-
1
-
-
14844307659
-
Modelling gene networks at different organisational levels
-
10.1016/j.febslet.2005.01.073 15763564
-
Schlitt T Brazma A Modelling gene networks at different organisational levels FEBS Lett 2005, 579(8):1859-1866 10.1016/j.febslet.2005.01.073 15763564
-
(2005)
FEBS Lett
, vol.579
, Issue.8
, pp. 1859-1866
-
-
Schlitt, T.1
Brazma, A.2
-
2
-
-
33646360604
-
Modelling in molecular biology: Describing transcription regulatory networks at different scales
-
10.1098/rstb.2005.1806 16524837
-
Schlitt T Brazma A Modelling in molecular biology: Describing transcription regulatory networks at different scales Philos Trans R Soc Lond B Biol Sci 2006, 361(1467):483-494 10.1098/rstb.2005.1806 16524837
-
(2006)
Philos Trans R Soc Lond B Biol Sci
, vol.361
, Issue.1467
, pp. 483-494
-
-
Schlitt, T.1
Brazma, A.2
-
3
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556 10802651
-
Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25(1):25-29 10.1038/75556 10802651
-
(2000)
Nat Genet
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
4
-
-
0033215210
-
Pathway alignment: Application to the comparative analysis of glycolytic enzymes
-
1220531 10493919 10.1042/0264-6021:3430115
-
Dandekar T Schuster S Snel B Huynen M Bork P Pathway alignment: application to the comparative analysis of glycolytic enzymes Biochem J 1999, 343(Pt 1):115-124 1220531 10493919 10.1042/0264-6021:3430115
-
(1999)
Biochem J
, vol.343
, Issue.PART 1
, pp. 115-124
-
-
Dandekar, T.1
Schuster, S.2
Snel, B.3
Huynen, M.4
Bork, P.5
-
5
-
-
0037252718
-
The Proteome Analysis database: A tool for the in silico analysis of whole proteomes
-
165552 12520037 10.1093/nar/gkg105
-
Pruess M Fleischmann W Kanapin A Karavidopoulou Y Kersey P Kriventseva E Mittard V Mulder N Phan I Servant F The Proteome Analysis database: A tool for the in silico analysis of whole proteomes Nucleic Acids Res 2003, 31(1):414-417 165552 12520037 10.1093/nar/gkg105
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 414-417
-
-
Pruess, M.1
Fleischmann, W.2
Kanapin, A.3
Karavidopoulou, Y.4
Kersey, P.5
Kriventseva, E.6
Mittard, V.7
Mulder, N.8
Phan, I.9
Servant, F.10
-
6
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
1251668 16214803 10.1093/nar/gki866
-
Overbeek R Begley T Butler RM Choudhuri JV Chuang HY Cohoon M de Crecy-Lagard V Diaz N Disz T Edwards R The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes Nucleic Acids Res 2005, 33(17):5691-5702 1251668 16214803 10.1093/nar/gki866
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.17
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
de Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
-
7
-
-
0032413411
-
Predicting gene regulatory elements in silico on a genomic scale
-
310790 9847082
-
Brazma A Jonassen I Vilo J Ukkonen E Predicting gene regulatory elements in silico on a genomic scale Genome Res 1998, 8(11):1202-1215 310790 9847082
-
(1998)
Genome Res
, vol.8
, Issue.11
, pp. 1202-1215
-
-
Brazma, A.1
Jonassen, I.2
Vilo, J.3
Ukkonen, E.4
-
8
-
-
3543042493
-
Periodic gene expression program of the fission yeast cell cycle
-
10.1038/ng1377 15195092
-
Rustici G Mata J Kivinen K Lio P Penkett CJ Burns G Hayles J Brazma A Nurse P Bahler J Periodic gene expression program of the fission yeast cell cycle Nat Genet 2004, 36(8):809-817 10.1038/ng1377 15195092
-
(2004)
Nat Genet
, vol.36
, Issue.8
, pp. 809-817
-
-
Rustici, G.1
Mata, J.2
Kivinen, K.3
Lio, P.4
Penkett, C.J.5
Burns, G.6
Hayles, J.7
Brazma, A.8
Nurse, P.9
Bahler, J.10
-
10
-
-
0037785111
-
Computer modeling of promoter organization as a tool to study transcriptional coregulation
-
10.1096/fj.02-0955rev
-
Werner T Fessele S Maier H Nelson PJ Computer modeling of promoter organization as a tool to study transcriptional coregulation Faseb J 2003, 17(10):1228-1237 10.1096/fj.02-0955rev 12832287
-
(2003)
Faseb J
, vol.17
, Issue.10
, pp. 1228-1237
-
-
Werner, T.1
Fessele, S.2
Maier, H.3
Nelson, P.J.4
-
11
-
-
16344369891
-
The identification and functional characterisation of conserved regulatory elements in developmental genes
-
10.1093/bfgp/3.4.332 15814024
-
Dickmeis T Muller F The identification and functional characterisation of conserved regulatory elements in developmental genes Brief Funct Genomic Proteomic 2005, 3(4):332-350 10.1093/bfgp/3.4.332 15814024
-
(2005)
Brief Funct Genomic Proteomic
, vol.3
, Issue.4
, pp. 332-350
-
-
Dickmeis, T.1
Muller, F.2
-
12
-
-
32544446322
-
Evaluating phylogenetic footprinting for human-rodent comparisons
-
(Oxford, England) 10.1093/bioinformatics/bti819 16332706
-
Sauer T Shelest E Wingender E Evaluating phylogenetic footprinting for human-rodent comparisons Bioinformatics (Oxford, England) 2006, 22(4):430-437 10.1093/bioinformatics/bti819 16332706
-
(2006)
Bioinformatics
, vol.22
, Issue.4
, pp. 430-437
-
-
Sauer, T.1
Shelest, E.2
Wingender, E.3
-
13
-
-
20844434817
-
Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites
-
1150811 15937122 10.1073/pnas.0409638102
-
Balhoff JP Wray GA Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites Proc Natl Acad Sci USA 2005, 102(24):8591-8596 1150811 15937122 10.1073/ pnas.0409638102
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.24
, pp. 8591-8596
-
-
Balhoff, J.P.1
Wray, G.A.2
-
14
-
-
0018199224
-
DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
-
342238 212715 10.1093/nar/5.9.3157
-
Galas DJ Schmitz A DNAse footprinting: A simple method for the detection of protein-DNA binding specificity Nucleic Acids Res 1978, 5(9):3157-3170 342238 212715 10.1093/nar/5.9.3157
-
(1978)
Nucleic Acids Res
, vol.5
, Issue.9
, pp. 3157-3170
-
-
Galas, D.J.1
Schmitz, A.2
-
15
-
-
0019878376
-
Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis
-
327619 6275366 10.1093/nar/9.23.6505
-
Fried M Crothers DM Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis Nucleic Acids Res 1981, 9(23):6505-6525 327619 6275366 10.1093/nar/9.23.6505
-
(1981)
Nucleic Acids Res
