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Author Correction: Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution

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Nature genetics 2020年第4期52卷 463页

作者： Michelle Chan-Seng-Yue Jaeseung C Kim Gavin W Wilson Karen Ng Eugenia Flores Figueroa Grainne M O'Kane Ashton A Connor Robert E Denroche Robert C Grant Jessica McLeod Julie M Wilson Gun Ho Jang Amy Zhang Sheng-Ben Liang Ayelet Borgida Dianne Chadwick Sangeetha Kalimuthu Ilinca Lungu John M S Bartlett Paul M Krzyzanowski Vandana Sandhu Hervé Tiriac Fieke E M Froeling Joanna M Karasinska James T Topham Daniel J Renouf David F Schaeffer Steven J M Jones Marco A Marra Janessa Laskin Runjan Chetty Lincoln D Stein George Zogopoulos Benjamin Haibe-Kains Peter J Campbell David A Tuveson Jennifer J Knox Sandra E Fischer Steven Gallinger Faiyaz Notta Princess Margaret Cancer Centre Toronto Ontario Canada. PanCuRx Translational Research Initiative Ontario Institute for Cancer Research Toronto Ontario Canada. Genomics Technology Program Ontario Institute for Cancer Research Toronto Ontario Canada. Wallace McCain Centre for Pancreatic Cancer Department of Medical Oncology Princess Margaret Centre University Health Network University of Toronto Toronto Ontario Canada. Hepatobiliary/Pancreatic Surgical Oncology Program University Health Network Toronto Ontario Canada. UHN Program in BioSpecimen Sciences University Health Network Toronto Ontario Canada. Lunenfeld-Tanenbaum Research Institute Mount Sinai Hospital Toronto Ontario Canada. Department of Pathology University Health Network and University of Toronto Toronto Ontario Canada. Diagnostic Development Ontario Institute for Cancer Research Toronto Ontario Canada. Cold Spring Harbor Laboratory Cold Spring Harbor NY USA. Lustgarten Foundation Pancreatic Cancer Research Laboratory Cold Spring Harbor NY USA. Department of Surgery University of California San Diego NCI-designated Comprehensive Cancer Center La Jolla CA USA. Department of Surgery and Cancer Imperial College London London UK. Pancreas Centre BC Vancouver British Columbia Canada. Department of Medical Oncology BC Cancer Vancouver British Columbia Canada. Department of Pathology and Laboratory Medicine Vancouver General Hospital Vancouver British Columbia Canada. Canada's Michael Smith Genome Sciences Centre Vancouver British Columbia Canada. Department of Medical Genetics University of British Columbia Vancouver British Columbia Canada. Bioinformatics Ontario Institute for Cancer Research Toronto Ontario Canada. Department of Molecular Genetics University of Toronto Toronto Ontario Canada. Research Institute of the McGill University Health Centre Montreal Quebec Canada. The Goodman Cancer Research Centre of McGill University Montreal Quebec Canada. Department of Medical

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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BIOM-24. PROTEIN SURFACE SIGNATURE ON SERUM EXTRACELLULAR VESICLES FOR NON-INVASIVE DETECTION OF TUMOR PROGRESSION IN GLIOBLASTOMA PATIENTS

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Neuro-Oncology 2021年第SUPPLEMENT_6期23卷 vi15-vi16页

