Access the full text.
Sign up today, get DeepDyve free for 14 days.
(1977)
Biophys. Mol. Biol
A. Groen, R. Wanders, H. Westerhoff, R. Meer, J. Tager (1982)
Quantification of the contribution of various steps to the control of mitochondrial respiration.The Journal of biological chemistry, 257 6
J. Tyson, James Murray (1989)
Cyclic AMP waves during aggregation of Dictyostelium amoebae.Development, 106 3
Z. Han, K. Ishizaki, K. Nishizawa, Tomohisa Kato, T. Todo, M. Ikenaga (1999)
A genetic effect of altered gravity: mutations induced by simulated hypogravity and hypergravity in microsatellite sequences of human tumor cells.Mutation research, 426 1
J. Papin, N. Price, Sharon Wiback, D. Fell, B. Palsson (2003)
Metabolic pathways in the post-genome era.Trends in biochemical sciences, 28 5
P. Glansdorff, I. Prigogine (1971)
Structure , stabilité et fluctuations
M. Elowitz, A. Levine, E. Siggia, P. Swain (2002)
Stochastic Gene Expression in a Single CellScience, 297
C. DeLisi (1988)
The Human Genome ProjectAmerican Scientist, 76
T. Smith, G. Lange, W. Marks (1996)
Fractal methods and results in cellular morphology — dimensions, lacunarity and multifractalsJournal of Neuroscience Methods, 69
J. Beckwith (1967)
Regulation of the Lac OperonScience, 156
D. Lane, S. Benchimol (1990)
p53: oncogene or anti-oncogene?Genes & development, 4 1
J. Wolf, J. Passarge, O. Somsen, J. Snoep, Reinhart Heinrich, H. Westerhoff (2000)
Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations.Biophysical journal, 78 3
W. Loomis, S. Thomas (1976)
Kinetic analysis of biochemical differentiation in Dictyostelium discoideum.The Journal of biological chemistry, 251 20
S. Newman, G. Forgacs, Gerd Muller (2006)
Before programs: the physical origination of multicellular forms.The International journal of developmental biology, 50 2-3
William Blake, Mads Kærn, C. Cantor, J. Collins (2003)
Noise in eukaryotic gene expressionNature, 422
L Rowen, G Magharias, L Hood (1997)
Sequencing the human genomeScience, 278
M. Mesarovic, S. Sreenath, J. Keene (2004)
Search for organising principles: understanding in systems biology.Systems biology, 1 1
T. Hammond, E. Benes, K. O’Reilly, D. Wolf, R. Linnehan, A. Taher, J. Kaysen, P. Allen, T. Goodwin (2000)
Mechanical culture conditions effect gene expression: gravity-induced changes on the space shuttle.Physiological genomics, 3 3
L. Herndon, Peter Schmeissner, Justyna Dudaronek, Paula Brown, Kristin Listner, Y. Sakano, M. Paupard, D. Hall, M. Driscoll (2002)
Stochastic and genetic factors influence tissue-specific decline in ageing C. elegansNature, 419
P. Glansdorff, I. Prigogine (1971)
Thermodynamic theory of structure, stability and fluctuations
P. Mitchell (1961)
Coupling of Phosphorylation to Electron and Hydrogen Transfer by a Chemi-Osmotic type of MechanismNature, 191
M. Levin (2003)
Bioelectromagnetics in morphogenesisBioelectromagnetics, 24
C. Nelson, R. Jean, J. Tan, Wendy Liu, N. Sniadecki, A. Spector, Christopher Chen (2005)
Emergent patterns of growth controlled by multicellular form and mechanics.Proceedings of the National Academy of Sciences of the United States of America, 102 33
A Turing (1952)
The chemical basis of morphogenesisPhil. Trans. Roy. Soc. London, Ser. B, 237
P Mitchell (1966)
Coupling in Oxidative and Photosynthetic Phosphorylation
M. Gerschenson, K. Graves, Steven Carson, R. Wells, G. Pierce (1986)
Regulation of melanoma by the embryonic skin.Proceedings of the National Academy of Sciences of the United States of America, 83 19
Xiaoyun Zhu, R. Assoian (1995)
Integrin-dependent activation of MAP kinase: a link to shape-dependent cell proliferation.Molecular biology of the cell, 6 3
D. Garfinkel, L. Garfinkel, M. Pring, S. Green, B. Chance (1970)
Computer applications to biochemical kinetics.Annual review of biochemistry, 39
D. Ingber (2005)
Mechanical control of tissue growth: function follows form.Proceedings of the National Academy of Sciences of the United States of America, 102 33
Maureen O’Malley, J. Dupré (2005)
Fundamental issues in systems biology.BioEssays : news and reviews in molecular, cellular and developmental biology, 27 12
Zhi-zhen Wang (2003)
[Central dogma of molecular biology].Sheng li ke xue jin zhan [Progress in physiology], 34 2
M. Aon, S. Cortassa (1994)
