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11 p, 3.5 MB |
The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs
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Murray, Gemma G. R. (University of Cambridge. Department of Veterinary Medicine) ;
Hossain, A. S. Md. Mukarram (Cancer Research UK Manchester Institute) ;
Miller, Eric L. (Haverford College. Department of Biology) ;
Bruchmann, Sebastian (University of Cambridge. Department of Veterinary Medicine) ;
Balmer, Andrew J. (University of Cambridge. Department of Veterinary Medicine) ;
Matuszewska, Marta (University of Cambridge. Department of Veterinary Medicine) ;
Herbert, Josephine (University of Portsmouth. Centre for Enzyme Innovation) ;
Hadjirin, Nazreen F. (University of Oxford. Nuffield Department of Population Health) ;
Mugabi, Robert (Iowa State University. College of Veterinary Medicine) ;
Li, Ganwu (Iowa State University. College of Veterinary Medicine) ;
Ferrando, Maria Laura (Wageningen University. Animal Sciences Department) ;
Fernandes de Oliveira, Isabela Maria (Wageningen University. Animal Sciences Department) ;
Nguyen, Thanh (Oxford University Clinical Research Unit) ;
Yen, Phung L. K. (Oxford University Clinical Research Unit) ;
Phuc, Ho D. (Oxford University Clinical Research Unit) ;
Zaw Moe, Aung (Livestock Breeding and Veterinary Department) ;
Su Wai, Thiri (Livestock Breeding and Veterinary Department) ;
Gottschalk, Marcelo (University of Montreal) ;
Aragon, Virginia (Unitat mixta d'investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal) ;
Valentin-Weigand, Peter (University of Veterinary Medicine Hannover. Institute for Microbiology) ;
Heegaard, Peter M. H. (Technical University of Denmark. Department of Health Technology) ;
Vrieling, Manouk (Wageningen Bioveterinary Research) ;
Thein Maw, Min (Livestock Breeding and Veterinary Department) ;
Thidar Myint, Hnin (Livestock Breeding and Veterinary Department) ;
Tun Win, Ye (Livestock Breeding and Veterinary Department) ;
Thi Hoa, Ngo (Ngoc Thach University of Medicine. Microbiology Department and Center for Tropical Medicine Research) ;
Bentley, Stephen D. (Wellcome Sanger Institute. Parasites and Microbes Programme) ;
Clavijo, Maria J. (Iowa State University. College of Veterinary Medicine) ;
Wells, Jerry M. (Wageningen University. Animal Sciences Department) ;
Tucker, Alexander W. (University of Cambridge. Department of Veterinary Medicine) ;
Weinert, Lucy A. (University of Cambridge. Department of Veterinary Medicine)
There is growing concern that rapid growth in livestock production and major changes in farming practices are driving the emergence of pathogens capable of causing disease in both livestock and humans. [...]
2023 -  10.1073/pnas.2307773120
Proceedings of the National Academy of Sciences of the United States of America, Vol. 120 (november 2023)
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3.
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11 p, 1.3 MB |
Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools
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García-Prieto, Carlos A (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Martínez Jiménez, Francisco (Institute for Research in Biomedicine (IRB Barcelona)) ;
Valencia, Alfonso (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
Motivation: The analysis of cancer genomes provides fundamental information about its etiology, the processes driving cell transformation or potential treatments. While researchers and clinicians are often only interested in the identification of oncogenic mutations, actionable variants or mutational signatures, the first crucial step in the analysis of any tumor genome is the identification of somatic variants in cancer cells (i. [...]
2022 - 10.1093/bioinformatics/btac306
Bioinformatics, Vol. 38 Núm. 12 (15 2022) , p. 3181-3191
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4.
