Jacky Snoep

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Snoep J L; Mrwebi M; Schuurmans J M; Rohwer J M; Teixeira de Mattos M J
Control of specific growth rate in Saccharomyces cerevisiae.
Pillay Ché S; Hofmeyr Jan-Hendrik S; Olivier Brett G; Snoep Jacky L; Rohwer Johann M
Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context.
Westerhoff Hans V; Kolodkin Alexey; Conradie Riaan; Wilkinson Stephen J; Bruggeman Frank J; Krab Klaas; van Schuppen Jan H; Hardin Hanna; Bakker Barbara M; Moné Martijn J; Rybakova Katja N; Eijken Marco; van Leeuwen Hans J P; Snoep Jacky L
Systems biology towards life in silico: mathematics of the control of living cells.

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2009: Snoep J L; Mrwebi M; Schuurmans J M; Rohwer J M; Teixeira de Mattos M J
Control of specific growth rate in Saccharomyces cerevisiae.
Microbiology (Reading, England) 2009;155(Pt 5):1699-707.
2009: Pillay Ché S; Hofmeyr Jan-Hendrik S; Olivier Brett G; Snoep Jacky L; Rohwer Johann M
Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context.
The Biochemical journal 2009;417(1):269-75.
2009: Westerhoff Hans V; Kolodkin Alexey; Conradie Riaan; Wilkinson Stephen J; Bruggeman Frank J; Krab Klaas; van Schuppen Jan H; Hardin Hanna; Bakker Barbara M; Moné Martijn J; Rybakova Katja N; Eijken Marco; van Leeuwen Hans J P; Snoep Jacky L
Systems biology towards life in silico: mathematics of the control of living cells.
Journal of mathematical biology 2009;58(1-2):7-34.
2008: Bruggeman F J; Snoep J L; Westerhoff H V
Control, responses and modularity of cellular regulatory networks: a control analysis perspective.
IET systems biology 2008;2(6):397-410.
2008: du Preez F B; Conradie R; Penkler G P; Holm K; van Dooren F L J; Snoep J L
A comparative analysis of kinetic models of erythrocyte glycolysis.
Journal of theoretical biology 2008;252(3):488-96.
2008: Jonker C M; Snoep J L; Treur J; Westerhoff H V; Wijngaards W C A
BDI-modelling of complex intracellular dynamics.
Journal of theoretical biology 2008;251(1):1-23.
2008: van Gend Carel; Snoep Jacky L
Systems biology model databases and resources.
Essays in biochemistry 2008;45():223-36.
2007: van Gend Carel; Conradie Riaan; du Preez Franco B; Snoep Jacky L
Data and model integration using JWS Online.
In silico biology 2007;7(2 Suppl):S27-35.
2006: Snoep J L; Westerhoff H V; Rohwer J M; Hofmeyr J H S
Is there an optimal ribosome concentration for maximal protein production?
Systems biology 2006;153(5):398-400.
2006: Uys L; Hofmeyr J H S; Snoep J L; Rohwer J M
Software tools that facilitate kinetic modelling with large data sets: an example using growth modelling in sugarcane.
Systems biology 2006;153(5):385-9.
2006: Hanekom A J; Hofmeyr J H S; Snoep J L; Rohwer J M
Experimental evidence for allosteric modifier saturation as predicted by the bi-substrate Hill equation.
Systems biology 2006;153(5):342-5.
2006: Rohwer J M; Hanekom A J; Crous C; Snoep J L; Hofmeyr J H S
Evaluation of a simplified generic bi-substrate rate equation for computational systems biology.
Systems biology 2006;153(5):338-41.
2006: Olivier B G; Rohwer J M; Snoep J L; Hofmeyr J H S
Comparing the regulatory behaviour of two cooperative, reversible enzyme mechanisms.
Systems biology 2006;153(5):335-7.
2006: Hofmeyr J H S; Rohwer J M; Snoep J L
Conditions for effective allosteric feedforward and feedback in metabolic pathways.
Systems biology 2006;153(5):327-31.
