-
1
-
-
0004001955
-
SPICE (simulation program with integrated circuit emphasis
-
University of California, Berkley
-
Nagel, L. W., and Pederson, D. O. (1973). SPICE (Simulation Program with Integrated Circuit Emphasis). Memorandum No. ERLM382 , University of California, Berkley.
-
(1973)
Memorandum No. ERLM382
-
-
Nagel, L.W.1
Pederson, D.O.2
-
2
-
-
28544451327
-
Foundations for engineering biology
-
DOI 10.1038/nature04342, PII N04342
-
Endy, D. (2005) Foundations for engineering biology, Nature 438 , 449-453. (Pubitemid 41742010)
-
(2005)
Nature
, vol.438
, Issue.7067
, pp. 449-453
-
-
Endy, D.1
-
3
-
-
33750617708
-
-
The MIT Press, Cambridge, MA
-
Szallasi, Z., Stelling, J., and Periwal (2006) System Modeling in Cellular Biology , The MIT Press, Cambridge, MA.
-
(2006)
System Modeling in Cellular Biology
-
-
Szallasi, Z.1
Stelling, J.2
Periwal3
-
4
-
-
9444266171
-
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
-
Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H. (2003) CellDesigner: a process diagram editor for gene-regulatory and biochemical networks, BIOSILICO 1 , 159-162.
-
(2003)
BIOSILICO
, vol.1
, pp. 159-162
-
-
Funahashi, A.1
Tanimura, N.2
Morohashi, M.3
Kitano, H.4
-
5
-
-
47949099328
-
CellDesigner 3.5: A versatile modeling tool for biochemical networks
-
ed
-
Funahashi, A., Matsuoka, Y., Jourako, A., Morohashi, M., Kikuchi, N., and Kitano, H. CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks, In Proceedings of the IEEE 8 ed., pp 1254-1265.
-
Proceedings of the IEEE
, vol.8
, pp. 1254-1265
-
-
Funahashi, A.1
Matsuoka, Y.2
Jourako, A.3
Morohashi, M.4
Kikuchi, N.5
Kitano, H.6
-
6
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
DOI 10.1093/bioinformatics/btg015
-
Hucka, M., and others. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics 19 , 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..
-
7
-
-
33644877164
-
BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
Novere, N. L., Bornstein, B., Broicher, A., Courtot, M. l., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B., Snoep, J. L., and Hucka, M. (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems, Nucleic Acids Res 34 , D689-D691.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Novere, N.L.1
Bornstein, B.2
Broicher, A.3
Courtot, M.I.4
Donizelli, M.5
Dharuri, H.6
Li, L.7
Sauro, H.8
Schilstra, M.9
Shapiro, B.10
Snoep, J.L.11
Hucka, M.12
-
8
-
-
0242490780
-
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
-
DOI 10.1101/gr.1239303
-
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res 13 , 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
-
9
-
-
77949504985
-
BisoGenet: A new tool for gene network building, visualization and analysis
-
Martin, A., Ochagavia, M. E., Rabasa, L. C., Miranda, J., de Cossio, J. F., and Bringas, R. BisoGenet: a new tool for gene network building, visualization and analysis, BMC Bioinformatics 11 :91.
-
BMC Bioinformatics
, vol.11
, pp. 91
-
-
Martin, A.1
Ochagavia, M.E.2
Rabasa, L.C.3
Miranda, J.4
De Cossio, J.F.5
Bringas, R.6
-
10
-
-
0242380634
-
CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
-
DOI 10.1093/nar/gkg461
-
Kurata, H., Matoba, N., and Shimizu, N. (2003) CADLIVE for constructing a large-scale biochemical network based on a simulationdirected notation and its application to yeast cell cycle, Nucleic Acids Res 31 , 4071-4084. (Pubitemid 37442287)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.14
, pp. 4071-4084
-
-
Kurata, H.1
Matoba, N.2
Shimizu, N.3
-
11
-
-
17844397967
-
CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models
-
DOI 10.1101/gr.3463705
-
Kurata, H., Masaki, K., Sumida, Y., and Iwasaki, R. (2005) CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models, Genome Res 15 , 590-600. (Pubitemid 41057822)
-
(2005)
Genome Research
, vol.15
, Issue.4
, pp. 590-600
-
-
Kurata, H.1
Masaki, K.2
Sumida, Y.3
Iwasaki, R.4
-
12
-
-
0035478586
-
The Virtual Cell: A software environment for computational cell biology
-
DOI 10.1016/S0167-7799(01)01740-1, PII S0167779901017401
-
Loew, L. M., and Schaff, J. C. (2001) The Virtual Cell: a software environment for computational cell biology, Trends Biotechnol 19 , 401-406. (Pubitemid 32925033)
-
(2001)
Trends in Biotechnology
, vol.19
, Issue.10
, pp. 401-406
-
-
Loew, L.M.1
Schaff, J.C.2
-
13
-
-
0347511691
-
Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration
-
Sauro, H. M., Hucka, M., Finney, A., Wellock, C., Bolouri, H., Doyle, J., and Kitano, H. (2003) Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration, OMICS 7 , 355-372. (Pubitemid 38018642)
-
(2003)
OMICS A Journal of Integrative Biology
, vol.7
, Issue.4
, pp. 355-372
-
-
Sauro, H.M.1
Hucka, M.2
Finney, A.3
Wellock, C.4
Bolouri, H.5
Doyle, J.6
Kitano, H.7
-
14
-
-
17644385076
-
Computational representation of developmental genetic regulatory networks
-
DOI 10.1016/j.ydbio.2005.04.023, PII S0012160605002575
-
Longabaugh, W. J. R., Davidson, E. H., and Bolouri, H. (2005) Computational representation of developmental genetic regulatory networks, Dev Biol 283 , 1-16. (Pubitemid 40828838)
-
(2005)
Developmental Biology
, vol.283
, Issue.1
, pp. 1-16
-
-
Longabaugh, W.J.R.1
Davidson, E.H.2
Bolouri, H.3
-
16
-
-
51449095986
-
Genetic design: Rising above the sequence
-
Goler, J. A., Bramlett, B. W., and Peccoud, J. (2008) Genetic design: rising above the sequence, Trends Biotechnol 26 , 538-544.
