AurelienMazurie's library 313 articles Export

	Functional cartography of complex metabolic networks. [My Copy] Nature, Vol. 433, No. 7028. (2005), pp. 895-900. by Roger Guimera, Luis posted to algorithm metabolic-networks modules by AurelienMazurie on 2008-09-12 13:12:29 as
	Extraction of phylogenetic network modules from prokayrote metabolic pathways. [My Copy] Genome Inform Ser, Vol. 15, No. 1. (2004), pp. 249-58. by Takuji Yamada, Susumu Goto, Minoru Kanehisa posted to metabolic-networks modules phylogeny by AurelienMazurie on 2008-09-12 13:12:29 as
	Metabolic functions of duplicate genes in Saccharomyces cerevisiae. [My Copy] Genome Res, Vol. 15, No. 10. (2005), pp. 1421-30. by Lars Kuepfer, Uwe Sauer, Lars M. Blank posted to essentiality flux-balance-analysis metabolic-networks by AurelienMazurie on 2008-09-12 13:12:29 as
	Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities. [My Copy] Bioinformatics, Vol. 21, No. 9. (2005), pp. 2008-16. by Marcin Imielinski, Calin Belta, Adam Halasz, Harvey Rubin posted to essentiality flux-balance-analysis metabolic-networks by AurelienMazurie on 2008-09-12 13:12:29 as
	Comparison of network-based pathway analysis methods. [My Copy] Trends Biotechnol, Vol. 22, No. 8. (2004), pp. 400-5. by Jason A. Papin, Joerg Stelling, Nathan D. Price, Steffen Klamt, Stefan Schuster, Bernhard O. Palsson posted to elementary-modes extreme-pathways metabolic-networks by AurelienMazurie on 2008-09-12 13:12:29 as
	Analysis of optimality in natural and perturbed metabolic networks. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 23. (2002), pp. 15112-7. by Daniel Segre, Dennis Vitkup, George M. Church posted to flux-balance-analysis metabolic-networks minimization-of-metabolic-adjustment by AurelienMazurie on 2008-09-12 13:12:29 as
	Expa: a program for calculating extreme pathways in biochemical reaction networks. [My Copy] Bioinformatics, Vol. 21, No. 8. (2005), pp. 1739-40. by Steven L. Bell, Bernhard O. Palsson posted to extreme-pathways metabolic-networks software by AurelienMazurie on 2008-09-12 13:12:29 as
	Modeling Lactococcus lactis using a genome-scale flux model. [My Copy] BMC Microbiol, Vol. 5, No. 1471-2180 (Electronic). (2005) by Ana P. Oliveira, Jens Nielsen, Jochen Forster posted to dataset flux-balance-analysis metabolic-networks minimization-of-metabolic-adjustment by AurelienMazurie on 2008-09-12 13:12:29 as
	Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. [My Copy] Genome Res, Vol. 14, No. 7. (2004), pp. 1298-309. by Natalie C. Duarte, Markus J. Herrgard, Bernhard O. Palsson posted to dataset flux-balance-analysis metabolic-networks by AurelienMazurie on 2008-09-12 13:12:29 as
	An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). [My Copy] Genome Biol, Vol. 4, No. 9. (2003) by Jennifer L. Reed, Thuy D. Vo, Christophe H. Schilling, Bernhard O. Palsson posted to dataset flux-balance-analysis metabolic-networks by AurelienMazurie on 2008-09-12 13:12:29 as
	The small world inside large metabolic networks. [My Copy] Proc Biol Sci, Vol. 268, No. 1478. (2001), pp. 1803-1810. by A. Wagner, D. A. Fell posted to metabolic-networks small-world topology by AurelienMazurie on 2008-09-12 13:12:29 as
	The metabolic world of Escherichia coli is not small. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 6. (2004), pp. 1543-7. by Masanori Arita posted to metabolic-networks quality small-world topology by AurelienMazurie on 2008-09-12 13:12:29 as
