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The IBEX Knowledge-Base: Achieving more together with open science

arXiv 2024年

作者： Radtke, Andrea J. Anidi, Ifeanyichukwu Arakkal, Leanne Arroyo-Mejias, Armando Beuschel, Rebecca T. Börner, Katy Chu, Colin J. Clark, Beatrice Clatworthy, Menna R. Colautti, Jake Croteau, Joshua Denha, Saven Dever, Rose Dutra, Walderez O. Fritzsche, Sonja Fullam, Spencer Gerner, Michael Y. Gola, Anita Gollob, Kenneth J. Hernandez, Jonathan M. Hor, Jyh Liang Ichise, Hiroshi Jing, Zhixin Jonigk, Danny Kandov, Evelyn Kastenmüller, Wolfgang Koenig, Joshua F.E. Kothurkar, Aanandita Kreins, Alexandra Y. Lamborn, Ian Lin, Yuri Morais, Katia Luciano Pereira Lunich, Aleksandra Luz, Jean C.S. MacDonald, Ryan B. Makranz, Chen Maltez, Vivien I. Moriaty, Ryan V. Ocampo-Godinez, Juan M. Olyntho, Vitoria M. Padhan, Kartika Remmert, Kirsten Richoz, Nathan Schrom, Edward C. Shang, Wanjing Shi, Lihong Shih, Rochelle M. Speranza, Emily Stierli, Salome Teichmann, Sarah A. Veres, Tibor Z. Vierhout, Megan Wachter, Brianna T. Wade-Vallance, Adam K. Williams, Margaret Zangger, Nathan Germain, Ronald N. Yaniv, Ziv Lymphocyte Biology Section Center for Advanced Tissue Imaging Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Critical Care Medicine and Pulmonary Branch National Heart Lung and Blood Institute National Institutes of Health BethesdaMD United States Lymphocyte Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Department of Intelligent Systems Engineering Indiana University BloomingtonIN United States UCL Institute of Ophthalmology NIHR Moorfields Biomedical Research Centre London United Kingdom Cambridge Institute for Therapeutic Immunology and Infectious Diseases University of Cambridge Department of Medicine Molecular Immunity Unit Laboratory of Molecular Biology Cambridge United Kingdom McMaster Immunology Research Centre Schroeder Allergy and Immunology Research Institute Department of Medicine Faculty of Health Sciences McMaster University HamiltonON Canada Department of Business Development BioLegend Inc. San DiegoCA United States Functional Immunogenomics Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institutes of Health BethesdaMD United States Laboratory of Cell-Cell Interactions Department of Morphology Institute of Biological Sciences Universidade Federal de Minas Gerais MG Belo Horizonte Brazil Spatial Proteomics Group Berlin Germany Division of Rheumatology Rush University Medical Center ChicagoIL United States Department of Immunology University of Washington School of Medicine SeattleWA United States Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development The Rockefeller University New YorkNY United States Hospital Israelita Albert Einstein SP Sao Paulo Brazil Surgical Oncology Program National Cancer Institute National Institutes of Health BethesdaMD United St

Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, p... 详细信息

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower

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Nature communications 2022年第1期13卷 7571页

作者： Shimin Shuai Steven Gallinger Lincoln D Stein Department of Molecular Genetics University of Toronto Toronto ON Canada M5S 1A8. shimin.shuai@mail.utoronto.ca. Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada M5G 0A3. shimin.shuai@mail.utoronto.ca. Division of General Surgery Toronto General Hospital Toronto ON Canada M5G 2C4. Lunenfeld-Tanenbaum Research Institute Mount Sinai Hospital Toronto ON Canada M5G 1X5. Department of Molecular Genetics University of Toronto Toronto ON Canada M5S 1A8. lincoln.stein@***. Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada M5G 0A3. lincoln.stein@***.

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Author Correction: m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome

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Nature Biotechnology 2023年 150页

作者： Lulu Hu Shun Liu Yong Peng Ruiqi Ge Bryan T. Harada Qing Dai Jiangbo Wei Lisheng Zhang Ziyang Hao Liangzhi Luo Huanyu Wang Yuru Wang Chuan He Mengjie Chen Rui Su Jianjun Chen Chamara Senevirathne Minkui Luo Department of Chemistry The University of Chicago Chicago IL USA Institute for Biophysical Dynamics The University of Chicago Chicago IL USA Howard Hughes Medical Institute The University of Chicago Chicago IL USA Fudan University Institutes of Biomedical Sciences Shanghai Cancer Center Shanghai Key Laboratory of Medical Epigenetics International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology) Shanghai Medical College of Fudan University Shanghai China Section of Genetic Medicine Department of Medicine The University of Chicago Chicago IL USA Department of Human Genetics The University of Chicago Chicago IL USA Department of Systems Biology Beckman Research Institute of City of Hope Monrovia CA USA City of Hope Comprehensive Cancer Center City of Hope Duarte CA USA Gehr Family Center for Leukemia Research City of Hope Duarte CA USA Chemical Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Program of Pharmacology Weill Cornell Medical College of Cornell University New York NY USA