, vol.9
, Issue.23
, pp. 6505-6525
-
-
Fried, M.1
Crothers, D.M.2
-
16
-
-
0019877067
-
A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system
-
327330 6269071 10.1093/nar/9.13.3047
-
Garner MM Revzin A A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system Nucleic Acids Res 1981, 9(13):3047-3060 327330 6269071 10.1093/nar/9.13.3047
-
(1981)
Nucleic Acids Res
, vol.9
, Issue.13
, pp. 3047-3060
-
-
Garner, M.M.1
Revzin, A.2
-
17
-
-
0036940469
-
Learning about gene regulatory networks from gene deletion experiments
-
10.1002/cfg.220
-
Schlitt T Brazma A Learning about gene regulatory networks from gene deletion experiments Comp Funct Genom 2002, 3:499-503 10.1002/cfg.220
-
(2002)
Comp Funct Genom
, vol.3
, pp. 499-503
-
-
Schlitt, T.1
Brazma, A.2
-
22
-
-
0033669189
-
A network of protein-protein interactions in yeast
-
10.1038/82360 11101803
-
Schwikowski B Uetz P Fields S A network of protein-protein interactions in yeast Nat Biotechnol 2000, 18(12):1257-1261 10.1038/82360 11101803
-
(2000)
Nat Biotechnol
, vol.18
, Issue.12
, pp. 1257-1261
-
-
Schwikowski, B.1
Uetz, P.2
Fields, S.3
-
23
-
-
0346752107
-
From gene networks to gene function
-
403798 14656964 10.1101/gr.1111403
-
Schlitt T Palin K Rung J Dietmann S Lappe M Ukkonen E Brazma A From gene networks to gene function Genome Res 2003, 13:2568-2576 403798 14656964 10.1101/gr.1111403
-
(2003)
Genome Res
, vol.13
, pp. 2568-2576
-
-
Schlitt, T.1
Palin, K.2
Rung, J.3
Dietmann, S.4
Lappe, M.5
Ukkonen, E.6
Brazma, A.7
-
24
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
10.1038/nature02800 15343339
-
Harbison CT Gordon DB Lee TI Rinaldi NJ Macisaac KD Danford TW Hannett NM Tagne JB Reynolds DB Yoo J Transcriptional regulatory code of a eukaryotic genome Nature 2004, 431(7004):99-104 10.1038/nature02800 15343339
-
(2004)
Nature
, vol.431
, Issue.7004
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
Yoo, J.10
-
25
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
10.1016/S0092-8674(00)00015-5 10929718
-
Hughes TR Marton MJ Jones AR Roberts CJ Stoughton R Armour CD Bennett HA Coffey E Dai H He YD Functional discovery via a compendium of expression profiles Cell 2000, 102(1):109-126 10.1016/S0092-8674(00)00015-5 10929718
-
(2000)
Cell
, vol.102
, Issue.1
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
-
26
-
-
0345928693
-
Building and analysing genome-wide gene disruption networks
-
(Oxford, England) 12386004
-
Rung J Schlitt T Brazma A Freivalds K Vilo J Building and analysing genome-wide gene disruption networks Bioinformatics (Oxford, England) 2002, 18(Suppl 2):S202-210 12386004
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 2
-
-
Rung, J.1
Schlitt, T.2
Brazma, A.3
Freivalds, K.4
Vilo, J.5
-
27
-
-
0141792394
-
Correlating protein-DNA and protein-protein interaction networks
-
10.1016/j.jmb.2003.08.004 14516744
-
Manke T Bringas R Vingron M Correlating protein-DNA and protein-protein interaction networks Journal of molecular biology 2003, 333(1):75-85 10.1016/j.jmb.2003.08.004 14516744
-
(2003)
Journal of Molecular Biology
, vol.333
, Issue.1
, pp. 75-85
-
-
Manke, T.1
Bringas, R.2
Vingron, M.3
-
28
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
10.1038/nature750
-
von Mering C Krause R Snel B Cornell M Oliver SG Fields S Bork P Comparative assessment of large-scale data sets of protein-protein interactions Nature 2002, 417(6887:399-403 10.1038/nature750 12000970
-
(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
-
29
-
-
0034721164
-
Error and attack tolerance of complex networks
-
10.1038/35019019 10935628
-
Albert R Jeong H Barabasi AL Error and attack tolerance of complex networks Nature 2000, 406(6794):378-382 10.1038/35019019 10935628
-
(2000)
Nature
, vol.406
, Issue.6794
, pp. 378-382
-
-
Albert, R.1
Jeong, H.2
Barabasi, A.L.3
-
30
-
-
0035945558
-
Correction: Error and attack tolerance of complex networks
-
Albert R Jeong H Barabasi AL correction: Error and attack tolerance of complex networks Nature 2001, 409(6819):542
-
(2001)
Nature
, vol.409
, Issue.6819
, pp. 542
-
-
Albert, R.1
Jeong, H.2
Barabasi, A.L.3
-
31
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
10.1038/nature02555 15190252
-
Han JD Bertin N Hao T Goldberg DS Berriz GF Zhang LV Dupuy D Walhout AJ Cusick ME Roth FP Evidence for dynamically organized modularity in the yeast protein-protein interaction network Nature 2004, 430(6995):88-93 10.1038/nature02555 15190252
-
(2004)
Nature
, vol.430
, Issue.6995
, pp. 88-93
-
-
Han, J.D.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.8
Cusick, M.E.9
Roth, F.P.10
-
32
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
10.1038/nature02782 15372033
-
Luscombe NM Babu MM Yu H Snyder M Teichmann SA Gerstein M Genomic analysis of regulatory network dynamics reveals large topological changes Nature 2004, 431(7006):308-312 10.1038/nature02782 15372033
-
(2004)
Nature
, vol.431
, Issue.7006
, pp. 308-312
-
-
Luscombe, N.M.1
Babu, M.M.2
Yu, H.3
Snyder, M.4
Teichmann, S.A.5
Gerstein, M.6
-
33
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
10.1126/science.298.5594.824 12399590
-
Milo R Shen-Orr S Itzkovitz S Kashtan N Chklovskii D Alon U Network motifs: Simple building blocks of complex networks Science 2002, 298(5594):824-827 10.1126/science.298.5594.824 12399590
-
(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
-
34
-
-
2442537233
-
Gene regulatory network growth by duplication
-
10.1038/ng1340 15107850
-
Teichmann SA Babu MM Gene regulatory network growth by duplication Nat Genet 2004, 36(5):492-496 10.1038/ng1340 15107850
-
(2004)
Nat Genet
, vol.36
, Issue.5
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.M.2
-
35
-
-
0033518234
-
From molecular to modular cell biology
-
10.1038/35011540 10591225
-
Hartwell LH Hopfield JJ Leibler S Murray AW From molecular to modular cell biology Nature 1999, 402(6761 Suppl):C47- 52 10.1038/35011540 10591225
-
(1999)
Nature
, vol.402
, Issue.6761 SUPPL.
