Publications

2023

• Kirschner M, Golebiewski M, Moser H, consortium E, 5 I2 (2023). ISO/TS 9491-1:2023 Biotechnology — Predictive computational models in personalized medicine research — Part 1: Constructing, verifying and validating models, ISO/TS 9491-1:2023 Biotechnology — Predictive computational models in personalized medicine research — Part 1: Constructing, verifying and validating models. International Organization for Standardization (ISO), Geneva, Switzerland. https://www.iso.org/standard/83516.html 1668
• Wittner R, Holub P, Mascia C, Frexia F, Müller H, Plass M, Allocca C, Betsou F, Burdett T, Cancio I, Chapman A, Chapman M, Courtot M, Curcin V, Eder J, Elliot M, Exter K, Goble C, Golebiewski M, Kisler B, Kremer A, Leo S, Lin‐Gibson S, Marsano A, Mattavelli M, Moore J, Nakae H, Perseil I, Salman A, Sluka J, Soiland‐Reyes S, Strambio‐De‐Castillia C, Sussman M, Swedlow JR, Zatloukal K, Geiger J (2023). Toward a common standard for data and specimen provenance in life sciences, Learning Health Systems,e10365 1655
• Dudas D, Wittig U, Rey M, Weidemann A, Muller W (2023). Improved insights into the SABIO-RK database via visualization., Database (Oxford). 2023 Mar 31;2023:baad011. doi: 10.1093/database/baad011. 1656
• Konig M, Gleeson P, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Schreiber F (2023). Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022., J Integr Bioinform. 2023 Mar 29;20(1):20230004. doi: 10.1515/jib-2023-0004. eCollection 2023 Mar 1. 1654
• Müller W, Mertova L (2023). ReStoRunT: Simple Recording, Storing, Running and Tracing changes in Spreadsheets, In: König-Ries, B., Scherzinger, S., Lehner, W. & Vossen, G. (Hrsg.), BTW 2023. Gesellschaft für Informatik e.V.. DOI: 10.18420/BTW2023-57 1666
• Lauterbach S, Dienhart H, Range J, Malzacher S, Sporing JD, Rother D, Pinto MF, Martins P, Lagerman CE, Bommarius AS, Host AV, Woodley JM, Ngubane S, Kudanga T, Bergmann FT, Rohwer JM, Iglezakis D, Weidemann A, Wittig U, Kettner C, Swainston N, Schnell S, Pleiss J (2023). EnzymeML: seamless data flow and modeling of enzymatic data., Nat Methods. 2023 Feb 9. doi: 10.1038/s41592-022-01763-1. 1612
• Leaman R, Islamaj R, Adams V, Alliheedi MA, Almeida JR, Antunes R, Bevan R, Chang Y, Erdengasileng A, Hodgskiss M, Ida R, Kim H, Li K, Mercer RE, Mertová L, Mobasher G, Shin H, Sung M, Tsujimura T, Yeh W, Lu Z (2023). Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII, Database 2023,baad005 1642
• Mobasher G, Müller W, Krebs O, Gertz M (2023). WeLT: Improving Biomedical Fine-tuned Pre-trained Language Models with Cost-sensitive Learning, Ghadeer Mobasher, Wolfgang Müller, Olga Krebs, and Michael Gertz. 2023. WeLT: Improving Biomedical Fine-tuned Pre-trained Language Models with Cost-sensitive Learning. In The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, pages 427–438, Toronto, Canada. Association for Computational Linguistics. 1684

