Literature DB >> 32827396

Towards standardization guidelines for in silico approaches in personalized medicine.

Søren Brunak1, Catherine Bjerre Collin1, Katharina Eva Ó Cathaoir1, Martin Golebiewski2, Marc Kirschner1,3, Ingrid Kockum4, Heike Moser5, Dagmar Waltemath6.   

Abstract

Despite the ever-progressing technological advances in producing data in health and clinical research, the generation of new knowledge for medical benefits through advanced analytics still lags behind its full potential. Reasons for this obstacle are the inherent heterogeneity of data sources and the lack of broadly accepted standards. Further hurdles are associated with legal and ethical issues surrounding the use of personal/patient data across disciplines and borders. Consequently, there is a need for broadly applicable standards compliant with legal and ethical regulations that allow interpretation of heterogeneous health data through in silico methodologies to advance personalized medicine. To tackle these standardization challenges, the Horizon2020 Coordinating and Support Action EU-STANDS4PM initiated an EU-wide mapping process to evaluate strategies for data integration and data-driven in silico modelling approaches to develop standards, recommendations and guidelines for personalized medicine. A first step towards this goal is a broad stakeholder consultation process initiated by an EU-STANDS4PM workshop at the annual COMBINE meeting (COMBINE 2019 workshop report in same issue). This forum analysed the status quo of data and model standards and reflected on possibilities as well as challenges for cross-domain data integration to facilitate in silico modelling approaches for personalized medicine.

Entities:  

Keywords:  zzm321990in silico modelling; data integration; personalized medicine; reproducibility; standards

Mesh:

Year:  2020        PMID: 32827396      PMCID: PMC7756614          DOI: 10.1515/jib-2020-0006

Source DB:  PubMed          Journal:  J Integr Bioinform        ISSN: 1613-4516


  42 in total

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Journal:  Prog Biophys Mol Biol       Date:  2004 Jun-Jul       Impact factor: 3.667

2.  Provenance Solutions for Medical Research in Heterogeneous IT-Infrastructure: An Implementation Roadmap.

Authors:  Marcel Parciak; Christian Bauer; Theresa Bender; Robert Lodahl; Björn Schreiweis; Erik Tute; Ulrich Sax
Journal:  Stud Health Technol Inform       Date:  2019-08-21

3.  The Importance of Data Compression in the Field of Genomics.

Authors:  Dan Greenfield; Vaughan Wittorff; Michael Hultner
Journal:  IEEE Pulse       Date:  2019 Mar-Apr       Impact factor: 0.924

4.  The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research.

Authors:  Jessica W Lau; Erik Lehnert; Anurag Sethi; Raunaq Malhotra; Gaurav Kaushik; Zeynep Onder; Nick Groves-Kirkby; Aleksandar Mihajlovic; Jack DiGiovanna; Mladen Srdic; Dragan Bajcic; Jelena Radenkovic; Vladimir Mladenovic; Damir Krstanovic; Vladan Arsenijevic; Djordje Klisic; Milan Mitrovic; Igor Bogicevic; Deniz Kural; Brandi Davis-Dusenbery
Journal:  Cancer Res       Date:  2017-11-01       Impact factor: 12.701

5.  Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Authors:  Falk Schreiber; Gary D Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nicolas Le Novère; Chris Myers; David Nickerson; Björn Sommer; Dagmar Walthemath
Journal:  J Integr Bioinform       Date:  2016-12-18

Review 6.  Harmonizing semantic annotations for computational models in biology.

Authors:  Maxwell Lewis Neal; Matthias König; David Nickerson; Göksel Mısırlı; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T Cooling; Daniel L Cook; Sharon Crook; Miguel de Alba; Samuel H Friedman; Alan Garny; John H Gennari; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nick Juty; Chris Myers; Brett G Olivier; Herbert M Sauro; Martin Scharm; Jacky L Snoep; Vasundra Touré; Anil Wipat; Olaf Wolkenhauer; Dagmar Waltemath
Journal:  Brief Bioinform       Date:  2019-03-22       Impact factor: 11.622