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
Murray, A.W.4
-
37
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
12740579
-
Segal E Shapira M Regev A Pe'er D Botstein D Koller D Friedman N Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data Nat Genet 2003, 34(2):166-176 12740579
-
(2003)
Nat Genet
, vol.34
, Issue.2
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Pe'er, D.4
Botstein, D.5
Koller, D.6
Friedman, N.7
-
38
-
-
0036699526
-
Revealing modular organization in the yeast transcriptional network
-
12134151
-
Ihmels J Friedlander G Bergmann S Sarig O Ziv Y Barkai N Revealing modular organization in the yeast transcriptional network Nat Genet 2002, 31(4):370-377 12134151
-
(2002)
Nat Genet
, vol.31
, Issue.4
, pp. 370-377
-
-
Ihmels, J.1
Friedlander, G.2
Bergmann, S.3
Sarig, O.4
Ziv, Y.5
Barkai, N.6
-
39
-
-
0037676107
-
Motifs, modules and games in bacteria
-
10.1016/S1369-5274(03)00033-X 12732301
-
Wolf DM Arkin AP Motifs, modules and games in bacteria Curr Opin Microbiol 2003, 6(2):125-134 10.1016/S1369-5274(03)00033-X 12732301
-
(2003)
Curr Opin Microbiol
, vol.6
, Issue.2
, pp. 125-134
-
-
Wolf, D.M.1
Arkin, A.P.2
-
40
-
-
1542286745
-
Quantifying modularity in the evolution of biomolecular systems
-
353226 14993205 10.1101/gr.1969504
-
Snel B Huynen MA Quantifying modularity in the evolution of biomolecular systems Genome Res 2004, 14(3):391-397 353226 14993205 10.1101/gr.1969504
-
(2004)
Genome Res
, vol.14
, Issue.3
, pp. 391-397
-
-
Snel, B.1
Huynen, M.A.2
-
41
-
-
25144498379
-
A human protein-protein interaction network: A resource for annotating the proteome
-
10.1016/j.cell.2005.08.029 16169070
-
Stelzl U Worm U Lalowski M Haenig C Brembeck FH Goehler H Stroedicke M Zenkner M Schoenherr A Koeppen S A human protein-protein interaction network: A resource for annotating the proteome Cell 2005, 122(6):957-968 10.1016/j.cell.2005.08.029 16169070
-
(2005)
Cell
, vol.122
, Issue.6
, pp. 957-968
-
-
Stelzl, U.1
Worm, U.2
Lalowski, M.3
Haenig, C.4
Brembeck, F.H.5
Goehler, H.6
Stroedicke, M.7
Zenkner, M.8
Schoenherr, A.9
Koeppen, S.10
-
42
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
10.1038/nature04209 16189514
-
Rual JF Venkatesan K Hao T Hirozane-Kishikawa T Dricot A Li N Berriz GF Gibbons FD Dreze M Ayivi-Guedehoussou N Towards a proteome-scale map of the human protein-protein interaction network Nature 2005, 437(7062):1173-1178 10.1038/nature04209 16189514
-
(2005)
Nature
, vol.437
, Issue.7062
, pp. 1173-1178
-
-
Rual, J.F.1
Venkatesan, K.2
Hao, T.3
Hirozane-Kishikawa, T.4
Dricot, A.5
Li, N.6
Berriz, G.F.7
Gibbons, F.D.8
Dreze, M.9
Ayivi-Guedehoussou, N.10
-
43
-
-
17044444207
-
Binary and graded responses in gene networks
-
12149512
-
Louis M Becskei A Binary and graded responses in gene networks Sci STKE 2002 2002, 143:PE33 12149512
-
(2002)
Sci STKE
, vol.2002
-
-
Louis, M.1
Becskei, A.2
-
44
-
-
0032549745
-
Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene
-
10.1126/science.279.5358.1896 9506933
-
Yuh CH Bolouri H Davidson EH Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene Science 1998, 279(5358):1896-1902 10.1126/science.279.5358.1896 9506933
-
(1998)
Science
, vol.279
, Issue.5358
, pp. 1896-1902
-
-
Yuh, C.H.1
Bolouri, H.2
Davidson, E.H.3
-
45
-
-
0036607698
-
A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo
-
10.1006/dbio.2002.0635 12027441
-
Davidson EH Rast JP Oliveri P Ransick A Calestani C Yuh CH Minokawa T Amore G Hinman V Arenas-Mena C A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo Dev Biol 2002, 246(1):162-190 10.1006/dbio.2002.0635 12027441
-
(2002)
Dev Biol
, vol.246
, Issue.1
, pp. 162-190
-
-
Davidson, E.H.1
Rast, J.P.2
Oliveri, P.3
Ransick, A.4
Calestani, C.5
Yuh, C.H.6
Minokawa, T.7
Amore, G.8
Hinman, V.9
Arenas-Mena, C.10
-
46
-
-
33646337667
-
A methodology for the structural and functional analysis of signaling and regulatory networks
-
1458363 16464248 10.1186/1471-2105-7-56
-
Klamt S Saez-Rodriguez J Lindquist JA Simeoni L Gilles ED A methodology for the structural and functional analysis of signaling and regulatory networks BMC Bioinformatics 2006, 7:56 1458363 16464248 10.1186/ 1471-2105-7-56
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 56
-
-
Klamt, S.1
Saez-Rodriguez, J.2
Lindquist, J.A.3
Simeoni, L.4
Gilles, E.D.5
-
47
-
-
0037270514
-
Towards reconstruction of gene networks from expression data by supervised learning
-
151290 12540298 10.1186/gb-2003-4-1-r6
-
Soinov LA Krestyaninova MA Brazma A Towards reconstruction of gene networks from expression data by supervised learning Genome Biol 2003, 4(1):R6 151290 12540298 10.1186/gb-2003-4-1-r6
-
(2003)
Genome Biol
, vol.4
, Issue.1
-
-
Soinov, L.A.1
Krestyaninova, M.A.2
Brazma, A.3
-
48
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
10.1089/106652700750050961 11108481
-