-
(2008)
Trends Biotechnol
, vol.26
, pp. 538-544
-
-
Goler, J.A.1
Bramlett, B.W.2
Peccoud, J.3
-
17
-
-
41149157016
-
TABASCO: A single molecule, base-pair resolved gene expression simulator
-
Kosuri, S., Kelly, J., and Endy, D. (2007) TABASCO: A single molecule, base-pair resolved gene expression simulator, BMC Bioinformatics 8 :480.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 480
-
-
Kosuri, S.1
Kelly, J.2
Endy, D.3
-
18
-
-
28544451327
-
Adventures in synthetic biology. Appeared in Foundations for engineering biology p449
-
Endy, D., Deese, I., and the, M. I. T. S. B. W. G. (2005). Adventures in synthetic biology. Appeared in Foundations for engineering biology p449, Nature , 438 , 449-453.
-
(2005)
Nature
, vol.438
, pp. 449-453
-
-
Endy, D.1
Deese, I.2
W, G.M.I.T.S.B.3
-
19
-
-
50549103571
-
Computational design of synthetic gene circuits with composable parts
-
Marchisio, M. A., and Stelling, J. (2008) Computational design of synthetic gene circuits with composable parts, Bioinformatics 24 , 1903-1910.
-
(2008)
Bioinformatics
, vol.24
, pp. 1903-1910
-
-
Marchisio, M.A.1
Stelling, J.2
-
20
-
-
70349775548
-
Synthetic gene network computational design
-
Marchisio, M. A., and Stelling, J. Synthetic gene network computational design, In Proc. IEEE International Symposium on Circuits and Systems, ISCAS 2009 , pp 309-312.
-
(2009)
Proc. IEEE International Symposium on Circuits and Systems, ISCAS
, pp. 309-312
-
-
Marchisio, M.A.1
Stelling, J.2
-
21
-
-
34548778155
-
Ribozymes, riboswitches and beyond: Regulation of gene expression without proteins
-
DOI 10.1038/nrg2172, PII NRG2172
-
Serganov, A., and Patel, D. J. (2007) Ribozymes, riboswitches and beyond: regulation of gene expression without proteins, Nat Rev Genet 8 , 776-790. (Pubitemid 47429208)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.10
, pp. 776-790
-
-
Serganov, A.1
Patel, D.J.2
-
22
-
-
61449140264
-
PROMOT: Modular modeling for systems biology
-
Mirschel, S., Steinmetz, K., Rempel, M., Ginkel, M., and Gilles, E. D. (2009) PROMOT: modular modeling for systems biology, Bioinformatics 25 , 687-689.
-
(2009)
Bioinformatics
, vol.25
, pp. 687-689
-
-
Mirschel, S.1
Steinmetz, K.2
Rempel, M.3
Ginkel, M.4
Gilles, E.D.5
-
23
-
-
0037715313
-
Modular modeling of cellular systems with ProMoT/Diva
-
DOI 10.1093/bioinformatics/btg128
-
Ginkel, M., Kremling, A., Nutsch, T., Rehner, R., and Gilles, E. D. (2003) Modular modeling of cellular systems with ProMoT/Diva, Bioinformatics 19 , 1169-1176. (Pubitemid 36790021)
-
(2003)
Bioinformatics
, vol.19
, Issue.9
, pp. 1169-1176
-
-
Ginkel, M.1
Kremling, A.2
Nutsch, T.3
Rehner, R.4
Gilles, E.D.5
-
24
-
-
33845368513
-
COPASI - A COmplex PAthway SImulator
-
DOI 10.1093/bioinformatics/btl485
-
Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, Jr., Simus, N., Singhal, M., Xu, L., Mendes, P., and Kummer, U. (2006) COPASI - a COmplex PAthway SImulator, Bioinformatics 22 , 3067-3074. (Pubitemid 44884083)
-
(2006)
Bioinformatics
, vol.22
, Issue.24
, pp. 3067-3074
-
-
Hoops, S.1
Gauges, R.2
Lee, C.3
Pahle, J.4
Simus, N.5
Singhal, M.6
Xu, L.7
Mendes, P.8
Kummer, U.9
-
25
-
-
46249085749
-
Asmparts: Assembly of biological model parts
-
Rodrigo, G., Carrera, J., and Jaramillo, A. (2008) Asmparts: assembly of biological model parts, Syst Synth Biol 1 , 167-170.
