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arXiv 2024年

作者： Amaro, R. Åqvist, J. Bahar, I. Battistini, F. Bellaiche, A. Beltran, D. Biggin, P.C. Bonomi, M. Bowman, G.R. Bryce, R. Bussi, G. Carloni, P. Case, D. Cavalli, A. Chang, C.A. Cheatham, T.E. Cheung, M.S. Chipot, C. Chong, L.T. Choudhary, P. Cisneros, G.A. Clementi, C. Collepardo-Guevara, R. Coveney, P. Covino, R. Crawford, T.D. Dal Peraro, M. de Groot, B. Delemotte, L. De Vivo, M. Essex, J. Fraternali, F. Gao, J. Gelpí, J.L. Gervasio, F.L. Gonzalez-Nilo, F.D. Grubmüller, H. Guenza, M.G. Guzman, H.V. Harris, S. Head-Gordon, T. Hernandez, R. Hospital, A. Huang, N. Huang, X. Hummer, G. Iglesias-Fernández, J. Jensen, J.H. Jha, S. Jiao, W. Jorgensen, W.L. Kamerlin, S.C.L. Khalid, S. Laughton, C. Levitt, M. Limongelli, V. Lindahl, E. Lindorff-Larsen, K. Loverde, S. Lundborg, M. Luo, Y.L. Luque, F.J. Lynch, C.I. MacKerell, A. Magistrato, A. Marrink, S.J. Martin, H. McCammon, J.A. Merz, K. Moliner, V. Mulholland, A. Murad, S. Naganathan, A.N. Nangia, S. Noe, F. Noy, A. Oláh, J. O'Mara, M. Ondrechen, M.J. Onuchic, J.N. Onufriev, A. Osuna, S. Palermo, G. Panchenko, A.R. Pantano, S. Parish, C. Parrinello, M. Perez, A. Perez-Acle, T. Perilla, J.R. Pettitt, B.M. Pietropaolo, A. Piquemal, J.-P. Poma, A. Praprotnik, M. Ramos, M.J. Ren, P. Reuter, N. Roitberg, A. Rosta, E. Rovira, C. Roux, B. Röthlisberger, U. Sanbonmatsu, K. Schlick, T. Shaytan, A.K. Simmerling, C. Smith, J.C. Sugita, Y. Świderek, K. Taiji, M. Tao, P. Tikhonova, I.G. Tirado-Rives, J. Tuñón, I. Van Der Kamp, M.W. Van der Spoel, D. Velankar, S. Voth, G.A. Wade, R. Warshel, A. Welborn, V.V. Wetmore, S. Wong, C.F. Yang, L.-W. Zacharias, M. Orozco, M. Department of Molecular Biology University of California San DiegoCA United States Department of Cell and Molecular Biology Uppsala University Uppsala Sweden Laufer Center for Physical and Quantitative Biology Renaissance School of Medicine Stony Brook University Stony BrookNY United States Department of Biochemistry and Cell Biology Renaissance School of Medicine Stony Brook University Stony BrookNY United States Barcelona Spain European Molecular Biology Laboratory European Bioinformatics Institute Hinxton United Kingdom Structural Bioinformatics and Computational Biochemistry Department of Biochemistry University of Oxford Oxford United Kingdom Institut Pasteur Université Paris Cité CNRS UMR 3528 Computational Structural Biology Unit Paris France Department of Biochemistry and Biophysics University of Pennsylvania PhiladelphiaPA United States Division of Pharmacy and Optometry University of Manchester Manchester United Kingdom Scuola Internazionale Superiore di Studi Avanzati-SISSA Trieste Italy Computational Biomedicine Institute of Advanced Simulations IAS-5 Institute for Neuroscience and Medicine INM-9 Forschungszentrum Jülich GmbH Jülich Germany Department of Physics and Universitätsklinikum RWTH Aachen University Aachen Germany Department of Chemistry & Chemical Biology Rutgers University PiscatawayNJ United States Istituto Italiano di Tecnologia Drug Discovery and Development Bologna Italy Lausanne Switzerland Department of Chemistry University of California RiversideCA United States Department of Medicinal Chemistry College of Pharmacy University of Utah Salt Lake CityUT United States Department of Physics University of Washington SeattleWA United States Pacific Northwest National Laboratory RichlandWA United States LIA CNRS-UIUC UMR n°7019 Université de Lorraine Vandœuvre-lès-Nancy France Department of Physics University of Illinois at Urbana-Champaign UrbanaIL United States Department of Biochemistry and Molecular Biol

