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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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20 p, 2.4 MB |
Ghost admixture in eastern gorillas
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Pawar, Harvinder (Institute of Evolutionary Biology) ;
Rymbekova, Aigerim (University of Vienna. Department of Evolutionary Anthropology) ;
Cuadros-Espinoza, Sebastian (Institute of Evolutionary Biology) ;
Huang, Xin (University of Vienna. Department of Evolutionary Anthropology) ;
de Manuel, Marc (Institute of Evolutionary Biology) ;
van der Valk, Tom (Swedish Museum of Natural History) ;
Lobón, Irene (Institute of Evolutionary Biology) ;
Alvarez-Estape, Marina (Institute of Evolutionary Biology) ;
Haber, Marc (University of Birmingham. Institute of Cancer and Genomic Sciences) ;
Dolgova, Olga (Parque Científico Tecnológico de Bizkaia. Centro de Investigación Cooperativa en Biociencias) ;
Han, Sojung 1984- (Institute of Evolutionary Biology) ;
Esteller-Cucala, Paula (Institute of Evolutionary Biology) ;
Juan, David (Institute of Evolutionary Biology) ;
Ayub, Qasim (Monash University Malaysia) ;
Bautista, Ruben (Wellcome Trust Sanger Institute (Regne Unit)) ;
Kelley, Joanna (University of California. Department of Ecology and Evolutionary Biology) ;
Cornejo, Omar E. (University of California. Department of Ecology and Evolutionary Biology) ;
Lao, Oscar (Institute of Evolutionary Biology) ;
Andrés, Aida M. (University College London. Department of Genetics, Evolution and Environment) ;
Guschanski, Katerina (University of Edinburgh) ;
Ssebide, Benard (Gorilla Doctors) ;
Cranfield, Mike (University of California Davis) ;
Tyler-Smith, Chris (Wellcome Trust Sanger Institute (Regne Unit)) ;
Xue, Yali (Wellcome Trust Sanger Institute (Regne Unit)) ;
Prado-Martinez, Javier (Institute of Evolutionary Biology) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Kuhlwilm, Martin (Institute of Evolutionary Biology)
Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. [...]
2023 - 10.1038/s41559-023-02145-2
Nature ecology & evolution, Vol. 7 (July 2023) , p. 1503-1514
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3.
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11 p, 1.1 MB |
Y chromosome sequence and epigenomic reconstruction across human populations
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Esteller-Cucala, Paula (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Palmada-Flores, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Kuderna, Lukas F. K. (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Fontsere, Claudia (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Serres-Armero, Aitor (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Dabad, Marc (Centre de Regulació Genòmica) ;
Torralvo, María (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Faella, Armida (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Ferrández-Peral, Luis (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Llovera, Laia (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Fornas, Òscar (Centre de Regulació Genòmica) ;
Julià, Eva (Centre de Regulació Genòmica) ;
Ramírez, Erika (Centre de Regulació Genòmica) ;
González, Irene (Centre de Regulació Genòmica) ;
Hecht, Jochen (Centre de Regulació Genòmica) ;
Lizano, Esther (Institut Català de Paleontologia Miquel Crusafont) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). [...]
2023 - 10.1038/s42003-023-05004-9
Communications Biology, Vol. 6 (June 2023) , art. 623
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4.