-
(2008)
Syst Synth Biol
, vol.1
, pp. 167-170
-
-
Rodrigo, G.1
Carrera, J.2
Jaramillo, A.3
-
26
-
-
77951969603
-
Standard virtual biological parts: A repository of modular modeling components for synthetic biology
-
Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J., and Wipat, A. Standard virtual biological parts: a repository of modular modeling components for synthetic biology, Bioinformatics 26 , 925-931.
-
Bioinformatics
, vol.26
, pp. 925-931
-
-
Cooling, M.T.1
Rouilly, V.2
Misirli, G.3
Lawson, J.4
Yu, T.5
Hallinan, J.6
Wipat, A.7
-
27
-
-
46249087691
-
Registry of BioBrick models using CellML
-
Rouilly, V., Canton, B., Nielsen, P., and Kitney, R. (2007) Registry of BioBrick models using CellML, BMC System Biology 1 Suppl 1, 79-80.
-
(2007)
BMC System Biology
, vol.1
, Issue.SUPPL. 1
, pp. 79-80
-
-
Rouilly, V.1
Canton, B.2
Nielsen, P.3
Kitney, R.4
-
28
-
-
1342329447
-
An overview of CellML 1.1, a biological model description language
-
Cuellar, A. A., Lloyd, C. M., Nielsen, P. F., Bullivant, D. P., Nickerson, D. P., and Hunter, P. J. (2003) An Overview of CellML 1.1, a Biological Model Description Language, Simulation 79 , 740-747.
-
(2003)
Simulation
, vol.79
, pp. 740-747
-
-
Cuellar, A.A.1
Lloyd, C.M.2
Nielsen, P.F.3
Bullivant, D.P.4
Nickerson, D.P.5
Hunter, P.J.6
-
29
-
-
48349089965
-
CellML and associated tools and techniques
-
Garny, A., Nickerson, D. P., Cooper, J., dos Santos, R. W., Miller, A. K., McKeever, S., Nielsen, P. M. F., and Hunter, P. J. (2008) CellML and associated tools and techniques, Philos Transact A Math Phys Eng Sci 366 , 3017-3043.
-
(2008)
Philos Transact A Math Phys Eng Sci
, vol.366
, pp. 3017-3043
-
-
Garny, A.1
Nickerson, D.P.2
Cooper, J.3
Dos Santos, R.W.4
Miller, A.K.5
McKeever, S.6
Nielsen, P.M.F.7
Hunter, P.J.8
-
30
-
-
71849095864
-
TinkerCell: Modular CAD tool for synthetic biology
-
Chandran, D., Bergmann, F. T., and Sauro, H. M. (2009) TinkerCell: modular CAD tool for synthetic biology, J Biol Eng 3 :19.
-
(2009)
J Biol Eng
, vol.3
, pp. 19
-
-
Chandran, D.1
Bergmann, F.T.2
Sauro, H.M.3
-
31
-
-
69849093395
-
Antimony: A modular model definition language
-
Smith, L. P., Bergmann, F. T., Chandran, D., and Sauro, H. M. (2009) Antimony: a modular model definition language, Bioinformatics 25 , 2452-2454.
-
(2009)
Bioinformatics
, vol.25
, pp. 2452-2454
-
-
Smith, L.P.1
Bergmann, F.T.2
Chandran, D.3
Sauro, H.M.4
-
32
-
-
54949133752
-
SynBioSS: The synthetic biology modeling suite
-
Hill, A. D., Tomshine, J. R., Weeding, E. M. B., Sotiropoulos, V., and Kaznessis, Y. N. (2008) SynBioSS: the synthetic biology modeling suite, Bioinformatics 24 , 2551-2553.
-
(2008)
Bioinformatics
, vol.24
, pp. 2551-2553
-
-
Hill, A.D.1
Tomshine, J.R.2
Weeding, E.M.B.3
Sotiropoulos, V.4
Kaznessis, Y.N.5
-
33
-
-
77955033157
-
SynBioSS designer: A web-based tool for the automated generation of kinetic models for synthetic biological constructs
-
Weeding, E., Houle, J., and Kaznessis, Y. N. SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs, Brief Bioinform 11 , 394-402.
-
Brief Bioinform
, vol.11
, pp. 394-402
-
-
Weeding, E.1
Houle, J.2
Kaznessis, Y.N.3
-
34
-
-
33645465102
-
Multiscale Hy3S: Hybrid stochastic simulation for supercomputers
-
Salis, H., Sotiropoulos, V., and Kaznessis, Y. N. (2006) Multiscale Hy3S: hybrid stochastic simulation for supercomputers, BMC Bioinformatics 7 :93.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 93
-
-
Salis, H.1
Sotiropoulos, V.2
Kaznessis, Y.N.3
-
35
-
-
10244219918
-
BioNetGen: Software for rule-based modeling of signal transduction based on the interactions of molecular domains
-
DOI 10.1093/bioinformatics/bth378
-
Blinov, M. L., Faeder, J. R., Goldstein, B., and Hlavacek, W. S. (2004) BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains, Bioinformatics 20 , 3289-3291. (Pubitemid 39619231)
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 3289-3291
-
-
Blinov, M.L.1
Faeder, J.R.2
Goldstein, B.3
Hlavacek, W.S.4
-
36
-
-
65649154507
-
Rule-based modeling of biochemical systems with BioNetGen
-
Faeder, J. R., Blinov, M. L., and Hlavacek, W. S. (2009) Rule-based modeling of biochemical systems with BioNetGen, Methods Mol Biol 500 , 113-167.
