-
3
-
-
85037030721
-
Design and synthesis of synchronization skeletons using branching time temporal logic
-
New York: Springer Berlin/Heidelberg
-
Clarke EM Emerson EA Design and synthesis of synchronization skeletons using branching time temporal logic Logic of Programs New York: Springer Berlin/Heidelberg 1982:52-71.
-
(1982)
Logic of Programs
, pp. 52-71
-
-
Clarke, E.M.1
Emerson, E.A.2
-
4
-
-
0020299274
-
Specification and verification of concurrent systems in CESAR
-
Queille JP Sifakis J Specification and verification of concurrent systems in CESAR Lecture Notes in Computer Science 1982, 137:337-351.
-
(1982)
Lecture Notes in Computer Science
, vol.137
, pp. 337-351
-
-
Queille, J.P.1
Sifakis, J.2
-
6
-
-
0142037521
-
Model building and model checking for biochemical processes
-
12794268
-
Antoniotti M Policriti A Ugel N Mishra B Model building and model checking for biochemical processes Cell Biochem Biophys 2003, 38(3):271-286. 12794268
-
(2003)
Cell Biochem Biophys
, vol.38
, Issue.3
, pp. 271-286
-
-
Antoniotti, M.1
Policriti, A.2
Ugel, N.3
Mishra, B.4
-
7
-
-
84860513120
-
Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli
-
15961457
-
Batt G Ropers D de Jong H Geiselmann J Mateescu R Page M Schneider D Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli Bioinformatics 2005, 21(Suppl 1):i19-i28. 15961457
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Batt, G.1
Ropers, D.2
de Jong, H.3
Geiselmann, J.4
Mateescu, R.5
Page, M.6
Schneider, D.7
-
9
-
-
34249725570
-
Predictive modeling of signaling crosstalk during C. elegans vulval development
-
1868774 17511512
-
Fisher J Piterman N Hajnal A Henzinger TA Predictive modeling of signaling crosstalk during C. elegans vulval development PLoS Comput Biol 2007, 3(5):e92. 1868774 17511512
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.5
-
-
Fisher, J.1
Piterman, N.2
Hajnal, A.3
Henzinger, T.A.4
-
12
-
-
49549083532
-
Temporal logic patterns for querying dynamic models of cellular interaction networks
-
18689830
-
Monteiro PT Ropers D Mateescu R Freitas AT de Jong H Temporal logic patterns for querying dynamic models of cellular interaction networks Bioinformatics 2008, 24(16):i227-i233. 18689830
-
(2008)
Bioinformatics
, vol.24
, Issue.16
-
-
Monteiro, P.T.1
Ropers, D.2
Mateescu, R.3
Freitas, A.T.4
de Jong, H.5
-
14
-
-
0035235039
-
Representation and simulation of biochemical processes using the pi-calculus process algebra
-
11262964
-
Regev A Silverman W Shapiro E Representation and simulation of biochemical processes using the pi-calculus process algebra Pac Symp Biocomput 2001, 459:-470. 11262964.