作者： Tzaridis, Theophilos Weller, Johannes Bachurski, Daniel Shakheri, Farhad Schaub, Christina Hau, Peter Buness, Andreas Schlegel, Uwe Steinbach, Joachim Seidel, Clemens Goldbrunner, Roland Schäfer, Niklas Wechsler-Reya, Robert Scheffler, Björn Glas, Martin Haeberle, Lothar Herrlinger, Ulrich Coch, Christoph Reiners, Katrin Hartmann, Gunther Tumor Initiation & Maintenance Program Sanford Burnham Presbys Medical Discovery Institute La Jolla CA USA Division of Clinical Neurooncology Department of Neurology University Hospital Bonn Bonn Germany Departmentof Internal Medicine Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf Partner Site Cologne Center for Molecular Medicine Cologne University of Cologne Cologne Germany Institute for Genomic Statistics and Bioinformatics University of Bonn Bonn Germany Department of Neurology and Wilhelm Sander NeuroOncology Unit University Hospital Regensburg Germany Department of Neurology University Hospital Knappschaftskrankenhaus Ruhr–University Bochum Bochum Germany Dr. Senckenbergisches Institut für Neuroonkologie Frankfurt Germany Department of Radiation Oncology University Hospital Leipzig Leipzig Germany Center for Neurosurgery Dept. of General Neurosurgery Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany Sanford Burnham Prebys Medical Discovery Institute La Jolla USA DKFZ-Division Translational Neurooncology at the West German Cancer Center German Cancer Consortium DKFZ Heidelberg & Partner Site University Hospital Essen Germany Essen Germany Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS) Division of Clinical Neurooncology University Medicine Essen University Duisburg-Essen Essen Germany Erlangen University Hospital Department of Gynecology and Obstetrics Comprehensive Cancer Center Erlangen-EMN Friedrich Alexander University of Erlangen–Nuremberg Germany Erlangen Germany Institute of Clinical Chemistry and Clinical Pharmacology University of Bonn Bonn Germany

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Publisher Correction: A terminal metabolite of niacin promotes vascular inflammation and contributes to cardiovascular disease risk

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Nature medicine 2024年第6期30卷 1791页

作者： Marc Ferrell Zeneng Wang James T Anderson Xinmin S Li Marco Witkowski Joseph A DiDonato James R Hilser Jaana A Hartiala Arash Haghikia Tomas Cajka Oliver Fiehn Naseer Sangwan Ilja Demuth Maximilian König Elisabeth Steinhagen-Thiessen Ulf Landmesser W H Wilson Tang Hooman Allayee Stanley L Hazen Department of Cardiovascular & Metabolic Sciences Lerner Research Institute Cleveland Clinic Cleveland OH USA. Systems Biology and Bioinformatics Program Department of Nutrition Case Western Reserve University Cleveland OH USA. Department of Cardiology Angiology and Intensive Care Deutsches Herzzentrum der Charité Campus Benjamin Franklin Berlin Germany. Department of Population and Public Health Sciences Keck School of Medicine University of Southern California Los Angeles CA USA. Department of Biochemistry & Molecular Medicine Keck School of Medicine University of Southern California Los Angeles CA USA. German Center for Cardiovascular Research (DZHK) Partner Site Berlin Berlin Germany. Berlin Institute of Health (BIH) Berlin Germany. Friede Springer Cardiovascular Prevention Center at Charité Berlin Germany. Charité - Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin Berlin Germany. West Coast Metabolomics Center University of California Davis Davis CA USA. Institute of Physiology of the Czech Academy of Sciences Prague Czech Republic. Department of Endocrinology and Metabolism Charité - Universitätsmedizin Berlin Berlin Germany. Berlin Institute of Health Center for Regenerative Therapies Berlin Germany. Department of Cardiovascular Medicine Heart Vascular and Thoracic Institute Cleveland Clinic Cleveland OH USA. Department of Cardiovascular & Metabolic Sciences Lerner Research Institute Cleveland Clinic Cleveland OH USA. hazens@***. Department of Cardiovascular Medicine Heart Vascular and Thoracic Institute Cleveland Clinic Cleveland OH USA. hazens@***.

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1964MO Alliance A031501: AMBASSADOR study of adjuvant pembrolizumab (Pembro) in muscle-invasive urothelial carcinoma (MIUC) vs observation (Obs): Extended follow-up disease-free survival (DFS) results and metastatic (met) disease recurrence distribution

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Annals of Oncology 2024年 35卷 S1135-S1136页

