-
2
-
-
3242675407
-
Glutathione-S-transferase-fusion based assays for studying protein-protein interactions
-
Glutathione-S-transferase-fusion based assays for studying protein-protein interactions. HG Vikis KL Guan, Methods Mol Biol 2004 261 175 186
-
(2004)
Methods Mol Biol
, vol.261
, pp. 175-186
-
-
Vikis, H.G.1
Guan, K.L.2
-
3
-
-
0034841844
-
The tandem affinity purification (TAP) method: A general procedure of protein complex purification
-
DOI 10.1006/meth.2001.1183
-
The tandem affinity purification (TAP) method: a general procedure of protein complex purification. O Puig F Caspary G Rigaut B Rutz E Bouveret E Bragado-Nilsson M Wilm B Seraphin, Methods 2001 24 3 218 229 (Pubitemid 32846428)
-
(2001)
Methods
, vol.24
, Issue.3
, pp. 218-229
-
-
Puig, O.1
Caspary, F.2
Rigaut, G.3
Rutz, B.4
Bouveret, E.5
Bragado-Nilsson, E.6
Wilm, M.7
Seraphin, B.8
-
4
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
DOI 10.1073/pnas.061034498
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome. T Ito T Chiba R Ozawa M Yoshida M Hattori Y Sakaki, Proc Natl Acad Sci USA 2001 98 8 4569 4574 (Pubitemid 32295017)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.8
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
5
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
DOI 10.1038/415141a
-
Functional organization of the yeast proteome by systematic analysis of protein complexes. AC Gavin M Bosche R Krause P Grandi M Marzioch A Bauer J Schultz JM Rick AM Michon CM Cruciat,, et al. Nature 2002 415 6868 141 147 (Pubitemid 34059510)
-
(2002)
Nature
, vol.415
, Issue.6868
, pp. 141-147
-
-
Gavin, A.-C.1
Bosche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
Bauer, A.6
Schultz, J.7
Rick, J.M.8
Michon, A.-M.9
Cruciat, C.-M.10
Remor, M.11
Hofert, C.12
Schelder, M.13
Brajenovic, M.14
Ruffner, H.15
Merino, A.16
Klein, K.17
Hudak, M.18
Dickson, D.19
Rudi, T.20
Gnau, V.21
Bauch, A.22
Bastuck, S.23
Huhse, B.24
Leutwein, C.25
Heurtier, M.-A.26
Copley, R.R.27
Edelmann, A.28
Querfurth, E.29
Rybin, V.30
Drewes, G.31
Raida, M.32
Bouwmeester, T.33
Bork, P.34
Seraphin, B.35
Kuster, B.36
Neubauer, G.37
Superti-Furga, G.38
more..
-
7
-
-
0036921994
-
Phage display: Practicalities and prospects
-
DOI 10.1023/A:1021215516430
-
Phage display: practicalities and prospects. WG Willats, Plant Mol Biol 2002 50 6 837 854 (Pubitemid 36034980)
-
(2002)
Plant Molecular Biology
, vol.50
, Issue.6
, pp. 837-854
-
-
Willats, W.G.T.1
-
8
-
-
10744230485
-
Global Mapping of the Yeast Genetic Interaction Network
-
DOI 10.1126/science.1091317
-
Global mapping of the yeast genetic interaction network. AH Tong G Lesage GD Bader H Ding H Xu X Xin J Young GF Berriz RL Brost M Chang,, et al. Science 2004 303 5659 808 813 (Pubitemid 38174652)
-
(2004)
Science
, vol.303
, Issue.5659
, pp. 808-813
-
-
Tong, A.H.Y.1
Lesage, G.2
Bader, G.D.3
Ding, H.4
Xu, H.5
Xin, X.6
Young, J.7
Berriz, G.F.8
Brost, R.L.9
Chang, M.10
Chen, Y.11
Cheng, X.12
Chua, G.13
Friesen, H.14
Goldberg, D.S.15
Haynes, J.16
Humphries, C.17
He, G.18
Hussein, S.19
Ke, L.20
Krogan, N.21
Li, Z.22
Levinson, J.N.23
Lu, H.24
Menard, P.25
Munyana, C.26
Parsons, A.B.27
Ryan, O.28
Tonikian, R.29
Roberts, T.30
Sdicu, A.-M.31
Shapiro, J.32
Sheikh, B.33
Suter, B.34
Wong, S.L.35
Zhang, L.V.36
Zhu, H.37
Burd, C.G.38
Munro, S.39
Sander, C.40
Rine, J.41
Greenblatt, J.42
Peter, M.43
Bretscher, A.44
Bell, G.45
Roth, F.P.46
Brown, G.W.47
Andrews, B.48
Bussey, H.49
Boone, C.50
more..
-
9
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. NJ Krogan G Cagney H Yu G Zhong X Guo A Ignatchenko J Li S Pu N Datta AP Tikuisis,, et al. Nature 2006 440 7084 637 643
-
(2006)
Nature
, vol.440
, Issue.7084
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
Ignatchenko, A.6
Li, J.7
Pu, S.8
Datta, N.9
Tikuisis, A.P.10
-
10
-
-
0033971642
-
DIP: The Database of Interacting Proteins
-
DIP: the database of interacting proteins. I Xenarios DW Rice L Salwinski MK Baron EM Marcotte D Eisenberg, Nucleic Acids Res 2000 28 1 289 291 (Pubitemid 30047782)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 289-291
-
-
Xenarios, I.1
Rice, D.W.2
Salwinski, L.3
Baron, M.K.4
Marcotte, E.M.5
Eisenberg, D.6
-
11
-
-
33644875537
-
MIPS: Analysis and annotation of proteins from whole genomes in 2005
-
MIPS: analysis and annotation of proteins from whole genomes in 2005. HW Mewes D Frishman KF Mayer M Munsterkotter O Noubibou P Pagel T Rattei M Oesterheld A Ruepp V Stumpflen, Nucleic Acids Res 2006 34 Database 169 172
-
(2006)
Nucleic Acids Res
, Issue.34 DATABASE
, pp. 4169-172
-
-
Mewes, H.W.1
Frishman, D.2
Mayer, K.F.3
Munsterkotter, M.4
Noubibou, O.5
Pagel, P.6
Rattei, T.7
Oesterheld, M.8
Ruepp, A.9
Stumpflen, V.10
-
12
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Proteome survey reveals modularity of the yeast cell machinery. AC Gavin P Aloy P Grandi R Krause M Boesche M Marzioch C Rau LJ Jensen S Bastuck B Dumpelfeld,, et al. Nature 2006 440 7084 631 636
-
(2006)
Nature
, vol.440
, Issue.7084
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
Marzioch, M.6
Rau, C.7
Jensen, L.J.8
Bastuck, S.9
Dumpelfeld, B.10
-
13
-
-
0032894060
-
The Yeast Proteome Database (YPD): A model for the organization and presentation of genome-wide functional data
-
DOI 10.1093/nar/27.1.69
-
The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. PE Hodges AH McKee BP Davis WE Payne JI Garrels, Nucleic Acids Res 1999 27 1 69 73 (Pubitemid 29209404)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.1
, pp. 69-73
-
-
Hodges, P.E.1
McKee, A.H.Z.2
Davis, B.P.3
Payne, W.E.4
Garrels, J.I.5
-
14
-
-
9144242935
-