The communities that embraced data archiving efforts decades ago are now, in the era of data-driven biology, those gaining the most from the AI revolution. The structural biology community was a pioneer in this regard by establishing the Protein data Bank (PDB) in 1971 and making data accessible using the FAIR (Findable, Accessible, Interoperable and Reusable) principles even before these were articulated [1, 2]. The genomics/bioinformatics community has followed the example, establishing many widely used databases [3, 4]. By contrast, molecular simulation has been anchored in usage paradigms dating back to the seventies, when molecular dynamics (MD) simulation was first applied to study biomacromolecules [5]. At that time, MD was used by theoretical physicists and chemists in "proof of concept" simulations. Still, fifty years later, MD has evolved into a cornerstone molecular biology technique that can provide accurate quantitative analysis and property prediction. MD is now employed by tens of thousands of researchers worldwide, accounting for roughly 15% of global supercomputer usage. Unfortunately, these rich and costly data are not systematically maintained, and when further analyses are required, simulations have to be rerun-an unacceptable situation from scientific, environmental and sustainability standpoints. In this letter, we argue for a collaborative endeavor to archive MD simulation data and describe ongoing efforts to establish cost-effective and sustainable data archiving strategies. © 2024, CC BY-NC-SA.

关键词： Biotic

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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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Author Correction: A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome

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Nature communications 2022年第1期13卷 7538页

作者： Poonam Chitale Alexander D Lemenze Emily C Fogarty Avi Shah Courtney Grady Aubrey R Odom-Mabey W Evan Johnson Jason H Yang A Murat Eren Roland Brosch Pradeep Kumar David Alland Ray V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens Rutgers University-New Jersey Medical School Newark NJ USA. Public Health Research Institute Rutgers University-New Jersey Medical School Newark NJ USA. Department of Pathology Immunology and Laboratory Medicine New Jersey Medical School Rutgers-The State University of New Jersey Newark NJ USA. Department of Medicine University of Chicago Chicago IL USA. Committee on Microbiology University of Chicago Chicago IL USA. Department of Microbiology Biochemistry and Molecular Genetics Rutgers University-New Jersey Medical School Newark NJ USA. Division of Computational Biomedicine Boston University School of Medicine and Bioinformatics Program Boston University Boston MA USA. Bioinformatics Program Boston University Boston MA USA. Center for Data Science Rutgers University-New Jersey Medical School Newark NJ USA. Helmholtz Institute for Functional Marine Biodiversity (HIFMB) Oldenburg Germany. Bay Paul Center Marine Biological Laboratory Woods Hole MA USA. Institut Pasteur Université Paris Cité Unit for Integrated Mycobacterial Pathogenomics CNRS UMR 6047 Paris France. Ray V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens Rutgers University-New Jersey Medical School Newark NJ USA. allandda@njms.rutgers.edu. Public Health Research Institute Rutgers University-New Jersey Medical School Newark NJ USA. allandda@njms.rutgers.edu.

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Addendum: The FAIR Guiding Principles for scientific data management and stewardship

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Scientific data 2019年第1期6卷 6页