作者： A.B. Apolo K. Ballman G.P. Sonpavde S. Berg W. Kim R. Parikh M.Y. Teo R.F. Sweis D. Geynisman P. Grivas G. Chatta Z. Reichert J.W. Kim M.A. Bilen B.A. McGregor S. Srinivas S. Halabi G. Perez Burbano M.J. Morris J.E. Rosenberg Genitourinary Malignancies Branch National Cancer Institute Bethesda MD USA Biostatistics Mayo Clinic Cancer Center Rochester MN USA Medical Oncology Genitourinary Section AdventHealth Cancer Institute Orlando FL USA Harvard Cancer Center Dana-Farber Cancer Institute Boston MA USA Department of Medicine UNC Lineberger Comprehensive Cancer Center Chapel Hill NC USA Genitourinary Cancer Program KUMC - University of Kansas Medical Center Kansas City KS USA Department of Medicine Memorial Sloan Kettering Cancer Center New York NY USA Medicine The University of Chicago Chicago IL USA Medical Oncology Department Fox Chase Cancer Center - Main Campus Philadelphia PA USA Medicine Oncology Dept. University of Washington Seattle WA USA Genitourinary Medicine Roswell Park Comprehensive Cancer Center Buffalo NY USA Internal Medicine University of Michigan Ann Arbor MI USA Medical Oncology Yale University School of Medicine - Yale Cancer Center New Haven CT USA Oncology Department Winship Cancer Institute of Emory University Atlanta GA USA Medical Oncology Department Dana Farber Cancer Institute Boston MA USA Medicine Department Stanford Comprehensive Cancer Institute Stanford CA USA Biostatistics and Bioinformatics Duke University Medical Center Durham NC USA Alliance Statistics and Data Management Center Mayo Clinic - Rochester Rochester MN USA Medicine Dept Memorial Sloan Kettering Cancer Center New York NY USA

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Corrigendum to "Dual regulatory effects of neferine on amyloid-β and tau aggregation studied by in silico, in vitro, and lab-on-a-chip technology" [Biomed. Pharmacother. 172 (2024) 1-14/116226]

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Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 2024年 181卷 117686页

作者： Yunkwon Nam Ritu Prajapati Sujin Kim Soo Jung Shin Da Yeon Cheong Yong Ho Park Hyun Ha Park Danyou Lim Yoojeong Yoon Gyudo Lee Hyun Ah Jung Insu Park Dong-Hyun Kim Jae Sue Choi Minho Moon Department of Biochemistry College of Medicine Konyang University 158 Gwanjeodong-ro Seo-gu Daejeon 35365 Republic of Korea. Department of Food and Life Science Pukyong National University Busan 48513 Republic of Korea. Department of Biochemistry College of Medicine Konyang University 158 Gwanjeodong-ro Seo-gu Daejeon 35365 Republic of Korea Research Institute for Dementia Science Konyang University 158 Gwanjeodong-ro Seo-gu Daejeon 35365 Republic of Korea. Department of Biotechnology and Bioinformatics Korea University Sejong 30019 Republic of Korea Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology Korea University Sejong 30019 Republic of Korea. Department of Biomedical Engineering Konyang University Daejeon 35365 Republic of Korea. Department of Food Science and Human Nutrition Chonbuk National University Jeonju 54896 Republic of Korea. Department of Biomedical Engineering Konyang University Daejeon 35365 Republic of Korea. Electronic address: insupark@konyang.ac.kr. Departments of Pharmacology and Advanced Translational Medicine School of Medicine Konkuk University Seoul 05029 Republic of Korea. Electronic address: mose79@kku.ac.kr. Department of Food and Life Science Pukyong National University Busan 48513 Republic of Korea. Electronic address: choijs@pknu.ac.kr. Research Institute for Dementia Science Konyang University 158 Gwanjeodong-ro Seo-gu Daejeon 35365 Republic of Korea. Electronic address: hominmoon@konyang.ac.kr.

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Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer's disease

npj metabolic health and disease

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npj metabolic health and disease 2024年第1期2卷 15页

