next up previous contents
Next: About this document ... Up: Network Analysis Tools (NeAT) Previous: Pathway inference   Contents

Bibliography

1
Masanori Arita.
In silico atomic tracing by substrate-product relationships in escherichia coli intermediary metabolism.
Genome Research, 13:2455-2466, 2003.

2
Sylvain Brohee and Jacques van Helden.
Evaluation of clustering algorithms for protein-protein interaction networks.
BMC Bioinformatics, 7:488, 2006.

3
R. Caspi, H. Foerster, C.A. Fulcher, P. Kaipa, M. Krummenacker, M. Latendresse, S. Paley, S.Y. Rhee, A.G. Shearer, C. Tissier, T.C. Walk, P. Zhang, and P.D. Karp.
The metacyc dat abase of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases.
Nucleic Acids Research, 36:D623-D631, 2008.

4
The Gene Ontology Consortium.
The gene ontology project in 2008.
Nucleic Acids Res, Nov 2007.

5
D. Croes, F. Couche, S. Wodak, and J. v. Helden.
Metabolic pathfinding: inferring relevant pathways in biochemical networks.
Nucleic Acids Research, 33:W326-W330, 2005.

6
D. Croes, F. Couche, S. Wodak, and J. v. Helden.
Inferring meaningful pathways in weighted metabolic networks.
J. Mol. Biol., 356:222-236, 2006.

7
A J Enright, S Van Dongen, and C A Ouzounis.
An efficient algorithm for large-scale detection of protein families.
Nucleic Acids Res, 30(7):1575-84, 2002.

8
J. Foerster, I. Famili, P. Fu, B.O. Palsson, and J. Nielsen.
Genome-scale reconstruction of the saccharomyces cerevisiae metabolic network.
Genome Research, 13:244-253, 2003.

9
Julien Gagneur, David B Jackson, and Georg Casari.
Hierarchical analysis of dependency in metabolic networks.
Bioinformatics, 19(8):1027-1034, May 2003.

10
Anne-Claude Gavin, Patrick Aloy, Paola Grandi, Roland Krause, Markus Boesche, Martina Marzioch, Christina Rau, Lars Juhl Jensen, Sonja Bastuck, Birgit Dümpelfeld, Angela Edelmann, Marie-Anne Heurtier, Verena Hoffman, Christian Hoefert, Karin Klein, Manuela Hudak, Anne-Marie Michon, Malgorzata Schelder, Markus Schirle, Marita Remor, Tatjana Rudi, Sean Hooper, Andreas Bauer, Tewis Bouwmeester, Georg Casari, Gerard Drewes, Gitte Neubauer, Jens M Rick, Bernhard Kuster, Peer Bork, Robert B Russell, and Giulio Superti-Furga.
Proteome survey reveals modularity of the yeast cell machinery.
Nature, 440(7084):631-636, Mar 2006.

11
Zhenjun Hu, David M Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M Stuart, and Charles DeLisi.
Visant 3.0: new modules for pathway visualization, editing, prediction and construction.
Nucleic Acids Res, 35(Web Server issue):W625-W632, Jul 2007.

12
C. Hyland, J.W. Pinney, G.A. McConkey, and D.R. Westhead.
metashark: a www platform for interactive exploration of metabolic networks.
Nucleic Acids Research, 34:W725-W728, 2006.

13
T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki.
A comprehensive two-hybrid analysis to explore the yeast protein interactome.
Proc Natl Acad Sci U S A, 98(8):4569-74., 2001.

14
H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A. L. Barabási.
The large-scale organization of metabolic networks.
Nature, 407(6804):651-654, Oct 2000.

15
M. Kanehisa, M. Araki, S. Goto, H. Masahiro, M. Hirakawa, M. Itoh, T. Katayama, S. Kawashima, S. Okuda, T. Tokimatsu, and Y. Yamanishi.
Kegg for linking genomes to life and the environment.
Nucleic Acids Research, 36:D480-D484, 2008.

16
A. D. King, N. Przulj, and I. Jurisica.
Protein complex prediction via cost-based clustering.
Bioinformatics, 20(17):3013-3020, Nov 2004.

17
C. Klukas and F. Schreiber.
Dynamic exploration and editing of kegg pathway diagrams.
Bioinformatics, 23:344-350, 2007.

18
M. Kotera, M. Hattori, M. Oh, R. Yamamoto, T. Komeno, J. Yabuzaki, K. Tonomura, S. Goto, and M. Kanehisa.
Rpair: a reactant-pair database representing chemical changes in enzymatic reactions.
Genome Informatics, 15:P062, 2004.