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23 p, 7.8 MB |
Deep learning applications in single-cell genomics and transcriptomics data analysis
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Erfanian, Nafiseh (Birjand University of Medical Sciences, Birjand, Iran) ;
Heydari, A.Ali (University of California, USA) ;
Feriz, Adib Miraki (Birjand University of Medical Sciences, Birjand, Iran) ;
Iañez, Pablo (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Derakhshani, Afshin (University of Calgary, Canada) ;
Ghasemigol, Mohammad (University of North Dakota, USA) ;
Farahpour, Mohsen (University of Birjand, Iran) ;
Razavi, Seyyed Mohammad (University of Birjand, Iran) ;
Nasseri, Saeed (Birjand University of Medical Sciences, Iran) ;
Safarpour, Hossein (Birjand University of Medical Sciences, Iran) ;
Sahebkar, Amirhossein (Mashhad University of Medical Sciences, Mashhad, Iran)
Traditional bulk sequencing methods are limited to measuring the average signal in a group of cells, potentially masking heterogeneity, and rare populations. The single-cell resolution, however, enhances our understanding of complex biological systems and diseases, such as cancer, the immune system, and chronic diseases. [...]
2023 - 10.1016/j.biopha.2023.115077
Biomedicine & pharmacotherapy, Vol. 165 (september 2023)
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5.
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9 p, 745.8 KB |
The EMIF-AD Multimodal Biomarker Discovery study : Design, methods and cohort characteristics
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Bos, Isabelle (Maastricht University) ;
Vos, Stephanie (Maastricht University) ;
Vandenberghe, Rik (Katholieke Universiteit Leuven) ;
Scheltens, Philip (Amsterdam UMC. University Medical Center) ;
Engelborghs, Sebastiaan (University of Antwerp) ;
Frisoni, Giovanni (IRCCS Instituto Centro San Giovanni di Dio Fatebenefratelli) ;
Molinuevo, José Luis (Fundació Pasqual Maragall) ;
Wallin, Anders (Institute of Neuroscience and Physiology) ;
Lleó, Alberto (Institut d'Investigació Biomèdica Sant Pau) ;
Popp, Julius (Lausanne University Hospital) ;
Martinez-Lage, Pablo (Centro de Investigación y Tecnología Agroalimentaria de Aragón) ;
Baird, Alison (University of Oxford) ;
Dobson, Richard (NIHR University College London Hospitals) ;
Legido-Quigley, Cristina (King's College London) ;
Sleegers, Kristel (University of Antwerp) ;
Van Broeckhoven, Christine (University of Antwerp) ;
Bertram, Lars (University of Oslo) ;
Ten Kate, Mara (Amsterdam UMC. University Medical Center) ;
Barkhof, Frederik (Amsterdam UMC. University Medical Center) ;
Zetterberg, Henrik (UK Dementia Research Institute) ;
Lovestone, Simon (University of Oxford) ;
Streffer, Johannes (Janssen Pharmaceutical Companies) ;
Visser, Pieter Jelle (Vrije Universiteit Amsterdam) ;
Universitat Autònoma de Barcelona
There is an urgent need for novel, noninvasive biomarkers to diagnose Alzheimer's disease (AD) in the predementia stages and to predict the rate of decline. Therefore, we set up the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD) study. [...]
2018 - 10.1186/s13195-018-0396-5
Alzheimer's research & therapy, Vol. 10 Núm. 1 (june 2018) , p. 64
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7.
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19 p, 8.7 MB |
Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation
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Jensen, Axel (Uppsala University. Department of Ecology and Genetics, Animal Ecology) ;
Swift, Frances (University of Edinburgh. School of Biological Sciences) ;
de Vries, Dorien (University of Salford. School of Science, Engineering and Environment) ;
Beck, Robin (University of Salford. School of Science, Engineering & Environment) ;
Kuderna, Lukas (Illumina Inc) ;
Knauf, Sascha (Federal Research Institute for Animal Health) ;
Chuma, Idrissa S. (Tanzania National Parks) ;
Keyyu, Julius (Tanzania Wildlife Research Institute) ;
Kitchener, Andrew (University of Edinburgh. University of Edinburgh) ;
Farh, Kyle (Illumina Inc) ;
Rogers, Jeffrey (Baylor College of Medicine. Human Genome Sequencing Center) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Detwiler, Kate (Florida Atlantic University. Department of Biological Sciences) ;
Roos, Christian (Leibniz Institute for Primate Research. German Primate Center) ;
Guschanski, Katerina (Uppsala University. Department of Ecology and Genetics)
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 (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. [...]
2023 - 10.1093/molbev/msad247
Molecular Biology and Evolution, Vol. 40, Issue 12 (December 2023) , art. msad247
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8.