作者： Annalise Schweickart Richa Batra Bryan J Neth Cameron Martino Liat Shenhav Anru R Zhang Pixu Shi Naama Karu Kevin Huynh Peter J Meikle Leyla Schimmel Amanda Hazel Dilmore Kaj Blennow Henrik Zetterberg Colette Blach Pieter C Dorrestein Rob Knight Suzanne Craft Rima Kaddurah-Daouk Jan Krumsiek Tri-Institutional Program in Computational Biology & Medicine Weill Cornell Medicine New York NY USA. Department of Physiology and Biophysics Weill Cornell Medicine Institute for Computational Biomedicine Englander Institute for Precision Medicine New York NY USA. Department of Neurology Mayo Clinic Rochester MN USA. Department of Pediatrics University of California San Diego La Jolla CA USA. Department of Microbiology New York University Grossman School of Medicine New York NY USA. Department of Biostatistics and Bioinformatics Duke University Durham NC USA. Tasmanian Independent Metabolomics and Analytical Chemistry Solutions (TIMACS) Hobart TAS Australia. Baker Heart and Diabetes Institute 75 Commercial Road Melbourne VIC Australia. Baker Department of Cardiovascular Research Translation and Implementation La Trobe University Bundoora VIC Australia. Department of Psychiatry and Behavioral Sciences Duke University Durham NC USA. Department of Psychiatry and Neurochemistry University of Gothenburg Gothenburg Sweden. Duke Molecular Physiology Institute Duke University Durham NC USA. Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA. Departments of Pediatrics Computer Science and Engineering Bioengineering University of California San Diego La Jolla CA USA. Department of Gerontology and Geriatric Medicine Wake Forest University School of Medicine Winston Salem NC USA. Duke Institute of Brain Sciences Duke University Durham NC USA. Department of Medicine Duke University Durham NC USA.

Alzheimer's disease (AD) is influenced by a variety of modifiable risk factors, including a person's dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a few studies have explored KD's metabolic impact, especially on blood and cerebrospinal fluid (CSF). Our study involved participants at risk for AD, either cognitively normal or with mild cognitive impairment. The participants consumed both a modified Mediterranean Ketogenic Diet (MMKD) and the American Heart Association diet (AHAD) for 6 weeks each, separated by a 6-week washout period. We employed nuclear magnetic resonance (NMR)-based metabolomics to profile serum and CSF and metagenomics profiling on fecal samples. While the AHAD induced no notable metabolic changes, MMKD led to significant alterations in both serum and CSF. These changes included improved modifiable risk factors, like increased HDL-C and reduced BMI, reversed serum metabolic disturbances linked to AD such as a microbiome-mediated increase in valine levels, and a reduction in systemic inflammation. Additionally, the MMKD was linked to increased amino acid levels in the CSF, a breakdown of branched-chain amino acids (BCAAs), and decreased valine levels. Importantly, we observed a strong correlation between metabolic changes in the CSF and serum, suggesting a systemic regulation of metabolism. Our findings highlight that MMKD can improve AD-related risk factors, reverse some metabolic disturbances associated with AD, and align metabolic changes across the blood-CSF barrier.

关键词： Diseases Metabolomics

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Author Correction: Determination of RNA structural diversity and its role in HIV-1 RNA splicing

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Nature 2020年第7837期588卷 E16页

作者： Phillip J Tomezsko Vincent D A Corbin Paromita Gupta Harish Swaminathan Margalit Glasgow Sitara Persad Matthew D Edwards Lachlan Mcintosh Anthony T Papenfuss Ann Emery Ronald Swanstrom Trinity Zang Tammy C T Lan Paul Bieniasz Daniel R Kuritzkes Athe Tsibris Silvi Rouskin Whitehead Institute for Biomedical Research Cambridge MA USA. Program in Virology Harvard Medical School Boston MA USA. Brigham and Women's Hospital Boston MA USA. Bioinformatics Division Walter and Eliza Hall Institute Parkville Victoria Australia. Department of Medical Biology The University of Melbourne Melbourne Victoria Australia. Massachusetts Institute of Technology Cambridge MA USA. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge MA USA. Peter MacCallum Cancer Centre Melbourne Victoria Australia. Department of Mathematics and Statistics University of Melbourne Melbourne Victoria Australia. Sir Peter MacCallum Department of Oncology The University of Melbourne Melbourne Victoria Australia. Curriculum in Genetics and Molecular Biology University of North Carolina at Chapel Hill Chapel Hill NC USA. Lineberger Comprehensive Cancer Center University of North Carolina at Chapel Hill Chapel Hill NC USA. Department of Microbiology and Immunology University of North Carolina at Chapel Hill Chapel Hill NC USA. Department of Biochemistry and Biophysics University of North Carolina at Chapel Hill Chapel Hill NC USA. Laboratory of Retrovirology The Rockefeller University New York NY USA. Howard Hughes Medical Institute The Rockefeller University New York NY USA. Department of Medicine Harvard Medical School Boston MA USA. Whitehead Institute for Biomedical Research Cambridge MA USA. srouskin@wi.mit.edu.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries (vol 55, pg 89, 2023)

