@article{BoteroMonkRodriguezCubillosetal.2020,
  author    = {Botero, David and Monk, Jonathan and Rodriguez Cubillos, Maria Juliana and Rodriguez Cubillos, Andres Eduardo and Restrepo, Mariana and Bernal-Galeano, Vivian and Reyes, Alejandro and Gonzalez Barrios, Andres and Palsson, Bernhard O. and Restrepo, Silvia and Bernal, Adriana},
  title     = {Genome-scale metabolic model of Xanthomonas phaseoli pv. manihotis},
  series = {Frontiers in genetics},
  volume    = {11},
  journal   = {Frontiers in genetics},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {1664-8021},
  doi       = {10.3389/fgene.2020.00837},
  pages     = {19},
  year      = {2020},
  abstract  = {Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)(+) balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species.},
  language  = {en}
}
@inproceedings{JacqminOezdemirFellKurbanetal.2021,
  author    = {Jacqmin, Julien and {\"O}zdemir, Paker Doğu and Fell Kurban, Caroline and Tun{\c{c}} Pekkan, Zelha and Koskinen, Johanna and Suonp{\"a}{\"a}, Maija and Seng, Cheyvuth and Carlon, May Kristine Jonson and Gayed, John Maurice and Cross, Jeffrey S. and Langseth, Inger and Jacobsen, Dan Yngve and Haugsbakken, Halvdan and Bethge, Joseph and Serth, Sebastian and Staubitz, Thomas and Wuttke, Tobias and Nordemann, Oliver and Das, Partha-Pratim and Meinel, Christoph and Ponce, Eva and Srinath, Sindhu and Allegue, Laura and Perach, Shai and Alexandron, Giora and Corti, Paola and Baudo, Valeria and Turr{\´o}, Carlos and Moura Santos, Ana and Nilsson, Charlotta and Maldonado-Mahauad, Jorge and Valdiviezo, Javier and Carvallo, Juan Pablo and Samaniego-Erazo, Nicolay and Poce, Antonella and Re, Maria Rosaria and Valente, Mara and Karp Gershon, Sa'ar and Ruip{\´e}rez-Valiente, Jos{\´e} A. and Despujol, Ignacio and Busquets, Jaime and Kerr, John and Lorenz, Anja and Sch{\"o}n, Sandra and Ebner, Martin and Wittke, Andreas and Beirne, Elaine and Nic Giolla Mhich{\´i}l, Mair{\´e}ad and Brown, Mark and Mac Lochlainn, Conch{\´u}r and Topali, Paraskevi and Chounta, Irene-Angelica and Ortega-Arranz, Alejandro and Villagr{\´a}-Sobrino, Sara L. and Mart{\´i}nez-Mon{\´e}s, Alejandra and Blackwell, Virginia Katherine and Wiltrout, Mary Ellen and Rami Gaddem, Mohamed and Hern{\´a}ndez Reyes, C{\´e}sar Augusto and Nagahama, Toru and Buchem, Ilona and Okatan, Ebru and Khalil, Mohammad and Casiraghi, Daniela and Sancassani, Susanna and Brambilla, Federica and Mihaescu, Vlad and Andone, Diana and Vasiu, Radu and Şahin, Muhittin and Egloffstein, Marc and Bothe, Max and Rohloff, Tobias and Schenk, Nathanael and Schwerer, Florian and Ifenthaler, Dirk and Hense, Julia and Bernd, Mike},
  title     = {EMOOCs 2021},
  editor    = {Meinel, Christoph and Staubitz, Thomas and Schweiger, Stefanie and Friedl, Christian and Kiers, Janine and Ebner, Martin and Lorenz, Anja and Ubachs, George and Mongenet, Catherine and Ruip{\´e}rez-Valiente, Jos{\´e} A. and Cortes Mendez, Manoel},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-512-5},
  doi       = {10.25932/publishup-51030},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-510300},
  pages     = {vii, 295},
  year      = {2021},
  abstract  = {From June 22 to June 24, 2021, Hasso Plattner Institute, Potsdam, hosted the seventh European MOOC Stakeholder Summit (EMOOCs 2021) together with the eighth ACM Learning@Scale Conference. Due to the COVID-19 situation, the conference was held fully online. The boost in digital education worldwide as a result of the pandemic was also one of the main topics of this year's EMOOCs. All institutions of learning have been forced to transform and redesign their educational methods, moving from traditional models to hybrid or completely online models at scale. The learnings, derived from practical experience and research, have been explored in EMOOCs 2021 in six tracks and additional workshops, covering various aspects of this field. In this publication, we present papers from the conference's Experience Track, the Policy Track, the Business Track, the International Track, and the Workshops.},
  language  = {en}
}