MIPS: Analysis and annotation of proteins from whole genomes
-
MIPS: analysis and annotation of proteins from whole genomes. HW Mewes C Amid R Arnold D Frishman U Guldener G Mannhaupt M Munsterkotter P Pagel N Strack V Stumpflen,, et al. Nucleic Acids Res 2004 32 Database 41 44
-
(2004)
Nucleic Acids Res
, Issue.32 DATABASE
, pp. 441-44
-
-
Mewes, H.W.1
Amid, C.2
Arnold, R.3
Frishman, D.4
Guldener, U.5
Mannhaupt, G.6
Munsterkotter, M.7
Pagel, P.8
Strack, N.9
Stumpflen, V.10
-
15
-
-
0037138406
-
MINT: A Molecular INTeraction database
-
DOI 10.1016/S0014-5793(01)03293-8, PII S0014579301032938
-
MINT: a Molecular INTeraction database. A Zanzoni L Montecchi-Palazzi M Quondam G Ausiello M Helmer-Citterich G Cesareni, FEBS Lett 2002 513 1 135 140 (Pubitemid 34242991)
-
(2002)
FEBS Letters
, vol.513
, Issue.1
, pp. 135-140
-
-
Zanzoni, A.1
Montecchi-Palazzi, L.2
Quondam, M.3
Ausiello, G.4
Helmer-Citterich, M.5
Cesareni, G.6
-
16
-
-
33846047770
-
IntAct - Open source resource for molecular interaction data
-
IntAct - open source resource for molecular interaction data. S Kerrien Y Alam-Faruque B Aranda I Bancarz A Bridge C Derow E Dimmer M Feuermann A Friedrichsen R Huntley,, et al. Nucleic Acids Res 2007 35 Database 561 565
-
(2007)
Nucleic Acids Res
, Issue.35 DATABASE
, pp. 4561-565
-
-
Kerrien, S.1
Alam-Faruque, Y.2
Aranda, B.3
Bancarz, I.4
Bridge, A.5
Derow, C.6
Dimmer, E.7
Feuermann, M.8
Friedrichsen, A.9
Huntley, R.10
-
17
-
-
0035171884
-
BIND - The Biomolecular Interaction Network Database
-
BIND - The Biomolecular Interaction Network Database. GD Bader I Donaldson C Wolting BF Ouellette T Pawson CW Hogue, Nucleic Acids Res 2001 29 1 242 245 (Pubitemid 32054459)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.1
, pp. 242-245
-
-
Bader, G.D.1
Donaldson, I.2
Wolting, C.3
Ouellette, B.F.F.4
Pawson, T.5
Hogue, C.W.V.6
-
19
-
-
58149193222
-
Human Protein Reference Database - 2009 update
-
Human Protein Reference Database - 2009 update. TS Keshava Prasad R Goel K Kandasamy S Keerthikumar S Kumar S Mathivanan D Telikicherla R Raju B Shafreen A Venugopal,, et al. Nucleic Acids Res 2009 37 Database 767 772
-
(2009)
Nucleic Acids Res
, Issue.37 DATABASE
, pp. 4767-772
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
Keerthikumar, S.4
Kumar, S.5
Mathivanan, S.6
Telikicherla, D.7
Raju, R.8
Shafreen, B.9
Venugopal, A.10
-
20
-
-
7244254458
-
HPID: The human protein interaction
-
DOI 10.1093/bioinformatics/bth253
-
HPID: the Human Protein Interaction Database. K Han B Park H Kim J Hong J Park, Bioinformatics 2004 20 15 2466 2470 (Pubitemid 39429921)
-
(2004)
Bioinformatics
, vol.20
, Issue.15
, pp. 2466-2470
-
-
Han, K.1
Park, B.2
Kim, H.3
Hong, J.4
Park, J.5
-
21
-
-
54949120007
-
DroID: The Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions
-
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. J Yu S Pacifico G Liu RL Finley Jr, BMC Genomics 2008 9 461
-
(2008)
BMC Genomics
, vol.9
, pp. 461
-
-
Yu, J.1
Pacifico, S.2
Liu, G.3
Finley Jr., R.L.4
-
23
-
-
58149193234
-
STRING 8 - A global view on proteins and their functional interactions in 630 organisms
-
STRING 8 - a global view on proteins and their functional interactions in 630 organisms. LJ Jensen M Kuhn M Stark S Chaffron C Creevey J Muller T Doerks P Julien A Roth M Simonovic,, et al. Nucleic Acids Res 2009 37 Database 412 416
-
(2009)
Nucleic Acids Res
, Issue.37 DATABASE
, pp. 4412-416
-
-
Jensen, L.J.1
Kuhn, M.2
Stark, M.3
Chaffron, S.4
Creevey, C.5
Muller, J.6
Doerks, T.7
Julien, P.8
Roth, A.9
Simonovic, M.10
-
24
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
The transcriptional landscape of the mammalian genome. Carninci Pea, Science 2005 309 1559 1563
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Pea, C.1
-
25
-
-
38549109487
-
NetworKIN: A resource for exploring cellular phosphorylation networks
-
NetworKIN: a resource for exploring cellular phosphorylation networks. Linding Rea, Nucleid Acids Res 2008 36 695 D699
-
(2008)
Nucleid Acids Res
, vol.36
-
-
Rea, L.1
-
26
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
DOI 10.1126/science.1075090
-
Transcriptional regulatory networks in Saccharomyces cerevisiae. TI Lee NJ Rinaldi F Robert DT Odom Z Bar-Joseph GK Gerber NM Hannett CT Harbison CM Thompson I Simon,, et al. Science 2002 298 5594 799 804 (Pubitemid 35231527)
-
(2002)
Science
, vol.298
, Issue.5594
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Benjamin Gordon, D.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.-B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
Young, R.A.21
more..
-
28
-
-
0029960055
-
TRANSFAC: A database on transcription factors and their DNA binding sites
-
DOI 10.1093/nar/24.1.238
-
TRANSFAC: a database on transcription factors and their DNA binding sites. E Wingender P Dietze H Karas R Knuppel, Nucleic Acids Res 1996 24 1 238 241 (Pubitemid 26085775)
-
(1996)
Nucleic Acids Research
, vol.24
, Issue.1
, pp. 238-241
-
-
Wingender, E.1
Dietze, P.2
Karas, H.3
Knuppel, R.4
-
29
-
-
0037208166
-
TRANSFAC®: Transcriptional regulation, from patterns to profiles
-
DOI 10.1093/nar/gkg108
-
TRANSFAC: transcriptional regulation, from patterns to profiles. V Matys E Fricke R Geffers E Gossling M Haubrock R Hehl K Hornischer D Karas AE Kel OV Kel-Margoulis,, et al. Nucleic Acids Res 2003 31 1 374 378 (Pubitemid 36150406)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gossling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.E.9
Kel-Margoulis, O.V.10
Kloos, D.-U.11
Land, S.12
Lewicki-Potapov, B.13
Michael, H.14
Munch, R.15
Reuter, I.16
Rotert, S.17
Saxel, H.18
Scheer, M.19
Thiele, S.20
Wingender, E.21
more..