	Scale-freeness and biological networks. [My Copy] J Biochem (Tokyo), Vol. 138, No. 1. (2005), pp. 1-4. by Masanori Arita posted to networks scale-free topology by AurelienMazurie on 2008-09-12 13:12:29 as
	The large-scale organization of metabolic networks. [My Copy] Nature, Vol. 407, No. 6804. (2000), pp. 651-4. by H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, A. L. Barabasi posted to cross-species metabolic-networks scale-free topology by AurelienMazurie on 2008-09-12 13:12:29 as
	Assessing experimentally derived interactions in a small world. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 8. (2003), pp. 4372-6. by Debra S. Goldberg, Frederick P. Roth posted to protein-networks small-world topology by AurelienMazurie on 2008-09-12 13:12:29 as
	The Small World Problem [My Copy] Psychology today, Vol. 2:1 (1967), pp. 60-67. by Milgram Stanley posted to networks small-world topology by AurelienMazurie on 2008-09-12 13:12:29 as
	Collective dynamics of 'small-world' networks. [My Copy] Nature, Vol. 393, No. 6684. (1998), pp. 440-2. by D. J. Watts, S. H. Strogatz posted to dynamics networks small-world topology by AurelienMazurie on 2008-09-12 13:12:29 as
	Diameter of the World-Wide Web [My Copy] Nature, Vol. 401 (1999), pp. 130-131. by Reka Albert, Hawoong Jeong, Albert L. Barabasi posted to networks scale-free topology by AurelienMazurie on 2008-09-12 13:12:28 as
	The identification of functional modules from the genomic association of genes. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 9. (2002), pp. 5890-5. by Berend Snel, Peer Bork, Martijn A. Huynen posted to algorithm modules protein-networks scale-free small-world by AurelienMazurie on 2008-09-12 13:12:28 as
	Interaction and domain networks of yeast. [My Copy] Proteomics, Vol. 2, No. 12. (2002), pp. 1715-23. by Stefan Wuchty posted to protein-networks scale-free small-world topology by AurelienMazurie on 2008-09-12 13:12:28 as
	Topological and causal structure of the yeast transcriptional regulatory network. [My Copy] Nat Genet, Vol. 31, No. 1. (2002), pp. 60-3. by Nabil Guelzim, Samuele Bottani, Paul Bourgine, Francois Kepes posted to dataset gene-networks scale-free topology by AurelienMazurie on 2008-09-12 13:12:28 as
	Network motifs in natural and artificial transcriptional regulatory networks [My Copy] Journal of Biological Physics and Chemistry, Vol. 4 (2004), pp. 85-92. by W. Banzhaf, P. D. Kuo posted to gene-networks modules motifs by AurelienMazurie on 2008-09-12 13:12:28 as
	Analyzing yeast protein-protein interaction data obtained from different sources. [My Copy] Nat Biotechnol, Vol. 20, No. 10. (2002), pp. 991-7. by Gary D. Bader, Christopher W. V. Hogue posted to protein-networks quality by AurelienMazurie on 2008-09-12 13:12:28 as
	Transcriptional regulatory networks in Saccharomyces cerevisiae. [My Copy] Science, Vol. 298, No. 5594. (2002), pp. 799-804. by Tong I. Lee, Nicola J. Rinaldi, Francois Robert, et al.Duncan T. Odom, Ziv B. Joseph, Georg K. Gerber, Nancy M. Hannett, Christopher T. Harbison, Craig M. Thompson, Itamar Simon, Julia Zeitlinger, Ezra G. Jennings, Heather L. Murray, Benjamin D. Gordon, Bing Ren, John J. Wyrick, Jean B. Tagne, Thomas L. Volkert, Ernest Fraenkel, David K. Gifford, Richard A. Young posted to dataset gene-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	The comprehensive updated regulatory network of Escherichia coli