2022

• Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, Leon MPd, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Pinero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Cristobal MGL, Meulder BD, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D’Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R (2022). A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms, biorxiv;2022.12.17.520865v1,[Preprint] 1563
• Golebiewski M (2022). ISO 20691:2022 Biotechnology — Requirements for data formatting and description in the life sciences, ISO 20691:2022 Biotechnology — Requirements for data formatting and description in the life sciences. International Organization for Standardization (ISO), Geneva, Switzerland. https://www.iso.org/standard/68848.html 1565
• Weidemann A, Dudas D, Rey M, Wittig U, Müller W (2022). More findability, more interoperability for SABIO-RK, the curated database for biochemical reaction kinetics 1637
• Ghosh S, Müller W, Wittig U, Rey M (2022). Towards Effortless Navigation of Scientific-Literature Screen Reading for Biocuration 1638
• Koetsenruijter J, Wronski P, Ghosh S, Muller W, Wensing M (2022). The Effect of an Additional Structured Methods Presentation on Decision-Makers’ Reading Time and Opinions on the Helpfulness of the Methods in a Quantitative Report: Nonrandomized Trial., JMIR Med Inform. 2022 Apr 12;10(4):e29813. doi: 10.2196/29813. 1558
• Lindstädt B, Shutsko A, Golebiewski M, Kipker D, Lettieri V, Klopfenstein S, Vorisek C, Löbe M, Schmidt CO (2022). Publication Policy of the National Research Data Infrastructure for Personal Health Data (NFDI4Health) and the NFDI4Health Task Force COVID-19, Lindstädt, Birte, & Shutsko, Aliaksandra. (2022). Publication Policy of the National Research Data Infrastructure for Personal Health Data (NFDI4Health) and the NFDI4Health Task Force COVID-19 (1.0). https://doi.org/10.4126/FRL01-006431467 1671
• Belling K, Caldara M, Collin CB, Gebhardt T, Golebiewski M, Karaderi T, Khan FM, Kirschner M, Krobitsch S, Küpfer L, Moser H, Tschinanu FM, Nassar M, Poli T, Rosenstiel P, Waltemath D, Wolkehnauer O, consortium E (2022). White Paper: Towards in silico approaches for personalised medicine – Recommendations for verifying and validating predictive computational models in EU collaborative research 1667
• Collin CB, Gebhardt T, Golebiewski M, Karaderi T, Hillemanns M, Khan FM, Salehzadeh-Yazdi A, Kirschner M, Krobitsch S, Pm ConsortiumE, Kuepfer L (2022). Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation., J Pers Med. 2022 Jan 26;12(2):166. doi: 10.3390/jpm12020166. 1562
• Santos VMd, Anton M, Szomolay B, Ostaszewski M, Arts I, Benfeitas R, Angel VDD, Ferk P, Fey D, Goble C, Golebiewski M, Gruden K, Heil KF, Hermjakob H, Kahlem P, Klapa MI, Koehorst J, Kolodkin A, Kutmon M, Leskošek B, Moretti S, Müller W, Pagni M, Rezen T, Rocha M, Rozman D, Šafránek D, Sheriff RSM, Diez MS, Steen KV, Westerhoff HV, Wittig U, Wolstencroft K, Zupanic A, Evelo CT, Hancock JM (2022). Systems Biology in ELIXIR: modelling in the spotlight, F1000Res 11:1265 1564

