Michael A Savageau

Title(s)Professor Emeritus, Biomedical Engineering
SchoolEngineering
Address228 Briggs Hall
CA 95616
Phone530-752-3047
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    Collapse Research 
    Collapse Research Activities and Funding
    International Conference on Molecular Systems Biology
    NIH/NIGMS R13GM071521Aug 1, 2004 - Jul 31, 2005
    Role: Principal Investigator
    Cellular Biotechnology Training Program (CBTP)
    NIH/NIGMS T32GM008353Jul 1, 1991 - Jun 30, 2022
    Role: Co-Principal Investigator
    Analysis of Molecular Networks and Control Systems
    NIH/NIGMS R01GM030054Apr 1, 1982 - Apr 30, 2016
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection. J Mol Evol. 2023 10; 91(5):687-710. Savageau MA. PMID: 37620617; PMCID: PMC10598110.
      View in: PubMed   Mentions: 1     Fields:    
    2. Phenotype-centric modeling for rational metabolic engineering. Metab Eng. 2022 07; 72:365-375. Valderrama-Gómez MÁ, Savageau MA. PMID: 35537663.
      View in: PubMed   Mentions:    Fields:    
    3. TaxisPy: A Python-based software for the quantitative analysis of bacterial chemotaxis. J Microbiol Methods. 2020 08; 175:105918. Valderrama-Gómez MÁ, Schomer RA, Savageau MA, Parales RE. PMID: 32512119.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    4. Mechanistic Modeling of Biochemical Systems without A Priori Parameter Values Using the Design Space Toolbox v.3.0. iScience. 2020 Jun 26; 23(6):101200. Valderrama-Gómez MÁ, Lomnitz JG, Fasani RA, Savageau MA. PMID: 32531747; PMCID: PMC7287267.
      View in: PubMed   Mentions: 1  
    5. Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation. Cell Rep. 2019 07 09; 28(2):342-351.e4. Turco GM, Rodriguez-Medina J, Siebert S, Han D, Valderrama-Gómez MÁ, Vahldick H, Shulse CN, Cole BJ, Juliano CE, Dickel DE, Savageau MA, Brady SM. PMID: 31291572.
      View in: PubMed   Mentions: 40     Fields:    Translation:Animals
    6. Phenotype-centric modeling for elucidation of biological design principles. J Theor Biol. 2018 10 14; 455:281-292. Valderrama-Gómez MA, Parales RE, Savageau MA. PMID: 30036529.
      View in: PubMed   Mentions: 3     Fields:    
    7. Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems. Sci Rep. 2016 08 31; 6:32375. Lomnitz JG, Savageau MA. PMID: 27578053; PMCID: PMC5006174.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    8. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems. Front Genet. 2016; 7:118. Lomnitz JG, Savageau MA. PMID: 27462346; PMCID: PMC4940394.
      View in: PubMed   Mentions: 6  
    9. Elucidating the genotype-phenotype map by automatic enumeration and analysis of the phenotypic repertoire. NPJ Syst Biol Appl. 2015; 1. Lomnitz JG, Savageau MA. PMID: 26998346; PMCID: PMC4794114.
      View in: PubMed   Mentions: 5     Fields:    
    10. Unrelated toxin-antitoxin systems cooperate to induce persistence. J R Soc Interface. 2015 Jul 06; 12(108):20150130. Fasani RA, Savageau MA. PMID: 26063817; PMCID: PMC4528579.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    11. Design principles of a conditional futile cycle exploited for regulation. Mol Biosyst. 2015 Jul; 11(7):1841-9. Tolla DA, Kiley PJ, Lomnitz JG, Savageau MA. PMID: 25851148; PMCID: PMC4470783.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    12. Evolution of a genome-encoded bias in amino acid biosynthetic pathways is a potential indicator of amino acid dynamics in the environment. Mol Biol Evol. 2014 Nov; 31(11):2865-78. Fasani RA, Savageau MA. PMID: 25118252; PMCID: PMC4209129.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    13. Strategy revealing phenotypic differences among synthetic oscillator designs. ACS Synth Biol. 2014 Sep 19; 3(9):686-701. Lomnitz JG, Savageau MA. PMID: 25019938; PMCID: PMC4210169.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    14. Relative amino acid composition signatures of organisms and environments. PLoS One. 2013; 8(10):e77319. Moura A, Savageau MA, Alves R. PMID: 24204807; PMCID: PMC3808408.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    15. Molecular mechanisms of multiple toxin-antitoxin systems are coordinated to govern the persister phenotype. Proc Natl Acad Sci U S A. 2013 Jul 02; 110(27):E2528-37. Fasani RA, Savageau MA. PMID: 23781105; PMCID: PMC3703989.
