Publications

Computational modeling

  • Goldberg AP, Szigeti B, Chew YH, Sekar JAP, Roth YD & Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 51, 97–102 (2018).
  • Szigeti B, Roth YD, Sekar JAP, Goldberg AP, Pochiraju SC & Karr JR. A blueprint for human whole-cell modeling. Curr Opin Syst Biol 7, 8–15 (2018).
  • Medley JK, Goldberg AP & Karr JR. Guidelines for reproducibly building and simulating systems biology models. IEEE Trans Biomed Eng 63, 2015–2020 (2016).
  • Waltemath D, Karr JR et al. Toward community standards and software for whole-cell modeling. IEEE Trans Biomed Eng 63, 2007–2014 (2016).
  • Karr JR, Takahasi K & Funahashi A. The principles of whole-cell modeling. Curr Opin Microbiol 27, 18–24 (2015).
  • Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI & Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389–401 (2012).

Genome engineering

  • Lartigue C, Vashee S, Algire MA, Chuang RY, Benders GA, Ma L, Noskov VN, Denisova EA, Gibson DG, Assad-Garcia N, Alperovich N, Thomas DW, Merryman C, Hutchison CA 3rd, Smith HO, Venter JC & Glass JI. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science 325, 1693–1696 (2009).
  • Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA 3rd, Smith HO & Venter JC. Genome transplantation in bacteria: changing one species to another. Science 317, 632–638 (2007).

Genomics

  • Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, Gavin AC, Bork P & Serrano L. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Mol Syst Biol 11, 780 (2015).
  • Lluch-Senar M, Luong K, Lloréns-Rico V, Delgado J, Fang G, Spittle K, Clark TA, Schadt E, Turner SW, Korlach J & Serrano L. Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet 9, e1003191 (2013).
  • Van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, Russell RB, Heck AJ, Bork P & Gavin AC. Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol 8, 571 (2012).
  • Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P & Serrano L. Transcriptome complexity in a genome-reduced bacterium. Science 326, 1268–1271 (2009).
  • Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P & Serrano L. Impact of genome reduction on bacterial metabolism and its regulation. Science 326, 1263–1268 (2009).
  • Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P & Gavin AC. Proteome organization in a genome-reduced bacterium. Science 326, 1235–1240 (2009).

Microbial pathogenesis

  • Citti C & Blanchard A. Mycoplasmas and their host: emerging and re-emerging minimal pathogens. Trends Microbiol 21, 196–203 (2013).
  • Großhennig S, Schmidl SR, Schmeisky G, Busse J & Stülke J. Implication of glycerol and phospholipid transporters in Mycoplasma pneumoniae growth and virulence. Infect Immun 81, 896–904 (2013).
  • Schmidl SR, Otto A, Lluch-Senar M, Piñol J, Busse J, Becher D & Stülke J. A trigger enzyme in Mycoplasma pneumoniae: impact of the glycerophosphodiesterase GlpQ on virulence and gene expression. PLoS Pathog 7, e1002263 (2011).
  • Hames C, Halbedel S, Hoppert M, Frey J & Stülke J. Glycerol metabolism is important for cytotoxicity of Mycoplasma pneumoniae. J Bacteriol 191, 747–753 (2009).
© Minicell Consortium 2015. Last updated March 30, 2018, 8:48 a.m..