Priv.-Doz. Dr. Wolfgang Müller

2023

• Linciano P, Quotadamo A, Luciani R, Santucci M, Zorn KM, Foil DH, Lane TR, Silva ACd, Santarem N, Moraes CB, Freitas-Junior L, Wittig U, Mueller W, Tonelli M, Ferrari S, Venturelli A, Gul S, Kuzikov M, Ellinger B, Reinshagen J, Ekins S, Costi MP (2023). High-Throughput Phenotypic Screening and Machine Learning Methods Enabled the Selection of Broad-Spectrum Low-Toxicity Antitrypanosomatidic Agents., J Med Chem. 2023 Nov 3. doi: 10.1021/acs.jmedchem.3c01322. 1734
• Meineke F, Golebiewski M, Hu X, Kirsten T, Löbe M, Klammt S, Sax U, Müller W (2023). NFDI4Health Local Data Hubs for Finding and Accessing Health Data, Proc Conf Res Data Infrastr 1 1797
• 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
• 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
• 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

• 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
• 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

• 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
• 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
• 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
• 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
• 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

• Müller M, Ghosh S, Rey M, Wittig U, Müller W, Strube M (2020). Reconstructing Manual Information Extraction with DB-to-Document Backprojection: Experiments in the Life Science Domain, In Proceedings of the First Workshop on Scholarly Document Processing, Online, November 2020, pp. 81-90. 1147

2019

• Moraes CB, Witt G, Kuzikov M, Ellinger B, Calogeropoulou T, Prousis KC, Mangani S, Pisa FD, Landi G, Iacono LD, Pozzi C, Freitas-Junior LH, Pascoalino BdS, Bertolacini CP, Behrens B, Keminer O, Leu J, Wolf M, Reinshagen J, Cordeiro-da-Silva A, Santarem N, Venturelli A, Wrigley S, Karunakaran D, Kebede B, Pöhner I, Müller W, Panecka-Hofman J, Wade RC, Fenske M, Clos J, Alunda JM, Corral MJ, Uliassi E, Bolognesi ML, Linciano P, Quotadamo A, Ferrari S, Santucci M, Borsari C, Costi MP, Gul S (2019). Accelerating Drug Discovery Efforts for Trypanosomatidic Infections Using an Integrated Transnational Academic Drug Discovery Platform, SLAS DISCOVERY: Advancing the Science of Drug Discovery 24(3):346-361 1075
• Ghosh S, Rey M, Wittig U, Müller W (2019). Bio-entity recognition for SABIO-RK database, F1000Research 8 1271

2018

• Linciano P, Pozzi C, Iacono Ld, Pisa Fd, Landi G, Bonucci A, Gul S, Kuzikov M, Ellinger B, Witt G, Santarem N, Baptista C, Franco C, Moraes CB, Müller W, Wittig U, Luciani R, Sesenna A, Quotadamo A, Ferrari S, Pöhner I, Cordeiro-da-Silva A, Mangani S, Costantino L, Costi MP (2018). Enhancement of Benzothiazoles as Pteridine Reductase-1 Inhibitors for the Treatment of Trypanosomatidic Infections, J. Med. Chem. 62(8):3989-4012 1008
• 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

• 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
• Linciano P, Dawson A, Pöhner I, Costa DM, Sá MS, Cordeiro-da-Silva A, Luciani R, Gul S, Witt G, Ellinger B, Kuzikov M, Gribbon P, Reinshagen J, Wolf M, Behrens B, Hannaert V, Michels PAM, Nerini E, Pozzi C, Pisa Fd, Landi G, Santarem N, Ferrari S, Saxena P, Lazzari S, Cannazza G, Freitas-Junior LH, Moraes CB, Pascoalino BS, Alcântara LM, Bertolacini CP, Fontana V, Wittig U, Müller W, Wade RC, Hunter WN, Mangani S, Costantino L, Costi MP (2017). Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma brucei Pteridine Reductase in Support of Early-Stage Drug Discovery, ACS Omega 2(9):5666-5683 270
• 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

• 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
• 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

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

2014

• 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

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

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