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NATURE GENETICS 2023年第3期55卷 519-520页

作者： Fernandez-Rozadilla, Ceres Timofeeva, Maria Chen, Zhishan Law, Philip Thomas, Minta Schmit, Stephanie Diez-Obrero, Virginia Hsu, Li Fernandez-Tajes, Juan Palles, Claire Sherwood, Kitty Briggs, Sarah Svinti, Victoria Donnelly, Kevin Farrington, Susan Blackmur, James Vaughan-Shaw, Peter Shu, Xiao-ou Long, Jirong Cai, Qiuyin Guo, Xingyi Lu, Yingchang Broderick, Peter Studd, James Huyghe, Jeroen Harrison, Tabitha Conti, David Dampier, Christopher Devall, Mathew Schumacher, Fredrick Melas, Marilena Rennert, Gad Obon-Santacana, Mireia Martin-Sanchez, Vicente Moratalla-Navarro, Ferran Oh, Jae Hwan Kim, Jeongseon Jee, Sun Ha Jung, Keum Ji Kweon, Sun-Seog Shin, Min-Ho Shin, Aesun Ahn, Yoon-Ok Kim, Dong-Hyun Oze, Isao Wen, Wanqing Matsuo, Keitaro Matsuda, Koichi Tanikawa, Chizu Ren, Zefang Gao, Yu-Tang Jia, Wei-Hua Hopper, John Jenkins, Mark Win, Aung Ko Pai, Rish Figueiredo, Jane Haile, Robert Gallinger, Steven Woods, Michael Newcomb, Polly Duggan, David Cheadle, Jeremy Kaplan, Richard Maughan, Timothy Kerr, Rachel Kerr, David Kirac, Iva Bohm, Jan Mecklin, Lukka-Pekka Jousilahti, Pekka Knekt, Paul Aaltonen, Lauri Rissanen, Harri Pukkala, Eero Eriksson, Johan Cajuso, Tatiana Hanninen, Ulrika Kondelin, Johanna Palin, Kimmo Tanskanen, Tomas Renkonen-Sinisalo, Laura Zanke, Brent Mannisto, Satu Albanes, Demetrius Weinstein, Stephanie Ruiz-Narvaez, Edward Palmer, Julie Buchanan, Daniel Platz, Elizabeth Visvanathan, Kala Ulrich, Cornelia Siegel, Erin Brezina, Stefanie Gsur, Andrea Campbell, Peter Chang-Claude, Jenny Hoffmeister, Michael Brenner, Hermann Slattery, Martha Potter, John Tsilidis, Konstantinos Schulze, Matthias Gunter, Marc Murphy, Neil Castells, Antoni Castellvi-Bel, Sergi Moreira, Leticia Arndt, Volker Shcherbina, Anna Stern, Mariana Pardamean, Bens Bishop, Timothy Giles, Graham Southey, Melissa Idos, Gregory McDonnell, Kevin Abu-Ful, Zomoroda Greenson, Joel Shulman, Katerina Lejbkowicz, Flavio Offit, Kenneth Su, Yu-Ru Steinfelder, Robert Keku, Temitope van Guelpen, Bethany Hudson, Thomas Hampel, Heather Pearlman, Edinburgh Cancer Research Centre Institute of Genomics and Cancer University of Edinburgh Edinburgh UK Genomic Medicine Group Instituto de Investigacion Sanitaria de Santiago Santiago de Compostela Spain Colon Cancer Genetics Group Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK Danish Institute for Advanced Study Department of Public Health University of Southern Denmark Odense Denmark Division of Epidemiology Department of Medicine Vanderbilt-Ingram Cancer Center Vanderbilt Epidemiology Center Vanderbilt University Medical Center Nashville TN USA Division of Genetics and Epidemiology Institute of Cancer Research London UK Public Health Sciences Division Fred Hutchinson Cancer Research Center Seattle WA USA Genomic Medicine Institute Cleveland Clinic Cleveland OH USA Population and Cancer Prevention Program Case Comprehensive Cancer Center Cleveland OH USA Colorectal Cancer Group ONCOBELL Program Bellvitge Biomedical Research Institute Barcelona Spain Oncology Data Analytics Program Catalan Institute of Oncology Barcelona Spain Consortium for Biomedical Research in Epidemiology and Public Health Madrid Madrid Spain Department of Clinical Sciences Faculty of Medicine University of Barcelona Barcelona Spain Department of Biostatistics School of Public Health University of Washington Seattle WA USA Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Birmingham UK Department of Public Health Richard Doll Building University of Oxford Oxford UK Department of Biomedical Informatics Vanderbilt University School of Medicine Nashville TN USA Department of Preventive Medicine USC Norris Comprehensive Cancer Center Keck School of Medicine University of Southern California Los Angeles CA USA Center for Public Health Genomics Department of Public Health Sciences University of Virginia Charlottesville VA USA Department of Populat

Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.

关键词： Colorectal cancer Epigenomics Genome-wide association studies Transcriptomics

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Author Correction: π-HuB: the proteomic navigator of the human body

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Nature 2025年第8046期637卷 E22页

作者： Fuchu He Ruedi Aebersold Mark S Baker Xiuwu Bian Xiaochen Bo Daniel W Chan Cheng Chang Luonan Chen Xiangmei Chen Yu-Ju Chen Heping Cheng Ben C Collins Fernando Corrales Jürgen Cox Weinan E Jennifer E Van Eyk Jia Fan Pouya Faridi Daniel Figeys George Fu Gao Wen Gao Zu-Hua Gao Keisuke Goda Wilson Wen Bin Goh Dongfeng Gu Changjiang Guo Tiannan Guo Yuezhong He Albert J R Heck Henning Hermjakob Tony Hunter Narayanan Gopalakrishna Iyer Ying Jiang Connie R Jimenez Lokesh Joshi Neil L Kelleher Ming Li Yang Li Qingsong Lin Cui Hua Liu Fan Liu Guang-Hui Liu Yansheng Liu Zhihua Liu Teck Yew Low Ben Lu Matthias Mann Anming Meng Robert L Moritz Edouard Nice Guang Ning Gilbert S Omenn Christopher M Overall Giuseppe Palmisano Yaojin Peng Charles Pineau Terence Chuen Wai Poon Anthony W Purcell Jie Qiao Roger R Reddel Phillip J Robinson Paola Roncada Chris Sander Jiahao Sha Erwei Song Sanjeeva Srivastava Aihua Sun Siu Kwan Sze Chao Tang Liujun Tang Ruijun Tian Juan Antonio Vizcaíno Chanjuan Wang Chen Wang Xiaowen Wang Xinxing Wang Yan Wang Tobias Weiss Mathias Wilhelm Robert Winkler Bernd Wollscheid Limsoon Wong Linhai Xie Wei Xie Tao Xu Tianhao Xu Liying Yan Jing Yang Xiao Yang John Yates Tao Yun Qiwei Zhai Bing Zhang Hui Zhang Lihua Zhang Lingqiang Zhang Pingwen Zhang Yukui Zhang Yu Zi Zheng Qing Zhong Yunping Zhu State Key Laboratory of Medical Proteomics Beijing Proteome Research Center National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing China. hefc@***. International Academy of Phronesis Medicine (Guangdong) Guangdong China. hefc@***. Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland. aebersold@imsb.biol.ethz.ch. Macquarie Medical School Macquarie University Sydney New South Wales Australia. Institute of Pathology and Southwest Cancer Center Southwest Hospital Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology Ministry of Education of China Chongqing China. Institute of Health Service and Transfusion Medicine Beijing China. Department of Pathology and The Sidney Kimmel Comprehensive Cancer Center Johns Hopkins University Baltimore MD USA. State Key Laboratory of Medical Proteomics Beijing Proteome Research Center National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing China. Key Laboratory of Systems Biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai China. Department of Nephrology First Medical Center of Chinese PLA General Hospital Nephrology Institute of the Chinese People's Liberation Army State Key Laboratory of Kidney Diseases National Clinical Research Center for Kidney Diseases Beijing Key Laboratory of Kidney Disease Research Beijing China. Institute of Chemistry Academia Sinica Taipei China. National Biomedical Imaging Center State Key Laboratory of Membrane Biology Institute of Molecular Medicine Peking-Tsinghua Center for Life Sciences College of Future Technology Peking University Beijing China. School of Biological Sciences Queen's University of Belfast Belfast UK. Functional Proteomics Laboratory Centro Nacional de Biotecnología-CSIC Madrid Spain. Computational Systems Biochemistry Research Group Ma