K-12. [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (2006) by H. Salgado, Santos A. Zavaleta, Gama S. Castro, et al.Peralta M. Gil, Penaloza M. I. Spinola, Martinez A. Antonio, P. D. Karp, Collado J. Vides posted to dataset gene-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	Large-scale identification of protein-protein interaction of Escherichia coli K-12. [My Copy] Genome Res, Vol. 16, No. 5. (2006), pp. 686-91. by Mohammad Arifuzzaman, Maki Maeda, Aya Itoh, et al.Kensaku Nishikata, Chiharu Takita, Rintaro Saito, Takeshi Ara, Kenji Nakahigashi, Hsuan C. Huang, Aki Hirai, Kohei Tsuzuki, Seira Nakamura, Mohammad, Taku Oshima, Tomoya Baba, Natsuko Yamamoto, Tomoyo Kawamura, Tomoko I. Nakamichi, Masanari Kitagawa, Masaru Tomita, Shigehiko Kanaya, Chieko Wada, Hirotada Mori posted to dataset protein-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	A protein interaction map of Drosophila melanogaster. [My Copy] Science, Vol. 302, No. 5651. (2003), pp. 1727-36. by L. Giot, J. S. Bader, C. Brouwer, et al.A. Chaudhuri, B. Kuang, Y. Li, Y. L. Hao, C. E. Ooi, B. Godwin, E. Vitols, G. Vijayadamodar, P. Pochart, H. Machineni, M. Welsh, Y. Kong, B. Zerhusen, R. Malcolm, Z. Varrone, A. Collis, M. Minto, S. Burgess, L. Mcdaniel, E. Stimpson, F. Spriggs, J. Williams, K. Neurath, N. Ioime, M. Agee, E. Voss, K. Furtak, R. Renzulli, N. Aanensen, S. Carrolla, E. Bickelhaupt, Y. Lazovatsky, A. Dasilva, J. Zhong, C. A. Stanyon, Jr R. L. Finley, K. P. White, M. Braverman, T. Jarvie, S. Gold, M. Leach, J. Knight, R. A. Shimkets, M. P. Mckenna, J. Chant, J. M. Rothberg posted to dataset protein-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	A comprehensive two-hybrid analysis to explore the yeast protein interactome. [My Copy] Proc Natl Acad Sci U S A, Vol. 98, No. 8. (2001), pp. 4569-74. by T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, Y. Sakaki posted to dataset protein-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	A map of the interactome network of the metazoan C. elegans. [My Copy] Science, Vol. 303, No. 5657. (2004), pp. 540-3. by Siming Li, Christopher M. Armstrong, Nicolas Bertin, et al.Hui Ge, Stuart Milstein, Mike Boxem, Pierre O. Vidalain, Jing, Alban Chesneau, Tong Hao, Debra S. Goldberg, Ning Li, Monica Martinez, Jean F. Rual, Philippe Lamesch, Lai Xu, Muneesh Tewari, Sharyl L. Wong, Lan V. Zhang, Gabriel F. Berriz, Laurent Jacotot, Philippe Vaglio, Jerome Reboul, Tomoko H. Kishikawa, Qianru Li, Harrison W. Gabel, Ahmed Elewa, Bridget Baumgartner, Debra J. Rose, Haiyuan Yu, Stephanie Bosak, Reynaldo Sequerra, Andrew Fraser, Susan E. Mango, William M. Saxton, Susan Strome, Sander Van Den Heuvel, Fabio Piano, Jean Vandenhaute, Claude Sardet, Mark Gerstein, Lynn D. Stamm, Kristin C. Gunsalus, Wade J. Harper, Michael E. Cusick, Frederick P. Roth, David E. Hill, Marc Vidal posted to dataset protein-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	Towards a proteome-scale map of the human protein-protein interaction network. [My Copy] Nature, Vol. 437, No. 7062. (2005), pp. 1173-8. by Jean F. Rual, Kavitha Venkatesan, Tong Hao, et al.Tomoko H. Kishikawa, Amelie Dricot, Ning Li, Gabriel F. Berriz, Francis D. Gibbons, Matija Dreze, Nono A. Guedehoussou, Niels Klitgord, Christophe Simon, Mike Boxem, Stuart Milstein, Jennifer Rosenberg, Debra S. Goldberg, Lan V. Zhang, Sharyl L. Wong, Giovanni Franklin, Siming Li, Joanna S. Albala, Janghoo Lim, Carlene