      View in: PubMed   Mentions: 64     Fields:    Translation:Cells
    16. Transcription factors in Escherichia coli prefer the holo conformation. PLoS One. 2013; 8(6):e65723. Balderas-Martínez YI, Savageau M, Salgado H, Pérez-Rueda E, Morett E, Collado-Vides J. PMID: 23776535; PMCID: PMC3680503.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    17. Phenotypic deconstruction of gene circuitry. Chaos. 2013 Jun; 23(2):025108. Lomnitz JG, Savageau MA. PMID: 23822506; PMCID: PMC3695976.
      View in: PubMed   Mentions: 9     Fields:    
    18. A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. Nucleic Acids Res. 2013 Jul; 41(12):6045-57. Williams K, Savageau MA, Blumenthal RM. PMID: 23630319; PMCID: PMC3695507.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    19. Regulatory design governing progression of population growth phases in bacteria. PLoS One. 2012; 7(2):e30654. Martínez-Antonio A, Lomnitz JG, Sandoval S, Aldana M, Savageau MA. PMID: 22363461; PMCID: PMC3283595.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    20. Design of the lac gene circuit revisited. Math Biosci. 2011 May; 231(1):19-38. Savageau MA. PMID: 21414326; PMCID: PMC3126112.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    21. Biomedical engineering strategies in system design space. Ann Biomed Eng. 2011 Apr; 39(4):1278-95. Savageau MA. PMID: 21203848; PMCID: PMC3074507.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    22. Phenotypic repertoire of the FNR regulatory network in Escherichia coli. Mol Microbiol. 2011 Jan; 79(1):149-65. Tolla DA, Savageau MA. PMID: 21166900; PMCID: PMC3075585.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    23. Relating mutant genotype to phenotype via quantitative behavior of the NADPH redox cycle in human erythrocytes. PLoS One. 2010 Sep 28; 5(9). Coelho PM, Salvador A, Savageau MA. PMID: 20927393; PMCID: PMC2946920.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    24. Automated construction and analysis of the design space for biochemical systems. Bioinformatics. 2010 Oct 15; 26(20):2601-9. Fasani RA, Savageau MA. PMID: 20823298; PMCID: PMC3025649.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    25. Regulation of aerobic-to-anaerobic transitions by the FNR cycle in Escherichia coli. J Mol Biol. 2010 Apr 09; 397(4):893-905. Tolla DA, Savageau MA. PMID: 20156450; PMCID: PMC2867928.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    26. Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination. Genetics. 2010 Apr; 184(4):1077-94. Reams AB, Kofoid E, Savageau M, Roth JR. PMID: 20083614; PMCID: PMC2865909.
      View in: PubMed   Mentions: 73     Fields:    Translation:Cells
    27. Qualitatively distinct phenotypes in the design space of biochemical systems. FEBS Lett. 2009 Dec 17; 583(24):3914-22. Savageau MA, Fasani RA. PMID: 19879266; PMCID: PMC2888490.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    28. Quantifying global tolerance of biochemical systems: design implications for moiety-transfer cycles. PLoS Comput Biol. 2009 Mar; 5(3):e1000319. Coelho PM, Salvador A, Savageau MA. PMID: 19300483; PMCID: PMC2650413.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    29. Phenotypes and tolerances in the design space of biochemical systems. Proc Natl Acad Sci U S A. 2009 Apr 21; 106(16):6435-40. Savageau MA, Coelho PM, Fasani RA, Tolla DA, Salvador A. PMID: 19279208; PMCID: PMC2672487.
      View in: PubMed   Mentions: 37     Fields:    
    30. Hysteretic and graded responses in bacterial two-component signal transduction. Mol Microbiol. 2008 Jun; 68(5):1196-215. Igoshin OA, Alves R, Savageau MA. PMID: 18363790; PMCID: PMC4372536.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    31. Distinctive topologies of partner-switching signaling networks correlate with their physiological roles. J Mol Biol. 2007 Jun 22; 369(5):1333-52. Igoshin OA, Brody MS, Price CW, Savageau MA. PMID: 17498739; PMCID: PMC2727513.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    32. Signalling network with a bistable hysteretic switch controls developmental activation of the sigma transcription factor in Bacillus subtilis. Mol Microbiol. 2006 Jul; 61(1):165-84. Igoshin OA, Price CW, Savageau MA. PMID: 16824103.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    33. Evolution of enzymes in a series is driven by dissimilar functional demands. Proc Natl Acad Sci U S A. 2006 Feb 14; 103(7):2226-31. Salvador A, Savageau MA. PMID: 16461898; PMCID: PMC1413729.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    34. Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes. Mol Microbiol. 2005 May; 56(4):1017-34. Alves R, Savageau MA. PMID: 15853887; PMCID: PMC1839009.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    35. Design of gene circuits: lessons from bacteria. Nat Rev Genet. 2004 Jan; 5(1):34-42. Wall ME, Hlavacek WS, Savageau MA. PMID: 14708014.