作者： Mark D Wilkinson Michel Dumontier Ijsbrand Jan Aalbersberg Gabrielle Appleton Myles Axton Arie Baak Niklas Blomberg Jan-Willem Boiten Luiz Bonino da Silva Santos Philip E Bourne Jildau Bouwman Anthony J Brookes Tim Clark Mercè Crosas Ingrid Dillo Olivier Dumon Scott Edmunds Chris T Evelo Richard Finkers Alejandra Gonzalez-Beltran Alasdair J G Gray Paul Groth Carole Goble Jeffrey S Grethe Jaap Heringa Peter A C 't Hoen Rob Hooft Tobias Kuhn Ruben Kok Joost Kok Scott J Lusher Maryann E Martone Albert Mons Abel L Packer Bengt Persson Philippe Rocca-Serra Marco Roos Rene van Schaik Susanna-Assunta Sansone Erik Schultes Thierry Sengstag Ted Slater George Strawn Morris A Swertz Mark Thompson Johan van der Lei Erik van Mulligen Andra Waagmeester Peter Wittenburg Katherine Wolstencroft Jun Zhao Barend Mons Center for Plant Biotechnology and Genomics Universidad Politécnica de Madrid Madrid 28223 Spain. Stanford University Stanford 94305-5411 USA. Elsevier Amsterdam 1043 NX The Netherlands. Nature Genetics New York 10004-1562 USA. Euretos and Phortos Consultants Rotterdam 2741 CA The Netherlands. ELIXIR Wellcome Genome Campus Hinxton CB10 1SA UK. Lygature Eindhoven 5656 AG The Netherlands. Vrije Universiteit Amsterdam Dutch Techcenter for Life Sciences Amsterdam 1081 HV The Netherlands. Office of the Director National Institutes of Health Rockville 20892 USA. TNO Zeist 3700 AJ The Netherlands. Department of Genetics University of Leicester Leicester LE1 7RH UK. Harvard Medical School Boston Massachusetts MA 02115 USA. Harvard University Cambridge Massachusetts MA 02138 USA. Data Archiving and Networked Services (DANS) The Hague 2593 HW The Netherlands. GigaScience Beijing Genomics Institute Shenzhen 518083 China. Department of Bioinformatics Maastricht University Maastricht 6200 MD The Netherlands. Wageningen UR Plant Breeding Wageningen 6708 PB The Netherlands. Oxford e-Research Center University of Oxford Oxford OX1 3QG UK. Heriot-Watt University Edinburgh EH14 4AS UK. School of Computer Science University of Manchester Manchester M13 9PL UK. Center for Research in Biological Systems School of Medicine University of California San Diego La Jolla California 92093-0446 USA. Dutch Techcenter for the Life Sciences Utrecht 3501 DE The Netherlands. Department of Human Genetics Leiden University Medical Center Dutch Techcenter for the Life Sciences Leiden 2300 RC The Netherlands. Dutch TechCenter for Life Sciences and ELIXIR-NL Utrecht 3501 DE The Netherlands. VU University Amsterdam Amsterdam 1081 HV The Netherlands. Leiden Center of Data Science Leiden University Leiden 2300 RA The Netherlands. Netherlands eScience Center Amsterdam 1098 XG The Netherlands. National Center for Microscopy and Imaging Research UCSD San Di

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POS0100 TARGETING NF-ΚB SIGNALLING IN B LINEAGE CELLS AS A POTENTIAL NOVEL TREATMENT STRATEGY FOR ANCA-ASSOCIATED VASCULITIS

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Annals of the Rheumatic Diseases 2023年 82卷 263-263页

作者： A. Merino-Vico J.P. Van Hamburg C. Bonasia P. Heeringa P. Tuijnenburg B. Helder M. Jansen A. Al-Soudi H.K. Olsson N. De Vries C. Stegeman J.S. Sanders A. Rutgers W. Abdulahad P. Lyons T. Bijma A. Jongejan T.W. Kuijpers S. Tas Amsterdam Rheumatology & immunology Center Amsterdam UMC/University of Amsterdam Department of Rheumatology and Clinical Immunology Amsterdam Netherlands Amsterdam UMC/University of Amsterdam Department of Experimental Immunology Amsterdam Netherlands University Medical Center Groningen Groningen the Netherlands Department of Rheumatology and Clinical Immunology Groningen Netherlands University Medical Center Groningen Groningen the Netherlands Department of Pathology and Medical Biology Groningen Netherlands Emma Children's Hospital Amsterdam UMC University of Amsterdam Department of Pediatric Immunology Rheumatology and Infectious diseases Amsterdam Netherlands AstraZeneca AstraZeneca Gothenburg Sweden Gothenburg Sweden University Medical Center Groningen Groningen the Netherlands Dept of Internal Medicine Division of Nephrology Groningen Netherlands University pf Cambridge School of Clinical Medicine University of Cambridge Dept of Medicine Cambridge United Kingdom Amsterdam Public Health Research Institute Amsterdam UMC University of Amsterdam Department of Epidemiology and Data Science Bioinformatics Laboratory Amsterdam Netherlands Sanquin Amsterdam Amsterdam & Department of Blood Cell Research Amsterdam Netherlands Academic Medical Center (AMC) Department of Pediatrics Amsterdam Netherlands

