Search results for 'systems biology' (try it on Scholar)

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  1. Ingo Brigandt (2013). Systems Biology and the Integration of Mechanistic Explanation and Mathematical Explanation. Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):477-492.score: 242.0
    The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation (as the analysis of a whole in terms of its structural parts and (...)
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  2. Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.) (2007). Systems Biology: Philosophical Foundations. Elsevier.score: 240.0
    Systems biology is a vigorous and expanding discipline, in many ways a successor to genomics and perhaps unprecendented in its combination of biology with a ...
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  3. I. C. Baianu (2006). Robert Rosen's Work and Complex Systems Biology. Axiomathes 16 (1-2):25-34.score: 240.0
    Complex Systems Biology approaches are here considered from the viewpoint of Robert Rosen’s (M,R)-systems, Relational Biology and Quantum theory, as well as from the standpoint of computer modeling. Realizability and Entailment of (M,R)-systems are two key aspects that relate the abstract, mathematical world of organizational structure introduced by Rosen to the various physicochemical structures of complex biological systems. Their importance for understanding biological function and life itself, as well as for designing new strategies for (...)
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  4. Fred C. Boogerd, Frank J. Bruggeman & Robert C. Richardson (2013). Mechanistic Explanations and Models in Molecular Systems Biology. Foundations of Science 18 (4):725-744.score: 240.0
    Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation (...)
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  5. Alexander Powell, Maureen A. O'Malley, Staffan Mueller-Wille, Jane Calvert & John Dupré (2007). Disciplinary Baptisms: A Comparison of the Naming Stories of Genetics, Molecular Biology, Genomics and Systems Biology. History and Philosophy of the Life Sciences 29 (1):5-32.score: 240.0
    Understanding how scientific activities use naming stories to achieve disciplinary status is important not only for insight into the past, but for evaluating current claims that new disciplines are emerging. In order to gain a historical understanding of how new disciplines develop in relation to these baptismal narratives, we compare two recently formed disciplines, systems biology and genomics, with two earlier related life sciences, genetics and molecular biology. These four disciplines span the twentieth century, a period in (...)
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  6. Jason Scott Robert, Jane Maienschein & Manfred D. Laubichler (2006). Systems Bioethics and Stem Cell Biology. Journal of Bioethical Inquiry 3 (1-2):19-31.score: 210.0
    The complexities of modern science are not adequately reflected in many bioethical discussions. This is especially problematic in highly contested cases where there is significant pressure to generate clinical applications fast, as in stem cell research. In those cases a more integrated approach to bioethics, which we call systems bioethics, can provide a useful framework to address ethical and policy issues. Much as systems biology brings together different experimental and methodological approaches in an integrative way, systems (...)
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  7. Jonathan Bard (2010). A Systems Biology View of Evolutionary Genetics. Bioessays 32 (7):559-563.score: 210.0
  8. Kurt Boonen, John W. Creemers & Liliane Schoofs (2009). Bioactive Peptides, Networks and Systems Biology. Bioessays 31 (3):300-314.score: 210.0
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  9. Jeffrey C. Way & Pamela A. Silver (2007). Systems Engineering Without an Engineer: Why We Need Systems Biology. Complexity 13 (2):22-29.score: 210.0
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  10. Marta Bertolaso, Alessandro Giuliani & Laura De Gara (2011). Systems Biology Reveals Biology of Systems. Complexity 16 (6):10-16.score: 210.0
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  11. Claudio Gutiérrez, Sebastián Jaramillo & Jorge Soto-Andrade (2011). Some Thoughts on A. H. Louie's “More Than Life Itself: A Reflection on Formal Systems and Biology”. [REVIEW] Axiomathes 21 (3):439-454.score: 204.0
    We review and discuss A. H. Louie’s book “More than Life Itself: A Reflexion on Formal Systems and Biology” from an interdisciplinary viewpoint, involving both biology and mathematics, taking into account new developments and related theories.
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  12. Melinda Fagan (2012). Waddington Redux: Models and Explanation in Stem Cell and Systems Biology. Biology and Philosophy 27 (2):179-213.score: 186.0
    Stem cell biology and systems biology are two prominent new approaches to studying cell development. In stem cell biology, the predominant method is experimental manipulation of concrete cells and tissues. Systems biology, in contrast, emphasizes mathematical modeling of cellular systems. For scientists and philosophers interested in development, an important question arises: how should the two approaches relate? This essay proposes an answer, using the model of Waddington’s landscape to triangulate between stem cell and (...)