-
31
-
-
13244289881
-
Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins
-
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. FCS Diella C Gemünd R Linding A Via B Kuster T Sicheritz-Pontén N Blom TJ Gibson, BMC Bioinformatics 2004 5
-
(2004)
BMC Bioinformatics
, vol.5
-
-
Diella, F.C.S.1
Gemünd, C.2
Linding, R.3
Via, A.4
Kuster, B.5
Sicheritz-Pontén, T.6
Blom, N.7
Gibson, T.J.8
-
32
-
-
55749111058
-
Linear motif atlas for phosphorylation-dependent signaling
-
Linear motif atlas for phosphorylation-dependent signaling. ML Miller,, et al. Sci Signal 2008 1 35
-
(2008)
Sci Signal
, vol.1
, Issue.35
-
-
Miller, M.L.1
-
33
-
-
44149105911
-
PHOSIDA (phosphorylation site database): Management, structural and evolutionary investigation, and prediction of phosphosites
-
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. F Gnad S Ren J Cox JV Olsen B Macek M Oroshi M Mann, Genome Biol 2007 8 11
-
(2007)
Genome Biol
, vol.8
, Issue.11
-
-
Gnad, F.1
Ren, S.2
Cox, J.3
Olsen, J.V.4
MacEk, B.5
Oroshi, M.6
Mann, M.7
-
35
-
-
33846090559
-
MiST: A microbial signal transduction database
-
MiST: a microbial signal transduction database. LE Ulrich IB Z, Nucleic Acids Res 2007 35 386 390
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 4386-390
-
-
Ulrich, L.E.1
Z, I.B.2
-
36
-
-
0037208158
-
TRANSPATH®: An integrated database on signal transduction and a tool for array analysis
-
DOI 10.1093/nar/gkg089
-
TRANSPATH: an integrated database on signal transduction and a tool for array analysis. M Krull N Voss C Choi S Pistor A Potapov E Wingender, Nucleic Acids Res 2003 31 1 97 100 (Pubitemid 36150343)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 97-100
-
-
Krull, M.1
Voss, N.2
Choi, C.3
Pistor, S.4
Potapov, A.5
Wingender, E.6
-
37
-
-
0034609791
-
The large-scale organization of metabolic networks
-
The large-scale organization of metabolic networks. H B Jeong R Tombor ZN Albert AL Oltvai, Nature 2000 407 651 654
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, B.1
Tombor, R.2
Albert, Z.N.3
Oltvai, A.L.4
-
40
-
-
75549090213
-
KEGG for representation and analysis of molecular networks involving diseases and drugs
-
KEGG for representation and analysis of molecular networks involving diseases and drugs. M Kanehisa S Goto M Furumichi M Tanabe M Hirakawa, Nucleic Acids Res 38 Database 355 360
-
Nucleic Acids Res
, Issue.38 DATABASE
, pp. 4355-360
-
-
Kanehisa, M.1
Goto, S.2
Furumichi, M.3
Tanabe, M.4
Hirakawa, M.5
-
41
-
-
58149179979
-
EcoCyc: A comprehensive view of Escherichia coli biology
-
EcoCyc: a comprehensive view of Escherichia coli biology. IM Keseler C Bonavides-Martinez J Collado-Vides S Gama-Castro RP Gunsalus DA Johnson M Krummenacker LM Nolan S Paley IT Paulsen,, et al. Nucleic Acids Res 2009 37 Database 464 470
-
(2009)
Nucleic Acids Res
, Issue.37 DATABASE
, pp. 4464-470
-
-
Keseler, I.M.1
Bonavides-Martinez, C.2
Collado-Vides, J.3
Gama-Castro, S.4
Gunsalus, R.P.5
Johnson, D.A.6
Krummenacker, M.7
Nolan, L.M.8
Paley, S.9
Paulsen, I.T.10
-
42
-
-
27244436714
-
Expansion of the Biocyc collection of pathway/genome databases to 160 genomes
-
DOI 10.1093/nar/gki892
-
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. PD Karp CA Ouzounis C Moore-Kochlacs L Goldovsky P Kaipa D Ahren S Tsoka N Darzentas V Kunin N Lopez-Bigas, Nucleic Acids Res 2005 33 19 6083 6089 (Pubitemid 41742547)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.19
, pp. 6083-6089
-
-
Karp, P.D.1
Ouzounis, C.A.2
Moore-Kochlacs, C.3
Goldovsky, L.4
Kaipa, P.5
Ahren, D.6
Tsoka, S.7
Darzentas, N.8
Kunin, V.9
Lopez-Bigas, N.10
-
44
-
-
0034615791
-
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
-
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. CH Schilling D Letscher BO Palsson, J Theor Biol 2000 203 3 229 248
-
(2000)
J Theor Biol
, vol.203
, Issue.3
, pp. 229-248
-
-
Schilling, C.H.1
Letscher, D.2
Palsson, B.O.3
-
45
-
-
0034615788
-
Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis
-
Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. CH Schilling BO Palsson, J Theor Biol 2000 203 3 249 283
-
(2000)
J Theor Biol
, vol.203
, Issue.3
, pp. 249-283
-
-
Schilling, C.H.1
Palsson, B.O.2
-
46
-
-
0033136109
-
Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era
-
DOI 10.1021/bp990048k
-
Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. CH Schilling S Schuster BO Palsson R Heinrich, Biotechnol Prog 1999 15 3 296 303 (Pubitemid 29270673)
-
(1999)
Biotechnology Progress
, vol.15
, Issue.3
, pp. 296-303
-
-
Schilling, C.H.1
Schuster, S.2
Palsson, B.O.3
Heinrich, R.4
-
47
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
-
DOI 10.1038/73786
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. S Schuster DA Fell T Dandekar, Nat Biotechnol 2000 18 3 326 332 (Pubitemid 30159487)
-
(2000)
Nature Biotechnology
, vol.18
, Issue.3
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
48
-
-
0033080396
-
Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
-
DOI 10.1016/S0167-7799(98)01290-6, PII S0167779998012906
-
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. S Schuster T Dandekar DA Fell, Trends Biotechnol 1999 17 2 53 60 (Pubitemid 29332898)
-
(1999)
Trends in Biotechnology
, vol.17
, Issue.2
, pp. 53-60
-
-
Schuster, S.1
Dandekar, T.2
Fell, D.A.3
-
49
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
DOI 10.1093/bioinformatics/btg015
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. M Hucka A Finney HM Sauro H Bolouri JC Doyle H Kitano AP Arkin BJ Bornstein D Bray A Cornish-Bowden,, et al. Bioinformatics 2003 19 4 524 531 (Pubitemid 36336519)
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
Cuellar, A.A.11
Dronov, S.12
Gilles, E.D.13
Ginkel, M.14
Gor, V.15
Goryanin, I.I.16
Hedley, W.J.17
Hodgman, T.C.18
Hofmeyr, J.-H.19
Hunter, P.J.20
Juty, N.S.21
Kasberger, J.L.22
Kremling, A.23
Kummer, U.24
Le Novere, N.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
Nakayama, Y.31
Nelson, M.R.32
Nielsen, P.F.33
Sakurada, T.34
Schaff, J.C.35
Shapiro, B.E.36
Shimizu, T.S.37
Spence, H.D.38
Stelling, J.39
Takahashi, K.40
Tomita, M.41
Wagner, J.42
Wang, J.43
more..
-
50
-
-
0348049802
-
Systems biology markup language: Level 2 and beyond
-
Systems biology markup language: Level 2 and beyond. A Finney M Hucka, Biochemical Society transactions 2003 31 Pt 6 1472 1473 (Pubitemid 38031003)
-
(2003)
Biochemical Society Transactions
, vol.31
, Issue.6
, pp. 1472-1473
-
-
Finney, A.1
Hucka, M.2
-
51
-
-
0742323374
-
The HUPO PSI's Molecular Interaction format - A community standard for the representation of protein interaction data
-
DOI 10.1038/nbt926
-
The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. H Hermjakob L Montecchi-Palazzi G Bader J Wojcik L Salwinski A Ceol S Moore S Orchard U Sarkans C von Mering,, et al. Nat Biotechnol 2004 22 2 177 183 (Pubitemid 38160532)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.2
, pp. 177-183
-
-
Hermjakob, H.1
Montecchi-Palazzi, L.2
Bader, G.3
Wojcik, J.4
Salwinski, L.5
Ceol, A.6
Moore, S.7
Orchard, S.8
Sarkans, U.9
Von Mering, C.10
Roechert, B.11
Poux, S.12
Jung, E.13
Mersch, H.14
Kersey, P.15
Lappe, M.16
Li, Y.17
Zeng, R.18
Rana, D.19
Nikolski, M.20
Husi, H.21
Brun, C.22
Shanker, K.23
Grant, S.G.N.24
Sander, C.25
Bork, P.26
Zhu, W.27
Pandey, A.28
Brazma, A.29
Jacq, B.30
Vidal, M.31
Sherman, D.32
Legrain, P.33
Cesareni, G.34
Xenarios, I.35
Eisenberg, D.36
Steipe, B.37
Hogue, C.38
Apweiler, R.39
more..