-
(2001)
Pac Symp Biocomput
, pp. 459-470
-
-
Regev, A.1
Silverman, W.2
Shapiro, E.3
-
15
-
-
0041344538
-
A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling
-
1223496 12691603
-
Hatakeyama M Kimura S Naka T Kawasaki T Yumoto N Ichikawa M Kim JH Saito K Saeki M Shirouzu M Yokoyama S Konagaya A A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling Biochem J 2003, 373(2):451-463. 1223496 12691603
-
(2003)
Biochem J
, vol.373
, Issue.2
, pp. 451-463
-
-
Hatakeyama, M.1
Kimura, S.2
Naka, T.3
Kawasaki, T.4
Yumoto, N.5
Ichikawa, M.6
Kim, J.H.7
Saito, K.8
Saeki, M.9
Shirouzu, M.10
Yokoyama, S.11
Konagaya, A.12
-
16
-
-
0345170900
-
Biopathways representation and simulation on hybrid functional Petri net
-
12954096
-
Matsuno H Tanaka Y Aoshima H Doi A Matsui M Miyano S Biopathways representation and simulation on hybrid functional Petri net In Silico Biol 2003, 3(3):389-404. 12954096
-
(2003)
In Silico Biol
, vol.3
, Issue.3
, pp. 389-404
-
-
Matsuno, H.1
Tanaka, Y.2
Aoshima, H.3
Doi, A.4
Matsui, M.5
Miyano, S.6
-
17
-
-
33845569068
-
Computational modeling of biological processes with Petri net based architecture
-
Springer Berlin Heidelberg Chen YP
-
Nagasaki M Doi A Matsuno H Miyano S Computational modeling of biological processes with Petri net based architecture Bioinformatics Technologies Springer Berlin Heidelberg Chen YP 2005
-
(2005)
Bioinformatics Technologies
-
-
Nagasaki, M.1
Doi, A.2
Matsuno, H.3
Miyano, S.4
-
18
-
-
18244391495
-
A versatile Petri net based architecture for modeling and simulation of complex biological processes
-
15712121
-
Nagasaki M Doi A Matsuno H Miyano S A versatile Petri net based architecture for modeling and simulation of complex biological processes Genome Inform 2004, 15(1):180-197. 15712121
-
(2004)
Genome Inform
, vol.15
, Issue.1
, pp. 180-197
-
-
Nagasaki, M.1
Doi, A.2
Matsuno, H.3
Miyano, S.4
-
19
-
-
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
-
20
-
-
33845569120
-
Petri net based descriptions for systematic understanding of biological pathways
-
E89-A
-
Matsuno H Li C Miyano S Petri net based descriptions for systematic understanding of biological pathways IEICE Trans Fundamentals 2006, E89-A(11):3166-3174.
-
(2006)
IEICE Trans Fundamentals
, Issue.11
, pp. 3166-3174
-
-
Matsuno, H.1
Li, C.2
Miyano, S.3
-
21
-
-
33947508946
-
Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets
-
17426385
-
Li C Ge QW Nakata M Matsuno H Miyano S Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets J Biosci 2007, 32(1):113-127. 17426385
-
(2007)
J Biosci
, vol.32
, Issue.1
, pp. 113-127
-
-
Li, C.1
Ge, Q.W.2
Nakata, M.3
Matsuno, H.4
Miyano, S.5
-
22
-
-
34548302044
-
Petri net modelling of biological networks
-
17626066
-
Chaouiya C Petri net modelling of biological networks Brief Bioinform 2007, 8(4):210-219. 17626066
-
(2007)
Brief Bioinform
, vol.8
, Issue.4
, pp. 210-219
-
-
Chaouiya, C.1
-
23
-
-
84889394191
-
Petri nets
-
A Wiley Interscience Publication Junker BH, Schreiber F
-
Koch I Heiner M Petri nets Analysis of Biological Networks A Wiley Interscience Publication Junker BH, Schreiber F 2008:139-180.
