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. B Goldenbogen, SO Adler, O Bodeit, JAH Wodke, A Korman, L Bonn, X Escalera-Fanjul, JEL Haffner, M Karnetzki, M Krantz, I Maintz, L Mallis, RU Moran Torres, H Prawitz, PS Segelitz, M Seeger, R Linding and E Klipp.
   Geospatial precision simulations of community confined human interactions during SARS-CoV-2 transmission reveals bimodal intervention outcomes.
   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

11. 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 S Malik 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.
    MEMOTE for standardized genome-scale metabolic model testing..
    March 2020.
    

12. Veera Raghavan Thangapandi, Oskar Knittelfelder, Mario Brosch, Eleonora Patsenker, Olga Vvedenskaya, Stephan Buch, Sebastian Hinz, Alexander Hendricks, Marina Nati, Alexander Herrmann, Devavrat Ravindra Rekhade, Thomas Berg, Madlen Matz-Soja, Klaus Huse, Edda Klipp, Josch K Pauling, Judith AH Wodke, Jacobo Miranda Ackerman, Malte Bonin, Elmar Aigner, Christian Datz, Witigo Schönfels, Sophie Nehring, Sebastian Zeissig, Christoph Röcken, Andreas Dahl, Triantafyllos Chavakis, Felix Stickel, Andrej Shevchenko, Clemens Schafmayer, Jochen Hampe and Pallavi Subramanian.
    Loss of hepatic Mboat7 leads to liver fibrosis.
    Gut 70(5):940–950, 2021.
    URL, DOI