-
52
-
-
0000554921
-
Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles
-
Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles. RP Murray RH S, Chem Inf Comput Sci 1999 39 928 942
-
(1999)
Chem Inf Comput Sci
, vol.39
, pp. 928-942
-
-
Murray, R.P.1
S, R.H.2
-
53
-
-
0035013293
-
Development of chemical markup language (CML) as a system for handling complex chemical content
-
DOI 10.1039/b008780g
-
Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content. P Murray-Rust HS Rzepa M Wright, New J Chem 2001 618 634 (Pubitemid 32523097)
-
(2001)
New Journal of Chemistry
, vol.25
, Issue.4
, pp. 618-634
-
-
Murray-Rust, P.1
Rzepa, H.S.2
Wright, M.3
-
55
-
-
2442595958
-
CellML: Its future, present and past
-
DOI 10.1016/j.pbiomolbio.2004.01.004, PII S007961070400015X
-
CellML: its future, present and past. CM Lloyd MD Halstead PF Nielsen, Progress in biophysics and molecular biology 2004 85 2-3 433 450 (Pubitemid 38629921)
-
(2004)
Progress in Biophysics and Molecular Biology
, vol.85
, Issue.2-3
, pp. 433-450
-
-
Lloyd, C.M.1
Halstead, M.D.B.2
Nielsen, P.F.3
-
60
-
-
3042514191
-
Coexpresion analysis of human genes across many microarray data sets
-
DOI 10.1101/gr.1910904
-
Coexpression analysis of human genes across many microarray data sets. HK Lee AK Hsu J Sajdak J Qin P Pavlidis, Genome Res 2004 14 6 1085 1094 (Pubitemid 38811545)
-
(2004)
Genome Research
, vol.14
, Issue.6
, pp. 1085-1094
-
-
Lee, H.K.1
Hsu, A.K.2
Sajdak, J.3
Qin, J.4
Pavlidis, P.5
-
64
-
-
49449086368
-
Survival of the sparsest: Robust gene networks are parsimonious
-
Survival of the sparsest: robust gene networks are parsimonious. RD Leclerc, Mol Syst Biol 2008 4 213
-
(2008)
Mol Syst Biol
, vol.4
, pp. 213
-
-
Leclerc, R.D.1
-
65
-
-
34147120474
-
A note on two problems in connexion with graphs
-
A note on two problems in connexion with graphs. EW Dijkstra, Numerische Mathematik 1959 1 269 271
-
(1959)
Numerische Mathematik
, vol.1
, pp. 269-271
-
-
Dijkstra, E.W.1
-
66
-
-
84945709831
-
Algorithm 97
-
Algorithm 97. RW Floyd, Comm ACM 1962 5-6 345
-
(1962)
Comm ACM
, vol.56
, pp. 345
-
-
Floyd, R.W.1
-
67
-
-
84976668743
-
Algorithm 457: Finding all cliques of an undirected graph
-
Algorithm 457: finding all cliques of an undirected graph. C Bron J Kerbosch, Commun ACM (ACM) 1973 16 9 575 577
-
(1973)
Commun ACM (ACM)
, vol.16
, Issue.9
, pp. 575-577
-
-
Bron, C.1
Kerbosch, J.2
-
69
-
-
33746617003
-
Extracting Gene Networks for Low-Dose Radiation Using Graph Theoretical Algorithms
-
Extracting Gene Networks for Low-Dose Radiation Using Graph Theoretical Algorithms. BH Voy JA Scharff AD Perkins AM Saxton B Borate EJ Chesler LK Branstetter MA Langston, PLoS Comput Biol 2006 2 7
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.7
-
-
Voy, B.H.1
Scharff, J.A.2
Perkins, A.D.3
Saxton, A.M.4
Borate, B.5
Chesler, E.J.6
Branstetter, L.K.7
Langston, M.A.8
-
70
-
-
33747814803
-
Arabidopsis Co-expression Tool (ACT): Web server tools for microarray-based gene expression analysis
-
Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. IW Manfield CH Jen JW Pinney I Michalopoulos JR Bradford PM Gilmartin DR Westhead, Nucleic Acids Res 2006 34 Web Server 504 509
-
(2006)
Nucleic Acids Res
, Issue.34 WEB SERVER
, pp. 23504-509
-
-
Manfield, I.W.1
Jen, C.H.2
Pinney, J.W.3
Michalopoulos, I.4
Bradford, J.R.5
Gilmartin, P.M.6
Westhead, D.R.7
-
71
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Bioconductor: open software development for computational biology and bioinformatics. RC Gentleman VJ Carey DM Bates B Bolstad M Dettling S Dudoit B Ellis L Gautier Y Ge J Gentry,, et al. Genome biology 2004 5 10 80
-
(2004)
Genome Biology
, vol.5
, Issue.10
, pp. 1880
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
-
72
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
DOI 10.1126/science.1073374
-
Hierarchical organization of modularity in metabolic networks. E Ravasz A Somera D Mongru Z Oltvai A-L Barabsi, Science 2002 297 1551 1555 (Pubitemid 34971002)
-
(2002)
Science
, vol.297
, Issue.5586
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.-L.5
-
74
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
DOI 10.1126/science.298.5594.824
-
Network motifs: simple building blocks of complex networks. R Milo S Shen-Orr S Itzkovitz N Kashtan D Chklovskii U Alon, Science 2002 298 5594 824 827 (Pubitemid 35231534)
-
(2002)
Science
, vol.298
, Issue.5594
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
75
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Network motifs in the transcriptional regulation network of Escherichia coli. S Shen-Orr R Milo S Mangan U Alon, Nat Genet 2002 31 64 68
-
(2002)
Nat Genet
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
76
-
-
33745780500
-
Network motifs: Structure does not determine function
-
Network motifs: structure does not determine function. PJ Ingram MP Stumpf J Stark, BMC Genomics 2006 7 108
-
(2006)
BMC Genomics
, vol.7
, pp. 108
-
-
Ingram, P.J.1
Stumpf, M.P.2
Stark, J.3
-
77
-
-
50949092459
-
Why do hubs in the yeast protein interaction network tend to be essential: Re-examining the connection between the network topology and essentiality
-
Why do hubs in the yeast protein interaction network tend to be essential: re-examining the connection between the network topology and essentiality. E Zotenko J Mestre DP O'Leary TM Przytycka, PLoS Comput Biol 2008 4 1 16
-
(2008)
PLoS Comput Biol
, vol.4
, pp. 1-16
-
-
Zotenko, E.1
Mestre, J.2
O'Leary, D.P.3
Przytycka, T.M.4
-
78
-
-
56849091295
-
Network hubs buffer environmental variation in Saccharomyces cerevisiae
-
Network hubs buffer environmental variation in Saccharomyces cerevisiae. SF Levy ML S, PLoS Biol 2008 6 11
-
(2008)
PLoS Biol
, vol.6
, Issue.11
-
-
Levy, S.F.1
S, M.L.2
-
79
-
-
0042093610
-