      View in: PubMed   Mentions: 82     Fields:    Translation:Cells
    36. Quantitative evolutionary design of glucose 6-phosphate dehydrogenase expression in human erythrocytes. Proc Natl Acad Sci U S A. 2003 Nov 25; 100(24):14463-8. Salvador A, Savageau MA. PMID: 14614139; PMCID: PMC283614.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    37. Design principles for regulator gene expression in a repressible gene circuit. J Mol Biol. 2003 Sep 26; 332(4):861-76. Wall ME, Hlavacek WS, Savageau MA. PMID: 12972257.
      View in: PubMed   Mentions: 19     Fields:    
    38. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell. 2003 May 30; 113(5):597-607. Atkinson MR, Savageau MA, Myers JT, Ninfa AJ. PMID: 12787501.
      View in: PubMed   Mentions: 240     Fields:    Translation:Cells
    39. Comparative analysis of prototype two-component systems with either bifunctional or monofunctional sensors: differences in molecular structure and physiological function. Mol Microbiol. 2003 Apr; 48(1):25-51. Alves R, Savageau MA. PMID: 12657043.
      View in: PubMed   Mentions: 42     Fields:    Translation:Cells
    40. Alternative designs for a genetic switch: analysis of switching times using the piecewise power-law representation. Math Biosci. 2002 Nov-Dec; 180:237-53. Savageau MA. PMID: 12387925.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    41. Design principles for elementary gene circuits: Elements, methods, and examples. Chaos. 2001 Mar; 11(1):142-159. Savageau MA. PMID: 12779449.
      View in: PubMed   Mentions: 62     Fields:    
    42. Irreversibility in unbranched pathways: preferred positions based on regulatory considerations. Biophys J. 2001 Mar; 80(3):1174-85. Alves R, Savageau MA. PMID: 11222282; PMCID: PMC1301313.
      View in: PubMed   Mentions: 8     Fields:    
    43. Effect of overall feedback inhibition in unbranched biosynthetic pathways. Biophys J. 2000 Nov; 79(5):2290-304. Alves R, Savageau MA. PMID: 11053109; PMCID: PMC1301117.
      View in: PubMed   Mentions: 14     Fields:    
    44. Extending the method of mathematically controlled comparison to include numerical comparisons. Bioinformatics. 2000 Sep; 16(9):786-98. Alves R, Savageau MA. PMID: 11108701.
      View in: PubMed   Mentions: 27     Fields:    
    45. Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways. Bioinformatics. 2000 Jun; 16(6):534-47. Alves R, Savageau MA. PMID: 10980151.
      View in: PubMed   Mentions: 16     Fields:    
    46. Comparing systemic properties of ensembles of biological networks by graphical and statistical methods. Bioinformatics. 2000 Jun; 16(6):527-33. Alves R, Savageau MA. PMID: 10980150.
      View in: PubMed   Mentions: 17     Fields:    
    47. Design of gene circuitry by natural selection: analysis of the lactose catabolic system in Escherichia coli. Biochem Soc Trans. 1999 Feb; 27(2):264-70. Savageau MA. PMID: 10093745.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    48. Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli. Genetics. 1998 Aug; 149(4):1677-91. Savageau MA. PMID: 9691028; PMCID: PMC1460280.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    49. Demand theory of gene regulation. I. Quantitative development of the theory. Genetics. 1998 Aug; 149(4):1665-76. Savageau MA. PMID: 9691027; PMCID: PMC1460276.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    50. Development of fractal kinetic theory for enzyme-catalysed reactions and implications for the design of biochemical pathways. Biosystems. 1998 Jun-Jul; 47(1-2):9-36. Savageau MA. PMID: 9715749.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    51. Rules for the evolution of gene circuitry. Pac Symp Biocomput. 1998; 54-65. Savageau MA. PMID: 9697171.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    52. Completely uncoupled and perfectly coupled gene expression in repressible systems. J Mol Biol. 1997 Feb 28; 266(3):538-58. Hlavacek WS, Savageau MA. PMID: 9067609.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    53. Model assessment and refinement using strategies from biochemical systems theory: application to metabolism in human red blood cells. J Theor Biol. 1996 Apr 21; 179(4):329-68. Ni TC, Savageau MA. PMID: 8763353.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    54. Application of biochemical systems theory to metabolism in human red blood cells. Signal propagation and accuracy of representation. J Biol Chem. 1996 Apr 05; 271(14):7927-41. Ni TC, Savageau MA. PMID: 8626472.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    55. Rules for coupled expression of regulator and effector genes in inducible circuits. J Mol Biol. 1996 Jan 12; 255(1):121-39. Hlavacek WS, Savageau MA. PMID: 8568860.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    56. Michaelis-Menten mechanism reconsidered: implications of fractal kinetics. J Theor Biol. 1995 Sep 07; 176(1):115-24. Savageau MA. PMID: 7475096.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    57. Subunit structure of regulator proteins influences the design of gene circuitry: analysis of perfectly coupled and completely uncoupled circuits. J Mol Biol. 1995 May 12; 248(4):739-55. Hlavacek WS, Savageau MA. PMID: 7752237.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    58. Influence of fractal kinetics on molecular recognition. J Mol Recognit. 1993 Dec; 6(4):149-57. Savageau MA. PMID: 7917410.