2006: Conradie R; Westerhoff H V; Rohwer J M; Hofmeyr J H S; Snoep J L
Summation theorems for flux and concentration control coefficients of dynamic systems.
Systems biology 2006;153(5):314-7.
2006: Snoep Jacky L; Rohwer Johann M; Hofmeyr Jan-Hendirk S
12th BTK meeting: 'Systems Biology: redefining BioThermoKinetics'.
Systems biology 2006;153(5):312-3.
2006: Snoep Jacky L; Bruggeman Frank; Olivier Brett G; Westerhoff Hans V
Towards building the silicon cell: a modular approach.
Bio Systems 2006;83(2-3):207-16.
2006: Le Novère Nicolas; Bornstein Benjamin; Broicher Alexander; Courtot Mélanie; Donizelli Marco; Dharuri Harish; Li Lu; Sauro Herbert; Schilstra Maria; Shapiro Bruce; Snoep Jacky L; Hucka Michael
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.
Nucleic acids research 2006;34(Database issue):D689-91.
2005: Le Novère Nicolas; Finney Andrew; Hucka Michael; Bhalla Upinder S; Campagne Fabien; Collado-Vides Julio; Crampin Edmund J; Halstead Matt; Klipp Edda; Mendes Pedro; Nielsen Poul; Sauro Herbert; Shapiro Bruce; Snoep Jacky L; Spence Hugh D; Wanner Barry L
Minimum information requested in the annotation of biochemical models (MIRIAM).
Nature biotechnology 2005;23(12):1509-15.
2005: Snoep Jacky L
The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level.
Current opinion in biotechnology 2005;16(3):336-43.
2005: Reijenga Karin A; van Megen Yvonne M G A; Kooi Bob W; Bakker Barbara M; Snoep Jacky L; van Verseveld Henk W; Westerhoff Hans V
Yeast glycolytic oscillations that are not controlled by a single oscillophore: a new definition of oscillophore strength.
Journal of theoretical biology 2005;232(3):385-98.
2004: Elbing Karin; Larsson Christer; Bill Roslyn M; Albers Eva; Snoep Jacky L; Boles Eckhard; Hohmann Stefan; Gustafsson Lena
Role of hexose transport in control of glycolytic flux in Saccharomyces cerevisiae.
Applied and environmental microbiology 2004;70(9):5323-30.
2004: Olivier Brett G; Snoep Jacky L
Web-based kinetic modelling using JWS Online.
Bioinformatics (Oxford, England) 2004;20(13):2143-4.
2004: Crowley Paula J; Svensäter Gunnel; Snoep Jacky L; Bleiweis Arnold S; Brady L Jeannine
An ffh mutant of Streptococcus mutans is viable and able to physiologically adapt to low pH in continuous culture.
FEMS microbiology letters 2004;234(2):315-24.
2004: Vadyvaloo Viveka; Snoep Jacky L; Hastings John W; Rautenbach Marina
Physiological implications of class IIa bacteriocin resistance in Listeria monocytogenes strains.
Microbiology (Reading, England) 2004;150(Pt 2):335-40.
2003: Snoep Jacky L; Olivier Brett G
JWS online cellular systems modelling and microbiology.
Microbiology (Reading, England) 2003;149(Pt 11):3045-7.
2003: Westerhoff Hans V; Bruggeman Frank; Hofmeyr Jan-Hendrik S; Snoep Jacky L
Attractive models: how to make the silicon cell relevant and dynamic.
Comparative and functional genomics 2003;4(1):155-8.
2002: Somsen Oscar J G; Siderius Marco; Bauer Florian F; Snoep Jacky L; Westerhoff Hans V
Selectivity in overlapping MAP kinase cascades.
Journal of theoretical biology 2002;218(3):343-54.
2002: de la Fuente Alberto; Snoep Jacky L; Westerhoff Hans V; Mendes Pedro
Metabolic control in integrated biochemical systems.
European journal of biochemistry / FEBS 2002;269(18):4399-408.