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16 p, 3.6 MB |
The population genomic legacy of the second plague pandemic
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Gopalakrishnan, Shyam (University of Copenhagen. The GLOBE Institute) ;
Ebenesersdóttir, S. Sunna (University of Iceland. Department of Anthropology) ;
Lundstrøm, Inge K.C. (University of Copenhagen. The GLOBE Institute) ;
Turner-Walker, Gordon (National Yunlin University of Science & Technology (Taiwan)) ;
Moore, Kristjan H.S. (deCODE Genetics (Reykjavík, Islàndia)) ;
Luisi, Pierre (Universidad Nacional de Córdoba (Argentina)) ;
Margaryan, Ashot (University of Copenhagen. The GLOBE Institute) ;
Martin, Michael D. (Norwegian University of Science and Technology. NTNU University Museum) ;
Ellegaard, Martin Rene (Norwegian University of Science and Technology. NTNU University Museum) ;
Magnússon, Ólafur þ. (deCODE Genetics (Reykjavík, Islàndia)) ;
Sigurðsson, Ásgeir (deCODE Genetics (Reykjavík, Islàndia)) ;
Snorradóttir, Steinunn (deCODE Genetics (Reykjavík, Islàndia)) ;
Magnúsdóttir, Droplaug N. (deCODE Genetics (Reykjavík, Islàndia)) ;
Laffoon, Jason E. (Leiden University. Department of Archaeological Sciences) ;
van Dorp, Lucy (University College London. Department of Genetics, Evolution and Environment) ;
Liu, Xiaodong (University of Copenhagen. Department of Biology) ;
Moltke, Ida (University of Copenhagen. Department of Biology) ;
Ávila-Arcos, Maria C (Universidad Nacional Autónoma de México. Laboratorio Internacional de Investigación sobre el Genoma Humano) ;
Schraiber, Joshua G. (Illumina Inc. Illumina Artificial Intelligence Laboratory (USA)) ;
Rasmussen, Simon (University of Copenhagen. Novo Nordisk Foundation Center for Protein Research) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Gelabert, Pere (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
de-Dios, Toni (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Fotakis, Anna K. (University of Copenhagen. The GLOBE Institute) ;
Iraeta-Orbegozo, Miren (University of Copenhagen. The GLOBE Institute) ;
Vågene, Åshild J. (Max Planck Institute for the Science of Human History) ;
Denham, Sean Dexter (University of Stavanger. Museum of Archaeology) ;
Christophersen, Axel (Norwegian University of Science and Technology. NTNU University Museum) ;
Stenøien, Hans K. (Norwegian University of Science and Technology. NTNU University Museum) ;
Garrett Vieira, Filipe (University of Copenhagen. The GLOBE Institute) ;
Liu, Shanlin (China National GeneBank) ;
Günther, Torsten (Evolutionsbiologisk Centrum EBC (Sweden)) ;
Kivisild, Toomas (University of Tartu. Institute of Genomics) ;
Moseng, Ole Georg (University of South-Eastern Norway. Department of Business, History and Social Sciences) ;
Skar, Birgitte (Norwegian University of Science and Technology. NTNU University Museum) ;
Cheung, Christina (Muséum National d'Histoire Naturelle (París, França)) ;
Sandoval-Velasco, Marcela (University of Copenhagen. The GLOBE Institute) ;
Wales, Nathan (University of York. Department of Archaeology) ;
Schroeder, Hannes (University of Copenhagen. The GLOBE Institute) ;
Campos, Paula F. (Universidade do Porto. Centro Interdisciplinar de Investigação Marinha e Ambiental) ;
Guðmundsdóttir, Valdís B. (University of Iceland. Department of Anthropology) ;
Sicheritz-Ponten, Thomas (AIMST University (Malàisia). Centre of Excellence for Omics-Driven Computational Biodiscovery) ;
Petersen, Bent (AIMST University (Malàisia). Centre of Excellence for Omics-Driven Computational Biodiscovery) ;
Halgunset, Jostein (Biobank1 (Norway)) ;
Gilbert, Edmund (School of Pharmacy and Biomolecular Sciences (Ireland)) ;
Cavalleri, Gianpiero L. (FutureNeuro SFI Research Centre (Ireland)) ;
Hovig, Eivind (University of Oslo. Center for Bioinformatics) ;
Kockum, Ingrid (Karolinska Institutet (Estocolm, Suècia). Department of Clinical Neuroscience) ;
Olsson, Tomas (Karolinska Institutet (Estocolm, Suècia). Department of Clinical Neuroscience) ;
Alfredsson, Lars (Karolinska Institutet (Estocolm, Suècia)) ;
Hansen, Thomas F. (Copenhagen Mental Health Services. Institute of Biological Psychiatry) ;
Werge, Thomas (Copenhagen Mental Health Services. Institute of Biological Psychiatry) ;
Willerslev, Eske (University of Cambridge. Department of Zoology) ;
Balloux, François (University College London. Department of Genetics, Evolution and Environment) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Lalueza-Fox, Carles (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Nielsen, Rasmus (University of California. Department of Integrative Biology) ;
Stefánsson, Kári (deCODE Genetics (Reykjavík, Islàndia)) ;
Helgason, Agnar (deCODE Genetics (Reykjavík, Islàndia)) ;
Gilbert, M. Thomas P. (Norwegian University of Science and Technology. University Museum)
Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%. [...]