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  13. Philippe De Backer, Danny De Waele & Linda Van Speybroeck (2010). Ins and Outs of Systems Biology Vis-à-Vis Molecular Biology: Continuation or Clear Cut? Acta Biotheoretica 58 (1).score: 180.0
    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems (...) ‘revolutionizes’ molecular biology and ‘transcends’ its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement. (shrink)
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  14. Maureen O'Malley, Jane Calvert & John Dupré (2007). The Study of Socioethical Issues in Systems Biology. American Journal of Bioethics 7 (4):67-78.score: 180.0
    Systems biology is the rapidly growing and heavily funded successor science to genomics. Its mission is to integrate extensive bodies of molecular data into a detailed mathematical understanding of all life processes, with an ultimate view to their prediction and control. Despite its high profile and widespread practice, there has so far been almost no bioethical attention paid to systems biology and its potential social consequences. We outline some of systems biology's most important socioethical (...)
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  15. Andrew Moore (2009). A Day of Systems and Synthetic Biology for Non‐Experts. Bioessays 31 (1):119-124.score: 180.0
  16. H. Goorhuis (2007). Towards a Constructivist Systems Biology? Review Of: F. C. Boogerd Et Al. (Eds.) (2006) Systems Biology. Constructivist Foundations 3 (1):57-57.score: 180.0
    Summary: Based on the book, the overall impression is that systems biology struggles with the limits of first-order cybernetics and tries to overcome it by mixing bottom up and top down methods from classical approaches such as genetics, molecular biology and enzymology. However, the contributors avoid the step from first-order to second-order cybernetics.
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  17. Kenneth F. Schaffner (2007). Theories, Models, and Equations in Systems Biology. In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Elsevier. 145--162.score: 180.0
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  18. Linda Van Speybroeck, Philippe De Backer, Joris Van Poucke & Danny De Waele (2005). The Conceptual Challenge of Systems Biology. Bioessays 27 (12):1305-1307.score: 180.0
    Report of the symposium 'Towards a Philosophy of Systems Biology' held at the Vrije Universiteit of Amsterdam (VUA), the Netherlands, from 2 to 3 June 2005.
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  19. William C. Wimsatt (2007). On Building Reliable Pictures with Unreliable Data: An Evolutionary and Developmental Coda for the New Systems Biology. In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Elsevier. 103--20.score: 180.0
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  20. Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (2007). Afterthoughts as Foundations for Systems Biology. In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Elsevier.score: 180.0
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  21. Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (2007). Towards Philosophical Foundations of Systems Biology: Introduction. In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Elsevier.score: 180.0
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  22. George Khushf (2008). Health as Intra-Systemic Integrity: Rethinking the Foundations of Systems Biology and Nanomedicine. Perspectives in Biology and Medicine 51 (3):432-449.score: 156.0
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  23. Athel Cornish-Bowden (2006). Putting the Systems Back Into Systems Biology. Perspectives in Biology and Medicine 49 (4):475-489.score: 156.0
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  24. Timothy Ravasi, Christine A. Wells & David A. Hume (2007). Systems Biology of Transcription Control in Macrophages. Bioessays 29 (12):1215-1226.score: 156.0
    The study of the mammalian immune system offers many advantages to systems biologists. The cellular components of the mammalian immune system are experimentally tractable; they can be isolated or differentiated from in vivo and ex vivo sources and have an essential role in health and disease. For these reasons, the major effectors cells of the innate immune system, macrophages, have been a particular focus in international genome and transcriptome consortia. Genomescale analysis of the transcriptome, and transcription initiation has enabled (...)