2021

• Range J, Halupczok C, Lohmann J, Swainston N, Kettner C, Bergmann FT, Weidemann A, Wittig U, Schnell S, Pleiss J (2021). EnzymeML-a data exchange format for biocatalysis and enzymology., FEBS J. 2022 Oct;289(19):5864-5874. doi: 10.1111/febs.16318. Epub 2021 Dec 26. 1413
• Wronski P, Wensing M, Ghosh S, Gärttner L, Müller W, Koetsenruijter J (2021). Use of a quantitative data report in a hypothetical decision scenario for health policymaking: a computer-assisted laboratory study, BMC Med Inform Decis Mak 21(1),32 1169
• König M, Grzegorzewski J, Golebiewski M, Hermjakob H, Hucka M, Olivier B, Keating S, Nickerson D, Schreiber F, Sheriff R, Waltemath D (2021). Ten Simple Rules for FAIR Sharing of Experimental and Clinical Data with the Modeling Community, [Preprint] 1672
• Darms J, Henke J, Hu X, Schmidt CO, Golebiewski M, Fluck J (2021). Improving the FAIRness of Health Studies in Germany: The German Central Health Study Hub COVID-19., Stud Health Technol Inform. 2021 Nov 18;287:78-82. doi: 10.3233/SHTI210818. 1450
• Mobasher G, Mertová L, Ghosh S, Krebs O, Heinlein B, Müller W (2021). Combining dictionary- and rule-based approximate entity linking with tuned BioBERT, biorxiv;2021.11.09.467905v1,[Preprint] 1440
• Schreiber F, Gleeson P, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, Konig M, Myers CJ, Nickerson DP, Sommer B, Waltemath D (2021). Specifications of standards in systems and synthetic biology: status and developments in 2021., J Integr Bioinform. 2021 Oct 22;18(3). pii: jib-2021-0026. doi: 10.1515/jib-2021-0026. 1451
• Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta‐Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Gómez LCM, Somers J, Hoch M, Gupta SK, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Leon MPd, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic‐Milacic M, Ribeiro AS, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, Waard Ad, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban‐Medina M, Peña‐Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, Meulder BD, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D’Eustachio P, Saez‐Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R (2021). COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms, Molecular Systems Biology 17(10),e10387 1291
• Matschinske J, Alcaraz N, Benis A, Golebiewski M, Grimm DG, Heumos L, Kacprowski T, Lazareva O, List M, Louadi Z, Pauling JK, Pfeifer N, Röttger R, Schwämmle V, Sturm G, Traverso A, Steen KV, Freitas MVd, Silva GCV, Wee L, Wenke NK, Zanin M, Zolotareva O, Baumbach J, Blumenthal DB (2021). The AIMe registry for artificial intelligence in biomedical research, Nat Methods 18(10):1128-1131 1344
• Ghosh S, Wronski P, Koetsenruijter J, Mueller W, Wensing M (2021). Watching people decide: decision prediction using heatmaps of reading of a decision-support document, Journal of Vision 21(9):2631 1318
• Mayer G, Muller W, Schork K, Uszkoreit J, Weidemann A, Wittig U, Rey M, Quast C, Felden J, Glockner FO, Lange M, Arend D, Beier S, Junker A, Scholz U, Schuler D, Kestler HA, Wibberg D, Puhler A, Twardziok S, Eils J, Eils R, Hoffmann S, Eisenacher M, Turewicz M (2021). Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases., Brief Bioinform. 2021 Sep 2;22(5). pii: 6135008. doi: 10.1093/bib/bbab010. 1355
• Schmidt CO, Fluck J, Golebiewski M, Grabenhenrich L, Hahn H, Kirsten T, Klammt S, Löbe M, Sax U, Thun S, Pigeot I, Ahrens W, Darms J, Henke J, Hu X, Klopfenstein S, Langnickel L, Lassen-Schmidt B, Pohlabeln H, Lieser M, Näher A, Scholz M, Vorisek C, Waltemath D, Wünsche H (2021). COVID-19-Forschungsdaten leichter zugänglich machen – Aufbau einer bundesweiten Informationsinfrastruktur, Bundesgesundheitsbl 64(9):1084-1092 1278
• König M, Grzegorzewski J, Golebiewski M, Hermjakob H, Hucka M, Olivier B, Keating S, Nickerson D, Schreiber F, Sheriff R, Waltemath D (2021). Ten Simple Rules for Sharing Experimental and Clinical Data with the Modeling Community, [Preprint] 1345
• Fluck J, Lindstädt B, Ahrens W, Beyan O, Buchner B, Darms J, Depping R, Dierkes J, Neuhausen H, Müller W, Zeeb H, Golebiewski M, Löffler M, Löbe M, Meineke F, Klammt S, Fröhlich H, Hahn H, Schulze M, Pischon T, Nöthlings U, Sax U, Kusch H, Grabenhenrich L, Schmidt CO, Waltemath D, Semler S, Gehrke J, Kirsten T, Praßer F, Thun S, Wieler L, Pigeot I (2021). NFDI4Health – Nationale Forschungsdateninfrastruktur für personenbezogene Gesundheitsdaten, Fluck, Juliane, Birte Lindstädt, Wolfgang Ahrens, Oya Beyan, Benedikt Buchner, Johannes Darms, Ralf Depping, Jens Dierkes, Hubertus Neuhausen, Wolfgang Müller, Hajo Zeeb, Martin Golebiewski, Markus Löffler, Matthias Löbe, Frank Meineke, Sebastian Klammt, Holger Fröhlich, Horst Hahn, Matthias Schulze, Tobias Pischon, Ute Nöthlings, Ulrich Sax, Harald Kusch, Linus Grabenhenrich, Carsten Oliver Schmidt, Dagmar Waltemath, Sebastian Semler, Juliane Gehrke, Toralf Kirsten, Fabian Praßer, Sylvia Thun, Lothar Wieler, und Iris Pigeot. 2021. „NFDI4Health – Nationale Forschungsdateninfrastruktur für Personenbezogene Gesundheitsdaten“. Bausteine Forschungsdatenmanagement, Nr. 2 (Juli). German:72-85. https://doi.org/10.17192/bfdm.2021.2.8331. 1670
• Schmidt CO, Darms J, Shutsko A, Lobe M, Nagrani R, Seifert B, Lindstadt 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 (2021). Facilitating Study and Item Level Browsing for Clinical and Epidemiological COVID-19 Studies., Stud Health Technol Inform. 2021 May 27;281:794-798. doi: 10.3233/SHTI210284. 1277
• Schmiester L, Schalte Y, Bergmann FT, Camba T, Dudkin E, Egert J, Frohlich F, Fuhrmann L, Hauber AL, Kemmer S, Lakrisenko P, Loos C, Merkt S, Muller W, Pathirana D, Raimundez E, Refisch L, Rosenblatt M, Stapor PL, Stadter P, Wang D, Wieland FG, Banga JR, Timmer J, Villaverde AF, Sahle S, Kreutz C, Hasenauer J, Weindl D (2021). PEtab-Interoperable specification of parameter estimation problems in systems biology., PLoS Comput Biol. 2021 Jan 26;17(1):e1008646. doi: 10.1371/journal.pcbi.1008646. eCollection 2021 Jan. 1449
• Rey M, Weidemann A, Wittig U, Dudas D, Ghosh S, Golebiewski M, Hu X, Müller W (2021). FAST, ADAPTED, CURATED FAIR DATA FOR COVID-19 RESEARCH 1212