The connectivity structure, giant strong component and centrality of metabolic networks
-
The connectivity structure, giant strong component and centrality of metabolic networks. H-W Ma A-P Z, Bioinformatics 2003 19 11
-
(2003)
Bioinformatics
, vol.19
, Issue.11
-
-
Ma, H.-W.1
Z, A.-P.2
-
81
-
-
47949110360
-
Centrality, Network Capacity, and Modularity as Parameters to Analyze the Core-Periphery Structure in Metabolic Networks
-
Centrality, Network Capacity, and Modularity as Parameters to Analyze the Core-Periphery Structure in Metabolic Networks. MR da Silva H Ma A-P Zeng, Proceedings of the IEEE 2008 96 8 1411 1420
-
(2008)
Proceedings of the IEEE
, vol.96
, Issue.8
, pp. 1411-1420
-
-
Da Silva, M.R.1
Ma, H.2
Zeng, A.-P.3
-
86
-
-
46249127253
-
Identifying gene-disease associations using centrality on a literature mined gene-interaction network
-
Identifying gene-disease associations using centrality on a literature mined gene-interaction network. A zgür T Vu G Erkan DR Radev, Bioinformatics 2008 24 13 277 i285
-
(2008)
Bioinformatics
, vol.24
, Issue.13
-
-
Zgür, A.1
Vu, T.2
Erkan, G.3
Radev, D.R.4
-
88
-
-
0036083434
-
Characterization of the folding degree of proteins
-
Characterization of the folding degree of proteins. E Estrada, Bioinformatics 2002 18 697 704 (Pubitemid 34679116)
-
(2002)
Bioinformatics
, vol.18
, Issue.5
, pp. 697-704
-
-
Estrada, E.1
-
89
-
-
0035159445
-
Recent advances on the role of topological indices in drug discovery research
-
Recent advances on the role of topological indices in drug discovery research. E Estrada E Uriarte, Curr Med Chem 2001 8 1699 1714
-
(2001)
Curr Med Chem
, vol.8
, pp. 1699-1714
-
-
Estrada, E.1
Uriarte, E.2
-
90
-
-
77649338567
-
Generalized walks-based centrality measures for complex biological networks
-
Generalized walks-based centrality measures for complex biological networks. E Estrada, J Theor Biol 2010 263 4 556 565
-
(2010)
J Theor Biol
, vol.263
, Issue.4
, pp. 556-565
-
-
Estrada, E.1
-
91
-
-
34547874681
-
Developmental time windows for spatial growth generate multiple-cluster small-world networks
-
DOI 10.1140/epjb/e2007-00214-4
-
Developmental time windows for spatial growth generate multiple-cluster small-world networks. F Nisbach M K, Eur Phys J B 2007 58 185 191 (Pubitemid 47254951)
-
(2007)
European Physical Journal B
, vol.58
, Issue.2
, pp. 185-191
-
-
Nisbach, F.1
Kaiser, M.2
-
92
-
-
34249999887
-
Predicting the connectivity of primate cortical networks from topological and spatial node properties
-
Predicting the connectivity of primate cortical networks from topological and spatial node properties. LdF Costa M Kaiser CC Hilgetag, BMC Syst Bio 2007 1
-
(2007)
BMC Syst Bio
, vol.1
-
-
Costa, L.F.1
Kaiser, M.2
Hilgetag, C.C.3
-
93
-
-
0035799707
-
Lethality and centrality in protein networks
-
DOI 10.1038/35075138
-
Lethality and centrality in protein networks. H Jeong SP Mason A-L Barabasi ZN Oltvai, Nature 2001 411 6833 41 42 (Pubitemid 32428180)
-
(2001)
Nature
, vol.411
, Issue.6833
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.-L.3
Oltvai, Z.N.4
-
94
-
-
16344381521
-
Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
-
DOI 10.1093/molbev/msi072
-
Comparative genomics of centrality and essentiality in three eukaryotic protein-protein interaction networks. M Hahn A K, Mol Biol Evol 2005 22 803 806 (Pubitemid 40471393)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.4
, pp. 803-806
-
-
Hahn, M.W.1
Kern, A.D.2
-
97
-
-
84867446322
-
Visone - Software for Visual Social Network Analysis
-
visone - Software for Visual Social Network Analysis. M Baur M Benkert U Brandes S Cornelsen M Gaertler B Köpf J Lerner D Wagner, Proc 9th Intl Symp Graph Drawing (GD '01), LNCS 2002 2265 463 464
-
(2002)
Proc 9th Intl Symp Graph Drawing (GD '01), LNCS
, vol.2265
, pp. 463-464
-
-
Baur, M.1
Benkert, M.2
Brandes, U.3
Cornelsen, S.4
Gaertler, M.5
Köpf, B.6
Lerner, J.7
Wagner, D.8
-
98
-
-
0002226683
-
Pajek - Program for Large Network Analysis
-
Pajek - Program for Large Network Analysis. V Batagelj A Mrvar, Connections 1998 21 47 57
-
(1998)
Connections
, vol.21
, pp. 47-57
-
-
Batagelj, V.1
Mrvar, A.2
-
100
-
-
27944493925
-
Scale-free networks in cell biology
-
Scale-free networks in cell biology. R Albert, Journal of Cell Science 2005 118
-
(2005)
Journal of Cell Science
, vol.118
-
-
Albert, R.1
-
101
-
-
72949090589
-
The powerful law of the power law and other myths in network biology
-
The powerful law of the power law and other myths in network biology. G Lima-Mendez J van Helden, Mol Biosyst 2009 5 12 1482 1493
-
(2009)
Mol Biosyst
, vol.5
, Issue.12
, pp. 1482-1493
-
-
Lima-Mendez, G.1
Van Helden, J.2
-
102
-
-
18744389789
-
Assortative Mixing in Networks
-
Assortative Mixing in Networks. MEJ Newman, Phys Rev Lett 2002 89 208701
-
(2002)
Phys Rev Lett
, vol.89
, pp. 208701
-
-
Newman, M.E.J.1
-
103
-
-
0038752085
-
Mixing patterns in networks
-
Mixing patterns in networks. MEJ Newman, Phys Rev 2003 67
-
(2003)
Phys Rev
, vol.67
-
-
Newman, M.E.J.1
-
104
-
-
43049149409
-
Networks: Teasing out the missing links
-
DOI 10.1038/453047a, PII 453047A
-
Networks: teasing out the missing links. S Redner, Nature 2008 453 47 48 (Pubitemid 351630319)
-
(2008)
Nature
, vol.453
, Issue.7191
, pp. 47-48
-
-
Redner, S.1
-
105
-
-
0000207615
-
On the strength of connectedness of a random graph
-
On the strength of connectedness of a random graph. P Erdös A R, Acta Math Acad Sci Hungar 1961 12 261 267
-
(1961)
Acta Math Acad Sci Hungar
, vol.12
, pp. 261-267
-
-
Erdös, P.1
R, A.2
-
106
-
-
0032482432
-
Collective dynamics of 'small-world' networks
-
DOI 10.1038/30918
-
Collective dynamics of 'small-world' networks. DJ Watts SH S, Nature 1998 393 440 442 (Pubitemid 28292183)
-
(1998)
Nature
, vol.393
, Issue.6684