-
(2009)
Methods Mol Biol
, vol.500
, pp. 113-167
-
-
Faeder, J.R.1
Blinov, M.L.2
Hlavacek, W.S.3
-
38
-
-
0034961694
-
STOCHSIM: Modelling of stochastic biomolecular processes
-
Novere, N. L., and Shimizu, T. S. (2001) STOCHSIM: modelling of stochastic biomolecular processes, Bioinformatics 17 , 575-576. (Pubitemid 32600510)
-
(2001)
Bioinformatics
, vol.17
, Issue.6
, pp. 575-576
-
-
Le Novere, N.1
Shimizu, T.S.2
-
39
-
-
66149151035
-
Internal coarse-graining of molecular systems
-
Feret, Jrm., Danos, V., Krivine, J., Harmer, R., and Fontana, W. (2009) Internal coarse-graining of molecular systems, Proc Natl Acad Sci USA 106 , 6453-6458.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 6453-6458
-
-
Feret, J.1
Danos, V.2
Krivine, J.3
Harmer, R.4
Fontana, W.5
-
40
-
-
20144377930
-
Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM
-
Fages, F., Soliman, S., and Chabrier-Rivier, N. (2004) Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM, Journal of Biological Physics and Chemistry 4 , 64-73.
-
(2004)
Journal of Biological Physics and Chemistry
, vol.4
, pp. 64-73
-
-
Fages, F.1
Soliman, S.2
Chabrier-Rivier, N.3
-
41
-
-
0035235039
-
Representation and simulation of biochemical processes using the pi-calculus process algebra
-
Regev, A., Silverman, W., and Shapiro, E. (2001) Representation and simulation of biochemical processes using the pi-calculus process algebra, Pac Symp Biocomput , 459-470.
-
(2001)
Pac Symp Biocomput
, pp. 459-470
-
-
Regev, A.1
Silverman, W.2
Shapiro, E.3
-
42
-
-
43049179364
-
Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
-
DOI 10.1016/j.entcs.2007.12.008, PII S1571066108000285
-
Ciocchetta, F., and Hillston, J. (2008) Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks, Electronic Notes in Theoretical Computational Science 194 , 103-117. (Pubitemid 351173025)
-
(2008)
Electronic Notes in Theoretical Computer Science
, vol.194
, Issue.3
, pp. 103-117
-
-
Ciocchetta, F.1
Hillston, J.2
-
43
-
-
67650663955
-
Towards programming languages for genetic engineering of living cells
-
Pedersen, M., and Phillips, A. (2009) Towards programming languages for genetic engineering of living cells, J R Soc Interface 6 Suppl 4 , S437-S450.
-
(2009)
J R Soc Interface
, vol.6
, Issue.SUPPL. 4
-
-
Pedersen, M.1
Phillips, A.2
-
44
-
-
35748938455
-
A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts
-
DOI 10.1093/bioinformatics/btm446
-
Cai, Y., Hartnett, B., Gustafsson, C., and Peccoud, J. (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts, Bioinformatics 23 , 2760-2767. (Pubitemid 350048342)
-
(2007)
Bioinformatics
, vol.23
, Issue.20
, pp. 2760-2767
-
-
Cai, Y.1
Hartnett, B.2
Gustafsson, C.3
Peccoud, J.4
-
45
-
-
67849130568
-
Writing DNA with GenoCAD
-
Czar, M. J., Cai, Y., and Peccoud, J. (2009) Writing DNA with GenoCAD, Nucleic Acids Res 37 , W40-W47.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Czar, M.J.1
Cai, Y.2
Peccoud, J.3
-
46
-
-
75649131791
-
A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks
-
Monteiro, P. T., Dumas, E., Besson, B., Mateescu, R., Page, M., Freitas, A. T., and de Jong, H. (2009) A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks, BMC Bioinformatics 10 :450.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 450
-
-
Monteiro, P.T.1
Dumas, E.2
Besson, B.3
Mateescu, R.4
Page, M.5
Freitas, A.T.6
De Jong, H.7
-
47
-
-
49549114493
-
Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules
-
Saez-Rodriguez, J., Gayer, S., Ginkel, M., and Gilles, E. D. (2008) Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules, Bioinformatics 24 , 213-219.
-
(2008)
Bioinformatics
, vol.24
, pp. 213-219
-
-
Saez-Rodriguez, J.1
Gayer, S.2
Ginkel, M.3
Gilles, E.D.4
-
48
-
-
33645677022
-
Infrastructure for engineered emergence on sensor/actuator networks
-
Beal, J., and Bachrach, J. (2006) Infrastructure for Engineered Emergence on Sensor/Actuator Networks, IEEE Intelligent Systems 21 (2) , 10-19.
-
(2006)
IEEE Intelligent Systems
, vol.21
, Issue.2
, pp. 10-19
-
-
Beal, J.1
Bachrach, J.2
-
49
-
-
64549144670
-
Programming with models: Modularity and abstraction provide powerful capabilities for systems biology
-
Mallavarapu, A., Thomson, M., Ullian, B., and Gunawardena, J. (2009) Programming with models: modularity and abstraction provide powerful capabilities for systems biology, J R Soc Interface 6 , 257-270.