      View in: PubMed   Mentions: 6     Fields:    
    59. The tricarboxylic acid cycle in Dictyostelium discoideum. Systemic effects of including protein turnover in the current model. J Biol Chem. 1993 Aug 15; 268(23):16917-28. Shiraishi F, Savageau MA. PMID: 8349583.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    60. The tricarboxylic acid cycle in Dictyostelium discoideum. III. Analysis of steady state and dynamic behavior. J Biol Chem. 1992 Nov 15; 267(32):22926-33. Shiraishi F, Savageau MA. PMID: 1429643.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    61. The tricarboxylic acid cycle in Dictyostelium discoideum. IV. Resolution of discrepancies between alternative methods of analysis. J Biol Chem. 1992 Nov 15; 267(32):22934-43. Shiraishi F, Savageau MA. PMID: 1429644.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    62. The tricarboxylic acid cycle in Dictyostelium discoideum. II. Evaluation of model consistency and robustness. J Biol Chem. 1992 Nov 15; 267(32):22919-25. Shiraishi F, Savageau MA. PMID: 1429642.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    63. The tricarboxylic acid cycle in Dictyostelium discoideum. I. Formulation of alternative kinetic representations. J Biol Chem. 1992 Nov 15; 267(32):22912-8. Shiraishi F, Savageau MA. PMID: 1429641.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    64. Metabolite channeling: implications for regulation of metabolism and for quantitative description of reactions in vivo. J Theor Biol. 1991 Sep 07; 152(1):85-92. Savageau MA. PMID: 1753775.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    65. Biochemical systems theory: operational differences among variant representations and their significance. J Theor Biol. 1991 Aug 21; 151(4):509-30. Savageau MA. PMID: 1943154.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    66. Reconstructionist molecular biology. New Biol. 1991 Feb; 3(2):190-7. Savageau MA. PMID: 2065013.
      View in: PubMed   Mentions: 4     Fields:    
    67. Constraints among molecular and systemic properties: implications for physiological genetics. J Theor Biol. 1989 Nov 08; 141(1):93-115. Savageau MA, Sorribas A. PMID: 2634164.
      View in: PubMed   Mentions: 11     Fields:    
    68. Accuracy of alternative representations for integrated biochemical systems. Biochemistry. 1987 Oct 20; 26(21):6869-80. Voit EO, Savageau MA. PMID: 3427048.
      View in: PubMed   Mentions: 18     Fields:    
    69. A theory of alternative designs for biochemical control systems. Biomed Biochim Acta. 1985; 44(6):875-80. Savageau MA. PMID: 4038287.
      View in: PubMed   Mentions: 13     Fields:    Translation:Animals
    70. Allometric morphogenesis of complex systems: Derivation of the basic equations from first principles. Proc Natl Acad Sci U S A. 1979 Dec; 76(12):6023-5. Savageau MA. PMID: 16592726; PMCID: PMC411791.
      View in: PubMed   Mentions: 11     Fields:    
    71. Growth of complex systems can be related to the properties of their underlying determinants. Proc Natl Acad Sci U S A. 1979 Nov; 76(11):5413-7. Savageau MA. PMID: 16592715; PMCID: PMC411657.
      View in: PubMed   Mentions: 9     Fields:    
    72. Genetic regulatory mechanisms and the ecological niche of Escherichia coli. Proc Natl Acad Sci U S A. 1974 Jun; 71(6):2453-5. Savageau MA. PMID: 4601590; PMCID: PMC388476.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    73. Biochemical systems analysis. 3. Dynamic solutions using a power-law approximation. J Theor Biol. 1970 Feb; 26(2):215-26. Savageau MA. PMID: 5434343.
      View in: PubMed   Mentions: 46     Fields:    Translation:Cells
    74. Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. J Theor Biol. 1969 Dec; 25(3):370-9. Savageau MA. PMID: 5387047.
      View in: PubMed   Mentions: 95     Fields:    Translation:Cells
    75. Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. J Theor Biol. 1969 Dec; 25(3):365-9. Savageau MA. PMID: 5387046.
      View in: PubMed   Mentions: 104     Fields:    
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