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Publisher Correction: Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

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Clinical epigenetics 2023年第1期15卷 3页

作者： Patricia Johansson Teresa Laguna Julio Ossowski Vera Pancaldi Martina Brauser Ulrich Dührsen Lara Keuneke Ana Queiros Julia Richter José I Martín-Subero Reiner Siebert Brigitte Schlegelberger Ralf Küppers Jan Dürig Eva M Murga Penas Enrique Carrillo-de Santa Pau Anke K Bergmann Faculty of Medicine Institute of Cell Biology (Cancer Research) University of Duisburg-Essen Virchowstr. 177 45122 Essen Germany. patricia.johansson@uk-essen.de. Computational Biology Group Precision Nutrition and Cancer Research Program IMDEA Food Institute 28049 Madrid Spain. teresa.laguna@***. Institute for Human Genetics Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein Campus Kiel Kiel Germany. Institute of Human Genetics Medical School Hannover (MHH) Hannover Germany. Centre de Recherches en Cancérologie de Toulouse (CRCT) Université de Toulouse CNRS Université Toulouse III-Paul Sabatier Centre de Recherches en Cancérologie de Toulouse INSERM U1037 31037 Toulouse France. Barcelona Supercomputing Center 08034 Barcelona Spain. Faculty of Medicine Institute of Cell Biology (Cancer Research) University of Duisburg-Essen Virchowstr. 177 45122 Essen Germany. Department of Hematology University Hospital Essen University of Duisburg-Essen Essen Germany. Institut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS) University of Barcelona 08036 Barcelona Spain. Institute for Pathology Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein Campus Kiel Kiel Germany. Institució Catalana de Recerca i Estudis Avançats (ICREA) 08010 Barcelona Spain. Institute of Human Genetics University of Ulm and University Medical Center Ulm Ulm Germany. Department of Internal Medicine University Hospital Essen St. Josef-Krankenhaus University Medicine Essen Essen Germany. Computational Biology Group Precision Nutrition and Cancer Research Program IMDEA Food Institute 28049 Madrid Spain.

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Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers

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Nature genetics 2023年第6期55卷 1078页

作者： Yuan Yuan Young Seok Ju Youngwook Kim Jun Li Yumeng Wang Christopher J Yoon Yang Yang Inigo Martincorena Chad J Creighton John N Weinstein Yanxun Xu Leng Han Hyung-Lae Kim Hidewaki Nakagawa Keunchil Park Peter J Campbell Han Liang Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon Korea. Department of Health Science and Technology Samsung Advanced Institute for Health Science and Technology Sungkyunkwan University School of Medicine Seoul Korea. Samsung Genome Institute Samsung Medical Center Seoul Korea. Quantitative and Computational Biosciences Graduate Program Baylor College of Medicine Houston TX USA. Division of Biostatistics The University of Texas Health Science Center at Houston School of Public Health Houston TX USA. Department of Medicine and Dan L. Duncan Cancer Center Division of Biostatistics Baylor College of Medicine Houston TX USA. Department of Systems Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Department of Applied Mathematics and Statistics Johns Hopkins University Baltimore MD USA. Department of Biochemistry and Molecular Biology The University of Texas Health Science Center at Houston McGovern Medical School Houston TX USA. Department of Biochemistry Ewha Womans University School of Medicine Seoul Korea. Laboratory for Cancer Genomics RIKEN Center for Integrative Medical Sciences Yokohama Japan. Division of Hematology/Oncology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea. kpark@skku.edu. Samsung Advanced Institute for Health Sciences and Technology Sungkyunkwan University School of Medicine Seoul South Korea. kpark@skku.edu. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. pc8@sanger.ac.uk. Department of Haematology University of Cambridge Cambridge UK. pc8@sanger.ac.uk. Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. hliang1@mdanderson.org. Quantitative and Comp

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Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction (vol 53, pg 65, 2021)

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NATURE genetics 2021年第3期53卷 413-413页