Fraughton, Estelle Llamosas, Sebiha Cevik, Camille Bex, Philippe Lamesch, Robert S. Sikorski, Jean Vandenhaute, Huda Y. Zoghbi, Alex Smolyar, Stephanie Bosak, Reynaldo Sequerra, Lynn D. Stamm, Michael E. Cusick, David E. Hill, Frederick P. Roth, Marc Vidal posted to dataset protein-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	A network of protein-protein interactions in yeast. [My Copy] Nat Biotechnol, Vol. 18, No. 12. (2000), pp. 1257-61. by B. Schwikowski, P. Uetz, S. Fields posted to dataset protein-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	A human protein-protein interaction network: a resource for annotating the proteome. [My Copy] Cell, Vol. 122, No. 6. (2005), pp. 957-68. by Ulrich Stelzl, Uwe Worm, Maciej Lalowski, et al.Christian Haenig, Felix H. Brembeck, Heike Goehler, Martin Stroedicke, Martina Zenkner, Anke Schoenherr, Susanne Koeppen, Jan Timm, Sascha Mintzlaff, Claudia Abraham, Nicole Bock, Silvia Kietzmann, Astrid Goedde, Engin Toksoz, Anja Droege, Sylvia Krobitsch, Bernhard Korn, Walter Birchmeier, Hans Lehrach, Erich E. Wanker posted to dataset protein-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. [My Copy] Nature, Vol. 403, No. 6770. (2000), pp. 623-7. by P. Uetz, L. Giot, G. Cagney, et al.T. A. Mansfield, R. S. Judson, J. R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, Qureshi A. Emili, Y. Li, B. Godwin, D. Conover, T. Kalbfleisch, G. Vijayadamodar, M. Yang, M. Johnston, S. Fields, J. M. Rothberg posted to dataset protein-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	hp-DPI: Helicobacter pylori database of protein interactomes--embracing experimental and inferred interactions. [My Copy] Bioinformatics, Vol. 21, No. 7. (2005), pp. 1288-90. by Chung Y. Lin, Chia L. Chen, Chi S. Cho, et al.Li M. Wang, Chia M. Chang, Pao Y. Chen, Chen Z. Lo, Chao A. Hsiung posted to database dataset protein-networks by AurelienMazurie on 2008-09-12 13:12:28 as
	Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. [My Copy] Bioinformatics, Vol. 19, No. 2. (2003), pp. 270-7. by Hong W. Ma, An P. Zeng posted to cross-species database dataset metabolic-networks quality topology by AurelienMazurie on 2008-09-12 13:12:27 as
	Hierarchical organization of modularity in metabolic networks. [My Copy] Science, Vol. 297, No. 5586. (2002), pp. 1551-5. by E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, A. L. Barabasi posted to metabolic-networks modules topology by AurelienMazurie on 2008-09-12 13:12:27 as
	Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. [My Copy] Trends Biochem Sci, Vol. 29, No. 12. (2004), pp. 641-7. by Jason A. Papin, Jennifer L. Reed, Bernhard O. Palsson posted to elementary-modes extreme-pathways metabolic-networks modules by AurelienMazurie on 2008-09-12 13:12:27 as
	Emergence of scaling in random networks [My Copy] Science, Vol. 286, No. 5439. (1999), pp. 509-12. by A. L. Barabasi, R. Albert posted to evolution networks preferential-attachment scale-free topology by AurelienMazurie on 2008-09-12 13:12:27 as
	Graph Theory [My Copy] (1969) by Frank Harary posted to graph-theory topology by AurelienMazurie on 2008-09-12 13:12:27 as
	The Development of Social Network Analysis: A Study in the Sociology of Science [My Copy] (2004) by L. C. Freeman posted to graph-theory topology by AurelienMazurie on 2008-09-12 13:12:27 as
	Graph Theory and Its Applications [My Copy] (2005) by J. L. Gross, J. Yellen posted to graph-theory topology by AurelienMazurie on 2008-09-12 13:12:27 as