-
(2009)
J R Soc Interface
, vol.6
, pp. 257-270
-
-
Mallavarapu, A.1
Thomson, M.2
Ullian, B.3
Gunawardena, J.4
-
50
-
-
34548747486
-
Robustness analysis and tuning of synthetic gene networks
-
DOI 10.1093/bioinformatics/btm362
-
Batt, Gg., Yordanov, B., Weiss, R., and Belta, C. (2007) Robustness analysis and tuning of synthetic gene networks, Bioinformatics 23 , 2415-2422. (Pubitemid 47423839)
-
(2007)
Bioinformatics
, vol.23
, Issue.18
, pp. 2415-2422
-
-
Batt, G.1
Yordanov, B.2
Weiss, R.3
Belta, C.4
-
51
-
-
0347635508
-
Design of genetic networks with specified functions by evolution in silico
-
DOI 10.1073/pnas.0304532101
-
Francois, P., and Hakim, V. (2004) Design of genetic networks with specified functions by evolution in silico, Proc Natl Acad Sci USA 101 , 580-585. (Pubitemid 38084679)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.2
, pp. 580-585
-
-
Francois, P.1
Hakim, V.2
-
52
-
-
33746593012
-
In silico evolution of functional modules in biochemical networks
-
DOI 10.1049/ip-syb:20050096
-
Paladugu, S. R., Chickarmane, V., Deckard, A., Frumkin, J. P., McCormack, M., and Sauro, H. M. (2006) In silico evolution of functional modules in biochemical networks, Syst Biol (Stevenage) 153 , 223-235. (Pubitemid 44151482)
-
(2006)
IEE Proceedings: Systems Biology
, vol.153
, Issue.4
, pp. 223-235
-
-
Paladugu, S.R.1
Chickarmane, V.2
Deckard, A.3
Frumkin, J.P.4
McCormack, M.5
Sauro, H.M.6
-
53
-
-
34547861255
-
Genetdes: Automatic design of transcriptional networks
-
DOI 10.1093/bioinformatics/btm237
-
Rodrigo, G., Carrera, J., and Jaramillo, A. (2007) Genetdes: automatic design of transcriptional networks, Bioinformatics 23 , 1857-1858. (Pubitemid 47250327)
-
(2007)
Bioinformatics
, vol.23
, Issue.14
, pp. 1857-1858
-
-
Rodrigo, G.1
Carrera, J.2
Jaramillo, A.3
-
54
-
-
26444479778
-
Optimization by simulated annealing
-
Kirkpatrick, S., Gelatt, C. D., and Vecchi, M. P. (1983) Optimization by Simulated Annealing, Science 220 , 671-680.
-
(1983)
Science
, vol.220
, pp. 671-680
-
-
Kirkpatrick, S.1
Gelatt, C.D.2
Vecchi, M.P.3
-
55
-
-
46249108209
-
Computational design of digital and memory biological devices
-
Rodrigo, G., and Jaramillo, A. (2007) Computational design of digital and memory biological devices, Syst Synth Biol 1 , 183-195.
-
(2007)
Syst Synth Biol
, vol.1
, pp. 183-195
-
-
Rodrigo, G.1
Jaramillo, A.2
-
56
-
-
42549159572
-
OptCircuit: An optimization based method for computational design of genetic circuits
-
Dasika, M. S., and Maranas, C. D. (2008) OptCircuit: an optimization based method for computational design of genetic circuits, BMC Syst Biol 2 :24.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 24
-
-
Dasika, M.S.1
Maranas, C.D.2
-
57
-
-
79952476417
-
Automatic design of digital synthetic gene circuits
-
Marchisio, M. A., and Stelling, Jr. (2011) Automatic Design of Digital Synthetic Gene Circuits, PLoS Comput Biol 7 , e1001083.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Marchisio, M.A.1
Stelling, J.2
-
59
-
-
77952513967
-
GeneDesign 3.0 is an updated synthetic biology toolkit
-
Richardson, S. M., Nunley, P. W., Yarrington, R. M., Boeke, J. D., and Bader, J. S. GeneDesign 3.0 is an updated synthetic biology toolkit, Nucleic Acids Res 38 , 2603-2606.
-
Nucleic Acids Res
, vol.38
, pp. 2603-2606
-
-
Richardson, S.M.1
Nunley, P.W.2
Yarrington, R.M.3
Boeke, J.D.4
Bader, J.S.5
-
60
-
-
33746788103
-
Gene Designer: A synthetic biology tool for constructing artificial DNA segments
-
Villalobos, A., Ness, J. E., Gustafsson, C., Minshull, J., and Govindarajan, S. (2006) Gene Designer: a synthetic biology tool for constructing artificial DNA segments, BMC Bioinformatics 7 :285.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 285
-
-
Villalobos, A.1
Ness, J.E.2
Gustafsson, C.3
Minshull, J.4
Govindarajan, S.5
-
61
-
-
19644370646
-
GeMS: An advanced software package for designing synthetic genes
-
DOI 10.1093/nar/gki614
-
Jayaraj, S., Reid, R., and Santi, D. V. (2005) GeMS: an advanced software package for designing synthetic genes, Nucleic Acids Res 33 , 3011-3016. (Pubitemid 41511238)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.9
, pp. 3011-3016
-
-
Jayaraj, S.1
Reid, R.2
Santi, D.V.3
-
62
-
-
0037095730
-
DNAWorks: An automated method for designing oligonucleotides for PCR-based gene synthesis
-
Hoover, D. M., and Lubkowski, J. (2002) DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis, Nucleic Acids Res 30 (10) :e43.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.10
-
-
Hoover, D.M.1
Lubkowski, J.2
-
63
-
-
3242888495
-
Gene2Oligo: Oligonucleotide design for in vitro gene synthesis
-
DOI 10.1093/nar/gkh401
-
Rouillard, J.-M., Lee, W., Truan, G., Gao, X., Zhou, X., and Gulari, E. (2004) Gene2Oligo: oligonucleotide design for in vitro gene synthesis, Nucleic Acids Res 32 , W176-W180. (Pubitemid 38997324)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.WEB. SERV. ISS.