2020

• Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frischman G, Gómez LCM, Somers J, Hoch M, Gupta SK, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Leon MPd, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker J, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Ribeiro AS, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, Waard Ad, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, Meulder BD, Dugourd A, Naldi A, Noel V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D’Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R (2020). COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms, biorxiv;2020.10.26.356014v1,[Preprint] 1211
• 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). The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE), Journal of Integrative Bioinformatics 17(2-3),20200005 1175
• Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik‐Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier‐Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M, Adams RR, Allen NA, Angermann BR, Antoniotti M, Bader GD, Červený J, Courtot M, Cox CD, Pezze PD, Demir E, Denney WS, Dharuri H, Dorier J, Drasdo D, Ebrahim A, Eichner J, Elf J, Endler L, Evelo CT, Flamm C, Fleming RM, Fröhlich M, Glont M, Gonçalves E, Golebiewski M, Grabski H, Gutteridge A, Hachmeister D, Harris LA, Heavner BD, Henkel R, Hlavacek WS, Hu B, Hyduke DR, Jong H, Juty N, Karp PD, Karr JR, Kell DB, Keller R, Kiselev I, Klamt S, Klipp E, Knüpfer C, Kolpakov F, Krause F, Kutmon M, Laibe C, Lawless C, Li L, Loew LM, Machne R, Matsuoka Y, Mendes P, Mi H, Mittag F, Monteiro PT, Natarajan KN, Nielsen PM, Nguyen T, Palmisano A, Pettit J, Pfau T, Phair RD, Radivoyevitch T, Rohwer JM, Ruebenacker OA, Saez‐Rodriguez J, Scharm M, Schmidt H, Schreiber F, Schubert M, Schulte R, Sealfon SC, Smallbone K, Soliman S, Stefan MI, Sullivan DP, Takahashi K, Teusink B, Tolnay D, Vazirabad I, Kamp A, Wittig U, Wrzodek C, Wrzodek F, Xenarios I, Zhukova A, Zucker J (2020). SBML Level 3: an extensible format for the exchange and reuse of biological models, Mol Syst Biol 16(8) 1178
• Brunak S, Collin CB, Cathaoir KEÓ, Golebiewski M, Kirschner M, Kockum I, Moser H, Waltemath D (2020). Towards standardization guidelines for in silico approaches in personalized medicine, Journal of Integrative Bioinformatics 17(2-3) 1210
• Schreiber F, Sommer B, Czauderna T, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D (2020). Specifications of standards in systems and synthetic biology: status and developments in 2020, Journal of Integrative Bioinformatics 17(2-3) 1213
• Group RCW (2020). RDA COVID-19 Recommendations and Guidelines, RDA COVID-19 Working Group. (2020). RDA COVID-19 Recommendations and Guidelines on Data Sharing. https://doi.org/10.15497/rda00052 1673

