Computational Systems Biology
Sauro Lab
University of Washington
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Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
4. WinSCAMP
5. Matlab Interface
6. Optimization
6. Bifurcation
 
maintained by Frank Bergmann
 
 
 
 

Research Impact

As a result of a number of requests for information, this page lists some of the research papers that have used the software available at this site, Jarnac citations are not listed yet. In all I estimate approximately 85 published papers which state that they used the software as part of the research described in the paper.

The software is also used by numerous teaching institutions as well as number of bioinformatic and pharmaceutical corporations.

The list is in chronological order, most recent first.

Bioinformatics

The first group cite the Bioinformatics paper: Computer Applications in the BioSciences. 9(4), 441-450, AUG 1993 SCAMP – A general purpose simulator and metabolic control analysis program.

0 Ingalls, B and Sauro, H. M Sensitivity Analysis of Stoichometric Networks: An Extension of Metabolic Control Analysis to Non-equilibrium Trajectories. J theor biol, in press, 2002

1 Cornish-Bowden A, Hofmeyr JHS The role of stoichiometric analysis in studies of metabolism: An example J THEOR BIOL 216 (2): 179-191 MAY 21 2002

2 de Atauri P, Fell DA, Chassagnole C, et al. Dependence of control coefficient distribution on the boundaries of a metabolic system: A generalized analysis of the effects of additional input and output reactions to a linear pathway. J THEOR BIOL 215 (2): 239-251 MAR 21 2002

3 Slepchenko BM, Schaff JC, Carson JH, et al. Computational cell biology: Spatiotemporal simulation of cellular events ANNU REV BIOPH BIOM 31: 423-441 2002

4 Cornish-Bowden A, Hofmeyr JHS, Cardenas ML Stoicheiometric analysis in studies of metabolism BIOCHEM SOC T 30: 43-46 Part 2 APR 2002

5 Kierzek AM STOCKS: STOChastic kinetic Simulations of biochemical systems with gillespie algorithm BIOINFORMATICS 18 (3): 470-481 MAR 2002

6 De Jong H Modeling and simulation of genetic regulatory systems: A literature review J COMPUT BIOL 9 (1): 67-103 2002

7 Moehren G, Markevich N, Demin O, et al. Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model BIOCHEMISTRY-US 41 (1): 306-320 JAN 8 2002

8 Cornish-Bowden A, Cardenas ML Information transfer in metabolic pathways - Effects of irreversible steps in computer models EUR J BIOCHEM 268 (24): 6616-6624 DEC 2001

9 Loew LM, Schaff JC The Virtual Cell: a software environment for computational cell biology TRENDS BIOTECHNOL 19 (10): 401-406 OCT 2001

10 Rohwer JM, Botha FC Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data BIOCHEM J 358: 437-445 Part 2 SEP 1 2001

11 Chassagnole C, Rais B, Quentin E, et al. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli BIOCHEM J 356: 415-423 Part 2 JUN 1 2001

12 Chassagnole C, Fell DA, Rais B, et al. Control of the threonine-synthesis pathway in Escherichia coli: a theoretical and experimental approach BIOCHEM J 356: 433-444 Part 2 JUN 1 2001

13 Tomita M Whole-cell simulation: a grand challenge of the 21st century TRENDS BIOTECHNOL 19 (6): 205-210 JUN 2001

14 Ichikawa K A-Cell: graphical user interface for the construction of biochemical reaction models BIOINFORMATICS 17 (5): 483-484 MAY 2001

15 Hofmeyr JHS, Westerhoff HV Building the cellular puzzle - Control in multi-level reaction networks J THEOR BIOL 208 (3): 261-285 FEB 7 2001

16 Somsen OJG, Hoeben MA, Esgalhado E, et al. Glucose and the ATP paradox in yeast BIOCHEM J 352: 593-599 Part 2 DEC 1 2000

17 Rohwer JM, Meadow ND, Roseman S, et al. Understanding glucose transport by the bacterial phosphoenolpyruvate : glucose phosphotransferase system on the basis of kinetic measurements in vitro J BIOL CHEM 275 (45): 34909-34921 NOV 10 2000

18 Bruggeman FJ, van Heeswijk WC, Boogerd FC, et al. Macromolecular intelligence in microorganisms BIOL CHEM 381 (9-10): 965-972 SEP-OCT 2000

19 Giersch C Mathematical modelling of metabolism CURR OPIN PLANT BIOL 3 (3): 249-253 JUN 2000

20 Poolman MG, Fell DA, Thomas S Modelling photosynthesis and its control J EXP BOT 51: 319-328 Sp. Iss. SI FEB 2000

21 Tomita M, Hashimoto K, Takahashi K, et al. The E-CELL project: Towards integrative simulation of cellular processes NEW GENERAT COMPUT 18 (1): 1-12 2000

