Pigeot I, Ahrens W, Darms J, Fluck J, Golebiewski M, Hahn HK, Hu X, Intemann T, Kasbohm E, Kirsten T, Klammt S, Klopfenstein SAI, Lassen-Schmidt B, Peters M, Sax U, Waltemath D, Schmidt CO (2024). Making Epidemiological and Clinical Studies FAIR Using the Example of COVID-19, Datenbank Spektrum 24(2):117-128 1862
Arend D, Conte AD, Feser M, Gadiya Y, Gaignard A, Castro LJ, Mičetić I, Moretti S, Neumann S, Rayya N, Tsueng G, Willighagen E, Wittig U (2024). Bioschemas Resource Index for Chem and Plants, osf.io/yxunp,[Preprint] 1777
D’Anna F, Jareborg N, Jetten M, Ahokas M, Alper P, Andrews R, Bösl K, D’Altri T, Faria D, Fatima N, Fuchs S, Garrard C, Gu W, Heil KF, Kallberg Y, Licciulli F, Lübke N, Melo AMP, Mičetić I, Oliveira J, Oulas A, Palagi PM, Poterlowicz K, Perez-Sitja X, Ruch P, Sansone S, Schnitzer H, Gelder Cv, Vergoulis T, Wibberg D, Wittig U, Leskošek B, Vondrasek J, Andrabi M (2024). A research data management (RDM) community for ELIXIR, F1000Res 13:230 1829
Abaza H, Shutsko A, Golebiewski M, Klopfenstein S, Schmidt CO, Vorisek C, Brünings-Kuppe C, Clemens V, Darms J, Hanß S, Intemann T, Jannasch F, Kasbohm E, Lindstädt B, Löbe M, Orban E, Perrar I, Peters M, Sax U, Schulze M, Schupp C, Schwarz F, Schwedhelm C, Strathmann S, Waltemath D, Wünsche H, Zeleke A (2023). The NFDI4Health Metadata Schema (V3_3)1780
Abaza H, Shutsko A, Golebiewski M, Klopfenstein S, Schmidt CO, Vorisek C, COVID-19 NTF, NFDI4Health , Brünings-Kuppe C, Clemens V, Darms J, Hanß S, Intemann T, Jannasch F, Kasbohm E, Lindstädt B, Löbe M, Orban E, Perrar I, Peters M, Sax U, Schulze M, Schupp C, Schwarz F, Schwedhelm C, Strathmann S, Waltemath D, Wünsche H, Zeleke A (2023). Metadata schema of the NFDI4Health and the NFDI4Health Task Force COVID-19 (V3_2)1779
Abaza H, Shutsko A, Golebiewski M, Klopfenstein S, Schmidt CO, Vorisek C, COVID-19 NTF, NFDI4Health , Brünings-Kuppe C, Clemens V, Darms J, Hanß S, Intemann T, Jannasch F, Kasbohm E, Lindstadt B, Lobe M, Orban E, Perrar I, Peters M, Sax U, Schulze M, Schupp C, Schwarz F, Schwedhelm C, Strathmann S, Waltemath D, Wünsche H, Zeleke AA (2023). Metadata schema of the NFDI4Health and the NFDI4Health Task Force COVID-19 (V3_1)1778
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
We use cookies on our website. Some of them are essential, while others help us improve this site and your experience.If you are under 16 and wish to give consent to optional services, you must ask your legal guardians for permission.We use cookies and other technologies on our website. Some of them are essential, while others help us to improve this website and your experience.Personal data may be processed (e.g. IP addresses), for example for personalized ads and content or ad and content measurement.You can find more information about the use of your data in our privacy policy.You can revoke or adjust your selection at any time under Settings.
If you are under 16 and wish to give consent to optional services, you must ask your legal guardians for permission.We use cookies and other technologies on our website. Some of them are essential, while others help us to improve this website and your experience.Personal data may be processed (e.g. IP addresses), for example for personalized ads and content or ad and content measurement.You can find more information about the use of your data in our privacy policy.Here you will find an overview of all cookies used. You can give your consent to entire categories or have further information displayed and thus select only certain cookies.