19
Nevan J Krogan, Gerard Cagney, Haiyuan Yu, Gouqing Zhong, Xinghua Guo, Alexandr Ignatchenko, Joyce Li, Shuye Pu, Nira Datta, Aaron P Tikuisis, Thanuja Punna, Jos� M Peregr�n-Alvarez, Michael Shales, Xin Zhang, Michael Davey, Mark D Robinson, Alberto Paccanaro, James E Bray, Anthony Sheung, Bryan Beattie, Dawn P Richards, Veronica Canadien, Atanas Lalev, Frank Mena, Peter Wong, Andrei Starostine, Myra M Canete, James Vlasblom, Samuel Wu, Chris Orsi, Sean R Collins, Shamanta Chandran, Robin Haw, Jennifer J Rilstone, Kiran Gandi, Natalie J Thompson, Gabe Musso, Peter St Onge, Shaun Ghanny, Mandy H Y Lam, Gareth Butland, Amin M Altaf-Ul, Shigehiko Kanaya, Ali Shilatifard, Erin O'Shea, Jonathan S Weissman, C. James Ingles, Timothy R Hughes, John Parkinson, Mark Gerstein, Shoshana J Wodak, Andrew Emili, and Jack F Greenblatt.
Global landscape of protein complexes in the yeast saccharomyces cerevisiae.
Nature, 440(7084):637-643, Mar 2006.

20
B. Samuel Lattimore, Stijn van Dongen, and M. James C Crabbe.
Genemcl in microarray analysis.
Comput Biol Chem, 29(5):354-359, Oct 2005.

21
Raphaël Leplae, Aline Hebrant, Shoshana J Wodak, and Ariane Toussaint.
Aclame: a classification of mobile genetic elements.
Nucleic Acids Res, 32(Database issue):D45-D49, Jan 2004.

22
I. Letunic, T. Yamada, M. Kanehisa, and P. Bork.
ipath: interactive exploration of biochemical pathways and networks.
Trends in biochemical sciences, 33:101-103, 2008.

23
H. W. Mewes, S. Dietmann, D. Frishman, R. Gregory, G. Mannhaupt, K. F X Mayer, M. Münsterkötter, A. Ruepp, M. Spannagl, V. Stümpflen, and T. Rattei.
Mips: analysis and annotation of genome information in 2007.
Nucleic Acids Res, Dec 2007.

24
Jose B Pereira-Leal, Anton J Enright, and Christos A Ouzounis.
Detection of functional modules from protein interaction networks.
Proteins, 54(1):49-57, Jan 2004.

25
M.G. Poolman, B.K. Bonde, A. Gevorgyan, H.H. Patel, and D.A. Fell.
Challenges to be faced in the reconstruction of metabolic networks from public databases.
Systems Biology, IEE Proceedings, 153:379-384, 2006.

26
S.A. Rahman, P. Advani, R. Schunk, R. Schrader, and D. Schomburg.
Metabolic pathway analysis web service (pathway hunter tool at cubic).
Bioinformatics, 21:1189-1193, 2005.

27
Roland Schwarz, Chunguang Liang, Christoph Kaleta, Mark Kühnel, Eik Hoffmann, Sergei Kuznetsov, Michael Hecker, Gareth Griffiths, Stefan Schuster, and Thomas Dandekar.
Integrated network reconstruction, visualization and analysis using yanasquare.
BMC Bioinformatics, 8, 2007.

28
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, and Trey Ideker.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome Res, 13(11):2498-2504, Nov 2003.

29
Roded Sharan, Igor Ulitsky, and Ron Shamir.
Network-based prediction of protein function.
Mol Syst Biol, 3:88, 2007.

30
P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein, and B. Futcher.
Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization.
Mol Biol Cell, 9:3273-3297, 1998.

31
Victor Spirin and Leonid A Mirny.
Protein complexes and functional modules in molecular networks.
Proc Natl Acad Sci U S A, 100(21):12123-12128, Oct 2003.

32
P. Uetz, L. Giot, G. Cagney, T. A. Mansfield, R. S. Judson, J. R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, A. Qureshi-Emili, Y. Li, B. Godwin, D. Conover, T. Kalbfleisch, G. Vijayadamodar, M. Yang, M. Johnston, S. Fields, and J. M. Rothberg.
A comprehensive analysis of protein-protein interactions in saccharomyces cerevisiae.
Nature, 403(6770):623-7., 2000.

33
Stijn Van Dongen.
Graph clustering by flow simulation.
PhD thesis, Centers for mathematics and computer science (CWI), University of Utrecht, 2000.

34
Jacques van Helden, David Gilbert, Lorenz Wernisch, Michael Schroeder, and Shoshana Wodak.
Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data.
Lecture Notes in Computer Science, 2066:147-165, 2001.

35
Christian von Mering, Lars J Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, and Peer Bork.
String 7-recent developments in the integration and prediction of protein interactions.
Nucleic Acids Res, 35(Database issue):D358-D362, Jan 2007.

36
J.D. Zhang and S. Wiemann.
Kegggraph: a graph approach to kegg pathway in r and bioconductor.
Bioinformatics, 25:1470-1471, 2009.



RSAT 2009-09-04