Background B cells are crucially important in the pathogenesis of many autoimmune diseases, including ANCA-associated vasculitis (AAV), which is further demonstrated by the beneficial clinical effects of rituximab (anti-CD20) B cell targeted therapy. Despite its advantages, this treatment strategy results in long-term B cell depletion and fails to target long-lived plasma cells, rendering an unmet need for more reversible and combined B and plasma cell targeting approaches to achieve long-term disease remission. This aim may be reached by targeting signalling pathways essential for different B cell functions. The canonical and non-canonical NF-κB signalling pathways regulate fundamental B and/or plasma cell responses downstream of various B cell surface receptors, including the B cell receptor, CD40, and TLRs. Objectives To study potential alterations in NF-κB signalling in B lineage cells and to evaluate the effects of targeting NF-κB on B cell responses in general, and more specifically on proliferation, plasmablast differentiation and (auto)antibody production in B cells from AAV patients. Methods Memory B cells were obtained from AAV patients and healthy donors (HD), and gene expression profiles were generated by RNA-sequencing. Functional assays were performed by culturing PMBCs from AAV patients and HD with stimuli mimicking T cell-dependent (anti-CD40/IL-21) and T cell-independent (CpG/IL-2) conditions. Pharmacological inhibitors of Inhibitor-of-κB-kinase-β (IKKβ, canonical pathway) or NF-κB inducing kinase (NIK, non-canonical pathway) were added to the cultures. Downstream NF-κB signalling was determined by Western blot. After 6-day cultures, B cell proliferation and differentiation were determined by flow cytometry, and ELISA was performed for the detection of (auto)antibody production. Results Memory B cells from AAV patients with active disease exhibited an increased expression of NF-κB-associated genes compared to patients in remission and HD. Targeting

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Author Correction: Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

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Nature communications 2023年第1期14卷 1072页

作者： Morgane Boone Pathmanaban Ramasamy Jasper Zuallaert Robbin Bouwmeester Berre Van Moer Davy Maddelein Demet Turan Niels Hulstaert Hannah Eeckhaut Elien Vandermarliere Lennart Martens Sven Degroeve Wesley De Neve Wim Vranken Nico Callewaert Center for Medical Biotechnology VIB Zwijnaarde Belgium. morganeboone@***. Department of Biochemistry and Microbiology Faculty of Sciences Ghent University Ghent Belgium. morganeboone@***. Department of Biochemistry and Biophysics UCSF San Francisco CA USA. morganeboone@***. Center for Medical Biotechnology VIB Zwijnaarde Belgium. Department of Biomolecular Medicine Faculty of Medicine and Health Sciences Ghent University Ghent Belgium. Structural Biology Brussels VUB Brussels Belgium. Structural Biology Research Center VIB Brussels Belgium. Interuniversity Institute of Bioinformatics in Brussels (IB)2 ULB-VUB Brussels Belgium. Department of Biochemistry and Microbiology Faculty of Sciences Ghent University Ghent Belgium. Center for Biotech Data Science Ghent University Global Campus Songdo Incheon South Korea. IDLab ELIS UGent Ghent Belgium. Center for Medical Biotechnology VIB Zwijnaarde Belgium. nico.callewaert@vib-ugent.be. Department of Biochemistry and Microbiology Faculty of Sciences Ghent University Ghent Belgium. nico.callewaert@vib-ugent.be.

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Author Correction: Inferring structural variant cancer cell fraction

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Nature communications 2022年第1期13卷 7568页

作者： Marek Cmero Ke Yuan Cheng Soon Ong Jan Schröder Niall M Corcoran Tony Papenfuss Christopher M Hovens Florian Markowetz Geoff Macintyre Department of Surgery Division of Urology Royal Melbourne Hospital and University of Melbourne Parkville VIC 3050 Australia. cmerom@unimelb.edu.au. The Epworth Prostate Centre Epworth Hospital Richmond VIC 3121 Australia. cmerom@unimelb.edu.au. Department of Computing and Information Systems University of Melbourne Parkville VIC 3010 Australia. cmerom@unimelb.edu.au. Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia. cmerom@unimelb.edu.au. Murdoch Children's Research Institute Parkville VIC 3052 Australia. cmerom@unimelb.edu.au. School of Computing Science University of Glasgow Sir Alwyn Williams Building Glasgow G12 8RZ UK. Cancer Research UK Cambridge Institute University of Cambridge Cambridge CB2 0RE UK. Electrical and Electronic Engineering University of Melbourne Parkville VIC 3010 Australia. Machine Learning Research Group Data61 Canberra ACT 2601 Australia. Research School of Computer Science Australian National University Canberra ACT 2601 Australia. Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia. Department of Surgery Division of Urology Royal Melbourne Hospital and University of Melbourne Parkville VIC 3050 Australia. The Epworth Prostate Centre Epworth Hospital Richmond VIC 3121 Australia. Department of Computing and Information Systems University of Melbourne Parkville VIC 3010 Australia. geoff.macintyre@cruk.cam.ac.uk. Cancer Research UK Cambridge Institute University of Cambridge Cambridge CB2 0RE UK. geoff.macintyre@cruk.cam.ac.uk.