2002: Koefoed Sarah; Otten Marijke; Koebmann Brian; Bruggeman Frank; Bakker Barbara; Snoep Jacky; Krab Klaas; van Spanning Rob; van Verseveld Henk; Jensen Peter; Koster Johanna; Westerhoff Hans
A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life.
Biochimica et biophysica acta 2002;1555(1-3):75-82.
2002: Koebmann Brian J; Westerhoff Hans V; Snoep Jacky L; Nilsson Dan; Jensen Peter R
The glycolytic flux in Escherichia coli is controlled by the demand for ATP.
Journal of bacteriology 2002;184(14):3909-16.
2002: Hoefnagel Marcel H N; Starrenburg Marjo J C; Martens Dirk E; Hugenholtz Jeroen; Kleerebezem Michiel; Van Swam Iris I; Bongers Roger; Westerhoff Hans V; Snoep Jacky L
Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis.
Microbiology (Reading, England) 2002;148(Pt 4):1003-13.
2002: Snoep Jacky L; van der Weijden Coen C; Andersen Heidi W; Westerhoff Hans V; Jensen Peter Ruhdal
DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase.
European journal of biochemistry / FEBS 2002;269(6):1662-9.
2002: Jonker Catholijn M; Snoep Jacky L; Treur Jan; Westerhoff Hans V; Wijngaards Wouter C A
Putting intentions into cell biochemistry: an artificial intelligence perspective.
Journal of theoretical biology 2002;214(1):105-34.
2002: Reijenga Karin A; Westerhoff Hans V; Kholodenko Boris N; Snoep Jacky L
Control analysis for autonomously oscillating biochemical networks.
Biophysical journal 2002;82(1 Pt 1):99-108.
2002: Stuger Rogier; Woldringh Conrad L; van der Weijden Coen C; Vischer Norbert O E; Bakker Barbara M; van Spanning Rob J M; Snoep Jacky L; Westerhoff Hans V
DNA supercoiling by gyrase is linked to nucleoid compaction.
Molecular biology reports 2002;29(1-2):79-82.
2002: Koebmann Brian J; Westerhoff Hans V; Snoep Jacky L; Solem Christian; Pedersen Martin B; Nilsson Dan; Michelsen Ole; Jensen Peter R
The extent to which ATP demand controls the glycolytic flux depends strongly on the organism and conditions for growth.
Molecular biology reports 2002;29(1-2):41-5.
2002: Snoep J L; Olivier B G
Java Web Simulation (JWS); a web based database of kinetic models.
Molecular biology reports 2002;29(1-2):259-63.
2002: Kroukamp O; Rohwer J M; Hofmeyr J H S; Snoep J L
Experimental supply-demand analysis of anaerobic yeast energy metabolism.
Molecular biology reports 2002;29(1-2):203-9.
2002: Hoefnagel M H N; van der Burgt A; Martens D E; Hugenholtz J; Snoep J L
Time dependent responses of glycolytic intermediates in a detailed glycolytic model of Lactococcus lactis during glucose run-out experiments.
Molecular biology reports 2002;29(1-2):157-61.
2002: Westerhoff Hans V; Getz Wayne M; Bruggeman Frank; Hofmeyr Jan-Hendrik S; Rohwer Johann M; Snoep Jacky L
ECA: control in ecosystems.
Molecular biology reports 2002;29(1-2):113-7.
2002: Hofmeyr J H S; Rohwer J M; Snoep J L; Westerhoff H V; Konings W N
How to distinguish between the vacuum cleaner and flippase mechanisms of the lmrA multi-drug transporter in Lactococcus lactis.
Molecular biology reports 2002;29(1-2):107-12.
2002: Westerhoff H V; Getz W M; van Verseveld H W; Hofmeyr J H S; Snoep J L
Bioinformatics, cellular flows, and calculation.
Ernst Schering Research Foundation workshop 2002;(38):221-43.
2001: Reijenga K A; Snoep J L; Diderich J A; van Verseveld H W; Westerhoff H V; Teusink B
Control of glycolytic dynamics by hexose transport in Saccharomyces cerevisiae.
Biophysical journal 2001;80(2):626-34.