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  25. Jason Scott Robert (2007). Molecular and Systems Biology and Bioethics. In David L. Hull & Michael Ruse (eds.), The Cambridge Companion to the Philosophy of Biology. Cambridge University Press.score: 156.0
  26. Orkun S. Soyer & Maureen A. O'Malley (2013). Evolutionary Systems Biology: What It is and Why It Matters. Bioessays 35 (8):696-705.score: 154.0
  27. Frank J. Bruggeman (2007). Systems Biology: At Last an Integrative Wet and Dry Biology. Biological Theory 2 (2):183-188.score: 152.0
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  28. Sara Green (2013). When One Model is Not Enough: Combining Epistemic Tools in Systems Biology. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (2):170-180.score: 152.0
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  29. Miles MacLeod & Nancy J. Nersessian (2013). Coupling Simulation and Experiment: The Bimodal Strategy in Integrative Systems Biology. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):572-584.score: 152.0
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  30. Jonathan F. Davies & Maureen A. O'Malley (2007). Toward a Philosophy of Systems Biology: Systems Biology: Philosophical Foundations, Fred C. Boogerd , Frank J. Bruggeman , Jan-Hendrik S. Hofmeyr , and Hans V. Westerhoff , Eds. Amsterdam: Elsevier, 2007, (360 Pp; €99.95 Hbk; ISBN 978-0-444-52085-2). [REVIEW] Biological Theory 2 (4):420-422.score: 152.0
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  31. Sara Green, Melinda Fagan & Johannes Jaeger (forthcoming). Explanatory Integration Challenges in Evolutionary Systems Biology. Biological Theory.score: 152.0
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  32. Annamaria Carusi (2014). Validation and Variability: Dual Challenges on the Path From Systems Biology to Systems Medicine. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 48:28-37.score: 152.0
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  33. Mihajlo Mesarovic & Sree N. Sreenath (2006). Beyond the Flat Earth Perspective in Systems Biology. Biological Theory 1 (1):33-34.score: 152.0
  34. Beckett Sterner, The Epistemology of Causal Selection: Insights From Systems Biology.score: 150.0
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  35. Lindell Bromham (2011). Wandering Drunks and General Lawlessness in Biology: Does Diversity and Complexity Tend to Increase in Evolutionary Systems? Biology and Philosophy 26 (6):915-933.score: 150.0
    Does biology have general laws that apply to all levels of biological organisation, across all evolutionary time? In their book “Biology’s first law: the tendency for diversity and complexity to increase in evolutionary systems” (2010), Daniel McShea and Robert Brandon propose that the most fundamental law of biology is that all levels of biological organisation have an underlying tendency to become more complex and diverse over time. A range of processes, most notably selection, can prevent the (...)
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  36. Jane Calvert (2012). Systems Biology, Synthetic Biology and Data-Driven Research: A Commentary on Krohs, Callebaut, and O'Malley and Soyer. Studies in History and Philosophy of Science Part C 43 (1):81-84.score: 150.0
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  37. Miles MacLeod & Nancy J. Nersessian (2013). Building Simulations From the Ground Up: Modeling and Theory in Systems Biology. Philosophy of Science 80 (4):533-556.score: 150.0
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  38. Maureen A. O'Malley & Orkun S. Soyer (2012). The Roles of Integration in Molecular Systems Biology. Studies in History and Philosophy of Science Part C 43 (1):58-68.score: 150.0
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  39. Jane Calvert & Joan H. Fujimura (2011). Calculating Life? Duelling Discourses in Interdisciplinary Systems Biology. Studies in History and Philosophy of Science Part C 42 (2):155-163.score: 150.0
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  40. Jacques Demongeot, Nicolas Glade & Andrés Moreira (forthcoming). Evolution and RNa Relics. A Systems Biology View. Acta Biotheoretica.score: 150.0
    The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only (...)
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  41. Morris Foster (2007). Everything Old is New Again, Including Systems Biology. American Journal of Bioethics 7 (4):85-86.score: 150.0
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  42. Fridolin Gross (2011). What Systems Biology Can Tell Us About Disease. History and Philosophy of the Life Sciences 33 (4).score: 150.0
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  43. Lenny Moss (2007). From Describing to Performing the Socioethical Engagement with Systems Biology. American Journal of Bioethics 7 (4):86-87.score: 150.0
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  44. Maureen O'Malley, Jane Calvert & John Dupré (2007). Response to Open Peer Commentaries on "The Study of Socioethical Issues in Systems Biology". American Journal of Bioethics 7 (4):7-9.score: 150.0
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  45. Sara Green & Olaf Wolkenhauer (forthcoming). Tracing Organizing Principles-Learning From the History of Systems Biology. History and Philosophy of the Life Sciences.score: 150.0
  46. James A. Marcum (2008). Whitehead's Philosophy of Organism and Systems Biology. Chromatikon: Annales de la Philosophie En Procès / Yearbook of Philosophy in Process 4:143-152.score: 150.0
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  47. Jason H. Moore & Scott M. Williams (2005). Traversing the Conceptual Divide Between Biological and Statistical Epistasis: Systems Biology and a More Modern Synthesis. Bioessays 27 (6):637-646.score: 150.0
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  48. Maureen A. O'Malley & John Dupré (2005). Fundamental Issues in Systems Biology. Bioessays 27 (12):1270-1276.score: 150.0
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  49. Nicolas Smith (2008). Well‐Designed Systems Biology Content. An Introduction to Systems Biology: Design Principles of Biological Circuits. (2007). By Uri Alon. Chapman and Hall/CRC Press. Paperback, 301 Pp. Price £28.99. ISBN: 1‐58488‐642‐0. [REVIEW] Bioessays 30 (2):189-190.score: 150.0
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  50. Jens Timmer, Adriano Henney, Andrew Moore & Ursula Klingmuller (2010). Systems Biology of Mammalian Cells: A Report From the Freiburg Conference. Bioessays 32 (12):1099-1104.score: 150.0
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