2022 - 10.1016/j.cub.2022.09.023
Current Biology, Vol. 32 (November 2022) , p. 1-9/e1-e6
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5.
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16 p, 5.0 MB |
Transcriptome innovations in primates revealed by single-molecule long-read sequencing
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Ferrández-Peral, Luis (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Zhan, Xiaoyu (BGI-Shenzhen) ;
Alvarez-Estape, Marina (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Chiva, Cristina (Centre de Regulació Genòmica) ;
Esteller-Cucala, Paula (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
García Perez, Raquel (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Julià, Eva (Centre de Regulació Genòmica) ;
Lizano, Esther (Institut Català de Paleontologia Miquel Crusafont) ;
Fornas, Òscar (Centre de Regulació Genòmica) ;
Sabidó, Eduard (Centre de Regulació Genòmica) ;
Li, Qiye (BGI-Shenzhen) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Zhang, Guojie
Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. [...]
2022 - 10.1101/gr.276395.121
Genome research, Published in Advance July 15, 2022
2 documents
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6.
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14 p, 1.9 MB |
Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes
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Lobón, Irene (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Solís-Moruno, Manuel (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Muhaisen, Ashraf (Universitat de Barcelona. Departament de Biologia Cel·lular, Fisiologia i Immunologia) ;
Abascal, Federico (Wellcome Trust Sanger Institute (Regne Unit)) ;
Esteller-Cucala, Paula (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
García Perez, Raquel (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Martí, Maria Josep (Universitat de Barcelona. Departament de Neurologia) ;
Tolosa, Eduardo (Universitat de Barcelona. Departament de Neurologia) ;
Ávila, Jesús (Centro de Biología Molecular Severo Ochoa) ;
Rahbari, Raheleh (Wellcome Trust Sanger Institute (Regne Unit)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Casals, Ferran (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut) ;
Soriano García, Eduardo (Institució Catalana de Recerca i Estudis Avançats)
The role of somatic mutations in complex diseases, including neurodevelopmental and neurodegenerative disorders, is becoming increasingly clear. However, to date, no study has shown their relation to Parkinson disease's phenotype. [...]
2022 - 10.3389/fragi.2022.851039
Frontiers in Aging, Vol. 3 (April 2022) , art. 851039
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7.
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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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8.
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17 p, 2.4 MB |
Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures
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García Perez, Raquel (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Esteller-Cucala, Paula (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Mas, Glòria (Centre de Regulació Genòmica) ;
Lobón, Irene (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Di Carlo, Valerio (Centre de Regulació Genòmica) ;
Riera, Meritxell (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Kuhlwilm, Martin (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Navarro, Arcadi, 1969- (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Blancher, Antoine (Centre de Physiopathologie Toulouse-Purpan) ;
Di Croce, Luciano (Centre de Regulació Genòmica) ;
Gomez-Skarmeta, José Luis (Centro Andaluz de Biología del Desarrollo) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
Changes in the epigenetic regulation of gene expression have a central role in evolution. Here, we extensively profiled a panel of human, chimpanzee, gorilla, orangutan, and macaque lymphoblastoid cell lines (LCLs), using ChIP-seq for five histone marks, ATAC-seq and RNA-seq, further complemented with whole genome sequencing (WGS) and whole genome bisulfite sequencing (WGBS). [...]
2021 - 10.1038/s41467-021-23397-1
Nature communications, Vol. 12 (May 2021) , art. 3116
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9.