2000: Somsen O J; Hoeben M A; Esgalhado E; Snoep J L; Visser D; van der Heijden R T; Heijnen J J; Westerhoff H V
Glucose and the ATP paradox in yeast.
The Biochemical journal 2000;352 Pt 2():593-9.
2000: Teusink B; Passarge J; Reijenga C A; Esgalhado E; van der Weijden C C; Schepper M; Walsh M C; Bakker B M; van Dam K; Westerhoff H V; Snoep J L
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.
European journal of biochemistry / FEBS 2000;267(17):5313-29.
2000: Ward D E; van Der Weijden C C; van Der Merwe M J; Westerhoff H V; Claiborne A; Snoep J L
Branched-chain alpha-keto acid catabolism via the gene products of the bkd operon in Enterococcus faecalis: a new, secreted metabolite serving as a temporary redox sink.
Journal of bacteriology 2000;182(11):3239-46.
2000: Wolf J; Passarge J; Somsen O J; Snoep J L; Heinrich R; Westerhoff H V
Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations.
Biophysical journal 2000;78(3):1145-53.
2000: Hillman J D; Brooks T A; Michalek S M; Harmon C C; Snoep J L; van Der Weijden C C
Construction and characterization of an effector strain of Streptococcus mutans for replacement therapy of dental caries.
Infection and immunity 2000;68(2):543-9.
2000: Snoep J L
Gearing up for a quantitative understanding of cell (dys)function.
Trends in biotechnology 2000;18(1):1-3.
1999: Jensen P R; Van Der Weijden C C; Jensen L B; Westerhoff H V; Snoep J L
Extensive regulation compromises the extent to which DNA gyrase controls DNA supercoiling and growth rate of Escherichia coli.
European journal of biochemistry / FEBS 1999;266(3):865-77.
1999: Ward D E; Ross R P; van der Weijden C C; Snoep J L; Claiborne A
Catabolism of branched-chain alpha-keto acids in Enterococcus faecalis: the bkd gene cluster, enzymes, and metabolic route.
Journal of bacteriology 1999;181(17):5433-42.
1999: de Graef M R; Alexeeva S; Snoep J L; Teixeira de Mattos M J
The steady-state internal redox state (NADH/NAD) reflects the external redox state and is correlated with catabolic adaptation in Escherichia coli.
Journal of bacteriology 1999;181(8):2351-7.
1999: van Heeswijk W C; Bakker B M; Teusink B; Kholodenko B N; Somsen O J; Snoep J L; Westerhoff H V
Live control of the living cell.
Biochemical Society transactions 1999;27(2):261-4.
1997: Neijssel O M; Snoep J L; Teixeira de Mattos M J
Regulation of energy source metabolism in streptococci.
Society for Applied Bacteriology symposium series 1997;26():12S-19S.
1996: Hillman J D; Chen A; Snoep J L
Genetic and physiological analysis of the lethal effect of L-(+)-lactate dehydrogenase deficiency in Streptococcus mutans: complementation by alcohol dehydrogenase from Zymomonas mobilis.
Infection and immunity 1996;64(10):4319-23.
1996: Snoep J L; Arfman N; Yomano L P; Westerhoff H V; Conway T; Ingram L O
Control of glycolytic flux in Zymomonas mobilis by glucose 6-phosphate dehydrogenase activity.
Biotechnology and bioengineering 1996;51(2):190-7.
1996: van Workum M; van Dooren S J; Oldenburg N; Molenaar D; Jensen P R; Snoep J L; Westerhoff H V
DNA supercoiling depends on the phosphorylation potential in Escherichia coli.
Molecular microbiology 1996;20(2):351-60.
1995: Wijker J E; Jensen P R; Snoep J L; Vaz Gomes A; Guiral M; Jongsma A P; de Waal A; Hoving S; van Dooren S; van der Weijden C C
Energy, control and DNA structure in the living cell.
Biophysical chemistry 1995;55(1-2):153-65.
1995: Jensen P R; Snoep J L; Molenaar D; van Heeswijk W C; Kholodenko B N; van der Gugten A A; Westerhoff H V
Molecular biology for flux control.