	Chemical Reaction Networks: A Graph-Theoretical Approach [My Copy] (1996) by O. N. Temkin, A. V. Zeigarnik, D. G. Bonchev posted to graph-theory topology by AurelienMazurie on 2008-09-12 13:12:27 as
	Topology in Chemistry: Discrete Mathematics of Molecules [My Copy] (2002) by Bruce King, Dennis Rouvray posted to graph-theory topology by AurelienMazurie on 2008-09-12 13:12:27 as
	Network motifs: simple building blocks of complex networks. [My Copy] Science, Vol. 298, No. 5594. (2002), pp. 824-7. by R. Milo, Shen S. Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon posted to modules motifs networks by AurelienMazurie on 2008-09-12 13:12:27 as
	Spontaneous evolution of modularity and network motifs. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 39. (2005), pp. 13773-8. by Nadav Kashtan, Uri Alon posted to evolution modules motifs networks by AurelienMazurie on 2008-09-12 13:12:27 as
	Are network motifs the spandrels of cellular complexity? [My Copy] Trends Ecol Evol, No. 0169-5347 (Print). (2006) by R. V. Sole, S. Valverde posted to modules motifs networks by AurelienMazurie on 2008-09-12 13:12:27 as
	Global transposon mutagenesis and essential gene analysis of Helicobacter pylori. [My Copy] J Bacteriol, Vol. 186, No. 23. (2004), pp. 7926-35. by Nina R. Salama, Benjamin Shepherd, Stanley Falkow posted to essentiality by AurelienMazurie on 2008-09-12 13:12:27 as
	Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. [My Copy] J Bacteriol, Vol. 187, No. 16. (2005), pp. 5818-30. by Ines Thiele, Thuy D. Vo, Nathan D. Price, Bernhard O. Palsson posted to dataset essentiality flux-balance-analysis metabolic-networks by AurelienMazurie on 2008-09-12 13:12:27 as
	Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. [My Copy] Bioinformatics, Vol. 21, No. 24. (2005), pp. 4401-7. by Lena Stromback, Patrick Lambrix posted to networks representation by AurelienMazurie on 2008-09-12 13:12:27 as
	The Database of Interacting Proteins: 2004 update. [My Copy] Nucleic Acids Res, Vol. 32, No. Database issue. (2004), pp. D449-51. by Lukasz Salwinski, Christopher S. Miller, Adam J. Smith, Frank K. Pettit, James U. Bowie, David Eisenberg posted to database dataset protein-networks by AurelienMazurie on 2008-09-12 13:12:27 as

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modules	119
protein-networks	97
algorithm	71
metabolic-networks	64
networks	63
gene-networks	59
topology	53
motifs	41
evolution	38
dataset	37
quality	30
essentiality	24
flux-balance-analysis	20
scale-free	19
dynamics	17
graph-theory	13
expression	13
review	12
small-world	10
comparison	8
representation	7
cross-species	7
signaling-networks	6
robustness	5
complexes	4
database	4
regulatory-networks	4
hubs	4
extreme-pathways	3
preferential-attachment	3
inference	3
relation-networks	2
feed-forward-loop	2
randomization	2
software	2
simulation	2
elementary-modes	2
minimization-of-metabolic-adjustment	2
models	1
glucosegeneticsmetabolism	1
genetic	1
humans	1
glycolysisgenetics	1
prediction	1
metabolismgenetics	1
entropy	1
signal-transductiongenetics	1
phylogeny	1
animals	1
adaptation	1
annotation	1
protein-biosynthesisgenetics	1
score	1
molecular	1
noise	1
constraints	1
genetic-interactions	1
lethality	1
computer-simulation	1
physiologicalgenetics	1
variation-geneticsgenetics	1
function	1
species-specificity	1

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