Friedman N Linial M Nachman I Pe'er D Using Bayesian networks to analyze expression data J Comput Biol 2000, 7(3-4):601-620 10.1089/ 106652700750050961 11108481
-
(2000)
J Comput Biol
, vol.7
, Issue.3-4
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
49
-
-
18144442687
-
Inferring subnetworks from perturbed expression profiles
-
(Oxford, England)
-
Pe'er D Regev A Elidan G Friedman N Inferring subnetworks from perturbed expression profiles Bioinformatics (Oxford, England) 2001, 17(Suppl1): S215-224 11473012
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Pe'er, D.1
Regev, A.2
Elidan, G.3
Friedman, N.4
-
50
-
-
10244230983
-
Reconstruction of gene networks using Bayesian learning and manipulation experiments
-
(Oxford, England) 10.1093/bioinformatics/bth337
-
Pournara I Wernisch L Reconstruction of gene networks using Bayesian learning and manipulation experiments Bioinformatics (Oxford, England) 2004, 20(17):2934-2942 10.1093/bioinformatics/bth337 15180938
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 2934-2942
-
-
Pournara, I.1
Wernisch, L.2
-
51
-
-
17644412264
-
Bayesian network analysis of signaling networks: A primer
-
10.1126/stke.2812005pl4 15855409
-
Pe'er D Bayesian network analysis of signaling networks: A primer Sci STKE 2005 2005, 281:pL4 10.1126/stke.2812005pl4 15855409
-
(2005)
Sci STKE
, vol.2005
-
-
Pe'er, D.1
-
52
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
10.1126/science.1094068 14764868
-
Friedman N Inferring cellular networks using probabilistic graphical models Science 2004, 303(5659):799-805 10.1126/science.1094068 14764868
-
(2004)
Science
, vol.303
, Issue.5659
, pp. 799-805
-
-
Friedman, N.1
-
53
-
-
0842309161
-
Discovering molecular pathways from protein interaction and gene expression data
-
(Oxford, England) 10.1093/bioinformatics/btg1037
-
Segal E Wang H Koller D Discovering molecular pathways from protein interaction and gene expression data Bioinformatics (Oxford, England) 2003, 19(Suppl 1):I264-I272 10.1093/bioinformatics/btg1037 12855469
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Segal, E.1
Wang, H.2
Koller, D.3
-
55
-
-
0036842375
-
Reverse engineers map the molecular switching yards
-
10.1016/S0167-7799(02)02051-6 124138110
-
Greller LD Somogyi R Reverse engineers map the molecular switching yards Trends Biotechnol 2002, 20(11):445-447 10.1016/S0167-7799(02)02051-6 124138110
-
(2002)
Trends Biotechnol
, vol.20
, Issue.11
, pp. 445-447
-
-
Greller, L.D.1
Somogyi, R.2
-
56
-
-
0031635563
-
Modeling the normal and neoplastic cell cycle with "realistic Boolean genetic networks": Their application for understanding carcinogenesis and assessing therapeutic strategies
-
9697172
-
Szallasi Z Liang S Modeling the normal and neoplastic cell cycle with "realistic Boolean genetic networks": Their application for understanding carcinogenesis and assessing therapeutic strategies Pac Symp Biocomput 1998, 66-76 9697172
-
(1998)
Pac Symp Biocomput
, pp. 66-76
-
-
Szallasi, Z.1
Liang, S.2
-
57
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
10380182
-
Akutsu T Miyano S Kuhara S Identification of genetic networks from a small number of gene expression patterns under the Boolean network model Pac Symp Biocomput 1999, 17-28 10380182
-
(1999)
Pac Symp Biocomput
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
58
-
-
0031616241
-
Reveal, a general reverse engineering algorithm for inference of genetic network architectures
-
9697168
-
Liang S Fuhrman S Somogyi R Reveal, a general reverse engineering algorithm for inference of genetic network architectures Pac Symp Biocomput 1998, 18-29 9697168
-
(1998)
Pac Symp Biocomput
, pp. 18-29
-
-
Liang, S.1
Fuhrman, S.2
Somogyi, R.3
-
59
-
-
0346158342
-
Petri Net representations in systems biology
-
14641101
-
Pinney JW Westhead DR McConkey GA Petri Net representations in systems biology Biochem Soc Trans 2003, 31(Pt 6):1513-1515 14641101
-
(2003)
Biochem Soc Trans
, vol.31
, Issue.PART 6
, pp. 1513-1515
-
-
Pinney, J.W.1
Westhead, D.R.2
McConkey, G.A.3
-
60
-
-
21644439156
-
Modeling and simulation of molecular biology systems using petri nets: Modeling goals of various approaches
-
10.1142/S0219720004000764 15617157
-
Hardy S Robillard PN Modeling and simulation of molecular biology systems using petri nets: Modeling goals of various approaches J Bioinform Comput Biol 2004, 2(4):595-613 10.1142/S0219720004000764 15617157
-
(2004)
J Bioinform Comput Biol
, vol.2
, Issue.4
, pp. 595-613
-
-
Hardy, S.1
Robillard, P.N.2
-
61
-
-
12844277447
-
Connecting the dots between genes, biochemistry, and disease susceptibility: Systems biology modeling in human genetics
-
10.1016/j.ymgme.2004.10.006 15670716
-
Moore JH Boczko EM Summar ML Connecting the dots between genes, biochemistry, and disease susceptibility: Systems biology modeling in human genetics Mol Genet Metab 2005, 84(2):104-111 10.1016/ j.ymgme.2004.10.006 15670716