22 Goryanin I, Hodgman TC, Selkov E Mathematical simulation and analysis of cellular metabolism and regulation BIOINFORMATICS 15 (9): 749-758 SEP 1999

23 de Atauri P, Curto R, Puigjaner J, et al. Advantages and disadvantages of aggregating fluxes into synthetic and degradative fluxes when modeling metabolic pathways EUR J BIOCHEM 265 (2): 671-679 OCT 1999

24 Hakman M, Groth T Object-oriented biomedical system modeling - The Rationale COMPUT METH PROG BIO 59 (1): 1-17 APR 1999

25 Tomita M, Hashimoto K, Takahashi K, et al. E-CELL: software environment for whole-cell simulation BIOINFORMATICS 15 (1): 72-84 JAN 1999

26 Mendes P, Kell DB Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation BIOINFORMATICS 14 (10): 869-883 1998

27 Rohwer JM, Postma PW, Kholodenko BN, et al. Implications of macromolecular crowding for signal transduction and metabolite channeling P NATL ACAD SCI USA 95 (18): 10547-10552 SEP 1 1998

28 McAdams HH, Arkin A Simulation of prokaryotic genetic circuits ANNU REV BIOPH BIOM 27: 199-224 1998

29 Kholodenko BN, Cascante M, Hoek JB, et al. Metabolic design: How to engineer a living cell to desired metabolite concentrations and fluxes BIOTECHNOL BIOENG 59 (2): 239-247 JUL 20 1998

30 Eisenthal R, Cornish-Bowden A Prospects for antiparasitic drugs - The case of Trypanosoma brucei, the causative agent of African sleeping sickness J BIOL CHEM 273 (10): 5500-5505 MAR 6 1998

31 Mendes P Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3 TRENDS BIOCHEM SCI 22 (9): 361-363 SEP 1997

32 Shymko RM, DeMeyts P, Thomas R Logical analysis of timing-dependent receptor signalling specificity: application to the insulin receptor metabolic and mitogenic signalling pathways BIOCHEM J 326: 463-469 Part 2 SEP 1 1997

33 Hofmeyr JHS, CornishBowden A The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models COMPUT APPL BIOSCI 13 (4): 377-385 AUG 1997

34 Okamoto M, Morita Y, Tominaga D, et al. Design of virtual-labo-system for metabolic engineering: Development of biochemical engineering system analyzing tool-kit (BEST KIT) COMPUT CHEM ENG 21: S745-S750 Suppl. S 1997

35 Woods JH, Sauro HM Elasticities in metabolic control analysis: Algebraic derivation of simplified expressions COMPUT APPL BIOSCI 13 (2): 123-130 APR 1997

36 Kacser H, Small JR How many phenotypes from one genotype? The case of prion diseases J THEOR BIOL 182 (3): 209-218 OCT 7 1996

37 Thomas S, Fell DA Design of metabolic control for large flux changes J THEOR BIOL 182 (3): 285-298 OCT 7 1996

38 Hofmeyr JHS, CornishBowden A Co-response analysis: A new experimental strategy for metabolic control analysis J THEOR BIOL 182 (3): 371-380 OCT 7 1996

39 Bieniasz LK A reaction compiler for electrochemical kinetics COMPUT CHEM 20 (4): 403-418 1996

40 Rohwer JM, Schuster S, Westerhoff HV How to recognize monofunctional units in a metabolic system J THEOR BIOL 179 (3): 213-228 APR 7 1996

41 Smits HP, Smits GJ, Postma PW, et al. High-affinity glucose uptake in Saccharomyces cerevisiae is not dependent on the presence of glucosephosphorylating enzymes YEAST 12 (5): 439-447 APR 1996

42 Kholodenko BN, Brown GC Paradoxical control properties of enzymes within pathways: Can activation cause an enzyme to have increased control? BIOCHEM J 314: 753-760 Part 3 MAR 15 1996

43 Mendes P, Kell DB, Westerhoff HV Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel BBA-GEN SUBJECTS 1289 (2): 175-186 MAR 15 1996

44 EHLDE M, ZACCHI G MIST - A USER-FRIENDLY METABOLIC SIMULATOR COMPUT APPL BIOSCI 11 (2): 201-207 APR 1995

45 KHOLODENKO BN, WESTERHOFF HV HOW TO REVEAL VARIOUS ASPECTS OF REGULATION IN GROUP-TRANSFER PATHWAYS BBA-BIOENERGETICS 1229 (2): 275-289 APR 26 1995

46 BROWN GC RATE CONTROL WITHIN THE NA+/GLUCOSE COTRANSPORTER BIOPHYS CHEM 54 (2): 181-189 APR 1995

47 SAURO HM MOIETY-CONSERVED CYCLES AND METABOLIC CONTROL ANALYSIS - PROBLEMS IN SEQUESTRATION AND METABOLIC CHANNELING BIOSYSTEMS 33 (1): 55-67 1994

48 ACERENZA L METABOLIC CONTROL DESIGN J THEOR BIOL 165 (1): 63-85 NOV 7 1993

Mathematical & Computer Modeling

The following group cited the Mathematical and Computer Modelling, 15 (12), 15-28, 1991 Sauro, HM, Fell, DA paper.

