Difference between revisions of "Team:Tuebingen/References"

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<p>
 
<p>
     <strong>(Hine &amp; Martin, 2015)</strong><br />
+
     <strong>(Büchel et al., 2013)</strong><br />
Hine, R., &amp; Martin, E. (2015). A Dictionary of Biology (7th ed.). OUP Oxford.
+
Büchel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., … Le Novère, N. (2013). Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Systems Biology, 7, 116. https://doi.org/10.1186/1752-0509-7-116
 
</p>
 
</p>
  
 
<p>
 
<p>
     <strong>(Orth et al., 2010)</strong><br />
+
     <strong>(Ebrahim, Lerman, Palsson, &amp; Hyduke, 2013)</strong><br />
Orth, Jeffrey D., Ines Thiele, and Bernhard Ø. Palsson. “What Is Flux Balance Analysis?” Nature Biotechnology 28, no. 3 (March 2010): 245–48. doi:10.1038/nbt.1614. Orth, J. D., Thiele, I., &amp; Palsson, B. Ø. (2010). What is flux balance analysis? Nature Biotechnology, 28(3), 245–248. https://doi.org/10.1038/nbt.1614
+
Ebrahim, A., Lerman, J. A., Palsson, B. O., &amp; Hyduke, D. R. (2013). COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Systems Biology, 7, 74. https://doi.org/10.1186/1752-0509-7-74
 
</p>
 
</p>
  
 
<p>
 
<p>
     <strong>(Wattam et al., 2014)</strong><br />
+
     <strong>(Hine &amp; Martin, 2015)</strong><br />
Wattam, A. R., Abraham, D., Dalay, O., Disz, T. L., Driscoll, T., Gabbard, J. L., … Sobral, B. W. (2014). PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Research, 42(Database issue), D581–D591. https://doi.org/10.1093/nar/gkt1099
+
Hine, R., &amp; Martin, E. (2015). A Dictionary of Biology (7th ed.). OUP Oxford.
 
</p>
 
</p>
  
Line 33: Line 33:
  
 
<p>
 
<p>
     <strong>(Ebrahim, Lerman, Palsson, &amp; Hyduke, 2013)</strong><br />
+
     <strong>(King et al., 2016)</strong><br />
Ebrahim, A., Lerman, J. A., Palsson, B. O., &amp; Hyduke, D. R. (2013). COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Systems Biology, 7, 74. https://doi.org/10.1186/1752-0509-7-74
+
King, Z. A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J. A., … Lewis, N. E. (2016). BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Research, 44(D1), D515–D522. https://doi.org/10.1093/nar/gkv1049
 +
</p>
 +
 
 +
 
 +
<p>
 +
    <strong>(Lee et al., 2010) </strong><br />
 +
Lee, H. J., Kim, E., & Kim, J. S. (2010). Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome research, 20(1), 81-89.
 +
</p>
 +
 
 +
<p>
 +
    <strong>(Li et al., 2010)</strong><br />
 +
Li, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., … Laibe, C. (2010). BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology, 4, 92. https://doi.org/10.1186/1752-0509-4-92
 +
</p>
 +
 
 +
<p>
 +
    <strong>(Liu et al., 1997) </strong><br />
 +
Liu, Q., Segal, D. J., Ghiara, J. B., & Barbas, C. F. (1997). Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. Proceedings of the National Academy of Sciences, 94(11), 5525-5530.
 +
</p>
 +
 
 +
<p>
 +
    <strong>(Lombardo et al., 2007) </strong><br />
 +
Lombardo, A., Genovese, P., Beausejour, C. M., Colleoni, S., Lee, Y. L., Kim, K. A., ... & Holmes, M. C. (2007). Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nature biotechnology, 25(11), 1298-1306.
 +
</p>
 +
 
 +
<p>
 +
    <strong>(Mutschler et al., 2011) </strong><br />
 +
Mutschler, H., Gebhardt, M., Shoeman, R. L., & Meinhart, A. (2011). A novel mechanism of programmed cell death in bacteria by toxin–antitoxin systems corrupts peptidoglycan synthesis. PLoS Biol, 9(3), e1001033.
 +
</p>
 +
 
 +
<p>
 +
    <strong>(Orth et al., 2010)</strong><br />
 +
Orth, Jeffrey D., Ines Thiele, and Bernhard Ø. Palsson. “What Is Flux Balance Analysis?” Nature Biotechnology 28, no. 3 (March 2010): 245–48. doi:10.1038/nbt.1614. Orth, J. D., Thiele, I., &amp; Palsson, B. Ø. (2010). What is flux balance analysis? Nature Biotechnology, 28(3), 245–248. https://doi.org/10.1038/nbt.1614
 
</p>
 
</p>
  
Line 43: Line 74:
  
 
<p>
 
<p>
     <strong>(Teusink et al., 2006)</strong><br />
+
     <strong>(Skerra, 1994) </strong><br />
Teusink, B., Wiersma, A., Molenaar, D., Francke, C., Vos, W. M. de, Siezen, R. J., &amp; Smid, E. J. (2006). Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model. Journal of Biological Chemistry, 281(52), 40041–40048. https://doi.org/10.1074/jbc.M606263200
+
Skerra, A. (1994). Use of the tetracycline promoter for the tightly regulated production of a murine antibody fragment in Escherichia coli. Gene, 151(1), 131-135.
 