-
(2005)
Mol Genet Metab
, vol.84
, Issue.2
, pp. 104-111
-
-
Moore, J.H.1
Boczko, E.M.2
Summar, M.L.3
-
62
-
-
33847304166
-
Qualitatively modelling and analysing genetic regulatory networks: A Petri net approach
-
10.1093/bioinformatics/btl596 17121774
-
Steggles LJ Banks R Shaw O Wipat A Qualitatively modelling and analysing genetic regulatory networks: A Petri net approach Bioinformatics (Oxford, England) 2007, 23(3):336-343 10.1093/bioinformatics/btl596 17121774
-
(2007)
Bioinformatics (Oxford, England)
, vol.23
, Issue.3
, pp. 336-343
-
-
Steggles, L.J.1
Banks, R.2
Shaw, O.3
Wipat, A.4
-
63
-
-
0032611513
-
Modeling gene expression with differential equations
-
10380183
-
Chen T He HL Church GM Modeling gene expression with differential equations Pac Symp Biocomput 1999, 29-40 10380183
-
(1999)
Pac Symp Biocomput
, pp. 29-40
-
-
Chen, T.1
He, H.L.2
Church, G.M.3
-
64
-
-
0032612220
-
Linear modeling of mRNA expression levels during CNS development and injury
-
10380184
-
D'Haeseleer P Wen X Fuhrman S Somogyi R Linear modeling of mRNA expression levels during CNS development and injury Pac Symp Biocomput 1999, 41-52 10380184
-
(1999)
Pac Symp Biocomput
, pp. 41-52
-
-
D'Haeseleer, P.1
Wen, X.2
Fuhrman, S.3
Somogyi, R.4
-
65
-
-
0036905483
-
The dynamics of cell cycle regulation
-
10.1002/bies.10191 12447975
-
Tyson JJ Csikasz-Nagy A Novak B The dynamics of cell cycle regulation Bioessays 2002, 24(12):1095-1109 10.1002/bies.10191 12447975
-
(2002)
Bioessays
, vol.24
, Issue.12
, pp. 1095-1109
-
-
Tyson, J.J.1
Csikasz-Nagy, A.2
Novak, B.3
-
66
-
-
0033782304
-
Modeling transcriptional control in gene networks-methods, recent results, and future directions
-
10.1006/bulm.1999.0155 10824430
-
Smolen P Baxter DA Byrne JH Modeling transcriptional control in gene networks-methods, recent results, and future directions Bull Math Biol 2000, 62(2):247-292 10.1006/bulm.1999.0155 10824430
-
(2000)
Bull Math Biol
, vol.62
, Issue.2
, pp. 247-292
-
-
Smolen, P.1
Baxter, D.A.2
Byrne, J.H.3
-
67
-
-
0033642487
-
Algorithms for inferring qualitative models of biological networks
-
10902178
-
Akutsu T Miyano S Kuhara S Algorithms for inferring qualitative models of biological networks Pac Symp Biocomput 2000, 293-304 10902178
-
(2000)
Pac Symp Biocomput
, pp. 293-304
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
68
-
-
0032879544
-
Genetic control of flower morphogenesis in Arabidopsis thaliana: A logical analysis
-
(Oxford, England) 10.1093/bioinformatics/15.7.593 10487867
-
Mendoza L Thieffry D Alvarez-Buylla ER Genetic control of flower morphogenesis in Arabidopsis thaliana: A logical analysis Bioinformatics (Oxford, England) 1999, 15(7-8):593-606 10.1093/bioinformatics/15.7.593 10487867
-
(1999)
Bioinformatics
, vol.15
, Issue.7-8
, pp. 593-606
-
-
Mendoza, L.1
Thieffry, D.2
Alvarez-Buylla, E.R.3
-
69
-
-
0014671878
-
Homeostasis and differentiation in random genetic control networks
-
10.1038/224177a0 5343519
-
Kauffman S Homeostasis and differentiation in random genetic control networks Nature 1969, 224(215):177-178 10.1038/224177a0 5343519
-
(1969)
Nature
, vol.224
, Issue.215
, pp. 177-178
-
-
Kauffman, S.1
-
70
-
-
0003737454
-
-
Oxford University Press Inc, USA
-
Kauffman SA Investigations Oxford University Press Inc, USA 2002
-
(2002)
Investigations
-
-
Kauffman, S.A.1
-
71
-
-
33344474684
-
Properties of attractors of canalyzing random Boolean networks
-
16605409
-
Paul U Kaufman V Drossel B Properties of attractors of canalyzing random Boolean networks Phys Rev E Stat Nonlin Soft Matter Phys 2006, 73(2 Pt 2):026118 16605409
-
(2006)
Phys Rev E Stat Nonlin Soft Matter Phys
, vol.73
, Issue.2 PART 2
, pp. 026118
-
-
Paul, U.1
Kaufman, V.2
Drossel, B.3
-
72
-
-
0033737840
-
Inferring qualitative relations in genetic networks and metabolic pathways
-
(Oxford, England) 10.1093/bioinformatics/16.8.727 11099258
-
Akutsu T Miyano S Kuhara S Inferring qualitative relations in genetic networks and metabolic pathways Bioinformatics (Oxford, England) 2000, 16(8):727-734 10.1093/bioinformatics/16.8.727 11099258
-
(2000)
Bioinformatics
, vol.16
, Issue.8
, pp. 727-734
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
73
-
-
0036184629
-
Probabilistic Boolean Networks: A rule-based uncertainty model for gene regulatory networks
-
(Oxford, England) 10.1093/bioinformatics/18.2.261 11847074
-
Shmulevich I Dougherty ER Kim S Zhang W Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks Bioinformatics (Oxford, England) 2002, 18(2):261-274 10.1093/ bioinformatics/18.2.261 11847074
-
(2002)
Bioinformatics
, vol.18
, Issue.2
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
74
-
-
0029267491
-
Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop- characteristic state
-
7703920
-
Thomas R Thieffry D Kaufman M Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop- characteristic state Bull Math Biol 1995, 57(2):247-276 7703920