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The generation challenge programme platform: Semantic standards and workbench for crop science

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International Journal of Plant Genomics 2008年第1期2008卷 369601页

作者： Bruskiewich, Richard Senger, Martin Davenport, Guy Ruiz, Manuel Rouard, Mathieu Hazekamp, Tom Takeya, Masaru Doi, Koji Satoh, Kouji Costa, Marcos Simon, Reinhard Balaji, Jayashree Akintunde, Akinnola Mauleon, Ramil Wanchana, Samart Shah, Trushar Anacleto, Mylah Portugal, Arllet Ulat, Victor Jun Thongjuea, Supat Braak, Kyle Ritter, Sebastian Dereeper, Alexis Skofic, Milko Rojas, Edwin Martins, Natalia Pappas, Georgios Alamban, Ryan Almodiel, Roque Barboza, Lord Hendrix Detras, Jeffrey Manansala, Kevin Mendoza, Michael Jonathan Morales, Jeffrey Peralta, Barry Valerio, Rowena Zhang, Yi Gregorio, Sergio Hermocilla, Joseph Echavez, Michael Yap, Jan Michael Farmer, Andrew Schiltz, Gary Lee, Jennifer Casstevens, Terry Jaiswal, Pankaj Meintjes, Ayton Wilkinson, Mark Good, Benjamin Wagner, James Morris, Jane Marshall, David Collins, Anthony Kikuchi, Shoshi Metz, Thomas McLaren, Graham Van Hintum, Theo Crop Research Informatics Laboratory International Rice Research Institute (IRRI) DAPO Box 7777 Metro Manila Philippines Crop Research Informatics Laboratory International Maize and Wheat Improvement Center (CIMMYT) DF 06600 Mexico Apdo. Postal 6-641 Mexico Centre International de Recherche Agronomique Pour le Développement (CIRAD) 34398 Montpellier Cedex 5 Avenue Agropolis France Bioversity International 00057 Maccarese (Fiumicino) Rome Via dei Tre Denari 472/a Italy National Institute for Agrobiological Sciences (NIAS) Tsukuba Ibaraki 305-8602 Kannondai 2-1-2 Japan Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA) Brasilia DF 70770-900 Parque Estaçao Biologia Final W5 Norte Brazil Centro Internacional de la Papa (CIP) Lima 12 Avenida La Molina 1895 La Molina Peru International Crops Research Institute for the Semi-Arid Tropics Patancheru Andhra Pradesh 502324 India International Center for Agricultural Research in the Dry Areas Aleppo P.O. Box 5466 Syrian Arab Republic National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Klong Luang Pathumthani 12120 Phahonyothin Road Klong 1 Thailand Institute of Computer Science College of Arts and Sciences University of the Philippines Los Banos Laguna 4031 Philippines Department of Computer Science University of the Philippines Melchor Hall Diliman Quezon City 1101 Philippines National Center for Genome Resources Santa Fe NM 87505 2935 Rodeo Park Drive East United States Scottish Crop Research Institute Invergowrie Dundee DD2 5DA United Kingdom Department of Plant Breeding Cornell University Ithaca NY 14853 United States African Centre for Gene Technologies Lynnwood Ridge 0040 P.O. Box 75011 South Africa Department of Medical Genetics Faculty of Medicine University of British Columbia Vancouver BC V6T 1Z3 Canada School of Computing Science Simon Fraser Universtiy Burnaby BC V5A 1S6 8888 University Drive Canada Bioinformatics Graduate Program Genome Sciences Centre BC

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform;(ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data;(iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making.

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