</p>
 
</p>
  
 
<p>
 
<p>
     <strong>(Li et al., 2010)</strong><br />
+
     <strong>(Teusink et al., 2006)</strong><br />
Li, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., … Laibe, C. (2010). BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology, 4, 92. https://doi.org/10.1186/1752-0509-4-92
+
Teusink, B., Wiersma, A., Molenaar, D., Francke, C., Vos, W. M. de, Siezen, R. J., &amp; Smid, E. J. (2006). Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model. Journal of Biological Chemistry, 281(52), 40041–40048. https://doi.org/10.1074/jbc.M606263200
 
</p>
 
</p>
  
 
<p>
 
<p>
     <strong>(King et al., 2016)</strong><br />
+
     <strong>(Wattam et al., 2014)</strong><br />
King, Z. A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J. A., … Lewis, N. E. (2016). BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Research, 44(D1), D515–D522. https://doi.org/10.1093/nar/gkv1049
+
Wattam, A. R., Abraham, D., Dalay, O., Disz, T. L., Driscoll, T., Gabbard, J. L., … Sobral, B. W. (2014). PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Research, 42(Database issue), D581–D591. https://doi.org/10.1093/nar/gkt1099
 
</p>
 
</p>
  
 
<p>
 
<p>
     <strong>(Büchel et al., 2013)</strong><br />
+
     <strong>(Young, 2002) </strong><br />
Büchel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., … Le Novère, N. (2013). Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Systems Biology, 7, 116. https://doi.org/10.1186/1752-0509-7-116
+
Young, R. Y. (2002). Bacteriophage holins: deadly diversity. Journal of molecular microbiology and biotechnology, 4(1), 21-36.
 
</p>
 
</p>
  

Revision as of 18:44, 18 October 2016

Bibliography

(Büchel et al., 2013)
Büchel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., … Le Novère, N. (2013). Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Systems Biology, 7, 116. https://doi.org/10.1186/1752-0509-7-116

(Ebrahim, Lerman, Palsson, & Hyduke, 2013)
Ebrahim, A., Lerman, J. A., Palsson, B. O., & Hyduke, D. R. (2013). COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Systems Biology, 7, 74. https://doi.org/10.1186/1752-0509-7-74

(Hine & Martin, 2015)
Hine, R., & Martin, E. (2015). A Dictionary of Biology (7th ed.). OUP Oxford.

(King et al., 2015)
King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLOS Comput Biol, 11(8), e1004321. https://doi.org/10.1371/journal.pcbi.1004321

(King et al., 2016)
King, Z. A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J. A., … Lewis, N. E. (2016). BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Research, 44(D1), D515–D522. https://doi.org/10.1093/nar/gkv1049

(Lee et al., 2010)
Lee, H. J., Kim, E., & Kim, J. S. (2010). Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome research, 20(1), 81-89.

(Li et al., 2010)
Li, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., … Laibe, C. (2010). BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology, 4, 92. https://doi.org/10.1186/1752-0509-4-92

(Liu et al., 1997)
Liu, Q., Segal, D. J., Ghiara, J. B., & Barbas, C. F. (1997). Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. Proceedings of the National Academy of Sciences, 94(11), 5525-5530.

(Lombardo et al., 2007)
Lombardo, A., Genovese, P., Beausejour, C. M., Colleoni, S., Lee, Y. L., Kim, K. A., ... & Holmes, M. C. (2007). Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nature biotechnology, 25(11), 1298-1306.

(Mutschler et al., 2011)
Mutschler, H., Gebhardt, M., Shoeman, R. L., & Meinhart, A. (2011). A novel mechanism of programmed cell death in bacteria by toxin–antitoxin systems corrupts peptidoglycan synthesis. PLoS Biol, 9(3), e1001033.

(Orth et al., 2010)
Orth, Jeffrey D., Ines Thiele, and Bernhard Ø. Palsson. “What Is Flux Balance Analysis?” Nature Biotechnology 28, no. 3 (March 2010): 245–48. doi:10.1038/nbt.1614. Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010). What is flux balance analysis? Nature Biotechnology, 28(3), 245–248. https://doi.org/10.1038/nbt.1614

(Perez & Granger, 2007)
Perez, F., & Granger, B. E. (2007). IPython: A System for Interactive Scientific Computing. Computing in Science Engineering, 9(3), 21–29. https://doi.org/10.1109/MCSE.2007.53

(Skerra, 1994)
Skerra, A. (1994). Use of the tetracycline promoter for the tightly regulated production of a murine antibody fragment in Escherichia coli. Gene, 151(1), 131-135.

(Teusink et al., 2006)
Teusink, B., Wiersma, A., Molenaar, D., Francke, C., Vos, W. M. de, Siezen, R. J., & Smid, E. J. (2006). Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model. Journal of Biological Chemistry, 281(52), 40041–40048. https://doi.org/10.1074/jbc.M606263200

(Wattam et al., 2014)
Wattam, A. R., Abraham, D., Dalay, O., Disz, T. L., Driscoll, T., Gabbard, J. L., … Sobral, B. W. (2014). PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Research, 42(Database issue), D581–D591. https://doi.org/10.1093/nar/gkt1099

(Young, 2002)
Young, R. Y. (2002). Bacteriophage holins: deadly diversity. Journal of molecular microbiology and biotechnology, 4(1), 21-36.