49 Teusink B, Passarge J, Reijenga CA, et al. Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry EUR J BIOCHEM 267 (17): 5313-5329 SEP 2000

50 Bakker BM, Michels PAM, Opperdoes FR, et al. What controls glycolysis in bloodstream form Trypanosoma brucei? J BIOL CHEM 274 (21): 14551-14559 MAY 21 1999

51 Teusink B, Walsh MC, van Dam K, et al. The danger of metabolic pathways with turbo design TRENDS BIOCHEM SCI 23 (5): 162-169 MAY 1998

52 Eisenthal R, Cornish-Bowden A Prospects for antiparasitic drugs - The case of Trypanosoma brucei, the causative agent of African sleeping sickness J BIOL CHEM 273 (10): 5500-5505 MAR 6 1998

53 Hofmeyr JHS, CornishBowden A The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models COMPUT APPL BIOSCI 13 (4): 377-385 AUG 1997

54 Holman RR, Smale AD, Pemberton E, et al. Randomized controlled pilot trial of a hand-held patient-oriented, insulin regimen optimizer MED INFORM 21 (4): 317-326 OCT-DEC 1996

55 Bakker BM, Michels PAM, Opperdoes FR, et al. Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes J BIOL CHEM 272 (6): 3207-3215 FEB 7 1997

56 Small and Kacser Design of metabolic control for large flux changes J THEOR BIOL 182 (3): 285-298 OCT 7 1996

57 Bieniasz LK A reaction compiler for electrochemical kinetics COMPUT CHEM 20 (4): 403-418 1996

58 Teusink B, Bakker BM, Westerhoff HV Control of frequency and amplitudes is shared by all enzymes in three models for yeast glycolytic oscillations BBA-BIOENERGETICS 1275 (3): 204-212 JUL 31 1996

59 Mendes P, Kell DB, Westerhoff HV Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel BBA-GEN SUBJECTS 1289 (2): 175-186 MAR 15 1996

60 Mendes P, Kell DB On the analysis of the inverse problem of metabolic pathways using artificial neural networks BIOSYSTEMS 38 (1): 15-28 1996

61 WOODS JH OBJECT-ORIENTED METABOLIC PROGRAMMING BIOCHEM SOC T 23 (2): S296-S296 MAY 1995

62 KHOLODENKO BN, SAURO HM, WESTERHOFF HV CONTROL BY ENZYMES, COENZYMES AND CONSERVED MOIETIES - A GENERALIZATION OF THE CONNECTIVITY THEOREM OF METABOLIC CONTROL ANALYSIS EUR J BIOCHEM 225 (1): 179-186 OCT 1 1994

63 MENDES P GEPASI - A SOFTWARE PACKAGE FOR MODELING THE DYNAMICS, STEADY-STATES AND CONTROL OF BIOCHEMICAL AND OTHER SYSTEMS COMPUT APPL BIOSCI 9 (5): 563-571 OCT 1993

64 SAURO HM SCAMP - A GENERAL-PURPOSE SIMULATOR AND METABOLIC CONTROL ANALYSIS PROGRAM COMPUT APPL BIOSCI 9 (4): 441-450 AUG 1993

65 THOMAS S, FELL DA A COMPUTER-PROGRAM FOR THE ALGEBRAIC DETERMINATION OF CONTROL COEFFICIENTS IN METABOLIC CONTROL ANALYSIS BIOCHEM J 292: 351-360 Part 2 JUN 1 1993

66 CORNISH-BOWDEN A, CARDENAS ML CHANNELING CAN AFFECT CONCENTRATIONS OF METABOLIC INTERMEDIATES AT CONSTANT NET FLUX - ARTIFACT OR REALITY EUR J BIOCHEM 213 (1): 87-92 APR 1 1993

67 EFFECTORS .2. THE LINEAR TREATMENT OF BRANCHED PATHWAYS AND METABOLITE CONCENTRATIONS - ASSESSMENT OF THE GENERAL NONLINEAR CASE EUR J BIOCHEM 213 (1): 625-640 APR 1 1993

68 FELL DA METABOLIC CONTROL ANALYSIS - A SURVEY OF ITS THEORETICAL AND EXPERIMENTAL DEVELOPMENT BIOCHEM J 286: 313-330 Part 2 SEP 1 1992

 
sysbio/researchimpact.txt · Last modified: 2007/07/17 11:52 by mallain
 

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