2019

• Golebiewski M, Waltemath D (2019). Proceedings of the 10th Computational Modeling in Biology Network (COMBINE) Meeting 2019, Golebiewski, Martin, & Waltemath, Dagmar. (2019). Proceedings of the 10th Computational Modeling in Biology Network (COMBINE) Meeting 2019. 10th Computational Modeling in Biology Network (COMBINE) meeting 2019 (COMBINE 2019), Heidelberg, Germany. Zenodo. https://doi.org/10.5281/zenodo.3763159 1669
• Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D (2019). Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019, Journal of Integrative Bioinformatics 16(2) 1071
• Sansone S, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M, Lister AL, Thurston M (2019). FAIRsharing as a community approach to standards, repositories and policies, Nat Biotechnol 37(4):358-367 1352
• Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, Alba Md, 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 (2019). Harmonizing semantic annotations for computational models in biology, Briefings in Bioinformatics 20(2):540-550 1072
• Stanford NJ, Scharm M, Dobson PD, Golebiewski M, Hucka M, Kothamachu VB, Nickerson D, Owen S, Pahle J, Wittig U, Waltemath D, Goble C, Mendes P, Snoep J (2019). Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices, Yeast Systems Biology 2049:285-314,Springer New York 489
• Golebiewski M (2019). Data Formats for Systems Biology and Quantitative Modeling, Encyclopedia of Bioinformatics and Computational Biology,pp.884-893,Elsevier 1070
• Wibberg D, Batut B, Belmann P, Blom J, Glöckner FO, Grüning B, Hoffmann N, Kleinbölting N, Rahn R, Rey M, Scholz U, Sharan M, Tauch A, Trojahn U, Usadel B, Kohlbacher O (2019). The de.NBI / ELIXIR-DE training platform – Bioinformatics training in Germany and across Europe within ELIXIR, F1000Res 8:1877 1073
• Ghosh S, Rey M, Wittig U, Müller W (2019). Bio-entity recognition for SABIO-RK database, F1000Research 8 1271

2018

• Halling P, Fitzpatrick PF, Raushel FM, Rohwer J, Schnell S, Wittig U, Wohlgemuth R, Kettner C (2018). An empirical analysis of enzyme function reporting for experimental reproducibility: Missing/incomplete information in published papers, Biophysical Chemistry 242:22-27 910
• Swainston N, Baici A, Bakker BM, Cornish‐Bowden A, Fitzpatrick PF, Halling P, Leyh TS, O’Donovan C, Raushel FM, Reschel U, Rohwer JM, Schnell S, Schomburg D, Tipton KF, Tsai M, Westerhoff HV, Wittig U, Wohlgemuth R, Kettner C (2018). STRENDA DB: enabling the validation and sharing of enzyme kinetics data, FEBS J 285(12):2193-2204 912
• Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D (2018). Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017, Journal of Integrative Bioinformatics 15(1) 913
• Wittig U, Rey M, Weidemann A, Kania R, Müller W (2018). SABIO-RK: an updated resource for manually curated biochemical reaction kinetics, Nucleic Acids Research 46(D1):D656-D660 911