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
107
-
-
0038483826
-
Emergence of scaling in random networks
-
Emergence of scaling in random networks. A-L Barabsi R A, Science 1999 286 509 512
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabsi, A.-L.1
A, R.2
-
108
-
-
12444301754
-
Structure and evolution of protein interaction networks: A statistical model for link dynamics and gene duplications
-
Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. J Berg M Lassig A Wagner, BMC Evol Biol 2004 4 1 51
-
(2004)
BMC Evol Biol
, vol.4
, Issue.1
, pp. 51
-
-
Berg, J.1
Lassig, M.2
Wagner, A.3
-
109
-
-
70350482286
-
Evolution of biomolecular networks - Lessons from metabolic and protein interactions
-
Evolution of biomolecular networks - lessons from metabolic and protein interactions. T Yamada P B, Nature Rev Molecular Cell Biology 2009 10 791 803
-
(2009)
Nature Rev Molecular Cell Biology
, vol.10
, pp. 791-803
-
-
Yamada, T.1
B, P.2
-
111
-
-
33749164066
-
Pattern Classification, ch.10: Unsupervised learning and clustering
-
Pattern Classification, ch.10: Unsupervised learning and clustering. RO Duda PE Hart DG Stork, Wiley, New York 2001 571
-
(2001)
Wiley, New York
, pp. 571
-
-
Duda, R.O.1
Hart, P.E.2
Stork, D.G.3
-
112
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
The neighbor-joining method: a new method for reconstructing phylogenetic trees. N Saitou M Nei, Mol Biol Evol 1987 4 4 406 425
-
(1987)
Mol Biol Evol
, vol.4
, Issue.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
114
-
-
70449448956
-
Threshold selection in gene co-expression networks using spectral graph theory techniques
-
Threshold selection in gene co-expression networks using spectral graph theory techniques. AD Perkins MA L, BMC Bioinformatics 2009 10
-
(2009)
BMC Bioinformatics
, vol.10
-
-
Perkins, A.D.1
L, M.A.2
-
115
-
-
0035375137
-
Computational analysis of microarray data
-
DOI 10.1038/35076576
-
Computational genetics: Computational analysis of microarray data. J Quackenbush, Nat Rev Genetics 2001 2 418 427 (Pubitemid 33673408)
-
(2001)
Nature Reviews Genetics
, vol.2
, Issue.6
, pp. 418-427
-
-
Quackenbush, J.1
-
117
-
-
0002510498
-
Unweighted Pair Group Method with Arithmetic Mean
-
San Francisco: Freeman
-
Unweighted Pair Group Method with Arithmetic Mean. PHA Sneath RR Sokal, Numerical Taxonomy San Francisco: Freeman 1973 230 234
-
(1973)
Numerical Taxonomy
, pp. 230-234
-
-
Sneath, P.H.A.1
Sokal, R.R.2
-
118
-
-
0000028423
-
A Quantitative Approach to a Problem in Classification
-
A Quantitative Approach to a Problem in Classification. CD Michener RR Sokal, Evolution 1957 11 2 130 162
-
(1957)
Evolution
, vol.11
, Issue.2
, pp. 130-162
-
-
Michener, C.D.1
Sokal, R.R.2
-
120
-
-
34250285795
-
U-Statistic Hierarchical Clustering
-
U-Statistic Hierarchical Clustering. R D'andrade, Psychometrika 1978 4 58 67
-
(1978)
Psychometrika
, vol.4
, pp. 58-67
-
-
D'Andrade, R.1
-
121
-
-
0014129195
-
Hierarchical Clustering Schemes
-
Hierarchical Clustering Schemes. SC Johnson, Psychometrika 1967 2 241 254
-
(1967)
Psychometrika
, vol.2
, pp. 241-254
-
-
Johnson, S.C.1
-
122
-
-
0036645183
-
Interactively Exploring Hierarchical Clustering Results
-
Interactively Exploring Hierarchical Clustering Results. J Seo B Shneiderman, Computer 2002 35 7 80 86
-
(2002)
Computer
, vol.35
, Issue.7
, pp. 80-86
-
-
Seo, J.1
Shneiderman, B.2
-
123
-
-
33645324706
-
An interactive power analysis tool for microarray hypothesis testing and generation
-
An interactive power analysis tool for microarray hypothesis testing and generation. J Seo H Gordish-Dressman EP Hoffman, Bioinformatics 2006 22 7 808 814
-
(2006)
Bioinformatics
, vol.22
, Issue.7
, pp. 808-814
-
-
Seo, J.1
Gordish-Dressman, H.2
Hoffman, E.P.3
-
124
-
-
3242810318
-
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
-
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. S Kumar K Tamura M Nei, Brief Bioinform 2004 5 2 150 163
-
(2004)
Brief Bioinform
, vol.5
, Issue.2
, pp. 150-163
-
-
Kumar, S.1
Tamura, K.2
Nei, M.3
-
125
-
-
34547781750
-
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
-
DOI 10.1093/molbev/msm092
-
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura D J M Nei K S, Molecular Biology and Evolution 2007 24 1596 1599 (Pubitemid 47236692)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1596-1599
-
-
Tamura, K.1
Dudley, J.2
Nei, M.3
Kumar, S.4
-
126
-
-
0036139211
-
MEGA2: Molecular evolutionary genetics analysis software
-
MEGA2: molecular evolutionary genetics analysis software. S Kumar K Tamura I Jakobsen M Nei, Bioinformatics 2001 17 12 1244 1245 (Pubitemid 33735359)
-
(2001)
Bioinformatics
, vol.17
, Issue.12
, pp. 1244-1245
-
-
Kumar, S.1
Tamura, K.2
Jakobsen, I.B.3
Nei, M.4
-
127
-
-
0028294049
-
MEGA: Molecular evolutionary genetics analysis software for microcomputers
-
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. S Kumar K Tamura M Nei, Comput Appl Biosci 1994 10 2 189 191 (Pubitemid 24125441)
-
(1994)
Computer Applications in the Biosciences
, vol.10
, Issue.2
, pp. 189-191
-
-
Kumar, S.1
Tamura, K.2
Nei, M.3
-
128
-
-
0037311919
-
TM4: A free, open-source system for microarray data management and analysis
-
TM4: a free, open-source system for microarray data management and analysis. AI Saeed V Sharov J White J Li W Liang N Bhagabati J Braisted M Klapa T Currier M Thiagarajan,, et al. BioTechniques 2003 34 2 374 378 (Pubitemid 36184095)
-
(2003)
BioTechniques
, vol.34
, Issue.2
, pp. 374-378
-
-
Saeed, A.I.1
Sharov, V.2
White, J.3
Li, J.4
Liang, W.5
Bhagabati, N.6
Braisted, J.7
Klapa, M.8
Currier, T.9
Thiagarajan, M.10
Sturn, A.11
Snuffin, M.12
Rezantsev, A.13
Popov, D.14
Ryltsov, A.15
Kostukovich, E.16
Borisovsky, I.17
Liu, Z.18
Vinsavich, A.19
Trush, V.20
Quackenbush, J.21
more..
