne) ;
Sornkom, J. (Sir Peter MacCallum Department of Oncology. University of Melbourne) ;
Hein, N. (ACRF Department of Cancer Biology and Therapeutics. John Curtin School of Medical Research. Australian National University) ;
Evers, M. (ACRF Department of Cancer Biology and Therapeutics. John Curtin School of Medical Research. Australian National University) ;
Pearson, R. B. (Department of Biochemistry and Molecular Biology. University of Melbourne) ;
McArthur, G. A. (St Vincent's Hospital (Sydney)) ;
Ganley, A. R. D. (School of Biological Sciences. The University of Auckland) ;
O'Sullivan, J. M. (Liggins Institute. The University of Auckland) ;
Hannan, R. D. (School of Biomedical Sciences. University of Queensland) ;
Poortinga, G. (St Vincent's Hospital (Sydney)) ;
Universitat Autònoma de Barcelona
The three-dimensional organization of the genome contributes to its maintenance and regulation. While chromosomal regions associate with nucleolar ribosomal RNA genes (rDNA), the biological significance of rDNA-genome interactions and whether they are dynamically regulated during disease remain unclear. [...]
2019 - 10.1038/s42003-019-0284-y
Communications Biology, Vol. 2 Núm. 1 (january 2019) , p. 39
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8.
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6 p, 757.8 KB |
Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual
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Kuderna, Lukas (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Solís Moruno, Manuel (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut) ;
Batlle-Masó, Laura (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut) ;
Julià, Eva (Institut Hospital del Mar d'Investigacions Mèdiques) ;
Lizano, Esther (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Anglada, Roger (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut) ;
Ramírez, Erika (Centre de Regulació Genòmica) ;
Bote, Alex (Centre de Regulació Genòmica) ;
Tormo, Marc (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Fornas, Òscar (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut) ;
Casals, Ferran (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut)
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 workflow to sequence native, unamplified DNA and applied it to the smallest human chromosome, the Y chromosome. [...]
2020 - 10.3389/fgene.2019.01315
Frontiers in genetics, Vol. 10 (January 2020) , art. 1315
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9.
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12 p, 1.0 MB |
Genome sequence of the olive tree, Olea europaea
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Cruz, Fernando (Universitat Pompeu Fabra) ;
Julca, Irene (Universitat Autònoma de Barcelona) ;
Gómez-Garrido, Jessica (Universitat Pompeu Fabra) ;
Loska, Damian (Centre de Regulació Genòmica) ;
Marcet-Houben, Marina (Centre de Regulació Genòmica) ;
Cano, Emilio (Consejo Superior de Investigaciones Científicas) ;
Galán, Beatriz (Consejo Superior de Investigaciones Científicas) ;
Frias, Leonor (Universitat Pompeu Fabra) ;
Ribeca, Paolo (Universitat Pompeu Fabra) ;
Derdak, Sophia (Universitat Pompeu Fabra) ;
Gut, Marta (Universitat Pompeu Fabra) ;
Sánchez Fernández, Manuel (Grupo Santander) ;
García, José Luis (Consejo Superior de Investigaciones Científicas) ;
Gut, Ivo (Universitat Pompeu Fabra) ;
Vargas, Pablo (Vargas Gómez) (Consejo Superior de Investigaciones Científicas. Real Jardín Botànico de Madrid) ;
Alioto, Tyler Scott (Centre Nacional d'Anàlisi Genòmica) ;
Gabaldón, Toni (Centre de Regulació Genòmica)
The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. [...]
2016 - 10.1186/s13742-016-0134-5
GigaScience, Vol. 5, Issue 1 (December 2016) , art. 29
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10.
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3 p, 131.9 KB |
Annotated features of domestic cat - Felis catus genome
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Tamazian, Gaik (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Simonov, Serguei (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Dobrynin, Pavel (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Makunin, Alexey (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Logachev, Anton (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Komissarov, Aleksey (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Shevchenko, Andrey (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Brukhin, Vladimir (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Cherkasov, Nikolay (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Svitin, Anton (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Koepfli, Klaus-Peter (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Pontius, Joan (Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University) ;
Driscoll, Carlos A. (Laboratory of Neurogenetics, NIAAA) ;
Blackistone, Kevin (Laboratory of Neurogenetics, NIAAA) ;
Barr, Cristina (Laboratory of Neurogenetics, NIAAA) ;
Goldman, David (Laboratory of Neurogenetics, NIAAA) ;
Antunes, Agostinho (CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto) ;
Quilez Oliete, Javier (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Lorente-Galdos, Belen (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Alkan, Can (Department of Computer Engineering, Bilkent University) ;
Marques-Bonet, Tomas 1975- (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Menotti-Raymond, Marylin (Laboratory of Genomic Diversity, Frederick National Laboratory for Cancer Research) ;
David, Victor A. (Laboratory of Genomic Diversity, Frederick National Laboratory for Cancer Research) ;
Narfström, Kristina (Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri) ;
O'Brien, Stephen J. (Oceanographic Center, Nova Southeastern University)
Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly human diseases, which include feline immunodeficiency virus, feline sarcoma virus and feline leukemia virus. [...]
2014 - 10.1186/2047-217X-3-13
GigaScience, Vol. 3 (august 2014) , p. 13
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