Biology Reference
In-Depth Information
•
Malca, H., Shomron, N. and Ast, G. (2003).
The U1 snRNP base pairs with the 5' splice site within a penta-snRNP
complex. Mol. Cell. Biol.
23
, 3442-3455.
•
Matsuno, H., Doi, A., Nagasaki, M. and Miyano, S. (2000). Hybrid Petri net representation of gene regulatory network.
Pac. Symp. Biocomput.
5
, 338-349.
•
Matsuno, H., Inouye, S.-I. T., Okitsu, Y., Fujii, Y. and Miyano, S. (2006). A new regulatory interaction suggested by
simulations for circadian genetic control mechanism in mammals. J. Bioinform. Comput. Biol.
4
, 139-153.
•
Mayas, R. M., Maita, H. and Staley, J. P. (2006). Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nat.
Struct. Mol. Biol.
13
, 482-490.
•
Modrek, B., Resch, A., Grasso, C. and Lee, C. (2001). Genome-wide detection of alternative splicing in expressed
sequences of human genes. Nucleic Acids Res.
29
, 2850-2859.
•
Nottrott, S., Urlaub, H. and L uhrmann, R. (2002). Hierarchical, clustered protein interactions with U4/U6 snRNA: a
biochemical role for U4/U6 proteins. EMBO J.
21
, 5527-5538.
•
Pandit, S., Lynn, B. and Rymond, B. C. (2006). Inhibition of a spliceosome turnover pathway suppresses splicing defects.
Proc. Natl. Acad. Sci. USA
103
, 13700-13705.
•
Papin, J. A., Stelling, J., Price, N. D., Klamt, S., Schuster, S. and Palsson, B. O. (2004). Comparison of network-based
pathway analysis methods. Trends Biotechnol.
22
, 400-405.
•
Park, J. W., Parisky, K., Celotto, A. M., Reenan, R. A. and Graveley, B. R. (2004). Identification of alternative splicing
regulators by RNA interference in
Drosophila
. Proc. Natl. Acad. Sci. USA
101
, 15974-15979.
•
Pawson, T. and Nash, P. (2000).
Protein-protein interactions define specificity in signal transduction.
Genes Dev.
14
,
1027-1047.
•
Perriman, R., Barta, I., Voeltz, G. K., Abelson, J. and Ares, M. jr. (2003). ATP requirement for Prp5p function is
determined by Cus2p and the structure of U2 small nuclear RNA. Proc. Natl. Acad. Sci. USA
100
, 13857-13862.
•
Pfeiffer, T., S anchez-Valdenebro, I., Nuno, J. C., Montero, F. and Schuster, S. (1999). METATOOL: for studying metabolic
networks. Bioinformatics
15
, 251-257.
•
Prieto, C. and De Las Rivas, J. (2006). APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res.
34
, W298-
W302.
•
Puig, O., Gottschalk, A., Fabrizio, P. and Seraphin, B. (1999). Interaction of the U1 snRNP with nonconserved intronic
sequences affects 5' splice site selection. Genes Dev.
13
, 569-580.
•
The R Development Core Team (2005).
R: A language and environment for statistical computing.
R Foundation for
Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
•
Reddy, V. N., Mavrovouniotis, M. L. and Liebman, M. N. (1993). Petri net representations in metabolic pathways. Proc.
Int. Conf. Intell. Syst. Mol. Biol.
1
, 328-336.
•
Reddy, V. N., Liebman, M. N. and Mavrovouniotis, M. L. (1996). Qualitative analysis of biochemical reaction systems.
Comput. Biol. Med.
26
, 9-24.
•
Rohr, C., Marwan, W. and Heiner, M. (2010). Snoopy - a unifying petri net framework to investigate biomolecular
networks. Bioinformatics
26
, published ahead of print.
•
Sackmann, A., Heiner, M. and Koch, I. (2006). Application of Petri net based analysis techniques to signal transduction
pathways. BMC Bioinformatics
7
, 482.
•
Sackmann, A., Formanowicz, D., Formanowicz, P., Koch, I. and Blazewicz, J. (2007). An analysis of the Petri net based
model of the human body iron homeostasis process. Comput. Biol. Chem.
31
, 1-10.
•
Schaffert, N., Hossbach, M., Heintzmann, R., Achsel, T. and Luhrmann, R. (2004). RNAi knockdown of hPrp31 leads to
an accumulation of 36 U4/U6 di-snRNPs in Cajal bodies. EMBO J.
23
, 3000-3009.
•
Schilling, C. H., Edwards, J. S. and Palsson, B. O. (1999). Toward metabolic phenomics: analysis of genomic data using
flux balances. Biotechnol. Prog.
15
, 288-295.
•
Schuster, S. and Hilgetag, C. (1994). On elementary flux modes in biochemical reaction systems at steady state. J. Biol.
Syst.
2
, 165-182.
•
Schuster, S., Dandekar, T. and Fell, D. A. (1999).
Detection of elementary flux modes in biochemical networks:
a
promising tool for pathway analysis and metabolic engineering. Trends Biotechnol.
17
, 53-60.
•
Schuster, S., Klipp, E. and Marhl, M. (2006). The Predictive Power of Molecular Network Modelling.
In
: Discovering
biomolecular mechanisms with computational biology, Eisenhaber, F. (ed.), Springer, pp. 95-103.
•
Schuster, S., von Kamp, A. and Pachkov, M. (2007).
Understanding the roadmap of metabolism by pathway analysis.
Methods Mol. Biol.
358
, 199-226.
•
Schwer, B. and Guthrie, C. (1991). PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome.
Nature
349
, 494-499.
•
Shen, H. and Green, M. R. (2004). A pathway of sequential arginine-serine-rich domain-splicing signal interactions during
mammalian spliceosome assembly. Mol. Cell.
16
, 363-373.
•
Shen, J., Zhang, L. and Zhao, R. (2007). Biochemical characterization of the ATPase and helicase activity of UAP56, an
essential pre-mRNA splicing and mRNA export factor. J. Biol. Chem.
282
, 22544-22550.