-
130
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
An efficient algorithm for large-scale detection of protein families. AJ Enright S Van Dongen CA Ouzounis, Nucleic Acids Res 2002 30 7 1575 1584 (Pubitemid 34679732)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
132
-
-
65449134296
-
Clustering algorithms for detecting functional modules in protein interaction networks
-
Clustering algorithms for detecting functional modules in protein interaction networks. L Gao PG Sun J Song, J Bioinform Comput Biol 2009 7 1 217 242
-
(2009)
J Bioinform Comput Biol
, vol.7
, Issue.1
, pp. 217-242
-
-
Gao, L.1
Sun, P.G.2
Song, J.3
-
133
-
-
26644466306
-
Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property
-
DOI 10.1109/TNB.2005.853667
-
Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property. W Zhong G Altun R Harrison PC Tai Y Pan, IEEE Trans Nanobioscience 2005 4 3 255 265 (Pubitemid 41441416)
-
(2005)
IEEE Transactions on Nanobioscience
, vol.4
, Issue.3
, pp. 255-265
-
-
Zhong, W.1
Altun, G.2
Harrison, R.3
Tai, P.C.4
Pan, Y.5
-
134
-
-
0005924596
-
Graph Clustering by Flow Simulation
-
University of Utrecht
-
Graph Clustering by Flow Simulation. S van Dogen, PhD thesis University of Utrecht 2000
-
(2000)
PhD Thesis
-
-
Van Dogen, S.1
-
135
-
-
65849100458
-
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
-
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. J Vlasblom SJ Wodak, BMC Bioinformatics 2009 10 99
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 99
-
-
Vlasblom, J.1
Wodak, S.J.2
-
136
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
An efficient algorithm for large-scale detection of protein families. AJ Enright S Van Dongen CA Ouzounis, Nucleic Acids Res 2002 30 7 1575 1584 (Pubitemid 34679732)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
137
-
-
0001457509
-
Some Methods for classification and Analysis of Multivariate Observations
-
Berkeley, University of California Press
-
Some Methods for classification and Analysis of Multivariate Observations. B MacQueen, Proceedings of 5-th Berkeley Symposium on Mathematical Statistics and Probability Berkeley, University of California Press 1967 1 281 297
-
(1967)
Proceedings of 5-th Berkeley Symposium on Mathematical Statistics and Probability
, vol.1
, pp. 281-297
-
-
MacQueen, B.1
-
138
-
-
13244255357
-
Incremental genetic K-means algorithm and its application in gene expression data analysis
-
Incremental genetic K-means algorithm and its application in gene expression data analysis. Y Lu S Lu F Fotouhi Y Deng SJ Brown, BMC Bioinformatics 2004 5 172
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 172
-
-
Lu, Y.1
Lu, S.2
Fotouhi, F.3
Deng, Y.4
Brown, S.J.5
-
139
-
-
33847172327
-
Clustering by passing messages between data points
-
DOI 10.1126/science.1136800
-
Clustering by passing messages between data points. BJ Frey D Dueck, Science 2007 315 5814 972 976 (Pubitemid 46281181)
-
(2007)
Science
, vol.315
, Issue.5814
, pp. 972-976
-
-
Frey, B.J.1
Dueck, D.2
-
140
-
-
10244264813
-
Protein complex prediction via cost-based clustering
-
DOI 10.1093/bioinformatics/bth351
-
Protein complex prediction via cost-based clustering. AD King N Przulj I Jurisica, Bioinformatics 2004 20 17 3013 3020 (Pubitemid 39619193)
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 3013-3020
-
-
King, A.D.1
Przulj, N.2
Jurisica, I.3
-
142
-
-
76749150479
-
Computational approaches for detecting protein complexes from protein interaction networks: A survey
-
Computational approaches for detecting protein complexes from protein interaction networks: a survey. X Li M Wu CK Kwoh SK Ng, BMC Genomics 2010 11 Suppl 1 3
-
(2010)
BMC Genomics
, vol.11
, Issue.SUPPL. 1
, pp. 193
-
-
Li, X.1
Wu, M.2
Kwoh, C.K.3
Ng, S.K.4
-
143
-
-
33751255087
-
Evaluation of clustering algorithms for protein-protein interaction networks
-
Evaluation of clustering algorithms for protein-protein interaction networks. S Brohee J van Helden, BMC Bioinformatics 2006 7 488
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 488
-
-
Brohee, S.1
Van Helden, J.2
-
144
-
-
65449162644
-
A survey of visualization tools for biological network analysis
-
A survey of visualization tools for biological network analysis. GA Pavlopoulos AL Wegener R Schneider, BioData Min 2008 1 12
-
(2008)
BioData Min
, vol.1
, pp. 12
-
-
Pavlopoulos, G.A.1
Wegener, A.L.2
Schneider, R.3
-
145
-
-
48449094106
-
NeAT: A toolbox for the analysis of biological networks, clusters, classes and pathways
-
NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. S Brohee K Faust G Lima-Mendez O Sand R Janky G Vanderstocken Y Deville J van Helden, Nucleic Acids Res 2008 36 Web Server 444 451
-
(2008)
Nucleic Acids Res
, Issue.36 WEB SER.
, pp. 23444-451
-
-
Brohee, S.1
Faust, K.2
Lima-Mendez, G.3
Sand, O.4
Janky, R.5
Vanderstocken, G.6
Deville, Y.7
Van Helden, J.8
-
147
-
-
33745590867
-
ArrayCluster: An analytic tool for clustering, data visualization and module finder on gene expression profiles
-
DOI 10.1093/bioinformatics/btl129
-
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. R Yoshida T Higuchi S Imoto S Miyano, Bioinformatics 2006 22 1538 1539 (Pubitemid 43985329)
-
(2006)
Bioinformatics
, vol.22
, Issue.12
, pp. 1538-1539
-
-
Yoshida, R.1
Higuchi, T.2
Imoto, S.3
Miyano, S.4
-
148
-
-
28944452690
-
Medusa: A simple tool for interaction graph analysis
-
DOI 10.1093/bioinformatics/bti696
-
Medusa: a simple tool for interaction graph analysis. SD Hooper P Bork, Bioinformatics 2005 21 24 4432 4433 (Pubitemid 41782941)
-
(2005)
Bioinformatics
, vol.21
, Issue.24
, pp. 4432-4433
-
-
Hooper, S.D.1
Bork, P.2
-
149
-
-
0242490780
-
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
-
DOI 10.1101/gr.1239303
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks. P Shannon A Markiel O Ozier NS Baliga JT Wang D Ramage N Amin B Schwikowski T Ideker, Genome Res 2003 13 11 2498 2504 (Pubitemid 37428274)
-
(2003)
Genome Research
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
151
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
DOI 10.1038/35001009
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. P Uetz L Giot G Cagney TA Mansfield RS Judson JR Knight D Lockshon V Narayan M Srinivasan P Pochart,, et al. Nature 2000 403 6770 623 627 (Pubitemid 30103994)
-
(2000)
Nature
, vol.403
, Issue.6770
, pp. 623-627
-
-
Uetz, P.1
Glot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
Lockshon, D.7
Narayan, V.8
Srinivasan, M.9
Pochart, P.10
Qureshi-Emlli, A.11
Li, Y.12
Godwin, B.13
Conover, D.14
Kalbfleisch, T.15
Vijayadamodar, G.16
Yang, M.17
Johnston, M.18
Fields, S.19
Rothberg, J.M.20
more..
-
152
-
-
0035843145
-
The protein-protein interaction map of Helicobacter pylori
-
DOI 10.1038/35051615
-
The protein-protein interaction map of Helicobacter pylori. JC Rain L Selig H De Reuse V Battaglia C Reverdy S Simon G Lenzen F Petel J Wojcik V Schachter,, et al. Nature 2001 409 6817 211 215 (Pubitemid 32144288)
-
(2001)
Nature
, vol.409
, Issue.6817
, pp. 211-215
-
-
Rain, J.-C.1
Selig, L.2
De Reuse, H.3
Battaglia, V.4
Reverdy, C.5
Simon, S.6
Lenzen, G.7
Petel, F.8
Wojcik, J.9
Schachter, V.10
Chemama, Y.11
Labigne, A.12
Legrain, P.13
-
153
-
-
0345600247
-
A Protein Interaction Map of Drosophila melanogaster
-
DOI 10.1126/science.1090289
-
A protein interaction map of Drosophila melanogaster. L Giot JS Bader C Brouwer A Chaudhuri B Kuang Y Li YL Hao CE Ooi B Godwin E Vitols,, et al. Science 2003 302 5651 1727 1736 (Pubitemid 37505730)
-
(2003)
Science
, vol.302
, Issue.5651
, pp. 1727-1736
-
-
Giot, L.1
Bader, J.S.2
Brouwer, C.3
Chaudhuri, A.4
Kuang, B.5
Li, Y.6
Hao, Y.L.7
Ooi, C.E.8
Godwin, B.9
Vitols, E.10
Vijayadamodar, G.11
Pochart, P.12
Machineni, H.13
Welsh, M.14
Kong, Y.15
Zerhusen, B.16
Malcolm, R.17
Varrone, Z.18
Collis, A.19
Minto, M.20
Burgess, S.21
McDaniel, L.22
Stimpson, E.23
Spriggs, F.24
Williams, J.25
Neurath, K.26
Ioime, N.27
Agee, M.28
Voss, E.29
Furtak, K.30
Renzulli, R.31
Aanensen, N.32
Carrolla, S.33
Bickelhaupt, E.34
Lazovatsky, Y.35
DaSilva, A.36
Zhong, J.37
Stanyon, C.A.38
Finley Jr., R.L.39
White, K.P.40
Braverman, M.41
Jarvie, T.42
Gold, S.43
Leach, M.44
Knight, J.45
Shimkets, R.A.46
McKenna, M.P.47
Chant, J.48
Rothberg, J.M.49
more..
