Publications

1. E Yus, T Maier, K Michalodimitrakis, V Noort, T Yamada, W-H Chen, J A H Wodke, M Güell, S Martínez, R Bourgeois, S Kühner, E Raineri, I Letunic, O V Kalinina, M Rode, R Herrmann, R Gutiérrez-Gallego, R B Russell, A-C Gavin, P Bork and L Serrano.
   Impact of genome reduction on bacterial metabolism and its regulation.
   Science 326 (5957):1263–1268, November 2009.
   URL

2. T Maier, J Marcos, J A H Wodke, B Paetzold, M Liebeke, R Gutiérrez-Gallego and L Serrano.
   Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae.
   Mol. Biosyst. 9:1743–1755, 2013.
   URL

3. J A H Wodke, J Puchałka, M Lluch-Senar, J Marcos, E Yus, M Godinho, R Gutiérrez-Gallego, V A P Martins dos Santos, L Serrano, E Klipp and T Maier.
   Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling.
   Mol. Syst. Biol. 9:653, 2013.
   URL

4. M Cvijovic, J Almquist, J Hagmar, S Hohmann, H-M Kaltenbach, E Klipp, M Krantz, P Mendes, S Nelander, J Nielsen, A Pagnani, N Przulj, A Raue, J Stelling, S Stoma, F Tobin, J A H Wodke, R Zecchina and M Jirstrand.
   Bridging the gaps in systems biology.
   Mol. Genet. Genomics 289 (5):727–734, October 2014.
   URL

5. M Lluch-Senar, J Delgado, W-H Chen, V Lloréns-Rico, F J O'Reilly, J A H Wodke, E B Unal, E Yus, S Martínez, R J Nichols, T Ferrar, A Vivancos, A Schmeisky, J Stülke, V Van Noort, A-C Gavin, P Bork and L Serrano.
   Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.
   Mol. Syst. Biol. 11 (1):780, 2015.
   URL

6. J A H Wodke, A Alibés, L Cozzuto, A Hermoso, E Yus, M Lluch-Senar, L Serrano and G Roma.
   MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae.
   Nucleic Acids Res. 43 (Database issue):D618–D623, 2015.
   URL

7. W-H Chen, V Van Noort, M Lluch-Senar, M L Hennrich, J A H Wodke, E Yus, A Alibés, G Roma, D R Mende, C Pesavento, A Typas, A-C Gavin, L Serrano and P Bork.
   Integration of multi-omics data of a genome-reduced bacterium: prevalence of post-transcriptional regulation and its correlation with protein abundances.
   Nucleic Acids Res. 44 (3):1192–1202, 2016.
   URL

8. J Theobald, X Cheng, A Ghanem, H Gaitantzi, G Song, E Klipp, J Wodke, H Becker, R Mrowka, K Breitkopf-Heinlein, S Dooley and S Wölfl.
   Monitoring cytochrome P450 activity in living hepatocytes by chromogenic substrates in response to drug treatment or during cell maturation.
   Arch. Toxicol. 92(3):1133–1149, 2018.
   URL

9. Stephan O Adler, Oliver Bodeit, Lasse Bonn, Bjoern Goldenbogen, Johanna E L Haffner, Maxim Karnetzki, Aviv Korman, Maria Krantz, Rune Linding, Ivo Maintz, Lisa Mallis, Ximena Martinez de la Escalera, Rafael U Moran Torres, Hannah Prawitz, Martin Seeger, Patrick Segelitz, Judith AH Wodke and Edda Klipp.
   Geospatially Referenced Demographic Agent-Based Modeling of SARS-CoV-2-Infection (COVID-19) Dynamics and Mitigation Effects in a Real-world Community.
   medRxiv, 2020.
   URL, DOI

10. Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman Malik S Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev and Cheng Zhang.
    Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.
    Nature biotechnology 38(4):504–504, 2020.
    URL