2017

• Myers CJ, Bader G, Gleeson P, Golebiewski M, Hucka M, Novere NL, Nickerson DP, Schreiber F, Waltemath D (2017). A brief history of COMBINE, 2017 Winter Simulation Conference (WSC),pp.884-895,IEEE 1347
• Wittig U, Rey M, Weidemann A, Müller W (2017). Data management and data enrichment for systems biology projects, Journal of Biotechnology 261:229-237 1177
• Müller W, Bittkowski M, Golebiewski M, Kania R, Rey M, Weidemann A, Wittig U (2017). SABIO-RK, von Daten in der Publikation zur Suchlösung für Spezialisten, Datenbank Spektrum 17(1):21-28 1346
• 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 (2017). FAIRDOMHub: a repository and collaboration environment for sharing systems biology research, Nucleic Acids Res 45(D1):D404-D407 9

2016

• Zakhartsev M, Medvedeva I, Orlov Y, Akberdin I, Krebs O, Schulze WX (2016). Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation, BMC Plant Biol 16(1) 29
• Touré V, Mazein A, Waltemath D, Balaur I, Saqi M, Henkel R, Pellet J, Auffray C (2016). STON: exploring biological pathways using the SBGN standard and graph databases., BMC Bioinformatics 17(1) 202
• Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D (2016). Notions of similarity for systems biology models., Brief Bioinform:bbw090 198
• Nickerson D, Atalag K, Bono Bd, Geiger J, Goble C, Hollmann S, Lonien J, Müller W, Regierer B, Stanford NJ, Golebiewski M, Hunter P (2016). The Human Physiome: how standards, software, and innovative service infrastructures are providing the building blocks to make it achievable., Interface Focus 6(2):20150103 200
• Regierer B, Hollmann S, Golebiewski M (2016). NORM-SYS – harmonizing standardization processes for model and data exchange in systems biology, EMBnet j. 21(A):813 1348
• Krebs O, Wolstencroft K, Stanford N, Morrison N, Golebiewski M, Owen S, Nguyen Q, Snoep J, Müller W, Goble C (2016). FAIRDOM approach for semantic interoperability of systems biology data and models., Proceedings International Conference on Biomedical Ontology, ICBO 2015. no. CEUR Workshop Proceedings 1515 199
• Schreiber F, Bader G, Gleeson P, Golebiewski M, Hucka M, Le N, Myers C, Nickerson D, Sommer B, Waltemath D (2016). Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016, Journal of Integrative Bioinformatics (2016) , 13:289 201

2015

• Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Novère NL, Mueller W, Snoep J, Goble C (2015). The evolution of standards and data management practices in systems biology, Mol Syst Biol 11(12):851 7
• 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 (2015). SEEK: a systems biology data and model management platform, BMC Syst Biol 9(1) 60
• 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 (2015). SEEK: a systems biology data and model management platform., BMC Syst Biol. 2015 Jul 11;9:33. doi: 10.1186/s12918-015-0174-y. 12
• Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S (2015). Specifications of Standards in Systems and Synthetic Biology, Journal of Integrative Bioinformatics 12(2):1-3 488
• Hucka M, Nickerson DP, Bader G, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Novère NL (2015). Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative, Front. Bioeng. Biotechnol. 3 1126

2014

• 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, Novère NL (2014). COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project, BMC Bioinformatics 15(1),369 1349
• Wittig U, Kania R, Bittkowski M, Wetsch E, Shi L, Jong L, Golebiewski M, Rey M, Weidemann A, Rojas I, Müller W (2014). Data extraction for the reaction kinetics database SABIO-RK, Perspectives in Science 1(1-6):33-40 10
• Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Novère NL, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E (2014). Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE), Stand. Genomic Sci. 9(3):1285-1301 1350

2013

• Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, Iersel Mv, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Novère NL (2013). Path2Models: large-scale generation of computational models from biochemical pathway maps, BMC Syst Biol 7(1),116 1351
• Wittig U, Rey M, Kania R, Bittkowski M, Shi L, Golebiewski M, Weidemann A, Muller W, Rojas I (2013). Challenges for an enzymatic reaction kinetics database., FEBS J. 2014 Jan;281(2):572-82. doi: 10.1111/febs.12562. Epub 2013 Oct 25. 11
• Shi L, Jong L, Wittig U, Lucarelli P, Stepath M, Mueller S, D’Alessandro LA, Klingmuller U, Muller W (2013). Excemplify: a flexible template based solution, parsing and managing data in spreadsheets for experimentalists., J Integr Bioinform. 2013 Apr 3;10(2):220. doi: 10.2390/biecoll-jib-2013-220. 26

