Towards standardization guidelines for in silico approaches in personalized medicine
暂无分享,去创建一个
Søren Brunak | Martin Golebiewski | Marc Kirschner | Dagmar Waltemath | Catherine Bjerre Collin | Katharina Eva Ó Cathaoir | Ingrid Kockum | Heike Moser | Catherine Bjerre Collin | S. Brunak | I. Kockum | M. Golebiewski | Marc Kirschner | K. Ó. Cathaoir | Heike Moser | Dagmar Waltemath | Martin Golebiewski | K. Cathaoir
[1] Steven N Goodman,et al. The research-treatment distinction: a problematic approach for determining which activities should have ethical oversight. , 2013, The Hastings Center report.
[2] C. Begley,et al. Reproducibility: Six red flags for suspect work , 2013, Nature.
[3] F. Prinz,et al. Believe it or not: how much can we rely on published data on potential drug targets? , 2011, Nature Reviews Drug Discovery.
[4] Jacky L. Snoep,et al. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language , 2011, BMC Systems Biology.
[5] Ricardo Henriques,et al. Standard and Super-Resolution Bioimaging Data Analysis: A Primer , 2017 .
[6] Rita Noumeir,et al. The digital imaging and communications in medicine , 2011 .
[7] Markus Hsi-Yang Fritz,et al. Efficient storage of high throughput DNA sequencing data using reference-based compression. , 2011, Genome research.
[8] Olaf Wolkenhauer,et al. Enabling multiscale modeling in systems medicine , 2014, Genome Medicine.
[9] Ingo Roeder,et al. Whither systems medicine? , 2018, Experimental & Molecular Medicine.
[10] Tudor Groza,et al. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species , 2019, Nucleic Acids Res..
[11] Rolf Backofen,et al. Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers , 2017, PLoS Comput. Biol..
[12] Arcadi Navarro,et al. Leveraging European infrastructures to access 1 million human genomes by 2022 , 2019, Nature Reviews Genetics.
[13] Chris J. Myers,et al. Harmonizing semantic annotations for computational models in biology , 2018, bioRxiv.
[14] Jun Fan,et al. The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience* , 2014, Molecular & Cellular Proteomics.
[15] R. Caporali,et al. The Clinical Value of Autoantibodies in Rheumatoid Arthritis , 2018, Front. Med..
[16] Daniel S. Katz,et al. Enforcing public data archiving policies in academic publishing: A study of ecology journals , 2018, Big Data Soc..
[17] Robert Uerpmann-Wittzack. Convention on Human Rights and Biomedicine , 2017 .
[18] Peter N. Robinson,et al. Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative , 2019, Front. Genet..
[19] Catherine M Lloyd,et al. CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.
[20] Begley Cg,et al. Ocean science: Arctic sea ice needs better forecasts , 2013, Nature.
[21] Lennart Martens,et al. mzML—a Community Standard for Mass Spectrometry Data* , 2010, Molecular & Cellular Proteomics.
[22] Tudor Groza,et al. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species , 2016, bioRxiv.
[23] Matthias König,et al. Executable Simulation Model of the Liver , 2020, bioRxiv.
[24] Michael R. Crusoe,et al. Common Workflow Language , 2015 .
[25] Gary D. Bader,et al. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019 , 2019, J. Integr. Bioinform..
[26] F. Scolari,et al. A model to predict disease progression in patients with autosomal dominant polycystic kidney disease (ADPKD): the ADPKD Outcomes Model , 2018, BMC Nephrology.
[27] U. Latza,et al. [Guidelines and recommendations for ensuring Good Epidemiological Practice (GEP) -- revised version after evaluation]. , 2005, Gesundheitswesen (Bundesverband der Arzte des Offentlichen Gesundheitsdienstes (Germany)).
[28] Chris J. Myers,et al. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core , 2018, J. Integr. Bioinform..
[29] F. Arnaud,et al. From core referencing to data re-use: two French national initiatives to reinforce paleodata stewardship (National Cyber Core Repository and LTER France Retro-Observatory) , 2017 .
[30] A. Nayarisseri,et al. Machine learning models to predict the precise progression of Tay-Sachs and Related Disease , 2019, Proceedings of MOL2NET 2019, International Conference on Multidisciplinary Sciences, 5th edition.
[31] Mikel Hernaez,et al. An introduction to MPEG-G, the new ISO standard for genomic information representation , 2018 .
[32] D. Lipman,et al. Rapid and sensitive protein similarity searches. , 1985, Science.
[33] A Värri,et al. A simple format for exchange of digitized polygraphic recordings. , 1992, Electroencephalography and clinical neurophysiology.
[34] Gary D Bader,et al. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016 , 2016, Journal of integrative bioinformatics.
[35] Rui Zhao,et al. Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients , 2018, PLoS Comput. Biol..
[36] Frank T. Bergmann,et al. SBML Level 3 Package: Flux Balance Constraints version 2 , 2018, J. Integr. Bioinform..
[37] David Brindley,et al. Decision Support Tools for Regenerative Medicine: Systematic Review , 2018, Journal of medical Internet research.
[38] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[39] I Goryanin,et al. Is there a Function for a Sex Pheromone Precursor? , 2019, J. Integr. Bioinform..
[40] Herbert M. Sauro,et al. Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology , 2018, PLoS Comput. Biol..
[41] Ann Wheeler. Digital Microscopy: Nature to Numbers , 2017 .
[42] Ulrich Sax,et al. Provenance Solutions for Medical Research in Heterogeneous IT-Infrastructure: An Implementation Roadmap , 2019, MedInfo.
[43] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[44] Pras Pathmanathan,et al. Advancing Regulatory Science With Computational Modeling for Medical Devices at the FDA's Office of Science and Engineering Laboratories , 2018, Front. Med..
[45] Matthew R. Pocock,et al. Synthetic Biology Open Language (SBOL) Version 2.3 , 2019, J. Integr. Bioinform..
[46] Nicolas Le Novère,et al. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project , 2014, BMC Bioinformatics.
[47] Irene Schmidtmann,et al. Guidelines and recommendations for ensuring Good Epidemiological Practice (GEP): a guideline developed by the German Society for Epidemiology , 2019, European Journal of Epidemiology.
[48] Dagmar Waltemath,et al. A call for virtual experiments: accelerating the scientific process. , 2015, Progress in biophysics and molecular biology.
[49] E. Birney,et al. Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022 , 2019, Nature Reviews Genetics.
[50] Steven N Goodman,et al. An ethics framework for a learning health care system: a departure from traditional research ethics and clinical ethics. , 2013, The Hastings Center report.
[51] Iain Hrynaszkiewicz,et al. The impact on authors and editors of introducing Data Availability Statements at Nature journals , 2018, bioRxiv.
[52] A. Sethi,et al. The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research. , 2017, Cancer research.
[53] Dan Greenfield,et al. The Importance of Data Compression in the Field of Genomics , 2019, IEEE Pulse.
[54] Nigel H. Goddard,et al. Towards NeuroML: model description methods for collaborative modelling in neuroscience. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[55] L Kuepfer,et al. Applied Concepts in PBPK Modeling: How to Build a PBPK/PD Model , 2016, CPT: pharmacometrics & systems pharmacology.
[56] David B. Allison,et al. Reproducibility: A tragedy of errors , 2016, Nature.