Biology Reference
In-Depth Information
•
Simao, E., Remy, E., Thieffry, D. and Chaouiya, C. (2005). Qualitative modelling of regulated metabolic pathways:
application to the tryptophan biosynthesis in
E. coli
. Bioinformatics
21 Suppl. 2
, ii190-ii196.
•
Small, E. C., Leggett, S. R., Winans, A. A. and Staley, J. P. (2006). The EF-G-like GTPase Snu114p regulates spliceosome
dynamics mediated by Brr2p, a DExD/H box ATPase. Mol. Cell.
23
, 389-399.
•
Spadaccini, R., Reidt, U., Dybkov, O., Will, C., Frank, R., Stier, G., Corsini, L., Wahl, M. C., L uhrmann, R. and Sattler,
M. (2006). Biochemical and NMR analyses of an SF3b155-p14-U2AF-RNA interaction network involved in branch point
definition during pre-mRNA splicing. RNA
12
, 410-425.
•
Staley, J. P. and Guthrie, C. (1998). Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell
92
,
315-326.
•
Stamm, S. (2002). Signals and their transduction pathways regulating alternative splicing: a new dimension of the human
genome. Hum. Mol. Genet.
11
, 2409-2416.
•
Starke, P. (1998).
INA - Integrated Net Analyzer Manual, Berlin.
HU Berlin, Dept.
of CS,
www2.informatik.hu-
•
Stevens, S. W., Barta, I., Ge, H. Y., Moore, R. E., Young, M. K., Lee, T. D. and Abelson, J. (2001). Biochemical and
genetic analyses of the U5, U6, and U4/U6 x U5 small nuclear ribonucleoproteins from
Saccharomyces cerevisiae
.RNA
7
, 1543-1553.
•
Stevens, S. W., Ryan, D. E., Ge, H. Y., Moore, R. E., Young, M. K., Lee, T. D. and Abelson, J. (2002). Composition and
functional characterization of the yeast spliceosomal penta-snRNP. Mol. Cell.
9
, 31-44.
•
Takai-Igarashi, T. (2005). Ontology based standardization of Petri net modeling for signaling pathways. In Silico Biol.
5
,
0047.
•
Tarn, W.-Y. and Steitz, J. A. (1994). SR proteins can compensate for the loss of U1 snRNP functions in vitro. Genes Dev.
8
, 2704-2717.
•
Thanaraj, T. A., Stamm, S., Clark, F., Riethoven, J.-J., Le Texier, V. and Muilu, J. (2004). ASD: the Alternative Splicing
Database. Nucleic Acids Res.
32
, D64-D69.
•
Thormann, A., Rudolph, K. and Koch, I. (2009). TInA (T-invariant analysis) - a tool box for exploring pathways in
biochemical systems at steady state.
In
: German Conference on Bioinformatics 2009, Short Papers and Abstracts, Grosse,
I., Neumann, S., Posch, S., Schreiber, F. and Stadler, P. (eds.), Halle, pp. 157-158.
•
Turner, I. A., Norman, C. M., Churcher, M. J. and Newman, A. J. (2004). Roles of the U5 snRNP in spliceosome dynamics
and catalysis. Biochem. Soc. Trans.
32
, 928-931.
•
Valadkhan, S., Mohammadi, A., Wachtel, C. and Manley, J. L. (2007).
Protein-free spliceosomal snRNAs catalyze a
reaction that resembles the first step of splicing. RNA
13
, 2300-2311.
•
van Nues, R. W. and Beggs, J. D. (2001). Functional contacts with a range of splicing proteins suggest a central role
for Brr2p in the dynamic control of the order of events in spliceosomes of
Saccharomyces cerevisiae
.
Genetics
157
,
1451-1467.
•
Venables, J. P. (2004). Aberrant and alternative splicing in cancer. Cancer Res.
64
, 7647-7654.
•
Villa, T. and Guthrie, C. (2005). The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to
regulate the fidelity of pre-mRNA splicing. Genes Dev.
19
, 1894-1904.
•
von Mering, C., Jensen, L. J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B. and Bork, P. (2007). STING 7 -
recent developments in the integration and prediction of protein interactions. Nucleic Acids Res.
35
, D358-D362.
•
Will, C. L. and L uhrmann, R. (2001). Spliceosomal UsnRNP biogenesis, structure and function. Curr. Opin. Cell Biol.
13
, 290-301.
•
Will, C. L. and L uhrmann, R. (2005). Splicing of a rare class of introns by the U12-dependent spliceosome. Biol. Chem.
386
, 713-724.
•
Will, C. L., Urlaub, H., Achsel, T., Gentzel, M., Wilm, M. and L uhrmann, R. (2002). Characterization of novel SF3b and
17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein. EMBO J.
21
, 4978-4988.
•
Xie, J., Beickman, K., Otte, E. and Rymond, B. C. (1998). Progression through the spliceosome cycle requires Prp38p
function for U4/U6 snRNA dissociation. EMBO J.
17
, 2938-2946.
•
Xiong, M., Zhao, J. and Xiong, H. (2004). Network-based regulatory pathways analysis. Bioinformatics
20
, 2056-2066.
•
Xu, Y.-Z., Newnham, C. M., Kameoka, S., Huang, T., Konarska, M. M. and Query, C. C. (2004). Prp5 bridges U1 and U2
snRNPs and enables stable U2 snRNP association with intron RNA. EMBO J.
23
, 376-385.
•
Zevedei-Oancea, I. and Schuster, S. (2003).
Topological analysis of metabolic networks based on Petri net theory.
In
Silico Biol.
3
, 0029.
•
Zhang, S., Jin, G., Zhang, X.-S. and Chen, L. (2007). Discovering functions and revealing mechanisms at molecular level
from biological networks. Proteomics
7
, 2856-2869.
•
Zhou, Z., Licklider, L. J., Gygi, S. P. and Reed, R. (2002). Comprehensive proteomic analysis of the human spliceosome.
Nature
419
, 182-185.