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SSRN 2020年

作者： Gonzalez-Teran, Barbara Pittman, Maureen Felix, Franco Richmond-Buccola, Desmond Thomas, Reuben Choudhary, Krishna Moroni, Elisabetta Colombo, Giorgio Alexanian, Michael Cole, Bonnie Samse-Knapp, Kaitlen McGregor, Michael Gifford, Casey A. Huttenhain, Ruth Gelb, Bruce D. Conklin, Bruce R. Black, Brian L. Bruneau, Benoit G. Krogan, Nevan J. Pollard, Katherine S. Srivastava, Deepak Gladstone Institutes San FranciscoCA United States SCITEC-CNR Milano Italy University of Pavia Department of Chemistry Pavia Italy Developmental and Stem Cell Biology PhD Program University of California San FranciscoCA United States Department of Cellular and Molecular Pharmacology University of California San Francisco San FranciscoCA United States Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New YorkNY United States Mindich Child Health and Development Institute Icahn School of Medicine at Mount Sinai New YorkNY United States Department of Pediatrics Icahn School of Medicine at Mount Sinai New YorkNY United States Cardiovascular Research Institute University of California San FranciscoCA United States Department of Pediatrics UCSF School of Medicine San FranciscoCA United States Roddenberry Center for Stem Cell Biology and Medicine at Gladstone San FranciscoCA United States University of California San Francisco San FranciscoCA United States Chan Zuckerberg Biohub San FranciscoCA United States Department of Epidemiology & Biostatistics Institute for Computational Health Sciences Institute for Human Genetics University of California San FranciscoCA United States Department of Biochemistry and Biophysics University of California San FranciscoCA United States Gladstone Institutes 1650 Owens St San FranciscoCA94158 United States

Congenital heart disease (CHD) is present in 1% of live births, yet identification of causal mutations remains a challenge despite large-scale genomic sequencing efforts. We hypothesized that genetic determinants for CHDs may lie in protein interactomes of GATA4 and TBX5, two transcription factors that cause CHDs. Defining their interactomes in human cardiac progenitors via affinity purification-mass spectrometry and integrating results with genetic data from the Pediatric Cardiac Genomic Consortium revealed an enrichment of de novo variants among proteins that interact with GATA4 or TBX5. A consolidative score that prioritized interactome members based on variant, gene, and proband features identified likely CHD-causing genes, including the epigenetic reader GLYR1. GLYR1 and GATA4 widely co-occupied cardiac developmental genes, resulting in co-activation, and the GLYR1 missense variant associated with CHD disrupted interaction with GATA4. This integrative proteomic and genetic approach provides a framework for prioritizing and interrogating the contribution of genetic variants in disease. © 2020, The Authors. All rights reserved.

关键词： Proteins

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Author Correction: L1CAM defines the regenerative origin of metastasis-initiating cells in colorectal cancer

Nature cancer

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Nature cancer 2020年第11期1卷 1128页

作者： Karuna Ganesh Harihar Basnet Yasemin Kaygusuz Ashley M Laughney Lan He Roshan Sharma Kevin P O'Rourke Vincent P Reuter Yun-Han Huang Mesruh Turkekul Ekrem Emrah Er Ignas Masilionis Katia Manova-Todorova Martin R Weiser Leonard B Saltz Julio Garcia-Aguilar Richard Koche Scott W Lowe Dana Pe'er Jinru Shia Joan Massagué Cancer Biology and Genetics Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. Department of Medicine Memorial Sloan Kettering Cancer Center New York NY USA. Molecular Pharmacology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. Louis V. Gerstner Jr. Graduate School of Biomedical Sciences Memorial Sloan Kettering Cancer Center New York NY USA. Institute for Computational Biomedicine Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA. Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. Department of Applied Physics and Applied Math Columbia University New York NY USA. New York Genome Center New York NY USA. Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program New York NY USA. Center for Epigenetics Research Memorial Sloan Kettering Cancer Center New York NY USA. Molecular Cytology Core Facility Memorial Sloan Kettering Cancer Center New York NY USA. Department of Physiology and Biophysics University of Illinois at Chicago Chicago IL USA. Department of Surgery Memorial Sloan Kettering Cancer Center New York NY USA. Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA. Cancer Biology and Genetics Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. j-massague@***.