-
(1995)
Bull Math Biol
, vol.57
, Issue.2
, pp. 247-276
-
-
Thomas, R.1
Thieffry, D.2
Kaufman, M.3
-
75
-
-
16344381707
-
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
-
(Oxford, England) 10.1093/bioinformatics/bti145 15546934
-
Koch I Junker BH Heiner M Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber Bioinformatics (Oxford, England) 2005, 21(7):1219-1226 10.1093/ bioinformatics/bti145 15546934
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 1219-1226
-
-
Koch, I.1
Junker, B.H.2
Heiner, M.3
-
76
-
-
0033670135
-
Pathway analysis in metabolic databases via differential metabolic display (DMD)
-
(Oxford, England) 10.1093/bioinformatics/16.9.825 11108705
-
Kuffner R Zimmer R Lengauer T Pathway analysis in metabolic databases via differential metabolic display (DMD) Bioinformatics (Oxford, England) 2000, 16(9):825-836 10.1093/bioinformatics/16.9.825 11108705
-
(2000)
Bioinformatics
, vol.16
, Issue.9
, pp. 825-836
-
-
Kuffner, R.1
Zimmer, R.2
Lengauer, T.3
-
77
-
-
0036188159
-
Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae
-
(Oxford, England) 10.1093/bioinformatics/18.2.351 11847093
-
Schuster S Pfeiffer T Moldenhauer F Koch I Dandekar T Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae Bioinformatics (Oxford, England) 2002, 18(2):351-361 10.1093/bioinformatics/18.2.351 11847093
-
(2002)
Bioinformatics
, vol.18
, Issue.2
, pp. 351-361
-
-
Schuster, S.1
Pfeiffer, T.2
Moldenhauer, F.3
Koch, I.4
Dandekar, T.5
-
79
-
-
0032600734
-
Nonlinear metabolic control analysis
-
10.1006/mben.1998.0108
-
Hatzimanikatis V Nonlinear metabolic control analysis Metab Eng 1999, 1(1):75-87 10.1006/mben.1998.0108 10935756
-
(1999)
Metab Eng
, vol.1
, Issue.1
, pp. 75-87
-
-
Hatzimanikatis, V.1
-
80
-
-
0034791625
-
Modeling genetic regulatory dynamics in neural development
-
10.1089/106652701752236223 11571076
-
Wahde M Hertz J Modeling genetic regulatory dynamics in neural development J Comput Biol 2001, 8(4):429-442 10.1089/106652701752236223 11571076
-
(2001)
J Comput Biol
, vol.8
, Issue.4
, pp. 429-442
-
-
Wahde, M.1
Hertz, J.2
-
81
-
-
0036843965
-
Gene networks: How to put the function in genomics
-
10.1016/S0167-7799(02)02053-X 12413821
-
Brazhnik P de la Fuente A Mendes P Gene networks: How to put the function in genomics Trends Biotechnol 2002, 20(11):467-472 10.1016/ S0167-7799(02)02053-X 12413821
-
(2002)
Trends Biotechnol
, vol.20
, Issue.11
, pp. 467-472
-
-
Brazhnik, P.1
de la Fuente, A.2
Mendes, P.3
-
82
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: A literature review
-
10.1089/10665270252833208 11911796
-
de Jong H Modeling and simulation of genetic regulatory systems: A literature review J Comput Biol 2002, 9(1):67-103 10.1089/ 10665270252833208 11911796
-
(2002)
J Comput Biol
, vol.9
, Issue.1
, pp. 67-103
-
-
de Jong, H.1
-
83
-
-
0033725197
-
Mathematical modeling of gene networks
-
10.1016/S0896-6273(00)81194-0 10896154
-
Smolen P Baxter DA Byrne JH Mathematical modeling of gene networks Neuron 2000, 26(3):567-580 10.1016/S0896-6273(00)81194-0 10896154
-
(2000)
Neuron
, vol.26
, Issue.3
, pp. 567-580
-
-
Smolen, P.1
Baxter, D.A.2
Byrne, J.H.3
-
85
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
10.1038/35018085 10910359
-
von Dassow G Meir E Munro EM Odell GM The segment polarity network is a robust developmental module Nature 2000, 406(6792):188-192 10.1038/ 35018085 10910359
-
(2000)
Nature
, vol.406
, Issue.6792
, pp. 188-192
-
-
von Dassow, G.1
Meir, E.2
Munro, E.M.3
Odell, G.M.4
-
86
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
(Oxford, England) 10.1093/bioinformatics/btg015 12611808
-
Hucka M Finney A Sauro HM Bolouri H Doyle JC Kitano H Arkin AP Bornstein BJ Bray D Cornish-Bowden A The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models Bioinformatics (Oxford, England) 2003, 19(4):524-531 10.1093/ bioinformatics/btg015 12611808
-
(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
-
87
-
-
0032499741
-
Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets
-
22622 9618484 10.1073/pnas.95.12.6750
-
Goss PJ Peccoud J Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets Proc Natl Acad Sci USA 1998, 95(12):6750-6755 22622 9618484 10.1073/pnas.95.12.6750
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, Issue.12
, pp. 6750-6755
-
-
Goss, P.J.1
Peccoud, J.2
-
88
-
-
33645299531
-
A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals
-
10.1142/S021972000600176X 16568547
-
Matsuno H Inouye ST Okitsu Y Fujii Y Miyano S A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals J Bioinform Comput Biol 2006, 4(1):139-153 10.1142/ S021972000600176X 16568547
-
(2006)
J Bioinform Comput Biol
, vol.4
, Issue.1
, pp. 139-153
-
-
Matsuno, H.1
Inouye, S.T.2
Okitsu, Y.3
Fujii, Y.4
Miyano, S.5
-
89
-
-
0029028963
-
Circuit simulation of genetic networks
-