Biochemical Society transactions 1995;23(2):367-70.
1995: Parker C; Barnell W O; Snoep J L; Ingram L O; Conway T
Characterization of the Zymomonas mobilis glucose facilitator gene product (glf) in recombinant Escherichia coli: examination of transport mechanism, kinetics and the role of glucokinase in glucose transport.
Molecular microbiology 1995;15(5):795-802.
1994: Snoep J L; Jensen P R; Groeneveld P; Molenaar D; Kholodenko B N; Westerhoff H V
How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox.
Biochemistry and molecular biology international 1994;33(5):1023-32.
1994: Snoep J L; Arfman N; Yomano L P; Fliege R K; Conway T; Ingram L O
Reconstruction of glucose uptake and phosphorylation in a glucose-negative mutant of Escherichia coli by using Zymomonas mobilis genes encoding the glucose facilitator protein and glucokinase.
Journal of bacteriology 1994;176(7):2133-5.
1994: Snoep J L; de Graef M R; Teixeira de Mattos M J; Neijssel O M
Effect of culture conditions on the NADH/NAD ratio and total amounts of NAD(H) in chemostat cultures of Enterococcus faecalis NCTC 775.
FEMS microbiology letters 1994;116(3):263-7.
1993: Snoep J L; de Graef M R; Westphal A H; de Kok A; Teixeira de Mattos M J; Neijssel O M
Differences in sensitivity to NADH of purified pyruvate dehydrogenase complexes of Enterococcus faecalis, Lactococcus lactis, Azotobacter vinelandii and Escherichia coli: implications for their activity in vivo.
FEMS microbiology letters 1993;114(3):279-83.
1993: Snoep J L; van Bommel M; Lubbers F; Teixeira de Mattos M J; Neijssel O M
The role of lipoic acid in product formation by Enterococcus faecalis NCTC 775 and reconstitution in vivo and in vitro of the pyruvate dehydrogenase complex.
Journal of general microbiology 1993;139 Pt 6():1325-9.
1992: Snoep J L; de Graef M R; Teixeira de Mattos M J; Neijssel O M
Pyruvate catabolism during transient state conditions in chemostat cultures of Enterococcus faecalis NCTC 775: importance of internal pyruvate concentrations and NADH/NAD+ ratios.
Journal of general microbiology 1992;138(10):2015-20.
1992: Snoep J L; Teixeira de Mattos M J; Starrenburg M J; Hugenholtz J
Isolation, characterization, and physiological role of the pyruvate dehydrogenase complex and alpha-acetolactate synthase of Lactococcus lactis subsp. lactis bv. diacetylactis.
Journal of bacteriology 1992;174(14):4838-41.
1992: Simons J A; Snoep J L; Feitz S; Teixeira de Mattos M J; Neijssel O M
Anaerobic 2-ketogluconate metabolism of Klebsiella pneumoniae NCTC 418 grown in chemostat culture: involvement of the pentose phosphate pathway.
Journal of general microbiology 1992;138(3):423-8.
1992: Snoep J L; Westphal A H; Benen J A; Teixeira de Mattos M J; Neijssel O M; de Kok A
Isolation and characterisation of the pyruvate dehydrogenase complex of anaerobically grown Enterococcus faecalis NCTC 775.
European journal of biochemistry / FEBS 1992;203(1-2):245-50.
1991: Hommes R W; Simons J A; Snoep J L; Postma P W; Tempest D W; Neijssel O M
Quantitative aspects of glucose metabolism by Escherichia coli B/r, grown in the presence of pyrroloquinoline quinone.
Antonie van Leeuwenhoek 1991;60(3-4):373-82.
1990: Snoep J L; Teixeira de Mattos M J; Postma P W; Neijssel O M
Involvement of pyruvate dehydrogenase in product formation in pyruvate-limited anaerobic chemostat cultures of Enterococcus faecalis NCTC 775.
Archives of microbiology 1990;154(1):50-5.

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Jacky Snoep

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