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14 p, 1.2 MB |
GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways
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López-Isac, Elena (Institute of Parasitology and Biomedicine López-Neyra) ;
Acosta-Herrera, Marialbert (Institute of Parasitology and Biomedicine López-Neyra) ;
Kerick, Martin (Institute of Parasitology and Biomedicine López-Neyra) ;
Assassi, Shervin (The University of Texas Health Science Center-Houston) ;
Satpathy, Ansuman (Stanford University) ;
Granja, Jeffrey (Stanford University) ;
Mumbach, Maxwell (Stanford University) ;
Beretta, Lorenzo (Referral Center for Systemic Autoimmune Diseases) ;
Simeón-Aznar, Carmen Pilar (Hospital Universitari Vall d'Hebron) ;
Carreira, Patricia E. (Hospital Universitario 12 de Octubre) ;
Ortego-Centeno, Norberto (San Cecilio Clinic University Hospital) ;
Castellvi, Ivan (Institut d'Investigació Biomèdica Sant Pau) ;
Bossini-Castillo, Lara (Wellcome Trust Sanger Institute (Regne Unit)) ;
Carmona, F. David (Universidad de Granada) ;
Orozco, Gisela (The University of Manchester) ;
Hunzelmann, Nicolas (University of Cologne) ;
Distler, Jörg H. W. (University of Erlangen-Nuremberg) ;
Franke, Andre (Christian-Albrechts-University of Kiel) ;
Lunardi, Claudio (Università degli Studi di Verona) ;
Moroncini, Gianluca (Università Politecnica delle Marche and Ospedali Riuniti) ;
Gabrielli, Armando (Università Politecnica delle Marche and Ospedali Riuniti) ;
de Vries-Bouwstra, Jeska (Leiden University Medical Center) ;
Wijmenga, Cisca (University of Groningen) ;
Koeleman, Bobby (University Medical Center Utrecht) ;
Nordin, Annika (Karolinska Institutet (Estocolm, Suècia)) ;
Padyukov, Leonid (Karolinska Institutet (Estocolm, Suècia)) ;
Hoffmann-Vold, Anna-Maria (Oslo University Hospital) ;
Lie, Benedicte A. (University of Oslo and Oslo University Hospital) ;
Ríos, Raquel (San Cecilio Clinic University Hospital) ;
Callejas Rubio, Jose Luis (San Cecilio Clinic University Hospital) ;
Vargas-Hitos, José Antonio (Hospital Virgen de las Nieves (Granada, Andalusia)) ;
García-Portales, Rosa (Hospital Universitario Virgen de la Victoria (Màlaga, Andalusia)) ;
Camps, María Teresa (Carlos Haya Hospital) ;
Fernández-Nebro, Antonio (Carlos Haya Hospital) ;
González-Escribano, Maria Francisca (Hospital Universitario Virgen del Rocío (Sevilla, Andalusia)) ;
García-Hernández, Francisco Jose (Hospital Universitario Virgen del Rocío (Sevilla, Andalusia)) ;
Castillo, María Jesús (Hospital Universitario Virgen del Rocío (Sevilla, Andalusia)) ;
Aguirre, Mª Angeles (Hospital Reina Sofía/IMIBIC) ;
Gómez-Gracia, Inmaculada (Hospital Reina Sofía/IMIBIC) ;
Fernández-Gutiérrez, B. (San Carlos Clinic Hospital) ;
Rodríguez-Rodríguez, L. (San Carlos Clinic Hospital) ;
García de la Peña, Paloma (Madrid Norte Sanchinarro Hospital) ;
Vicente-Rabaneda, Esther Francisca (Hospital Universitario de la Princesa (Madrid)) ;
Andréu, José Luis (Puerta de Hierro Hospital-Majadahonda) ;
Fernández de Castro, Mónica (Puerta de Hierro Hospital-Majadahonda) ;
López-Longo, Francisco Javier (Hospital General Universitario Gregorio Marañón) ;
Martínez, Lina Patricia (Hospital General Universitario Gregorio Marañón) ;
Fonollosa, Vicenç (Hospital Universitari Vall d'Hebron) ;
Guillén, Alfredo Chávez (Hospital Universitari Vall d'Hebron) ;
Espinosa, Gerard (Hospital Clínic i Provincial de Barcelona) ;
Tolosa-Vilella, Carles (Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí (I3PT)) ;
Pros, Ana (Hospital del Mar (Barcelona, Catalunya)) ;
Rodríguez-Carballeira, M. (Hospital Universitari MútuaTerrassa) ;
