Literature for Seminar "Systems Biology"


Hutchison, C.A., 3rd, Chuang, R.Y., Noskov, V.N., Assad-Garcia, N., Deerinck, T.J., Ellisman, M.H., Gill, J., Kannan, K., Karas, B.J., Ma, L., Pelletier, J.F., Qi, Z.Q., Richter, R.A., Strychalski, E.A., Sun, L., Suzuki, Y., Tsvetanova, B., Wise, K.S., Smith, H.O., Glass, J.I., Merryman, C., Gibson, D.G. and Venter, J.C. (2016) Design and synthesis of a minimal bacterial genome. Science, 351, aad6253.

Mackenzie, R.J., Lawless, C., Holman, S.W., Lanthaler, K., Beynon, R.J., Grant, C.M., Hubbard, S.J. and Eyers, C.E. (2016) Absolute protein quantification of the yeast chaperome under conditions of heat shock. Proteomics, 16, 2128-2140.

Werth, E.G., McConnell, E.W., Gilbert, T.S., Couso Lianez, I., Perez, C.A., Manley, C.K., Graves, L.M., Umen, J.G. and Hicks, L.M. (2017) Probing the global kinome and phosphoproteome in Chlamydomonas reinhardtii via sequential enrichment and quantitative proteomics. Plant J., 89, 416-426.


Goloubinoff, P., Sassi, A.S., Fauvet, B., Barducci, A. and De Los Rios, P. (2018) Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins. Nat. Chem. Biol., 14, 388-395.

Majsec, K., Bhuiyan, N.H., Sun, Q., Kumari, S., Kumar, V., Ware, D. and van Wijk, K.J. (2017) The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis. Plant Cell, 29, 2687-2710.

Lukoszek, R., Feist, P., and Ignatova, Z. (2016). Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq. BMC Plant Biol. 16, 221.


Datlinger, P., Rendeiro, A.F., Schmidl, C., Krausgruber, T., Traxler, P., Klughammer, J., Schuster, L.C., Kuchler, A., Alpar, D. and Bock, C. (2017) Pooled CRISPR screening with single-cell transcriptome readout. Nature methods, 14, 297-301.

Roberts, A.M., Miyamoto, D.K., Huffman, T.R., Bateman, L.A., Ives, A.N., Akopian, D., Heslin, M.J., Contreras, C.M., Rape, M., Skibola, C.F. and Nomura, D.K. (2017) Chemoproteomic Screening of Covalent Ligands Reveals UBA5 As a Novel Pancreatic Cancer Target. ACS Chem. Biol., 12, 899-904.

Savitski, M.M., Reinhard, F.B., Franken, H., Werner, T., Savitski, M.F., Eberhard, D., Martinez Molina, D., Jafari, R., Dovega, R.B., Klaeger, S., Kuster, B., Nordlund, P., Bantscheff, M., and Drewes, G. (2014). Tracking cancer drugs in living cells by thermal profiling of the proteome. Science 346, 1255784.


Alon, U. (2007). Network motifs: theory and experimental approaches. Nature reviews. Genetics 8, 450-461.

Chang, R.L., Ghamsari, L., Manichaikul, A., Hom, E.F., Balaji, S., Fu, W., Shen, Y., Hao, T., Palsson, B.O., Salehi-Ashtiani, K., and Papin, J.A. (2011). Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol. Syst. Biol. 7, 518.

Kovary, K.M., Taylor, B., Zhao, M.L., and Teruel, M.N. (2018). Expression variation and covariation impair analog and enable binary signaling control. Mol. Syst. Biol. 14, e7997.

Reshef, D.N., Reshef, Y.A., Finucane, H.K., Grossman, S.R., McVean, G., Turnbaugh, P.J., Lander, E.S., Mitzenmacher, M., and Sabeti, P.C. (2011). Detecting Novel Associations in Large Data Sets. Science 334, 1518-1524.

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