Dr. Ulrike Wittig

2024

• 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

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
• 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
• 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

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
• 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
• 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
• Müller M, Ghosh S, Wittig U, Rey M (2021). Word-Level Alignment of Paper Documents with their Electronic Full-Text Counterparts, In Proceedings of the 20th SIGBioMed Workshop on Biomedical Language Processing, BioNLP 2021, Online, June 11, 2021. 1265
• 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

• 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
• 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

• 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
• 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
• 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
• 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
• 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

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

• 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

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

2008

• 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

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

• 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