作者： Conti, David V. Darst, Burcu F. Moss, Lilit C. Saunders, Edward J. Sheng, Xin Chou, Alisha Schumacher, Fredrick R. Al Olama, Ali Amin Benlloch, Sara Dadaev, Tokhir Brook, Mark N. Sahimi, Ali Hoffmann, Thomas J. Takahashi, Atushi Matsuda, Koichi Momozawa, Yukihide Fujita, Masashi Muir, Kenneth Lophatananon, Artitaya Wan, Peggy Le Marchand, Loic Wilkens, Lynne R. Stevens, Victoria L. Gapstur, Susan M. Carter, Brian D. Schleutker, Johanna Tammela, Teuvo L. J. Sipeky, Csilla Auvinen, Anssi Giles, Graham G. Southey, Melissa C. MacInnis, Robert J. Cybulski, Cezary Wokolorczyk, Dominika Lubinski, Jan Neal, David E. Donovan, Jenny L. Hamdy, Freddie C. Martin, Richard M. Nordestgaard, Borge G. Nielsen, Sune F. Weischer, Maren Bojesen, Stig E. Roder, Martin Andreas Iversen, Peter Batra, Jyotsna Chambers, Suzanne Moya, Leire Horvath, Lisa Clements, Judith A. Tilley, Wayne Risbridger, Gail P. Gronberg, Henrik Aly, Markus Szulkin, Robert Eklund, Martin Nordstrom, Tobias Pashayan, Nora Dunning, Alison M. Ghoussaini, Maya Travis, Ruth C. Key, Tim J. Riboli, Elio Park, Jong Y. Sellers, Thomas A. Lin, Hui-Yi Albanes, Demetrius Weinstein, Stephanie J. Mucci, Lorelei A. Giovannucci, Edward Lindstrom, Sara Kraft, Peter Hunter, David J. Penney, Kathryn L. Turman, Constance Tangen, Catherine M. Goodman, Phyllis J. Thompson, Ian M., Jr. Hamilton, Robert J. Fleshner, Neil E. Finelli, Antonio Parent, Marie-Elise Stanford, Janet L. Ostrander, Elaine A. Geybels, Milan S. Koutros, Stella Freeman, Laura E. Beane Stampfer, Meir Wolk, Alicja Hakansson, Niclas Andriole, Gerald L. Hoover, Robert N. Machiela, Mitchell J. Sorensen, Karina Dalsgaard Borre, Michael Blot, William J. Zheng, Wei Yeboah, Edward D. Mensah, James E. Lu, Yong-Jie Zhang, Hong-Wei Feng, Ninghan Mao, Xueying Wu, Yudong Zhao, Shan-Chao Sun, Zan Thibodeau, Stephen N. McDonnell, Shannon K. Schaid, Daniel J. West, Catharine M. L. Burnet, Neil Barnett, Gill Maier, Christiane Schnoeller, Thomas Luedeke, Manuel Kibel, Adam S. Drake, Bettina F. Cussenot, Olivier Cancel-Tassin, Gerald Center for Genetic Epidemiology Department of Preventive Medicine Keck School of Medicine University of Southern California/Norris Comprehensive Cancer Center Los Angeles CA USA The Institute of Cancer Research London UK Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA Seidman Cancer Center University Hospitals Cleveland OH USA Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care University of Cambridge Strangeways Research Laboratory Cambridge UK Stroke Research Group Department of Clinical Neurosciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics University of California San Francisco CA USA Institute for Human Genetics University of California San Francisco CA USA Laboratory for Statistical Analysis RIKEN Center for Integrative Medical Sciences Yokohama Japan Department of Genomic Medicine National Cerebral and Cardiovascular Center Research Institute Suita Japan Laboratory of Clinical Genome Sequencing Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Tokyo Japan Biobank Tokyo Japan Laboratory for Genotyping Development RIKEN Center of Integrative Medical Sciences Yokohama Japan Laboratory for Cancer Genomics RIKEN Center of Integrative Medical Sciences Yokohama Japan Division of Population Health Health Services Research and Primary Care School of Health Sciences Faculty of Biology Medicine and Health University of Manchester Manchester UK Warwick Medical School University of Warwick Coventry UK Epidemiology Program University of Hawaii Cancer Center Honolulu HI USA Behavioral and Epidemiology Research Group Research Program American Cancer Society Atlanta GA USA Institute of Biomedicine University of Turku Turku Finland Department of Medical Genetics Genomics Laboratory Division Turku University Hospital Turku Finland Department of Urolog

Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,2... 详细信息

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BPS2025 - Development and benchmarking of the open force field initiative self-consistent force field for proteins and small molecules

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Biophysical Journal 2025年第3期124卷 483a-484a页

作者： Chapin E. Cavender Pavan K. Behara Anika J. Friedman Joshua T. Horton Alexandra R. McIsaac Louis G. Smith Matthew W. Thompson Jeffrey Wagner Lily Wang Brent R. Westbrook John D. Chodera Daniel Cole David L. Mobley Michael R. Shirts Michael K. Gilson Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA Center for Neurotherapeutics University of California Irvine Irvine CA USA Department of Chemical and Biological Engineering University of Colorado Boulder Boulder CO USA School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne United Kingdom Open Force Field Consortium Open Molecular Software Foundation Davis CA USA Department of Biochemistry and Biophysics University of Pennsylvania Philadelphia PA USA Computational & Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Pharmaceutical Sciences and Department of Chemistry University of California Irvine Irvine CA USA