-
(2008)
Analysis of Biological Networks
, pp. 139-180
-
-
Koch, I.1
Heiner, M.2
-
26
-
-
2642533799
-
Genomic Object Net: I. A platform for modelling and simulating biopathways
-
15130806
-
Nagasaki M Doi A Matsuno H Miyano S Genomic Object Net: I. A platform for modelling and simulating biopathways Appl Bioinformatics 2003, 2(3):181-184. 15130806
-
(2003)
Appl Bioinformatics
, vol.2
, Issue.3
, pp. 181-184
-
-
Nagasaki, M.1
Doi, A.2
Matsuno, H.3
Miyano, S.4
-
27
-
-
10044242838
-
Constructing biological pathway models with hybrid functional Petri nets
-
15724280
-
Doi A Fujita S Matsuno H Nagasaki M Miyano S Constructing biological pathway models with hybrid functional Petri nets In Silico Biol 2004, 4(3):271-291. 15724280
-
(2004)
In Silico Biol
, vol.4
, Issue.3
, pp. 271-291
-
-
Doi, A.1
Fujita, S.2
Matsuno, H.3
Nagasaki, M.4
Miyano, S.5
-
28
-
-
2642527148
-
Abstract Genomic Object Net: II. modelling biopathways by hybrid functional Petri net with extension
-
15130807
-
Doi A Nagasaki M Fujita S Matsuno H Miyano S Abstract Genomic Object Net: II. modelling biopathways by hybrid functional Petri net with extension Appl Bioinformatics 2003 2(3):185-188. 15130807
-
(2003)
Appl Bioinformatics
, vol.2
, Issue.3
, pp. 185-188
-
-
Doi, A.1
Nagasaki, M.2
Fujita, S.3
Matsuno, H.4
Miyano, S.5
-
30
-
-
0041627864
-
Boundary formation by notch signaling in Drosophila multicellular systems: Experimental observations and gene network modeling by Genomic Object Net
-
12603025
-
Matsuno H Murakami R Yamane R Yamasaki N Fujita S Yoshimori H Miyano S Boundary formation by notch signaling in Drosophila multicellular systems: Experimental observations and gene network modeling by Genomic Object Net Pac Symp Biocomput 2003:152-163. 12603025
-
(2003)
Pac Symp Biocomput
, pp. 152-163
-
-
Matsuno, H.1
Murakami, R.2
Yamane, R.3
Yamasaki, N.4
Fujita, S.5
Yoshimori, H.6
Miyano, S.7
-
31
-
-
33845595564
-
Modeling and simulation with hybrid functional Petri nets of the role of interleukin-6 in human early haematopoiesis
-
17094258
-
Troncale S Tahi F Campard D Vannier JP Guespin J Modeling and simulation with hybrid functional Petri nets of the role of interleukin-6 in human early haematopoiesis Pac Symp Biocomput 2006:427-438. 17094258
-
(2006)
Pac Symp Biocomput
, pp. 427-438
-
-
Troncale, S.1
Tahi, F.2
Campard, D.3
Vannier, J.P.4
Guespin, J.5
-
32
-
-
0024309272
-
The combined action of two intercellular signaling pathways specifies three cell fates during vulval induction in C. elegans
-
2548732
-
Sternberg PW Horvitz HR The combined action of two intercellular signaling pathways specifies three cell fates during vulval induction in C. elegans Cell 1989, 58(4):679-693. 2548732
-
(1989)
Cell
, vol.58
, Issue.4
, pp. 679-693
-
-
Sternberg, P.W.1
Horvitz, H.R.2
-
34
-
-
33645117792
-
LIN-12/Notch signaling in C. elegans
-
Greenwald I LIN-12/Notch signaling in C. elegans Worm Book 2005, 8:1-16.