-
154
-
-
9144264169
-
A Map of the Interactome Network of the Metazoan C. elegans
-
DOI 10.1126/science.1091403
-
A map of the interactome network of the metazoan C. elegans. S Li CM Armstrong N Bertin H Ge S Milstein M Boxem PO Vidalain JD Han A Chesneau T Hao,, et al. Science 2004 303 5657 540 543 (Pubitemid 38120855)
-
(2004)
Science
, vol.303
, Issue.5657
, pp. 540-543
-
-
Li, S.1
Armstrong, C.M.2
Bertin, N.3
Ge, H.4
Milstein, S.5
Boxem, M.6
Vidalain, P.-O.7
Han, J.-D.J.8
Chesneau, A.9
Hao, T.10
Goldberg, D.S.11
Li, N.12
Martinez, M.13
Rual, J.-F.14
Lamesch, P.15
Xu, L.16
Tewari, M.17
Wong, S.L.18
Zhang, L.V.19
Berriz, G.F.20
Jacotot, L.21
Vaglio, P.22
Reboul, J.23
Hirozane-Kishikawa, T.24
Li, Q.25
Gabel, H.W.26
Elewa, A.27
Baumgartner, B.28
Rose, D.J.29
Yu, H.30
Bosak, S.31
Sequerra, R.32
Fraser, A.33
Mango, S.E.34
Saxton, W.M.35
Strome, S.36
Van Den Heuvel, S.V.37
Piano, F.38
Vandenhaute, J.39
Sardet, C.40
Gerstein, M.41
Doucette-Stamm, L.42
Gunsalus, K.C.43
Harper, J.W.44
Cusick, M.E.45
Roth, F.P.46
Hill, D.E.47
Vidal, M.48
more..
-
155
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
Comparative assessment of large-scale data sets of protein-protein interactions. C von Mering R Krause B Snel M Cornell SG Oliver S Fields P Bork, Nature 2002 417 6887 399 403 (Pubitemid 34563526)
-
(2002)
Nature
, vol.417
, Issue.6887
, pp. 399-403
-
-
Von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
156
-
-
77956381678
-
Construction and analysis of protein-protein interaction networks
-
Construction and analysis of protein-protein interaction networks. K Raman, Autom Exp 2010 2 1 2
-
(2010)
Autom Exp
, vol.2
, Issue.1
, pp. 2
-
-
Raman, K.1
-
157
-
-
30644465547
-
The comprehensive updated regulatory network of Escherichia coli K-12
-
The comprehensive updated regulatory network of Escherichia coli K-12. H Salgado A Santos-Zavaleta S Gama-Castro M Peralta-Gil MI Penaloza-Spinola A Martinez-Antonio PD Karp J Collado-Vides, BMC Bioinformatics 2006 7 5
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 5
-
-
Salgado, H.1
Santos-Zavaleta, A.2
Gama-Castro, S.3
Peralta-Gil, M.4
Penaloza-Spinola, M.I.5
Martinez-Antonio, A.6
Karp, P.D.7
Collado-Vides, J.8
-
158
-
-
33644873438
-
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions
-
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. H Salgado S Gama-Castro M Peralta-Gil E Diaz-Peredo F Sanchez-Solano A Santos-Zavaleta I Martinez-Flores V Jimenez-Jacinto C Bonavides-Martinez J Segura-Salazar,, et al. Nucleic Acids Res 2006 34 Database 394 397
-
(2006)
Nucleic Acids Res
, Issue.34 DATABASE
, pp. 4394-397
-
-
Salgado, H.1
Gama-Castro, S.2
Peralta-Gil, M.3
Diaz-Peredo, E.4
Sanchez-Solano, F.5
Santos-Zavaleta, A.6
Martinez-Flores, I.7
Jimenez-Jacinto, V.8
Bonavides-Martinez, C.9
Segura-Salazar, J.10
-
159
-
-
33746207758
-
Bacterial regulatory networks are extremely flexible in evolution
-
Bacterial regulatory networks are extremely flexible in evolution. I Lozada-Chavez SC Janga J Collado-Vides, Nucleic Acids Res 2006 34 12 3434 3445
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.12
, pp. 3434-3445
-
-
Lozada-Chavez, I.1
Janga, S.C.2
Collado-Vides, J.3
-
160
-
-
33646113855
-
Evolutionary dynamics of prokaryotic transcriptional regulatory networks
-
Evolutionary dynamics of prokaryotic transcriptional regulatory networks. M Madan Babu SA Teichmann L Aravind, J Mol Biol 2006 358 2 614 633
-
(2006)
J Mol Biol
, vol.358
, Issue.2
, pp. 614-633
-
-
Madan Babu, M.1
Teichmann, S.A.2
Aravind, L.3
-
162
-
-
0041828241
-
Scaling laws in the functional content of genomes
-
DOI 10.1016/S0168-9525(03)00203-8
-
Scaling laws in the functional content of genomes. E van Nimwegen, Trends Genet 2003 19 9 479 484 (Pubitemid 37101085)
-
(2003)
Trends in Genetics
, vol.19
, Issue.9
, pp. 479-484
-
-
Van Nimwegen, E.1
-
163
-
-
0033555859
-
Emergent properties of networks of biological signaling pathways
-
Emergent properties of networks of biological signaling pathways. US Bhalla R Iyengar, Science 1999 283 5400 381 387
-
(1999)
Science
, vol.283
, Issue.5400
, pp. 381-387
-
-
Bhalla, U.S.1
Iyengar, R.2
-
165
-
-
0036578654
-
Topological and causal structure of the yeast transcriptional regulatory network
-
Topological and causal structure of the yeast transcriptional regulatory network. N Guelzim S Bottani P Bourgine F Kepes, Nat Genet 2002 31 1 60 63
-
(2002)
Nat Genet
, vol.31
, Issue.1
, pp. 60-63
-
-
Guelzim, N.1
Bottani, S.2
Bourgine, P.3
Kepes, F.4
-
166
-
-
0037316239
-
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
-
DOI 10.1093/bioinformatics/19.2.270
-
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. H Ma AP Zeng, Bioinformatics 2003 19 2 270 277 (Pubitemid 36181913)
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 270-277
-
-
Ma, H.1
Zeng, A.-P.2
-
168
-
-
0038281450
-
Hierarchical analysis of dependency in metabolic networks
-
DOI 10.1093/bioinformatics/btg115
-
Hierarchical analysis of dependency in metabolic networks. J Gagneur DB Jackson G Casari, Bioinformatics 2003 19 8 1027 1034 (Pubitemid 36675825)
-
(2003)
Bioinformatics
, vol.19
, Issue.8
, pp. 1027-1034
-
-
Gagneur, J.1
Jackson, D.B.2
Casari, G.3
-
169
-
-
0037345719
-
Subnetwork hierarchies of biochemical pathways
-
DOI 10.1093/bioinformatics/btg033
-
Subnetwork hierarchies of biochemical pathways. P Holme M Huss H Jeong, Bioinformatics 2003 19 4 532 538 (Pubitemid 36342252)
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 532-538
-
-
Holme, P.1
Huss, M.2
Jeong, H.3
|