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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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Genomics and epidemiology for gastric adenocarcinomas (GE4GAC): a Brazilian initiative to study gastric cancer

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Applied Cancer Research 2019年第1期39卷 1-4页

作者： Bartelli, Thais F. Senda de Abrantes, Lais L. Freitas, Helano C. Thomas, Andrew M. Silva, Jordana M. Albuquerque, Gabriela E. Araújo, Luiza F. Branco, Gabriela P. de Amorim, Maria G. Serpa, Marianna S. Takenaka, Isabella K. T. M. Souza, Deborah T. Monção, Lucas O. Moda, Bruno S. Valieris, Renan Defelicibus, Alexandre Borges, Rodrigo Drummond, Rodrigo D. Alves, Francisco I. A. Santos, Monize N. P. Bobrovnitchaia, Irina G. Elhaik, Eran Coelho, Luiz G. V. Khayat, André Demachki, Samia Assumpção, Paulo P. Santiago, Karina M. Torrezan, Giovana T. Carraro, Dirce M. Peres, Stela V. Calsavara, Vinícius F. Burbano, Rommel Nóbrega, Calebe R. Baladão, Graziela P. P. Pereira, Ana C. C. Gatti, Camila M. Fagundes, Marcela A. Araújo, Marília S. Miranda, Tayana V. Barbosa, Monica S. Cardoso, Daniela M. M. Carneiro, Lilian C. Brito, Alexandre M. Ramos, Amanda F. P. L. Silva, Lucas L. L. Pontes, Jaqueline C. Tiengo, Tatiane Arantes, Paola E. Santana, Vilma Cordeiro, Milena Sant’Ana, Rosane O. Andrade, Hanna B. Anaissi, Ana K. M. Sampaio, Sara V. Abdallah, Emne A. Chinen, Ludmilla T. D. Braun, Alexcia C. Flores, Bianca C. T. Mello, Celso A. L. Claro, Laura C. L. Sztokfisz, Claudia Z. Altamirano, Carlos C. Carter, David R. F. Jesus, Victor H. F. Riechelmann, Rachel Medina, Tiago Gollob, Kenneth J. Martins, Vilma R. Setúbal, João C. Pelosof, Adriane G. Coimbra, Felipe J. Costa-Jr, Wilson L. Silva, Israel T. Nunes, Diana N. Curado, Maria P. Dias-Neto, Emmanuel Lab of Medical Genomics A.C.Camargo Cancer Center Sao Paulo Brazil International Research Center A.C.Camargo Cancer Center Sao Paulo Brazil Clinical Oncology Department A.C. Camargo Cancer Center São Paulo Brazil Department CIBIO University of Trento Trento Italy Biochemistry Department Chemistry Institute Universidade de São Paulo São Paulo Brazil Lab. of Bioinformatics and Computational Biology A.C.Camargo Cancer Center Sao Paulo Brazil Data Science group International Research Center A.C.Camargo Cancer Center Sao Paulo Brazil Department of Animal & Plant Sciences University of Sheffield Sheffield UK Instituto Alfa de Gastroenterologia Hospital das Clínicas Universidade Federal de Minas Gerais Belo Horizonte Brazil Instituto de Ciências Biológicas Universidade Federal do Pará Belém Brazil Núcleo de Pesquisas em Oncologia Universidade Federal do Pará Belém Brazil Lab. de Genômica e Biologia Molecular A.C.Camargo Cancer Center Sao Paulo Brazil Epidemiology and Statistics Group A.C.Camargo Cancer Center Sao Paulo Brazil Laboratório de Biologia Molecular Hospital Ophir Loyola Belém Brazil Universidade Federal de Goiás IPTESP – Instituto de Patologia Tropical e Saúde Pública Goiânia Brazil Department of Abdominal Surgery Hospital Araujo Jorge Goiânia Brazil Instituto de Saúde Coletiva da Universidade Federal da Bahia Salvador Brazil Instituto do Cancer do Ceará Fortaleza Brazil Department of Pathology A.C.Camargo Cancer Center São Paulo Brazil Endoscopy sector A.C.Camargo Cancer Center São Paulo Brazil Instituto Nacional de Enfermedades Neoplásicas Surquillo Peru Dept. of Biological and Medical Sciences Faculty of Health and Life Sciences Oxford Brookes University Oxford UK Translational Immuno-oncology Group A.C.Camargo Cancer Center Sao Paulo Brazil Tumor Biology and Biomarkers Group A.C.Camargo Cancer Center Sao Paulo Brazil Department of Abdominal Surgery A.C.Camargo Cancer Center São Paulo Brazil