On the fractal nature of cytoplasmFEBS Letters, 344
H. Siegelmann (1999)
Neural networks and analog computation - beyond the Turing limit
M. Maffini, A. Soto, J. Calabro, A. Ucci, C. Sonnenschein (2004)
The stroma as a crucial target in rat mammary gland carcinogenesisJournal of Cell Science, 117
Matthias Scherf, A. Klingenhoff, Thomas Werner (2000)
Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach.Journal of molecular biology, 297 3
S. Guerroui, J. Deschatrette, C. Wolfrom (2005)
Prolonged perturbation of the oscillations of hepatoma Fao cell proliferation by a single small dose of methotrexate.Pathologie-biologie, 53 5
R. Brent (2004)
A partnership between biology and engineeringNature Biotechnology, 22
C. Auffray, S. Imbeaud, M. Roux-Rouquié, L. Hood (2003)
Self–organized living systems: conjunction of a stable organization with chaotic fluctuations in biological space–timePhilosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences, 361
H. Westerhoff, K. Dam (1987)
Thermodynamics and Control of Biological Free-Energy Transduction
(1943)
What is life? The physical aspects of the living cell Based on Lectures Delivered under the Auspices of the Dublin Institute for Advanced Studies at Trinity College
S. Kauffman (1991)
Origins of Order: self-organization and selection in evolution
M. Savageau (1969)
Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions.Journal of theoretical biology, 25 3
B. Palsson (2002)
In silico biology through “omics”Nature Biotechnology, 20
P. Kenny, M. Bissell (2003)
Tumor reversion: Correction of malignant behavior by microenvironmental cuesInternational Journal of Cancer, 107
E. Kellenberger (2004)
The evolution of molecular biologyEMBO reports, 5
J. Bolker (2000)
Modularity in Development and Why It Matters to Evo-Devo1, 40
Sui Huang (1999)
Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discoveryJournal of Molecular Medicine, 77
B. Wright (1970)
The use of kinetic models to analyze differentiation.Behavioral science, 15 1
Conrad Waddington (1957)
The strategy of the genes
P. Anderson (1972)
More is different.Science, 177 4047
H. Umbarger, B. Brown (1956)
THREONINE DEAMINATION IN ESCHERICHIA COLI IJournal of Bacteriology, 71
J. Binney, N. Dowrick, A. Fisher, M. Newman (1992)
The Theory of Critical Phenomena: An Introduction to the Renormalization Group
A. Kurakin (2004)
Self-organization vs Watchmaker: stochastic gene expression and cell differentiationDevelopment Genes and Evolution, 215
J. Needham (1943)
Biochemistry and morphogenesis
L. Onsager (1931)
Reciprocal Relations in Irreversible Processes. II.Physical Review, 37
R. Strohman (1997)
The coming Kuhnian revolution in biologyNature Biotechnology, 15
B. Teusink, Barbara Bakker, H. Westerhoff (1996)
Control of frequency and amplitudes is shared by all enzymes in three models for yeast glycolytic oscillations.Biochimica et biophysica acta, 1275 3
S. Kanamura, K. Kanai, J. Watanabe (1990)
Fine structure and function of hepatocytes during development.Journal of electron microscopy technique, 14 2
B. Novák, J. Tyson (1995)
Quantitative analysis of a molecular model of mitotic control in fission yeastJournal of Theoretical Biology, 173
O. Toussaint, E. Schneider (1998)
The thermodynamics and evolution of complexity in biological systems.Comparative biochemistry and physiology. Part A, Molecular & integrative physiology, 120 1
R. Yates, A. Pardee (1957)
Control by uracil of formation of enzymes required for orotate synthesis.The Journal of biological chemistry, 227 2
Reinhart Heinrich, S. Rapoport, T. Rapoport (1977)
Metabolic regulation and mathematical models.Progress in biophysics and molecular biology, 32 1
Attila Becskei, L. Serrano (2000)
Engineering stability in gene networks by autoregulationNature, 405
S. Lelièvre, V. Weaver, J. Nickerson, C. Larabell, Ankan Bhaumik, O. Petersen, M. Bissell (1998)
Tissue phenotype depends on reciprocal interactions between the extracellular matrix and the structural organization of the nucleus.Proceedings of the National Academy of Sciences of the United States of America, 95 25
T. Hunkapiller, R. Kaiser, B. Koop, L. Hood (1991)
Large-scale and automated DNA sequence determination.Science, 254 5028
J. Clegg (1984)
Intracellular water and the cytomatrix: some methods of study and current viewsThe Journal of Cell Biology, 99