-
-
Rouillard, J.-M.1
Lee, W.2
Truan, G.3
Gao, X.4
Zhou, X.5
Gulari, E.6
-
64
-
-
33747816812
-
Zinc Finger Tools: Custom DNA-binding domains for transcription factors and nucleases
-
DOI 10.1093/nar/gkl209
-
Mandell, J. G., and Barbas, C. F. (2006) Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases, Nucleic Acids Res 34 , W516-W523. (Pubitemid 44529824)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.WEB. SERV. ISS.
-
-
Mandell, J.G.1
Barbas III, C.F.2
-
65
-
-
0042622239
-
NEBcutter: A program to cleave DNA with restriction enzymes
-
DOI 10.1093/nar/gkg526
-
Vincze, T., Posfai, J., and Roberts, R. J. (2003) NEBcutter: A program to cleave DNA with restriction enzymes, Nucleic Acids Res 31 , 3688-3691. (Pubitemid 37442224)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3688-3691
-
-
Vincze, T.1
Posfai, J.2
Roberts, R.J.3
-
66
-
-
77952521011
-
CLONEQC: Lightweight sequence verification for synthetic biology
-
Lee, P. A., Dymond, J. S., Scheifele, L. Z., Richardson, S. M., Foelber, K. J., Boeke, J. D., and Bader, J. S. CLONEQC: lightweight sequence verification for synthetic biology, Nucleic Acids Res 38 , 2617-2623.
-
Nucleic Acids Res
, vol.38
, pp. 2617-2623
-
-
Lee, P.A.1
Dymond, J.S.2
Scheifele, L.Z.3
Richardson, S.M.4
Foelber, K.J.5
Boeke, J.D.6
Bader, J.S.7
-
67
-
-
84934438960
-
UNAFold: Software for nucleic acid folding and hybridization
-
Markham, N. R., and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization, Methods Mol Biol 453 , 3-31.
-
(2008)
Methods Mol Biol
, vol.453
, pp. 3-31
-
-
Markham, N.R.1
Zuker, M.2
-
68
-
-
23144440350
-
DINAMelt web server for nucleic acid melting prediction
-
DOI 10.1093/nar/gki591
-
Markham, N. R., and Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction, Nucleic Acids Res 33 , W577-W581. (Pubitemid 44529988)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Markham, N.R.1
Zuker, M.2
-
69
-
-
34249772381
-
Fast folding and comparision of rna secondary strucutre
-
Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, L. S., Tacker, M., and Schuster, P. (1994) Fast Folding and Comparision of RNA Secondary Strucutre, Monatshefte fuer Chemie 125 , 167-188.
-
(1994)
Monatshefte fuer Chemie
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, L.S.4
Tacker, M.5
Schuster, P.6
-
70
-
-
0043123153
-
Vienna RNA secondary structure server
-
DOI 10.1093/nar/gkg599
-
Hofacker, I. L. (2003) Vienna RNA secondary structure server, Nucleic Acids Res 31 , 3429-3431. (Pubitemid 37442172)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3429-3431
-
-
Hofacker, I.L.1
-
71
-
-
77951796655
-
RNA FRABASE 2.0: An advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures
-
Popenda, M., Szachniuk, M., Blazewicz, M., Wasik, S., Burke, E. K., Blazewicz, J., and Adamiak, R. W. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures, BMC Bioinformatics 11 :231.
-
BMC Bioinformatics
, vol.11
, pp. 231
-
-
Popenda, M.1
Szachniuk, M.2
Blazewicz, M.3
Wasik, S.4
Burke, E.K.5
Blazewicz, J.6
Adamiak, R.W.7
-
72
-
-
0032612579
-
Ab initio protein structure prediction of CASP III targets using ROSETTA
-
DOI 10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z
-
Simons, K. T., Bonneau, R., Ruczinski, I., and Baker, D. (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA, Proteins Suppl 3 , 171-176. (Pubitemid 29463528)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.37
, Issue.SUPPL. 3
, pp. 171-176
-
-
Simons, K.T.1
Bonneau, R.2
Ruczinski, I.3
Baker, D.4
-
73
-
-
0242369082
-
RAPTOR: Optimal protein threading by linear programming
-
Xu, J., Li, M., Kim, D., and Xu, Y. (2003) RAPTOR: optimal protein threading by linear programming, J Bioinform Comput Biol 1 , 95-117.
-
(2003)
J Bioinform Comput Biol
, vol.1
, pp. 95-117
-
-
Xu, J.1
Li, M.2
Kim, D.3
Xu, Y.4
-
74
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
DOI 10.1093/nar/gki408
-
Soeding, J., Biegert, A., and Lupas, A. N. (2005) The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res 33 , W244-W248. (Pubitemid 44529917)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Soding, J.1
Biegert, A.2
Lupas, A.N.3
-
75
-
-
48849113878
-
Comparative protein structure modeling using MODELLER
-
Unit 2.9
-
Eswar, N., Webb, B., Marti-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M.-Y., Pieper, U., and Sali, A. (2007) Comparative protein structure modeling using MODELLER, Curr Protoc Protein Sci Chapter 2:Unit 2.9.
