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Publications

2021

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms. Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, et al. (2021). Molecular Systems Biology 17(10): e10387. Full Text

Facilitating Study and Item Level Browsing for Clinical and Epidemiological COVID-19 Studies. Schmidt CO, Darms J, Shutsko A, Löbe M, Nagrani R, Seifert B, Lindstädt B, Golebiewski M, Koleva S, Bender T, Bauer CR, Sax U, Hu X, Lieser M, Junker V, Klopfenstein S, Zeleke A, Waltemath D, Pigeot I, Fluck J and the NFDI4Health Task Force COVID-19 (May 2021) . Studies in health technology and informatics, 281:794-798. Full Text

Making COVID-19 research data more accessible-building a nationwide information infrastructure [in German: COVID-19-Forschungsdaten leichter zugänglich machen – Aufbau einer bundesweiten Informationsinfrastruktur] . Schmidt CO, Fluck J, Golebiewski M, et al. (23 July 2021). Bundesgesundheitsblatt 64, 1084–1092. Full Text

2020

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). Waltemath D, Golebiewski M, Blinov ML, Gleeson P, Hermjakob H, Hucka M, Inau ET, Keating SM, König M, Krebs O, Malik-Sheriff RS, Nickerson D, Oberortner E, Sauro HM, Schreiber F, Smith L, Stefan MI, Wittig U, Myers CJ (2020). Journal of Integrative Bioinformatics. 2020;17(2-3): 20200005. Full Text

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms. Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, et al. (2020). bioRxiv 2020.10.26.356014 ( preprint) Full Text

SBML Level 3: an extensible format for the exchange and reuse of biological models. Keating SM, Waltemath D, König M, Zhang F, et al. (2020). Molecular Systems Biology 16(8): e9110. Full Text

Specifications of standards in systems and synthetic biology: status and developments in 2020. Schreiber F, Sommer B, Czauderna T, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, Konig M, Myers C, Nickerson D, Waltemath D (2020). Journal of Integrative Bioinformatics. 2020;17(2-3): 20200022. Full Text

2019

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Natalie J. Stanford, Martin Scharm, Paul D. Dobson, Martin Golebiewski, Michael Hucka, Varun B. Kothamachu, David Nickerson, Stuart Owen, Jürgen Pahle, Ulrike Wittig, Dagmar Waltemath, Carole Goble, Pedro Mendes, Jacky Snoep. Methods in Molecular Biology 2019;2049:285-314. Full Text

Harmonizing semantic annotations for computational models in biology, Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. Brief Bioinform, 2019 Mar 22;20(2):540-550. Full Text

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D (2019). Journal of Integrative Bioinformatics 16(2): 20190035. Full Text

Data Formats for Systems Biology and Quantitative Modeling, Golebiewski M, in: Encyclopedia of Bioinformatics and Computational Biology, 2019, Volume 2, Pages 884-893. Full Text

2018

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017, Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D, J Integr Bioinform, 2018 Mar 29;15(1). Full Text

2017

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research, Wolstencroft K, Krebs O, Snoep JL, Stanford NJ, Bacall F, Golebiewski M, Kuzyakiv R, Nguyen Q, Owen S, Soiland-Reyes S, Straszewski J, van Niekerk DD, Williams AR, Malmström L, Rinn B, Müller W, Goble C, Nucleic Acids Research, 2017 Jan 4;45(D1): D404-D407. Full Text

Data management and data enrichment for systems biology projects, Wittig U, Rey M, Weidemann A, Müller W. J Biotechnol. 2017 Nov 10;261:229-237.Full Text

2016

The Human Physiome: how standards, software, and innovative service infrastructures are providing the building blocks to make it achievable. Nickerson D, Atalag K, de Bono B, Geiger J, Goble C, Hollmann S, Lonien J, Müller W, Regierer B, Stanford NJ, Golebiewski M, Hunter P. Interface Focus (2016) 6: 20150103. Full Text

The FAIR Guiding Principles for scientific data management and stewardship, Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, ‘t Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B, Scientific Data, 3,

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openBIS ELN-LIMS: an open-source database for academic laboratories, Barillari C, Ottoz DS, Fuentes-Serna JM, Ramakrishnan C, Rinn B, Rudolf F, Bioinformatics, 4, 638-40,

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2015

SEEK: a systems biology data and model management platform, Wolstencroft K, Owen S, Krebs O, Nguyen Q, Stanford NJ, Golebiewski M, Weidemann A, Bittkowski M, An L, Shockley D, Snoep JL, Mueller W, Goble C, BMC Systems Biology, 9:33,

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The evolution of standards and data management practices in systems biology, Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C, Molecular Systems Biology, 11:12, 2015. Full Text

2014

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project, Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N, BMC Bioinformatics, 15:1, 369,

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2013

Why linked data is not enough for scientists, Bechhofer S, Buchan I, De Roure D, Missier P, Ainsworth J, Bhagat J, Couch P, Cruickshank D, Delderfield M, Dunlop I, Gamble M, Michaelides D, Owen S, Newman D, Sufi S, Goble C, Future Generation Computer Systems, 29:2, 599-611, 2013. Full Text

Stealthy annotation of experimental biology by spreadsheets, Wolstencroft K, Owen S, Horridge M, Jupp S, Krebs O, Snoep J, du Preez F, Mueller W, Stevens R, Goble C, Concurrency and Computation: Practice and Experience, 25:4, 467 – 480,

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Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform, Wolstencroft K, Owen S, Krebs O, Mueller W, Nguyen Q, Snoep JL, Goble C, Springer, Berlin, Heidelberg, 2013.

2012

Toward interoperable bioscience data, Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W, Nature Genetics, 44:2, 121-126, 2012. Full Text

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