7.  Synthetic Biology Open Language (SBOL) Version 2.3.

Authors:  Curtis Madsen; Angel Goñi Moreno; Umesh P; Zachary Palchick; Nicholas Roehner; Christian Atallah; Bryan Bartley; Kiri Choi; Robert Sidney Cox; Thomas Gorochowski; Raik Grünberg; Chris Macklin; James McLaughlin; Xianwei Meng; Tramy Nguyen; Matthew Pocock; Meher Samineni; James Scott-Brown; Ysis Tarter; Michael Zhang; Zhen Zhang; Zach Zundel; Jacob Beal; Michael Bissell; Kevin Clancy; John H Gennari; Goksel Misirli; Chris Myers; Ernst Oberortner; Herbert Sauro; Anil Wipat
Journal:  J Integr Bioinform       Date:  2019-06-13

8.  The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Authors:  Kent A Shefchek; Nomi L Harris; Michael Gargano; Nicolas Matentzoglu; Deepak Unni; Matthew Brush; Daniel Keith; Tom Conlin; Nicole Vasilevsky; Xingmin Aaron Zhang; James P Balhoff; Larry Babb; Susan M Bello; Hannah Blau; Yvonne Bradford; Seth Carbon; Leigh Carmody; Lauren E Chan; Valentina Cipriani; Alayne Cuzick; Maria Della Rocca; Nathan Dunn; Shahim Essaid; Petra Fey; Chris Grove; Jean-Phillipe Gourdine; Ada Hamosh; Midori Harris; Ingo Helbig; Maureen Hoatlin; Marcin Joachimiak; Simon Jupp; Kenneth B Lett; Suzanna E Lewis; Craig McNamara; Zoë M Pendlington; Clare Pilgrim; Tim Putman; Vida Ravanmehr; Justin Reese; Erin Riggs; Sofia Robb; Paola Roncaglia; James Seager; Erik Segerdell; Morgan Similuk; Andrea L Storm; Courtney Thaxon; Anne Thessen; Julius O B Jacobsen; Julie A McMurry; Tudor Groza; Sebastian Köhler; Damian Smedley; Peter N Robinson; Christopher J Mungall; Melissa A Haendel; Monica C Munoz-Torres; David Osumi-Sutherland
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

9.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand 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; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

10.  Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.

Authors:  J Kyle Medley; Kiri Choi; Matthias König; Lucian Smith; Stanley Gu; Joseph Hellerstein; Stuart C Sealfon; Herbert M Sauro
Journal:  PLoS Comput Biol       Date:  2018-06-15       Impact factor: 4.475

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  4 in total

1.  Artificial Intelligence in Medicine: A Multinational Multi-Center Survey on the Medical and Dental Students' Perception.

Authors:  Sotirios Bisdas; Constantin-Cristian Topriceanu; Zosia Zakrzewska; Alexandra-Valentina Irimia; Loizos Shakallis; Jithu Subhash; Maria-Madalina Casapu; Jose Leon-Rojas; Daniel Pinto Dos Santos; Dilys Miriam Andrews; Claudia Zeicu; Ahmad Mohammad Bouhuwaish; Avinindita Nura Lestari; Lua'i Abu-Ismail; Arsal Subbah Sadiq; Almu'atasim Khamees; Khaled M G Mohammed; Estelle Williams; Aya Ibrahim Omran; Dima Y Abu Ismail; Esraa Hasan Ebrahim
Journal:  Front Public Health       Date:  2021-12-24

2.  Phase-In to Phase-Out-Targeted, Inclusive Strategies Are Needed to Enable Full Replacement of Animal Use in the European Union.

Authors:  Lindsay J Marshall; Helder Constantino; Troy Seidle
Journal:  Animals (Basel)       Date:  2022-03-29       Impact factor: 2.752

3.  Simulation of the crosstalk between glucose and acetaminophen metabolism in a liver zonation model.

Authors:  Kazuhiro Maeda; Shuta Hagimori; Masahiro Sugimoto; Yasuyuki Sakai; Masaki Nishikawa
Journal:  Front Pharmacol       Date:  2022-09-23       Impact factor: 5.988

4.  Specifications of standards in systems and synthetic biology: status and developments in 2020.

Authors:  Falk Schreiber; Björn Sommer; Tobias Czauderna; Martin Golebiewski; Thomas E Gorochowski; Michael Hucka; Sarah M Keating; Matthias König; Chris Myers; David Nickerson; Dagmar Waltemath
Journal:  J Integr Bioinform       Date:  2020-06-29
  4 in total

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