2019

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. 10.1093/bib/bby087

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). 10.1515/jib-2018-0013

Data Formats for Systems Biology and Quantitative Modeling, Golebiewski M,  in: Encyclopedia of Bioinformatics and Computational Biology (Editor-in-ChiefsShoba Ranganathan Kenta Nakai Christian Schonbach), Pages 884-893 (Published Date: 31st August 2018)

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. 10.1093/nar/gkw1032

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. 10.1016/j.jbiotec.2017.06.007

2016

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, 2016. 10.1038/sdata.2016.18.

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, 2016. 10.1093/bioinformatics/btv606.

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,  2015. 10.1186/s12918-015-0174-y.

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. 10.15252/msb.20156053.

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, 2014. 10.1186/s12859-014-0369-z.

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. 10.1016/j.future.2011.08.004.

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, 2013. 10.1002/cpe.2941.

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. 10.1038/ng.1054.

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