10.1126/science.7624793 7624793
-
McAdams HH Shapiro L Circuit simulation of genetic networks Science 1995, 269(5224):650-656 10.1126/science.7624793 7624793
-
(1995)
Science
, vol.269
, Issue.5224
, pp. 650-656
-
-
McAdams, H.H.1
Shapiro, L.2
-
90
-
-
33748532797
-
Reconstruction of gene regulatory networks under the Finite State Linear Model
-
16901105
-
Ruklisa D Brazma A Viksna J Reconstruction of gene regulatory networks under the Finite State Linear Model Genome informatics 2005, 16(2):225-236 16901105
-
(2005)
Genome Informatics
, vol.16
, Issue.2
, pp. 225-236
-
-
Ruklisa, D.1
Brazma, A.2
Viksna, J.3
-
91
-
-
2942572373
-
Reverse engineering of gene regulatory networks: A finite state linear model
-
10.1186/gb-2003-4-6-p5
-
Brazma A Schlitt T Reverse engineering of gene regulatory networks: A finite state linear model Genome Biology 2003, 4(6):P5 10.1186/ gb-2003-4-6-p5
-
(2003)
Genome Biology
, vol.4
, Issue.6
-
-
Brazma, A.1
Schlitt, T.2
-
93
-
-
0032567081
-
Dissecting the regulatory circuitry of a eukaryotic genome
-
10.1016/S0092-8674(00)81641-4 9845373
-
Holstege FC Jennings EG Wyrick JJ Lee TI Hengartner CJ Green MR Golub TR Lander ES Young RA Dissecting the regulatory circuitry of a eukaryotic genome Cell 1998, 95(5):717-728 10.1016/S0092-8674(00)81641-4 9845373
-
(1998)
Cell
, vol.95
, Issue.5
, pp. 717-728
-
-
Holstege, F.C.1
Jennings, E.G.2
Wyrick, J.J.3
Lee, T.I.4
Hengartner, C.J.5
Green, M.R.6
Golub, T.R.7
Lander, E.S.8
Young, R.A.9
-
94
-
-
0031029852
-
Stochastic mechanisms in gene expression
-
19596 9023339 10.1073/pnas.94.3.814
-
McAdams HH Arkin A Stochastic mechanisms in gene expression Proc Natl Acad Sci USA 1997, 94(3):814-819 19596 9023339 10.1073/pnas.94.3.814
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, Issue.3
, pp. 814-819
-
-
McAdams, H.H.1
Arkin, A.2
-
95
-
-
2942718723
-
Control of stochasticity in eukaryotic gene expression
-
1410811 15166317 10.1126/science.1098641
-
Raser JM O'Shea EK Control of stochasticity in eukaryotic gene expression Science 2004, 304(5678):1811-1814 1410811 15166317 10.1126/ science.1098641
-
(2004)
Science
, vol.304
, Issue.5678
, pp. 1811-1814
-
-
Raser, J.M.1
O'Shea, E.K.2
-
96
-
-
0842285841
-
Summing up the noise in gene networks
-
10.1038/nature02257 14749823
-
Paulsson J Summing up the noise in gene networks Nature 2004, 427(6973):415-418 10.1038/nature02257 14749823
-
(2004)
Nature
, vol.427
, Issue.6973
, pp. 415-418
-
-
Paulsson, J.1
-
97
-
-
0037687416
-
Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
-
156306 12730377 10.1073/pnas.0933416100
-
Tegner J Yeung MK Hasty J Collins JJ Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling Proc Natl Acad Sci USA 2003, 100(10):5944-5949 156306 12730377 10.1073/pnas.0933416100
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.10
, pp. 5944-5949
-
-
Tegner, J.1
Yeung, M.K.2
Hasty, J.3
Collins, J.J.4
-
98
-
-
2342578714
-
Spatiotemporal control of gene expression with pulse-generating networks
-
404049 15096621 10.1073/pnas.0307571101
-
Basu S Mehreja R Thiberge S Chen MT Weiss R Spatiotemporal control of gene expression with pulse-generating networks Proc Natl Acad Sci USA 2004, 101(17):6355-6360 404049 15096621 10.1073/pnas.0307571101
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.17
, pp. 6355-6360
-
-
Basu, S.1
Mehreja, R.2
Thiberge, S.3
Chen, M.T.4
Weiss, R.5
-
99
-
-
17144456808
-
Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion
-
125456 11350942 10.1093/emboj/20.10.2528
-
Becskei A Seraphin B Serrano L Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion EMBO J 2001, 20(10):2528-2535 125456 11350942 10.1093/emboj/20.10.2528
-
(2001)
EMBO J
, vol.20
, Issue.10
, pp. 2528-2535
-
-
Becskei, A.1
Seraphin, B.2
Serrano, L.3
-
100
-
-
0034212551
-
Engineering stability in gene networks by autoregulation
-
10.1038/35014651 10850721
-
Becskei A Serrano L Engineering stability in gene networks by autoregulation Nature 2000, 405(6786):590-593 10.1038/35014651 10850721
-
(2000)
Nature
, vol.405
, Issue.6786
, pp. 590-593
-
-
Becskei, A.1
Serrano, L.2
-
101
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
10.1038/35002125 10659856
-
Elowitz MB Leibler S A synthetic oscillatory network of transcriptional regulators Nature 2000, 403(6767):335-338 10.1038/35002125 10659856
-
(2000)
Nature
, vol.403
, Issue.6767
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
102
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
10.1038/35002131 10659857
-
Gardner TS Cantor CR Collins JJ Construction of a genetic toggle switch in Escherichia coli Nature 2000, 403(6767):339-342 10.1038/35002131 10659857
-
(2000)
Nature
, vol.403
, Issue.6767
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
103
-
-
2942614884
-
Programmable cells: Interfacing natural and engineered gene networks
-
420408 15159530 10.1073/pnas.0402940101
-