R. Strohman (2000)
Organization becomes cause in the matterNature Biotechnology, 18
Brian Goodwin (2000)
The life of form. Emergent patterns of morphological transformation.Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie, 323 1
P. Mitchell (1966)
CHEMIOSMOTIC COUPLING IN OXIDATIVE AND PHOTOSYNTHETIC PHOSPHORYLATIONBiological Reviews, 41
E. Coen (1999)
The Art of Genes
N. Farinella-Ferruzza (1956)
The transformation of a tail into limb after xenoplastic transplantationExperientia, 12
B. Kholodenko, H. Westerhoff (2004)
Metabolic engineering in the post genomic era
X. Xie, H. Lu (1999)
Single-molecule Enzymology*The Journal of Biological Chemistry, 274
M. Cassman (2005)
Barriers to progress in systems biologyNature, 438
Abhay Joshi, Bernhard Palsson (1989)
Metabolic dynamics in the human red cell. Part I--A comprehensive kinetic model.Journal of theoretical biology, 141 4
H. Umbarger, B. Brown (1956)
Threonine deamination in Escherichia coli. I. D- and L-threonine deaminase activities of cell-free extracts.Journal of bacteriology, 71 4
E. Keller (2000)
The Century of the Gene
E. Knust (2000)
Control of epithelial cell shape and polarity.Current opinion in genetics & development, 10 5
F. Heylighen (1999)
The Science of Self-Organization and Adaptivity
B. Mandelbrot (1985)
Self-Affine Fractals and Fractal DimensionPhysica Scripta, 32
David Hume (2000)
Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression.Blood, 96 7
A. Zaikin, A. Zhabotinsky (1970)
Concentration Wave Propagation in Two-dimensional Liquid-phase Self-oscillating SystemNature, 225
E. Schrödinger (1944)
What is life? : the physical aspect of the living cell
Barbara Bakker, H. Assmus, F. Bruggeman, J. Haanstra, E. Klipp, H. Westerhoff (2004)
Network-Based Selectivity of Antiparasitic InhibitorsMolecular Biology Reports, 29
HE Umbarger, B Brown (1957)
Threonine deamination in Escherichia coli. II. Evidence for two L-threonine deaminasesJ. Bacteriol., 73
J. Cutting, Jeffrey Garvin (1987)
Fractal curves and complexityPerception & Psychophysics, 42
P Mitchell (1961)
Chemiosmotic Coupling of phosphorylation to electron and hydrogen transfer by a chemiosmotic type of mechanismNature, 191
C. Woese (2004)
A New Biology for a New CenturyMicrobiology and Molecular Biology Reviews, 68
R. McBeath, Dana Pirone, C. Nelson, K. Bhadriraju, Christopher Chen (2004)
Cell shape, cytoskeletal tension, and RhoA regulate stem cell lineage commitment.Developmental cell, 6 4
S. Gilbert, J. Opitz, R. Raff (1996)
Resynthesizing evolutionary and developmental biology.Developmental biology, 173 2
J. Kupiec (1997)
A Darwinian theory for the origin of cellular differentiationMolecular and General Genetics MGG, 255
B. Hess, A. Boiteux (1971)
Oscillatory phenomena in biochemistry.Annual review of biochemistry, 40
Sui Huang, D. Ingber (2000)
Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks.Experimental cell research, 261 1
M. Aon, S. Cortassa, D. Lloyd (2000)
CHAOTIC DYNAMICS AND FRACTAL SPACE IN BIOCHEMISTRY: SIMPLICITY UNDERLIES COMPLEXITYCell Biology International, 24
A. Lloyd, D. Lloyd (1995)
CHAOS: ITS SIGNIFICANCE AND DETECTION IN BIOLOGYBiological Rhythm Research, 26
F. Schock, N. Perrimon (2002)
Molecular mechanisms of epithelial morphogenesis.Annual review of cell and developmental biology, 18
D. Ingber (1997)
Tensegrity: the architectural basis of cellular mechanotransduction.Annual review of physiology, 59
H. Stapp (1971)
S-MATRIX INTERPRETATION OF QUANTUM THEORY.Physical Review D, 3
T. Dewey (1998)
Fractals in Molecular Biophysics
R. Laughlin, 京都大学基礎物理学研究所 (2005)
A Different Universe
B. Chance, R. Estabrook, A. Ghosh (1964)
DAMPED SINUSOIDAL OSCILLATIONS OF CYTOPLASMIC REDUCED PYRIDINE NUCLEOTIDE IN YEAST CELLS.Proceedings of the National Academy of Sciences of the United States of America, 51
H. Atlan, Moshe Koppel (1990)
The cellular computer DNA: Program or dataBulletin of Mathematical Biology, 52
J. Edwards, B. Palsson (1999)
Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype*The Journal of Biological Chemistry, 274
P. Weiss (1947)
The Problem of Specificity in Growth and Development *The Yale Journal of Biology and Medicine, 19
Christopher Chen, M. Mrksich, Sui Huang, G. Whitesides, D. Ingber (1997)
Geometric control of cell life and death.Science, 276 5317