Gastric cancer (GC) is the fifth most common type of cancer worldwide with high incidences in Asia, Central, and South American countries. This patchy distribution means that GC studies are neglected by large research centers from developed countries. The need for further understanding of this complex disease, including the local importance of epidemiological factors and the rich ancestral admixture found in Brazil, stimulated the implementation of the GE4GAC project. GE4GAC aims to embrace epidemiological, clinical, molecular and microbiological data from Brazilian controls and patients with malignant and pre-malignant gastric disease. In this letter, we summarize the main goals of the project, including subject and sample accrual and current findings.

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PLUMED Tutorials: a collaborative, community-driven learning ecosystem

arXiv

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arXiv 2024年

作者： Tribello, Gareth A. Bonomi, Massimiliano Bussi, Giovanni Camilloni, Carlo Armstrong, Blake I. Arsiccio, Andrea Aureli, Simone Ballabio, Federico Bernetti, Mattia Bonati, Luigi Brookes, Samuel G.H. Faidon Brotzakis, Z. Capelli, Riccardo Ceriotti, Michele Chan, Kam-Tung Cossio, Pilar Dasetty, Siva Donadio, Davide Ensing, Bernd Ferguson, Andrew L. Fraux, Guillaume Gale, Julian D. Gervasio, Francesco Luigi Giorgino, Toni Herringer, Nicholas S.M. Hocky, Glen M. Hoff, Samuel E. Invernizzi, Michele Languin-Cattoën, Olivier Leone, Vanessa Limongelli, Vittorio Lopez-Acevedo, Olga Marinelli, Fabrizio Martinez, Pedro Febrer Masetti, Matteo Mehdi, Shams Michaelides, Angelos Murtada, Mhd Hussein Parrinello, Michele Piaggi, Pablo M. Pietropaolo, Adriana Pietrucci, Fabio Pipolo, Silvio Pritchard, Claire Raiteri, Paolo Raniolo, Stefano Rapetti, Daniele Rizzi, Valerio Rydzewski, Jakub Salvalaglio, Matteo Schran, Christoph Seal, Aniruddha Zadeh, Armin Shayesteh Silva, Tomás F.D. Spiwok, Vojtěch Stirnemann, Guillaume Sucerquia, Daniel Tiwary, Pratyush Valsson, Omar Vendruscolo, Michele Voth, Gregory A. White, Andrew D. Wu, Jiangbo Centre for Quantum Materials and Technology School of Mathematics and Physics Queen’s University Belfast United Kingdom Institut Pasteur Université Paris Cité CNRS UMR 3528 Computational Structural Biology Unit Paris France Via Bonomea 265 Trieste34136 Italy Department of Biosciences University of Milano Milano Italy School of Molecular and Life Sciences Curtin University GPO Box U1987 PerthWA6845 Australia Coriolis Pharma Fraunhoferstrasse 18b Martinsried82152 Germany School of Pharmaceutical Sciences University of Geneva Rue Michel-Servet 1 GenevaCH-1206 Switzerland Institute of Pharmaceutical Sciences of Western Switzerland University of Geneva GenevaCH-1206 Switzerland Swiss Bioinformatics Institute University of Geneva GenevaCH-1206 Switzerland Via Celoria 26 Milan20133 Italy Department of Biomolecular Sciences University of Urbino "Carlo Bo" Piazza Rinascimento 6 Urbino61029 Italy Department of Pharmacy and Biotechnology Alma Mater Studiorum University of Bologna Via Belmeloro 6 Bologna40126 Italy Atomistic Simulations Italian Institute of Technology Genova Italy Yusuf Hamied Department of Chemistry University of Cambridge CambridgeCB2 1EW United Kingdom Institute for Bioinnovation Biomedical Sciences Research Center "Alexander Fleming" Vari16672 Greece Laboratory of Computational Science and Modeling Institut des Matériaux École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Chemistry University of California Davis DavisCA95616 United States Center for Computational Mathematics Flatiron Institute New YorkNY10010 United States Center for Computational Biology Flatiron Institute New YorkNY10010 United States Pritzker School of Molecular Engineering University of Chicago ChicagoIL60637 United States AI4Science Lab Informatics Institute University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Computational Chemistry Group Van’t Hoff Institute for Molecular Sciences Unive

In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software’s functionalities. To address these issues, here we introduce "PLUMED Tutorials", a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources. © 2024, CC BY.

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