-
(2007)
Curr Protoc Protein Sci Chapter
, vol.2
-
-
Eswar, N.1
Webb, B.2
Marti-Renom, M.A.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.-Y.6
Pieper, U.7
Sali, A.8
-
76
-
-
14144256681
-
Energy functions for protein design: Adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
-
DOI 10.1016/j.jmb.2004.12.019
-
Pokala, N., and Handel, T. M. (2005) Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity, J Mol Biol 347 , 203-227. (Pubitemid 40283639)
-
(2005)
Journal of Molecular Biology
, vol.347
, Issue.1
, pp. 203-227
-
-
Pokala, N.1
Handel, T.M.2
-
77
-
-
77649187057
-
PROTDES: CHARMM toolbox for computational protein design
-
Suarez, M., Tortosa, P., and Jaramillo, A. (2008) PROTDES: CHARMM toolbox for computational protein design, Syst Synth Biol 2 , 105-113.
-
(2008)
Syst Synth Biol
, vol.2
, pp. 105-113
-
-
Suarez, M.1
Tortosa, P.2
Jaramillo, A.3
-
78
-
-
33744471931
-
Enhanced automated function prediction using distantly related sequences and contextual association by PFP
-
DOI 10.1110/ps.062153506
-
Hawkins, T., Luban, S., and Kihara, D. (2006) Enhanced automated function prediction using distantly related sequences and contextual association by PFP, Protein Sci 15 , 1550-1556. (Pubitemid 43800030)
-
(2006)
Protein Science
, vol.15
, Issue.6
, pp. 1550-1556
-
-
Hawkins, T.1
Luban, S.2
Kihara, D.3
-
79
-
-
59849089151
-
PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data
-
Hawkins, T., Chitale, M., Luban, S., and Kihara, D. (2009) PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data, Proteins 74 , 566-582.
-
(2009)
Proteins
, vol.74
, pp. 566-582
-
-
Hawkins, T.1
Chitale, M.2
Luban, S.3
Kihara, D.4
-
80
-
-
63849246525
-
Protein structure prediction on the Web: A case study using the Phyre server
-
Kelley, L. A., and Sternberg, M. J. E. (2009) Protein structure prediction on the Web: a case study using the Phyre server, Nat Protoc 4 , 363-371.
-
(2009)
Nat Protoc
, vol.4
, pp. 363-371
-
-
Kelley, L.A.1
Sternberg, M.J.E.2
-
81
-
-
77954065271
-
I-TASSER: A unified platform for automated protein structure and function prediction
-
Roy, A., Kucukural, A., and Zhang, Y. I-TASSER: a unified platform for automated protein structure and function prediction, Nat Protoc 5 , 725-738.
-
Nat Protoc
, vol.5
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
82
-
-
70349932423
-
AutoDock4 and AutoDockTools4: Automated docking with selective receptor fl exibility
-
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., and Olson, A. J. (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor fl exibility, J Comput Chem 30 , 2785-2791.
-
(2009)
J Comput Chem
, vol.30
, pp. 2785-2791
-
-
Morris, G.M.1
Huey, R.2
Lindstrom, W.3
Sanner, M.F.4
Belew, R.K.5
Goodsell, D.S.6
Olson, A.J.7
-
83
-
-
77954275738
-
HexServer: An FFT-based protein docking server powered by graphics processors
-
Macindoe, G., Mavridis, L., Venkatraman, V., Devignes, M.-D., and Ritchie, D. W. HexServer: an FFT-based protein docking server powered by graphics processors, Nucleic Acids Res 38 Suppl , W445-W449.
-
Nucleic Acids Res
, vol.38
, Issue.SUPPL.
-
-
MacIndoe, G.1
Mavridis, L.2
Venkatraman, V.3
Devignes, M.-D.4
Ritchie, D.W.5
-
84
-
-
34147192127
-
Biskit - A software platform for structural bioinformatics
-
DOI 10.1093/bioinformatics/btl655
-
Gruenberg, R., Nilges, M., and Leckner, J. (2007) Biskit-a software platform for structural bioinformatics, Bioinformatics 23 , 769-770. (Pubitemid 46554731)
-
(2007)
Bioinformatics
, vol.23
, Issue.6
, pp. 769-770
-
-
Grunberg, R.1
Nilges, M.2
Leckner, J.3
-
85
-
-
46949091517
-
Refinement and standardization of synthetic biological parts and devices
-
DOI 10.1038/nbt1413, PII NBT1413
-
Canton, B., Labno, A., and Endy, D. (2008) Refinement and standardization of synthetic biological parts and devices, Nat Biotechnol 26 , 787-793. (Pubitemid 351961452)
-
(2008)
Nature Biotechnology
, vol.26
, Issue.7
, pp. 787-793
-
-
Canton, B.1
Labno, A.2
Endy, D.3
-
86
-
-
4344703213
-
BioLogic gates enable logical transcription control in mammalian cells
-
DOI 10.1002/bit.20142
-
Kramer, B. P., Fischer, C., and Fussenegger, M. (2004) BioLogic gates enable logical transcription control in mammalian cells, Biotechnol Bioeng 87 , 478-484. (Pubitemid 39150049)
-
(2004)
Biotechnology and Bioengineering
, vol.87
, Issue.4
, pp. 478-484
-
-
Kramer, B.P.1
Fischer, C.2
Fussenegger, M.3
-
87
-
-
34548856538
-
Rational design of memory in eukaryotic cells
-
DOI 10.1101/gad.1586107
-
Ajo-Franklin, C. M., Drubin, D. A., Eskin, J. A., Gee, E. P. S., Landgraf, D., Phillips, I., and Silver, P. A. (2007) Rational design of memory in eukaryotic cells, Genes Dev 21 , 2271-2276. (Pubitemid 47443332)
-
(2007)
Genes and Development
, vol.21
, Issue.18
, pp. 2271-2276
-
-
Ajo-Franklin, C.M.1
Drubin, D.A.2
Eskin, J.A.3
Gee, E.P.S.4
Landgraf, D.5
Phillips, I.6
Silver, P.A.7
-
88
-
-
58249117722
-
A tunable synthetic mammalian oscillator
-
Tigges, M., Marquez-Lago, T. T., Stelling, J., and Fussenegger, M. (2009) A tunable synthetic mammalian oscillator, Nature 457 , 309-312.