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Publisher Correction: Immune landscape in invasive ductal and lobular breast cancer reveals a divergent macrophage-driven microenvironment

Nature cancer

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Nature cancer 2023年第4期4卷 582页

作者： Sayali Onkar Jian Cui Jian Zou Carly Cardello Anthony R Cillo Mostofa Rafid Uddin April Sagan Marion Joy Hatice U Osmanbeyoglu Katherine L Pogue-Geile Priscilla F McAuliffe Peter C Lucas George C Tseng Adrian V Lee Tullia C Bruno Steffi Oesterreich Dario A A Vignali Department of Immunology University of Pittsburgh School of Medicine Pittsburgh PA USA. Tumor Microenvironment Center UPMC Hillman Cancer Center Pittsburgh PA USA. Graduate Program in Microbiology and Immunology University of Pittsburgh School of Medicine Pittsburgh PA USA. Department of Biostatistics University of Pittsburgh Pittsburgh PA USA. Computational Biology Department Carnegie Mellon University Pittsburgh PA USA. Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology Pittsburgh PA USA. Department of Biomedical Informatics University of Pittsburgh Pittsburgh PA USA. UPMC Hillman Cancer Center Pittsburgh PA USA. NSABP Foundation Pittsburgh PA USA. Department of Bioengineering University of Pittsburgh Pittsburgh PA USA. Section of Breast Surgery Division of Surgical Oncology Department of Surgery University of Pittsburgh College of Medicine Magee Women's Hospital of UPMC Pittsburgh PA USA. Women's Cancer Research Center UPMC Hillman Cancer Center Magee-Womens Research Institute University of Pittsburgh Pittsburgh PA USA. Department of Pathology University of Pittsburgh Pittsburgh PA USA. Cancer Biology Program UPMC Hillman Cancer Center Pittsburgh PA USA. Department of Pharmacology and Chemical Biology University of Pittsburgh Pittsburgh PA USA. Cancer Immunology and Immunotherapy Program UPMC Hillman Cancer Center Pittsburgh PA USA. Women's Cancer Research Center UPMC Hillman Cancer Center Magee-Womens Research Institute University of Pittsburgh Pittsburgh PA USA. oesterreichs@upmc.edu. Cancer Biology Program UPMC Hillman Cancer Center Pittsburgh PA USA. oesterreichs@upmc.edu. Department of Pharmacology and Chemical Biology University of Pittsburgh Pittsburgh PA USA. oesterreichs@upmc.edu. Department of Immunology University of Pittsburgh School of Medicine Pittsburgh PA USA. dvignali@pitt.edu. Tumor Microenvironment Center UPMC Hillman Cancer Center Pittsburgh PA USA. dvignali@pi

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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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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26th Annual computational Neuroscience Meeting (CNS*2017) of the Organization for computational Neuroscience Antwerp, Belgium, July 15-20, 2017

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BMC NEUROSCIENCE 2017年第Sup1期18卷 1-79页

作者： [Anonymous] Indiana University Purdue University Indianapolis Indianapolis IN 46032 USA Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN 46032 USA Department of Mathematics East Carolina University Greenville NC 27858 USA Jülich Supercomputing Centre Forschungszentrum Jülich 52425 Jülich Germany Future Systems Swiss National Supercomputing Centre 8092 Zurich Switzerland User Engagement and Support Swiss National Supercomputing Centre 6900 Lugano Switzerland Institut de Neurosciences des Systèmes Aix Marseille Univ 13005 Marseille France Simulation Lab Neuroscience Forschungszentrum Jülich Jülich Germany Department of Experimental Psychology Ghent University 9000 Ghent Belgium Donders Center for Cognitive Neuroimaging Radboud University 6525HR Nijmegen The Netherlands Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO 80309 USA Department of Neurosurgery Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Neurology Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Otolaryngology Johns Hopkins School of Medicine Baltimore MD 21287 USA INSERM U968 Paris France Sorbonne Universités UPMC University Paris 06 UMR_S 968 Institut de la Vision Paris France CNRS UMR_7210 Paris France Department of Computer Architecture and Technology University of Granada (CITIC) Granada Spain Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Institut de la Vision Paris France Department of Adaptive Machine Systems Osaka University Osaka Japan Department of Computer Science University of Cergy-Pontoise Cergy-Pontoise France Department of Physics and Astronomy College of Charleston Charleston SC 29424 USA School of Physics Faculty of Science University of Sydney Sydney NSW 2006 Australia Center of Excellence for Integrative Brain Function Australian Research Council Sydney Australia Max Planck Institute for Human Cognitive and Bra

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Author Correction: Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants

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Nature medicine 2024年第1期30卷 307页

作者： Nicole L Welch Meilin Zhu Catherine Hua Juliane Weller Marzieh Ezzaty Mirhashemi Tien G Nguyen Sreekar Mantena Matthew R Bauer Bennett M Shaw Cheri M Ackerman Sri Gowtham Thakku Megan W Tse Jared Kehe Marie-Martine Uwera Jacqueline S Eversley Derek A Bielwaski Graham McGrath Joseph Braidt Jeremy Johnson Felecia Cerrato Gage K Moreno Lydia A Krasilnikova Brittany A Petros Gabrielle L Gionet Ewa King Richard C Huard Samantha K Jalbert Michael L Cleary Nicholas A Fitzgerald Stacey B Gabriel Glen R Gallagher Sandra C Smole Lawrence C Madoff Catherine M Brown Matthew W Keller Malania M Wilson Marie K Kirby John R Barnes Daniel J Park Katherine J Siddle Christian T Happi Deborah T Hung Michael Springer Bronwyn L MacInnis Jacob E Lemieux Eric Rosenberg John A Branda Paul C Blainey Pardis C Sabeti Cameron Myhrvold Broad Institute of MIT and Harvard Cambridge MA USA. nicole_welch@g.harvard.edu. Harvard Program in Virology Division of Medical Sciences Harvard Medical School Boston MA USA. nicole_welch@g.harvard.edu. Broad Institute of MIT and Harvard Cambridge MA USA. Department of Biological Engineering Massachusetts Institute of Technology Cambridge MA USA. Division of Infectious Diseases Department of Medicine Massachusetts General Hospital Boston MA USA. Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK. Harvard Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA. Division of Health Sciences and Technology Harvard Medical School and Massachusetts Institute of Technology Cambridge MA USA. Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA. Harvard/Massachusetts Institute of Technology MD-PhD Program Harvard Medical School Boston MA USA. Department of Systems Biology Harvard Medical School Boston MA USA. State Health Laboratories Rhode Island Department of Health Providence RI USA. Massachusetts Department of Public Health Boston MA USA. Influenza Division National Center for Immunization and Respiratory Diseases Centers for Disease Control and Prevention Atlanta GA USA. African Centre of Excellence for Genomics of Infectious Diseases Redeemer's University Ede Nigeria. Department of Biological Sciences College of Natural Sciences Redeemer's University Ede Nigeria. Molecular Biology Department and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA USA. Department of Immunology and Infectious Disease Harvard T.H. Chan School of Public Health Harvard University Boston MA USA. Department of Pathology Massachusetts General Hospital and Harvard Medical School Boston MA USA. Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology Cambridge MA USA. Broad Institute of MIT and Harvard Cambridge MA USA. pardis

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Author Correction: Low-intensity pulsed ultrasound stimulation (LIPUS) modulates microglial activation following intracortical microelectrode implantation

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Nature communications 2024年第1期15卷 7618页

作者： Fan Li Jazlyn Gallego Natasha N Tirko Jenna Greaser Derek Bashe Rudra Patel Eric Shaker Grace E Van Valkenburg Alanoud S Alsubhi Steven Wellman Vanshika Singh Camila Garcia Padilla Kyle W Gheres John I Broussard Roger Bagwell Maureen Mulvihill Takashi D Y Kozai Department of Bioengineering University of Pittsburgh Pittsburgh PA USA. Center for Neural Basis of Cognition Pittsburgh PA USA. Computational Modeling and Simulation PhD Program University of Pittsburgh Pittsburgh PA USA. Department of Biochemistry and Molecular Biology Pennsylvania State University University Park PA USA. Actuated Medical Bellefonte PA USA. Washington University in St. Louis St. Louis MO USA. Department of Neuroscience University of Pittsburgh Pittsburgh PA USA. Columbia University New York NY USA. Department of Bioengineering University of Pittsburgh Pittsburgh PA USA. TK.Kozai@pitt.edu. Center for Neural Basis of Cognition Pittsburgh PA USA. TK.Kozai@pitt.edu. Center for Neuroscience University of Pittsburgh Pittsburgh PA USA. TK.Kozai@pitt.edu. McGowan Institute of Regenerative Medicine University of Pittsburgh Pittsburgh PA USA. TK.Kozai@pitt.edu. NeuroTech Center University of Pittsburgh Brain Institute Pittsburgh PA USA. TK.Kozai@pitt.edu.

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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