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Author Correction: A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing

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Nature communications 2022年第1期13卷 2828页

作者： Sanju Sinha Karina Barbosa Kuoyuan Cheng Mark D M Leiserson Prashant Jain Anagha Deshpande David M Wilson Bríd M Ryan Ji Luo Ze'ev A Ronai Joo Sang Lee Aniruddha J Deshpande Eytan Ruppin Cancer Data Science Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda MD 20892 USA. Laboratory of Human Carcinogenesis Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda MD 20850 USA. Center for Bioinformatics and Computational Biology University of Maryland College Park MD 20742 USA. Tumor Initiation Program Cancer Center Sanford Burnham Prebys Medical Discovery Institute La Jolla CA 92037 USA. Laboratory of Molecular Gerontology National Institute on Aging Intramural Research Program National Institutes of Health Baltimore MD 21224 USA. Laboratory of Cancer Biology and Genetics Center for Cancer Research National Cancer Institute National Institute of Health Bethesda MD 20850 USA. Samsung Medical Center Sungkyunkwan University School of Medicine Suwon 16419 Republic of Korea. Department of Precision Medicine School of Medicine and Department of Artificial Intelligence Sungkyunkwan University Suwon 16419 Republic of Korea. Tumor Initiation Program Cancer Center Sanford Burnham Prebys Medical Discovery Institute La Jolla CA 92037 USA. adeshpande@***. Cancer Data Science Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda MD 20892 USA. eytan.ruppin@nih.gov.

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Guidelines and definitions for research on epithelial-mesenchymal transition (vol 21, pg 341, 2020)

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NATURE REVIEWS MOLECULAR CELL biology 2021年第12期22卷 834-834页

作者： Yang, Jing Antin, Parker Berx, Geert Blanpain, Cedric Brabletz, Thomas Bronner, Marianne Campbell, Kyra Cano, Amparo Casanova, Jordi Christofori, Gerhard Dedhar, Shoukat Derynck, Rik Ford, Heide L. Fuxe, Jonas Garcia de Herreros, Antonio Goodall, Gregory J. Hadjantonakis, Anna-Katerina Huang, Ruby Y. J. Kalcheim, Chaya Kalluri, Raghu Kang, Yibin Khew-Goodall, Yeesim Levine, Herbert Liu, Jinsong Longmore, Gregory D. Mani, Sendurai A. Massague, Joan Mayor, Roberto McClay, David Mostov, Keith E. Newgreen, Donald F. Nieto, M. Angela Puisieux, Alain Runyan, Raymond Savagner, Pierre Stanger, Ben Stemmler, Marc P. Takahashi, Yoshiko Takeichi, Masatoshi Theveneau, Eric Thiery, Jean Paul Thompson, Erik W. Weinberg, Robert A. Williams, Elizabeth D. Xing, Jianhua Zhou, Binhua P. Sheng, Guojun Departments of Pharmacology and Pediatrics Moores Cancer Center University of California San Diego La Jolla CA USA Department of Cellular and Molecular Medicine University of Arizona Tucson AZ USA Molecular and Cellular Oncology Lab Department of Biomedical Molecular Biology Ghent University Cancer Research Institute Ghent (CRIG) VIB Center for Inflammation Research Ghent Belgium Laboratory of Stem Cells and Cancer Université Libre de Bruxelles Bruxelles Belgium Department of Experimental Medicine 1 Nikolaus-Fiebiger-Center for Molecular Medicine Friedrich-Alexander-University Erlangen-Nürnberg Erlangen Germany Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA Department of Biomedical Science and Bateson Centre University of Sheffield Sheffield UK Departamento de Bioquímica Universidad Autónoma de Madrid (UAM) Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM) IdiPAZ & Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Madrid Spain Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology/Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona Spain Department of Biomedicine University of Basel Basel Switzerland Department of Biochemistry and Molecular Biology University of British Columbia and British Columbia Cancer Research Centre Vancouver BC Canada Departments of Cell and Tissue Biology and Anatomy University of California at San Francisco San Francisco CA USA Department of Pharmacology University of Colorado Anschutz Medical Campus Aurora CO USA Department of Laboratory Medicine (LABMED) Division of Pathology Karolinska University Hospital and Department of Microbiology Tumor and Cell Biology (MTC) Karolinska Institutet Stockholm Sweden Programa de Recerca en Càncer Institut Hospital del Mar d’Investigacions Mèdiques (IMIM) and Departament de Ciències Experimentals i de la Salut Universitat Pompeu Fabra Barcelona Spain C

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