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32 p, 2.0 MB |
Comprehensive identification of somatic nucleotide variants in human brain tissue
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Wang, Yifan (University of Michigan Medical School. Department of Computational Medicine and Bioinformatics) ;
Bae, Taejeong (Mayo Clinic. Center for Individualized Medicine. Department of Health Sciences Research) ;
Thorpe, Jeremy (Johns Hopkins School of Medicine. Program in Biochemistry, Cellular and Molecular Biology) ;
Sherman, Maxwell A. (Harvard Medical School) ;
Jones, Attila G. (Icahn School of Medicine at Mount Sinai. Department of Genetics and Genomic Sciences) ;
Cho, Sean (Kennedy Krieger Institute. Department of Neurology) ;
Daily, Kenneth (Sage Bionetworks (Seattle, Estats Units)) ;
Dou, Yanmei (Harvard Medical School. Department of Biomedical Informatics) ;
Ganz, Javier (Harvard Medical School. Departments of Neurology and Pediatrics) ;
Galor, Alon (Harvard Medical School. Department of Biomedical Informatics) ;
Lobón, Irene (Universitat de Barcelona. Departament de Biologia Cel·lular, Fisiologia i Immunologia) ;
Pattni, Reenal (Stanford University School of Medicine. Department of Genetics) ;
Rosenbluh, Chaggai (Icahn School of Medicine at Mount Sinai. Department of Cell, Developmental and Regenerative Biology) ;
Tomasi, Simone (Yale University. Child Study Center) ;
Tomasini, Livia (Yale University. Child Study Center) ;
Yang, Xiaoxu (Rady Children's Institute for Genomic Medicine) ;
Zhou, Bo (Stanford University School of Medicine. Department of Genetics) ;
Akbarian, Schahram (Icahn School of Medicine at Mount Sinai. Department of Psychiatry) ;
Ball, Laurel L. (Rady Children's Institute for Genomic Medicine) ;
Bizzotto, Sara (Broad Institute of MIT and Harvard) ;
Emery, Sarah B. (University of Michigan Medical School. Department of Human Genetics) ;
Doan, Ryan (Broad Institute of MIT and Harvard) ;
Fasching, Liana (Yale University. Child Study Center) ;
Jang, Yeongjun (Mayo Clinic. Center for Individualized Medicine. Department of Health Sciences Research) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Lizano, Esther (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Luquette, Lovelace J. (Harvard Medical School. Department of Biomedical Informatics) ;
Moldovan, John B. (University of Michigan Medical School. Department of Human Genetics) ;
Narurkar, Rujuta (Lieber Institute for Brain Development) ;
Oetjens, Matthew T. (University of Michigan Medical School. Department of Human Genetics) ;
Rodin, Rachel E. (Broad Institute of MIT and Harvard) ;
Sekar, Shobana (Mayo Clinic. Center for Individualized Medicine. Department of Health Sciences Research) ;
Shin, Joo Heon (Johns Hopkins School of Medicine. Department of Neurology) ;
Soriano García, Eduardo (Universitat de Barcelona. Departament de Biologia Cel·lular, Fisiologia i Immunologia) ;
Straub, Richard E. (Lieber Institute for Brain Development) ;
Zhou, Weichen (University of Michigan Medical School. Department of Computational Medicine and Bioinformatics) ;
Chess, Andrew (Icahn School of Medicine at Mount Sinai. Department of Genetics and Genomic Sciences) ;
Gleeson, Joseph G. (Rady Children's Institute for Genomic Medicine) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Park, Peter J. (Harvard Medical School. Department of Biomedical Informatics) ;
Peters, Mette A. (Sage Bionetworks) ;
Pevsner, Jonathan (Johns Hopkins School of Medicine. Department of Psychiatry and Behavioral Sciences) ;
Walsh, Christopher A. (Broad Institute of MIT and Harvard) ;
Weinberger, Daniel R. (Johns Hopkins School of Medicine. Department of Neuroscience) ;
Vaccarino, Flora M. (Yale University. Department of Neuroscience) ;
Moran, John V. (University of Michigan Medical School. Department of Internal Medicine) ;
Urban, Alexander E. (Stanford University School of Medicine. Department of Psychiatry and Behavioral Sciences) ;
Kidd, Jeffrey M. (University of Michigan Medical School. Department of Computational Medicine and Bioinformatics) ;
Mills, Ryan E. (University of Michigan Medical School. Department of Computational Medicine and Bioinformatics) ;
Abyzov, Alexej (Mayo Clinic. Center for Individualized Medicine. Department of Health Sciences Research) ;
Brain Somatic Mosaicism Network
Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. [...]
2021 - 10.1186/s13059-021-02285-3
Genome biology, Vol. 22 (march 2021)
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9 p, 2.2 MB |
Extreme differences between human germline and tumor mutation densities are driven by ancestral human-specific deviations
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Heredia-Genestar, José María (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Navarro, Arcadi, 1969- (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Mutations do not accumulate uniformly across the genome. Human germline and tumor mutation density correlate poorly, and each is associated with different genomic features. Here, we use non-human great ape (NHGA) germlines to determine human germline- and tumor-specific deviations from an ancestral-like great ape genome-wide mutational landscape. [...]
2020 - 10.1038/s41467-020-16296-4
Nature communications, Vol. 11 (May 2020) , art. 2512
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