-
(2005)
Worm Book
, vol.8
, pp. 1-16
-
-
Greenwald, I.1
-
35
-
-
0442272485
-
Crosstalk between the EGFR and LIN-12/Notch pathways in C. elegans vulval development
-
14752159
-
Yoo A Bais C Greenwald I Crosstalk between the EGFR and LIN-12/Notch pathways in C. elegans vulval development Science 2004, 303(5658):663-666. 14752159
-
(2004)
Science
, vol.303
, Issue.5658
, pp. 663-666
-
-
Yoo, A.1
Bais, C.2
Greenwald, I.3
-
36
-
-
0030014642
-
lag-1, a gene required for lin-12 and glp-1 signaling in Caenorhabditis elegans, is homologous to human CBF1 and Drosophila Su(H)
-
8625826
-
Christensen S Kodoyianni V Bosenberg M Friedman L Kimble J lag-1, a gene required for lin-12 and glp-1 signaling in Caenorhabditis elegans, is homologous to human CBF1 and Drosophila Su(H) Development 1996, 122(5):1373-1383. 8625826
-
(1996)
Development
, vol.122
, Issue.5
, pp. 1373-1383
-
-
Christensen, S.1
Kodoyianni, V.2
Bosenberg, M.3
Friedman, L.4
Kimble, J.5
-
37
-
-
33646515073
-
SynMuv genes redundantly inhibit lin-3/EGF expression to prevent inappropriate vulval induction in C. elegans
-
16678779
-
Cui M Chen J Myers TR Hwang BJ Sternberg PW Greenwald I Han M SynMuv genes redundantly inhibit lin-3/EGF expression to prevent inappropriate vulval induction in C. elegans Dev Cell 2006, 10(5):667-672. 16678779
-
(2006)
Dev Cell
, vol.10
, Issue.5
, pp. 667-672
-
-
Cui, M.1
Chen, J.2
Myers, T.R.3
Hwang, B.J.4
Sternberg, P.W.5
Greenwald, I.6
Han, M.7
-
38
-
-
0027196007
-
lin-31, a Caenorhabditis elegans HNF-3/fork head transcription factor homolog, specifies three alternative cell fates in vulval development
-
8504934
-
Miller LM Gallegos ME Morisseau B Kim S lin-31, a Caenorhabditis elegans HNF-3/fork head transcription factor homolog, specifies three alternative cell fates in vulval development Genes Dev 1993, 7(6):933-947. 8504934
-
(1993)
Genes Dev
, vol.7
, Issue.6
, pp. 933-947
-
-
Miller, L.M.1
Gallegos, M.E.2
Morisseau, B.3
Kim, S.4
-
39
-
-
0022500775
-
Pattern formation during vulval development in C. elegans
-
3753901
-
Sternberg PW Horvitz HR Pattern formation during vulval development in C. elegans Cell 1986, 44(5):761-772. 3753901
-
(1986)
Cell
, vol.44
, Issue.5
, pp. 761-772
-
-
Sternberg, P.W.1
Horvitz, H.R.2
-
40
-
-
0028107517
-
A MAP kinase homolog, mpk-1, is involved in ras-mediated induction of vulval cell fates in Caenorhabditis elegans
-
8299936
-
Lackner M Kornfeld K Miller LM Horvitz HR Kim S A MAP kinase homolog, mpk-1, is involved in ras-mediated induction of vulval cell fates in Caenorhabditis elegans Genes Dev 1994, 8(2):160-173. 8299936
-
(1994)
Genes Dev
, vol.8
, Issue.2
, pp. 160-173
-
-
Lackner, M.1
Kornfeld, K.2
Miller, L.M.3
Horvitz, H.R.4
Kim, S.5
-
41
-
-
0037069661
-
Endocytosis-mediated downregulation of LIN-12/Notch upon Ras activation in Caenorhabditis elegans
-
12478297
-
Shaye DD Greenwald I Endocytosis-mediated downregulation of LIN-12/Notch upon Ras activation in Caenorhabditis elegans Nature 2002, 420(6916):686-690. 12478297
-
(2002)
Nature
, vol.420
, Issue.6916
, pp. 686-690
-
-
Shaye, D.D.1
Greenwald, I.2
-
42
-
-
33751333097
-
Vulval development
-
Sternberg PW Vulval development Worm Book 2005, 25:1-28
-
(2005)
Worm Book
, vol.25
, pp. 1-28
-
-
Sternberg, P.W.1
-
45
-
-
0032524912
-