Narváez, Francisco J. (Hospital Universitari de Bellvitge) ;
Rubio Rivas, Manuel (Hospital Universitari de Bellvitge) ;
Ortiz-Santamaría, None (Hospital Granollers) ;
Madroñero, A.B. (Hospital General Universitario San Jorge (Osca, Aragó)) ;
González-Gay, M.A. (Universidad de Cantabria) ;
Díaz, B. (Hospital Universitario Central de Asturias) ;
Trapiella, L. (Hospital Universitario Central de Asturias) ;
Sousa, A. (Hospital Xeral-Complexo Hospitalario Universitario de Vigo) ;
Egurbide, M.V. (Hospital Universitario Cruces) ;
Fanlo-Mateo, P. (Hospital Virgen del Camino (Pamplona)) ;
Sáez-Comet, L. (Hospital Universitario Miguel Servet (Saragossa)) ;
Díaz, F. (Hospital Universitario de Canarias) ;
Hernández, None (Hospital Universitario de Canarias) ;
Beltrán, E. (Hospital General Universitario de Valencia) ;
Román-Ivorra, J.A. (Hospital Universitari i Politècnic La Fe de València) ;
Grau, E. (Hospital Universitari i Politècnic La Fe de València) ;
Alegre-Sancho, Juan José (Hospital Universitari Doctor Peset) ;
Freire, M. (Complexo Hospitalario Universitario de Vigo) ;
Blanco-García, F.J (INIBIC-Hospital Universitario A Coruña) ;
Oreiro, N. (INIBIC-Hospital Universitario A Coruña) ;
Witte, T. (Hannover Medical School) ;
Kreuter, A. (Ruhr University Bochum) ;
Riemekasten, G. (University of Lübeck) ;
Airò, Paolo (Service of Rheumatology and Clinic Immunology Spedali Civili) ;
Magro-Checa, César (Leiden University Medical Center) ;
Voskuyl, A.E. (Amsterdam UMC. University Medical Center) ;
Vonk, Madelon C. (Radboud University Nijmegen Medical Center) ;
Hesselstrand, Roger (Lund University) ;
Proudman, Susanna (Royal Adelaide Hospital and University of Adelaide) ;
Stevens, Wendy (St. Vincent's Hospital) ;
Nikpour, Mandana (The University of Melbourne at St. Vincent's Hospital) ;
Zochling, Jane M. (University of Tasmania) ;
Sahhar, Joanne (Monash Medical Centre) ;
Roddy, Janet (Cincinnati Children's Hospital Medical Center (CCHMC). Center for Fetal and Placental Research) ;
Nash, Peter (Sunshine Coast Rheumatology) ;
Tymms, Kathleen (Canberra Rheumatology) ;
Rischmueller, Maureen (The Queen Elizabeth Hospital) ;
Lester, S. (The Queen Elizabeth Hospital) ;
Vyse, Timothy (King's College London) ;
Herrick, Ariane (NIHR Manchester Biomedical Research Centre) ;
Worthington, Jane (The University of Manchester) ;
Denton, Christopher P (Royal Free and University College Medical School) ;
Allanore, Yannick (Paris Descartes University) ;
Brown, Matthew A. (Princess Alexandra Hospital) ;
Radstake, Timothy R. D. J. (University Medical Center Utrecht) ;
Fonseca, Carmen (Royal Free and University College Medical School) ;
Chang, Howard Y. (Stanford University) ;
Mayes, Maureen D (The University of Texas Health Science Center-Houston) ;
Martín, Javier (Institute of Parasitology and Biomedicine López-Neyra) ;
Universitat Autònoma de Barcelona
Systemic sclerosis (SSc) is an autoimmune disease that shows one of the highest mortality rates among rheumatic diseases. We perform a large genome-wide association study (GWAS), and meta-analysis with previous GWASs, in 26,679 individuals and identify 27 independent genome-wide associated signals, including 13 new risk loci. [...]
2019 - 10.1038/s41467-019-12760-y
Nature communications, Vol. 10 Núm. 1 (january 2019) , p. 4955
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9.
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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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10.
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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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