2011

• Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, Algaa E, Weidemann A, Sauer-Danzwith H, Mir S, Krebs O, Bittkowski M, Wetsch E, Rojas I, Muller W (2011). SABIO-RK–database for biochemical reaction kinetics., Nucleic Acids Res. 2012 Jan;40(Database issue):D790-6. doi: 10.1093/nar/gkr1046. Epub 2011 Nov 18. 8
• Müller W, Rojas I, Eberhart A, Haase P, Schmidt M (2011). A-R-E: The Author-Review-Execute Environment, Procedia Computer Science 4:627-636 16
• Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Novère NL (2011). Controlled vocabularies and semantics in systems biology, Mol Syst Biol 7(1):543 1353

2010

• Swainston N, Golebiewski M, Messiha HL, Malys N, Kania R, Kengne S, Krebs O, Mir S, Sauer-Danzwith H, Smallbone K, Weidemann A, Wittig U, Kell DB, Mendes P, Muller W, Paton NW, Rojas I (2010). Enzyme kinetics informatics: from instrument to browser., FEBS J. 2010 Sep;277(18):3769-79. doi: 10.1111/j.1742-4658.2010.07778.x. Epub 2010 Aug 3. 18

2009

• Drager A, Planatscher H, Wouamba DM, Schroder A, Hucka M, Endler L, Golebiewski M, Muller W, Zell A (2009). SBML2LATEX: Conversion of SBML files into human-readable reports, Bioinformatics 25(11):1455-1456 1354

2008

• Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, Pierre SS, Twigger S, White O, Rhee SY (2008). Big data: The future of biocuration, Nature 455(7209):47-50 28
• Wittig U, Weidemann A, Kania R, Peiss C, Rojas I (2008). Classification of chemical compounds to support complex queries in a pathway database., Comp Funct Genomics. 2004;5(2):156-62. doi: 10.1002/cfg.387. 22
• Ratsch E, Schultz J, Saric J, Lavin PC, Wittig U, Reyle U, Rojas I (2008). Developing a protein-interactions ontology., Comp Funct Genomics. 2003;4(1):85-9. doi: 10.1002/cfg.244. 23
• Weidemann A, Richter S, Stein M, Sahle S, Gauges R, Gabdoulline R, Surovtsova I, Semmelrock N, Besson B, Rojas I, Wade R, Kummer U (2008). SYCAMORE–a systems biology computational analysis and modeling research environment, Bioinformatics 24(12):1463-1464 27

2007

• Rojas I, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Wittig U (2007). Storing and annotating of kinetic data., In Silico Biol. 2007;7(2 Suppl):S37-44. 20
• Krebs O, Golebiewski M, Kania R, Mir S, Saric J, Weidemann A, Wittig U, Rojas I (2007). SABIO-RK: A data warehouse for biochemical reactions and their kinetics, Journal of Integrative Bioinformatics 4(1):22-30 1356

2006

• Wittig U, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Anstein S, Saric J, Rojas I (2006). SABIO-RK: Integration and Curation of Reaction Kinetics Data, Data Integration in the Life Sciences 4075:94-103,Springer Berlin Heidelberg 1357

2004

• Sosa N, Kremling A, Ratsch E, Rojas I (2004). Web-based visualisation of the transcriptional control network of Escherichia coli., In Silico Biol. 2004;4(4):507-15. 15
• Rojas I, Ratsch E, Saric J, Wittig U (2004). Notes on the use of ontologies in the biochemical domain., In Silico Biol. 2004;4(1):89-96. Epub 2004 Mar 15. 24

2002

• Rojas I, Bernardi L, Ratsch E, Kania R, Wittig U, Saric J (2002). A database system for the analysis of biochemical pathways., In Silico Biol. 2002;2(2):75-86. 25

2001

• Wittig U, Beuckelaer AD (2001). Analysis and comparison of metabolic pathway databases., Brief Bioinform. 2001 May;2(2):126-42. 21