MAP kinase signaling specificity mediated by the LIN-1 Ets/LIN-31 WH transcription factor complex during C. elegans vulval induction
-
9604932
-
Tan PB Lackner MR Kim SK MAP kinase signaling specificity mediated by the LIN-1 Ets/LIN-31 WH transcription factor complex during C. elegans vulval induction Cell 1998, 93(4):569-580. 9604932
-
(1998)
Cell
, vol.93
, Issue.4
, pp. 569-580
-
-
Tan, P.B.1
Lackner, M.R.2
Kim, S.K.3
-
46
-
-
0035137910
-
Notch inhibition of RAS signaling through MAP kinase phosphatase LIP-1 during C. elegans vulval development
-
11161219
-
Berset T Hoier EF Battu G Canevascini S Hajnal A Notch inhibition of RAS signaling through MAP kinase phosphatase LIP-1 during C. elegans vulval development Science 2001, 291(5506):1055-1058. 11161219
-
(2001)
Science
, vol.291
, Issue.5506
, pp. 1055-1058
-
-
Berset, T.1
Hoier, E.F.2
Battu, G.3
Canevascini, S.4
Hajnal, A.5
-
47
-
-
41849092276
-
Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways
-
18467775
-
Jeong E Nagasaki M Saito A Miyano S Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways In Silico Biol 2007, 7(6):623-638. 18467775
-
(2007)
In Silico Biol
, vol.7
, Issue.6
, pp. 623-638
-
-
Jeong, E.1
Nagasaki, M.2
Saito, A.3
Miyano, S.4
-
48
-
-
67651221266
-
-
Pnuts http://www.pnuts.org/
-
Pnuts
-
-
-
49
-
-
0017618537
-
Post-embryonic cell lineages of the nematode, Caenorhabditis elegans
-
838129
-
Sulston JE Horvitz HR Post-embryonic cell lineages of the nematode, Caenorhabditis elegans Dev Biol 1977, 56(1):110-156. 838129
-
(1977)
Dev Biol
, vol.56
, Issue.1
, pp. 110-156
-
-
Sulston, J.E.1
Horvitz, H.R.2
-
50
-
-
22344439386
-
The C. elegans homolog of the mammalian tumor suppressor Dep-1/Scc1 inhibits EGFR signaling to regulate binary cell fate decisions
-
1142556 15901674
-
Berset TA Hoier EF Hajnal A The C. elegans homolog of the mammalian tumor suppressor Dep-1/Scc1 inhibits EGFR signaling to regulate binary cell fate decisions Genes Dev 2005, 19(11):1328-1340. 1142556 15901674
-
(2005)
Genes Dev
, vol.19
, Issue.11
, pp. 1328-1340
-
-
Berset, T.A.1
Hoier, E.F.2
Hajnal, A.3
-
51
-
-
0023090512
-
A genetic pathway for the specification of the vulval cell lineages of Caenorhabditis elegans
-
2881214
-
Ferguson EL Sternberg PW Horvitz HR A genetic pathway for the specification of the vulval cell lineages of Caenorhabditis elegans Nature 1987, 326(6110):259-267. 2881214
-
(1987)
Nature
, vol.326
, Issue.6110
, pp. 259-267
-
-
Ferguson, E.L.1
Sternberg, P.W.2
Horvitz, H.R.3
-
52
-
-
0019891530
-
Alterations in cell lineage following laser ablation of cells in the somatic gonad of Caenorhabditis elegans
-
7286433
-
Kimble J Alterations in cell lineage following laser ablation of cells in the somatic gonad of Caenorhabditis elegans Dev Biol 1981, 87(2):286-300. 7286433
-
(1981)
Dev Biol
, vol.87
, Issue.2
, pp. 286-300
-
-
Kimble, J.1
-
53
-
-
0025647293
-
The let-60 locus controls the switch between vulval and nonvulval cell fates in Caenorhabditis elegans
-
1204287 2076820
-
Han M Aroian RV Sternberg PW The let-60 locus controls the switch between vulval and nonvulval cell fates in Caenorhabditis elegans Genetics 1990, 126(4):899-913. 1204287 2076820
-
(1990)
Genetics
, vol.126
, Issue.4
, pp. 899-913
-
-
Han, M.1
Aroian, R.V.2
Sternberg, P.W.3
|