R. Singhvi, Ashok Kumar, G. López, G. Stephanopoulos, Daniel Wang, G. Whitesides, D. Ingber (1994)
Engineering cell shape and function.Science, 264 5159
(1963)
Oscillatory Organization in Cells, a Dynamic Theory of Cellular Control Processes
A. Turing (1952)
The chemical basis of morphogenesisBulletin of Mathematical Biology, 52
W. Goldmann (2002)
MECHANICAL ASPECTS OF CELL SHAPE REGULATION AND SIGNALINGCell Biology International, 26
D'arcy Thompson
On Growth and FormNature, 100
H. Kitano (2002)
Systems Biology: A Brief OverviewScience, 295
C. Jamora, E. Fuchs (2002)
Intercellular adhesion, signalling and the cytoskeletonNature Cell Biology, 4
D. Ingber (1999)
How cells (might) sense microgravityThe FASEB Journal, 13
J. Beckwith (1967)
Regulation of the lac operon. Recent studies on the regulation of lactose metabolism in Escherichia coli support the operon model.Science, 156 3775
M. Chicurel, R. Singer, C. Meyer, D. Ingber (1998)
Integrin binding and mechanical tension induce movement of mRNA and ribosomes to focal adhesionsNature, 392
J. Barrow-Green (1996)
Poincare and the Three Body Problem
I. Prigogine (1995)
La fin des certitudes, 2
R. Waterston, E. Lander, J. Sulston (2002)
On the sequencing of the human genomeProceedings of the National Academy of Sciences of the United States of America, 99
Stephen Day, Pareena Lawrence (2000)
Measuring dimensions: the regulation of size and shape.Development, 127 14
Hans Westerhoff, Hans Westerhoff, Jannie Hofmeyr, B. Kholodenko, B. Kholodenko (1994)
Getting to the inside of cells using metabolic control analysis.Biophysical chemistry, 50 3
J. Till (1981)
Cellular diversity in the blood-forming system.American scientist, 69 5
M. Bissell, D. Farson, A. Tung (2010)
Cell shape and hexose transport in normal and virus-transformed cells in culture.Journal of supramolecular structure, 6 1
Hui Ge, A. Walhout, M. Vidal (2003)
Integrating 'omic' information: a bridge between genomics and systems biology.Trends in genetics : TIG, 19 10
M. Paszek, Nastaran Zahir, Kandice Johnson, J. Lakins, G. Rozenberg, A. Gefen, C. Reinhart-King, S. Margulies, M. Dembo, D. Boettiger, D. Hammer, V. Weaver (2005)
Tensional homeostasis and the malignant phenotype.Cancer cell, 8 3
P. Lawrence (1992)
The making of a fly
C. Gershenson, F. Heylighen (2004)
How can we think the complexarXiv: Adaptation and Self-Organizing Systems
P. Uetz, L. Giot, G. Cagney, T. Mansfield, R. Judson, James Knight, D. Lockshon, Vaibhav Narayan, Maithreyan Srinivasan, P. Pochart, Alia Qureshi-Emili, Ying Li, B. Godwin, D. Conover, T. Kalbfleisch, G. Vijayadamodar, Meijia Yang, M. Johnston, S. Fields, J. Rothberg (2000)
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiaeNature, 403
H. Rottenberg, S. Caplan, A. Essig (1967)
Stoichiometry and Coupling: Theories of Oxidative PhosphorylationNature, 216
J. Rosai (2001)
The Continuing Role of Morphology in the Molecular AgeModern Pathology, 14
H. Westerhoff, Yi-der Chen (1984)
How do enzyme activities control metabolite concentrations? An additional theorem in the theory of metabolic control.European journal of biochemistry, 142 2
G. Fankhauser (1945)
Maintenance of normal structure in heteroploid salamander larvae, through compensation of changes in cell size by adjustment of cell number and cell shape.The Journal of experimental zoology, 100
R. Ibarra, J. Edwards, B. Palsson (2002)
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growthNature, 420
K. Strange (2005)
The end of "naive reductionism": rise of systems biology or renaissance of physiology?American journal of physiology. Cell physiology, 288 5
Systems analysis has historically been performed in many areas of biology, including ecology, developmental biology and immunology. More recently, the genomics revolution has catapulted molecular biology into the realm of systems biology. In unicellular organisms and well-defined cell lines of higher organisms, systems approaches are making definitive strides toward scientific understanding and biotechnological applications. We argue here that two distinct lines of inquiry in molecular biology have converged to form contemporary systems biology.
Nature Biotechnology – Springer Journals
Published: Oct 6, 2004
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.