Kobayashi H Kaern M Araki M Chung K Gardner TS Cantor CR Collins JJ Programmable cells: Interfacing natural and engineered gene networks Proc Natl Acad Sci USA 2004, 101(22):8414-8419 420408 15159530 10.1073/ pnas.0402940101
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.22
, pp. 8414-8419
-
-
Kobayashi, H.1
Kaern, M.2
Araki, M.3
Chung, K.4
Gardner, T.S.5
Cantor, C.R.6
Collins, J.J.7
-
104
-
-
0035165508
-
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data
-
29796 11125055 10.1093/nar/29.1.80
-
Ball CA Jin H Sherlock G Weng S Matese JC Andrada R Binkley G Dolinski K Dwight SS Harris MA Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data Nucleic Acids Res 2001, 29(1):80-81 29796 11125055 10.1093/nar/29.1.80
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.1
, pp. 80-81
-
-
Ball, C.A.1
Jin, H.2
Sherlock, G.3
Weng, S.4
Matese, J.C.5
Andrada, R.6
Binkley, G.7
Dolinski, K.8
Dwight, S.S.9
Harris, M.A.10
-
105
-
-
0642336165
-
The engineering of gene regulatory networks
-
10.1146/annurev.bioeng.5.040202.121553 14527313
-
Kaern M Blake WJ Collins JJ The engineering of gene regulatory networks Annu Rev Biomed Eng 2003, 5:179-206 10.1146/ annurev.bioeng.5.040202.121553 14527313
-
(2003)
Annu Rev Biomed Eng
, vol.5
, pp. 179-206
-
-
Kaern, M.1
Blake, W.J.2
Collins, J.J.3
-
106
-
-
0032112293
-
A genome-wide transcriptional analysis of the mitotic cell cycle
-
10.1016/S1097-2765(00)80114-8 9702192
-
Cho RJ Campbell MJ Winzeler EA Steinmetz L Conway A Wodicka L Wolfsberg TG Gabrielian AE Landsman D Lockhart DJ A genome-wide transcriptional analysis of the mitotic cell cycle Mol Cell 1998, 2(1):65-73 10.1016/ S1097-2765(00)80114-8 9702192
-
(1998)
Mol Cell
, vol.2
, Issue.1
, pp. 65-73
-
-
Cho, R.J.1
Campbell, M.J.2
Winzeler, E.A.3
Steinmetz, L.4
Conway, A.5
Wodicka, L.6
Wolfsberg, T.G.7
Gabrielian, A.E.8
Landsman, D.9
Lockhart, D.J.10
-
107
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
25624 9843569
-
Spellman PT Sherlock G Zhang MQ Iyer VR Anders K Eisen MB Brown PO Botstein D Futcher B Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization Mol Biol Cell 1998, 9(12):3273-3297 25624 9843569
-
(1998)
Mol Biol Cell
, vol.9
, Issue.12
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
108
-
-
12244267727
-
Global transcriptional responses of fission yeast to environmental stress
-
140239 12529438 10.1091/mbc.E02-08-0499
-
Chen D Toone WM Mata J Lyne R Burns G Kivinen K Brazma A Jones N Bahler J Global transcriptional responses of fission yeast to environmental stress Mol Biol Cell 2003, 14(1):214-229 140239 12529438 10.1091/ mbc.E02-08-0499
-
(2003)
Mol Biol Cell
, vol.14
, pp. 214-229
-
-
Chen, D.1
Toone, W.M.2
Mata, J.3
Lyne, R.4
Burns, G.5
Kivinen, K.6
Brazma, A.7
Jones, N.8
Bahler, J.9
-
109
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
15070 11102521
-
Gasch AP Spellman PT Kao CM Carmel-Harel O Eisen MB Storz G Botstein D Brown PO Genomic expression programs in the response of yeast cells to environmental changes Mol Biol Cell 2000, 11(12):4241-4257 15070 11102521
-
(2000)
Mol Biol Cell
, vol.11
, Issue.12
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
110
-
-
0035805255
-
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
-
10.1126/science.292.5518.929 11340206
-
Ideker T Thorsson V Ranish JA Christmas R Buhler J Eng JK Bumgarner R Goodlett DR Aebersold R Hood L Integrated genomic and proteomic analyses of a systematically perturbed metabolic network Science 2001, 292(5518):929-934 10.1126/science.292.5518.929 11340206
-
(2001)
Science
, vol.292
, Issue.5518
, pp. 929-934
-
-
Ideker, T.1
Thorsson, V.2
Ranish, J.A.3
Christmas, R.4
Buhler, J.5
Eng, J.K.6
Bumgarner, R.7
Goodlett, D.R.8
Aebersold, R.9
Hood, L.10
-
111
-
-
13244284551
-
Dynamic complex formation during the yeast cell cycle
-
10.1126/science.1105103 15692050
-
de Lichtenberg U Jensen LJ Brunak S Bork P Dynamic complex formation during the yeast cell cycle Science 2005, 307(5710):724-727 10.1126/ science.1105103 15692050
-
(2005)
Science
, vol.307
, Issue.5710
, pp. 724-727
-
-
de Lichtenberg, U.1
Jensen, L.J.2
Brunak, S.3
Bork, P.4
-
112
-
-
0037135134
-
Systematic identification of pathways that couple cell growth and division in yeast
-
10.1126/science.1070850 12089449
-
Jorgensen P Nishikawa JL Breitkreutz BJ Tyers M Systematic identification of pathways that couple cell growth and division in yeast Science 2002, 297(5580):395-400 10.1126/science.1070850 12089449
-
(2002)
Science
, vol.297
, Issue.5580
, pp. 395-400
-
-
Jorgensen, P.1
Nishikawa, J.L.2
Breitkreutz, B.J.3
Tyers, M.4
-
113
-
-
0015823097
-
Boolean formalization of genetic control circuits
-
10.1016/0022-5193(73)90247-6 4588055
-
Thomas R Boolean formalization of genetic control circuits J Theor Biol 1973, 42(3):563-585 10.1016/0022-5193(73)90247-6 4588055
-
(1973)
J Theor Biol
, vol.42
, Issue.3
, pp. 563-585
-
-
Thomas, R.1
|