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50 p, 28.5 MB |
Pan-cancer proteogenomics connects oncogenic drivers to functional states
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Li, Yize (Washington University in St. Louis) ;
Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Tokheim, Collin (Harvard T.H. Chan School of Public Health) ;
Bailey, Matthew H. (Brigham Young University) ;
Yaron, Tomer (Weill Cornell Medicine) ;
Stathias, Vasileios (University of Miami Miller School of Medicine) ;
Geffen, Yifat (Massachusetts General Hospital) ;
Imbach, Kathleen (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Cao, Song (McDonnell Genome Institute) ;
Anand, Shankara (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Akiyama, Yo (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Liu, Wenke (NYU Grossman School of Medicine) ;
Wyczalkowski, Matthew A. (McDonnell Genome Institute) ;
Song, Yizhe (McDonnell Genome Institute) ;
Storrs, Erik P. (McDonnell Genome Institute) ;
Wendl, Michael C. (Washington University in St. Louis) ;
Zhang, Wubing (Dana-Farber Cancer Institute (Boston, Estats Units)) ;
Sibai, Mustafa (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ruiz-Serra, Victoria (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Liang, Wen-Wei (McDonnell Genome Institute) ;
Terekhanova, Nadezhda V. (McDonnell Genome Institute) ;
Martins Rodrigues, Fernanda (McDonnell Genome Institute) ;
Clauser, Karl R. (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Heiman, David I. (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Zhang, Qing (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Aguet, Francois (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Calinawan, Anna Pamela (Icahn School of Medicine at Mount Sinai) ;
Dhanasekaran, Saravana Mohan (University of Michigan) ;
Birger, Chet (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Satpathy, Shankha (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Zhou, Daniel Cui (McDonnell Genome Institute) ;
Wang, Liang-Bo (McDonnell Genome Institute) ;
Baral, Jessika (McDonnell Genome Institute) ;
Johnson, Jared L. (Weill Cornell Medicine) ;
Huntsman, Emily M. (Weill Cornell Medicine) ;
Pugliese, Pietro (University of Sannio (Benevento, Itàlia)) ;
Colaprico, Antonio (University of Miami Miller School of Medicine) ;
Iavarone, Antonio (University of Miami Miller School of Medicine) ;
Chheda, Milan G. (Washington University in St. Louis) ;
Ricketts, Christopher J. (National Institutes of Health) ;
Fenyö, David (NYU Grossman School of Medicine) ;
Payne, Samuel H. (Brigham Young University) ;
Rodriguez, Henry (Office of Cancer Clinical Proteomics Research) ;
Robles, Ana I. (Office of Cancer Clinical Proteomics Research) ;
Gillette, Michael A. (Harvard Medical School) ;
Kumar-Sinha, Chandan (University of Michigan) ;
Lazar, Alexander (The University of Texas MD Anderson Cancer Center) ;
Cantley, Lewis (Weill Cornell Medicine) ;
Getz, Gad A. (Harvard Medical School) ;
Ding, Li (Siteman Cancer Center) ;
An, Eunkyung ;
Anurag, Meenakshi ;
Bavarva, Jasmin ;
Birrer, Michael J. ;
Ceccarelli, Michele ;
Chan, Daniel W. ;
Chinnaiyan, Arul M. ;
Cho, Hanbyul ;
Chowdhury, Shrabanti ;
Cieslik, Marcin P. ;
da Veiga Leprevost, Felipe ;
Day, Corbin ;
Domagalski, Marcin J. ;
Dou, Yongchao ;
Druker, Brian J. ;
Edwards, Nathan ;
Ellis, Matthew J. ;
Selvan, Myvizhi Esai ;
Foltz, Steven M. ;
Francis, Alicia ;
Gonzalez Robles, Tania J. ;
Gosline, Sara J. C. ;
Gümüş, Zeynep H. ;
Hiltke, Tara ;
Hong, Runyu ;
Hostetter, Galen ;
Hu, Yingwei ;
Huang, Chen ;
Huntsman, Emily ;
Jaehnig, Eric J. ;
Jewel, Scott D. ;
Ji, Jiayi ;
Jiang, Wen ;
Katsnelson, Lizabeth ;
Ketchum, Karen A. ;
Kolodziejczak, Iga ;
Lei, Jonathan T. ;
Liao, Yuxing ;
Lindgren, Caleb M. ;
Liu, Tao ;
Ma, Weiping ;
McKerrow, Wilson ;
Nesvizhskii, Alexey I. ;
Newton, Chelsea ;
Oldroyd, Robert ;
Omenn, Gilbert S. ;
Paulovich, Amanda G. ;
Petralia, Francesca ;
Reva, Boris ;
Rodland, Karin D. ;
Ruggles, Kelly V. ;
Rykunov, Dmitry ;
Savage, Sara R. ;
Schadt, Eric E. ;
Schnaubelt, Michael ;
Schraink, Tobias ;
Shi, Zhiao ;
Smith, Richard D. ;
Song, Xiaoyu ;
Tan, Jimin ;
Thangudu, Ratna R. ;
Tignor, Nicole ;
Wang, Joshua M. ;
Wang, Pei ;
Wang, Ying Cindy ;
Wen, Bo ;
Wiznerowicz, Maciej ;
Yi, Xinpei ;
Zhang, Bing ;
Zhang, Hui ;
Zhang, Xu ;
Zhang, Zhen ;
Universitat Autònoma de Barcelona
Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here, our multi-omics pan-cancer analysis uncovers insights into the impacts of cancer drivers by identifying their significant cis-effects and distal trans-effects quantified at the RNA, protein, and phosphoprotein levels. [...]
2023 -  10.1016/j.cell.2023.07.014
Cell, Vol. 186 Núm. 18 (31 2023) , p. 3921-3944.e25
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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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