-
(2009)
Nature
, vol.457
, pp. 309-312
-
-
Tigges, M.1
Marquez-Lago, T.T.2
Stelling, J.3
Fussenegger, M.4
-
89
-
-
33646582649
-
RNA synthetic biology
-
Isaacs, F. J., Dwyer, D. J., and Collins, J. J. (2006) RNA synthetic biology, Nat Biotechnol 24 , 545-554.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 545-554
-
-
Isaacs, F.J.1
Dwyer, D.J.2
Collins, J.J.3
-
90
-
-
41349118107
-
Complex riboswitches
-
DOI 10.1126/science.1152621
-
Breaker, R. R. (2008) Complex riboswitches, Science 319 , 1795-1797. (Pubitemid 351451558)
-
(2008)
Science
, vol.319
, Issue.5871
, pp. 1795-1797
-
-
Breaker, R.R.1
-
91
-
-
54249113318
-
Higher-order cellular information processing with synthetic RNA devices
-
Win, M. N., and Smolke, C. D. (2008) Higher-order cellular information processing with synthetic RNA devices, Science 322 , 456-460.
-
(2008)
Science
, vol.322
, pp. 456-460
-
-
Win, M.N.1
Smolke, C.D.2
-
92
-
-
21444457242
-
Programmable ligand-controlled riboregulators of eukaryotic gene expression
-
DOI 10.1038/nbt1069
-
Bayer, T. S., and Smolke, C. D. (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression, Nat Biotechnol 23 , 337-343. (Pubitemid 41094422)
-
(2005)
Nature Biotechnology
, vol.23
, Issue.3
, pp. 337-343
-
-
Bayer, T.S.1
Smolke, C.D.2
-
93
-
-
62649171253
-
Frameworks for programming biological function through RNA parts and devices
-
Win, M. N., Liang, J. C., and Smolke, C. D. (2009) Frameworks for programming biological function through RNA parts and devices, Chem Biol 16 , 298-310.
-
(2009)
Chem Biol
, vol.16
, pp. 298-310
-
-
Win, M.N.1
Liang, J.C.2
Smolke, C.D.3
-
95
-
-
77952473769
-
Strategies for protein synthetic biology
-
Gruenberg, R., and Serrano, L. (2010) Strategies for protein synthetic biology, Nucleic Acids Res 38 , 2663-2675.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 2663-2675
-
-
Gruenberg, R.1
Serrano, L.2
-
96
-
-
77956517750
-
BioNetCAD: Design, simulation and experimental validation of synthetic biochemical networks
-
Rialle, S. p., Felicori, L., Dias-Lopes, C., Peres, S., Atia, S. E., Thierry, A. R., Amar, P., and Molina, F. BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks, Bioinformatics 26 (18) , 2298-2304.
-
Bioinformatics
, vol.26
, Issue.18
, pp. 2298-2304
-
-
Rialle, S.P.1
Felicori, L.2
Dias-Lopes, C.3
Peres, S.4
Atia, S.E.5
Thierry, A.R.6
Amar, P.7
Molina, F.8
-
97
-
-
77952521393
-
Algorithms for automated DNA assembly
-
Densmore, D., Hsiau, T. H. C., Kittleson, J. T., DeLoache, W., Batten, C., and Anderson, J. C. Algorithms for automated DNA assembly, Nucleic Acids Res 38 , 2607-2616.
-
Nucleic Acids Res
, vol.38
, pp. 2607-2616
-
-
Densmore, D.1
Hsiau, T.H.C.2
Kittleson, J.T.3
Deloache, W.4
Batten, C.5
Anderson, J.C.6
-
98
-
-
43249106821
-
Recursive construction of perfect DNA molecules from imperfect oligonucleotides
-
Linshiz, G., Yehezkel, T. B., Kaplan, S., Gronau, I., Ravid, S., Adar, R., and Shapiro, E. (2008) Recursive construction of perfect DNA molecules from imperfect oligonucleotides, Mol Syst Biol 4 :191
-
(2008)
Mol Syst Biol
, vol.4
, pp. 191
-
-
Linshiz, G.1
Yehezkel, T.B.2
Kaplan, S.3
Gronau, I.4
Ravid, S.5
Adar, R.6
Shapiro, E.7
|