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  1. E. Ahmed (1998). Ideas in Theoretical Biology. Acta Biotheoretica 46 (2).
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  2. Mike Ainsworth (1993). Abpl. Acta Biotheoretica 41 (1-2).
    Computer analysis of biological systems, using approaches such as metabolic control analysis is common. A typical example is a language like Herbert Sauro's SCAMP (Sauro & Fell, 1991), which allows simulations of enzyme systems, and calculation of control coefficients and elasticities. However such systems are motivated by the underlying biochemical theory and often have limitations as programming languages which mean that they can only be applied to particular classes of problems.ABPL (a biochemical programming language) extends these ideas by adding all (...)
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  3. J. McKenzie Alexander (2010). Robustness, Optimality, and the Handicap Principle. Biology and Philosophy 25 (5).
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  4. Hedi Ben Amor, Fabien Corblin, Eric Fanchon, Adrien Elena, Laurent Trilling, Jacques Demongeot & Nicolas Glade (forthcoming). Formal Methods for Hopfield-Like Networks. Acta Biotheoretica.
    Building a meaningful model of biological regulatory network is usually done by specifying the components (e.g. the genes) and their interactions, by guessing the values of parameters, by comparing the predicted behaviors to the observed ones, and by modifying in a trial-error process both architecture and parameters in order to reach an optimal fitness. We propose here a different approach to construct and analyze biological models avoiding the trial-error part, where structure and dynamics are represented as formal constraints. We apply (...)
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  5. Henri Atlan (1998). Paradigms in Immunology and Modern, Post-Modern, Post-Post-Modern, _ Philosophy. A Review of Alfred I. Tauber, the Immune Self: Theory or Metaphor? [REVIEW] Biology and Philosophy 13 (1):125-131.
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  6. Pierre M. Auger & Robert Roussarie (1994). Complex Ecological Models with Simple Dynamics: From Individuals to Populations. Acta Biotheoretica 42 (2-3).
    The aim of this work is to study complex ecological models exhibiting simple dynamics. We consider large scale systems which can be decomposed into weakly coupled subsystems. Perturbation Theory is used in order to get a reduced set of differential equations governing slow time varying global variables. As examples, we study the influence of the individual behaviour of animals in competition and predator-prey models. The animals are assumed to do many activities all day long such as searching for food of (...)
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  7. Pierre Auger, Ali Moussaoui & Gauthier Sallet (forthcoming). Basic Reproduction Ratio for a Fishery Model in a Patchy Environment. Acta Biotheoretica.
    Abstract We present a dynamical model of a multi-site fishery. The fish stock is located on a discrete set of fish habitats where it is catched by the fishing fleet. We assume that fishes remain on fishing habitats while the fishing vessels can move at a fast time scale to visit the different fishing sites. We use the existence of two time scales to reduce the dimension of the model : we build an aggregated model considering the habitat fish densities (...)
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  8. Pierre Auger & Jean-Christophe Poggiale (1996). Aggregation and Emergence in Hierarchically Organized Systems: Population Dynamics. Acta Biotheoretica 44 (3-4).
    The aim of this work is to present aggregation methods of hierarchically organized systems allowing one to replace the initial micro-system by a macro-system described by a few global variables. We also study the relations between the fast micro-dynamics and the slow macro-dynamics which can produce global properties. Emergence corresponds to a bottom-up coupling that is the result effected by a micro-level at a macro-level. As an example, we present prey-predator models with different time scales in an heterogeneous environment. A (...)
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  9. Melvin Avrami (1941). Geometry and Dynamics of Populations. Philosophy of Science 8 (1):115-132.
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  10. Nazneen Aziz (1995). Animal Models of Polycystic Kidney Disease. Bioessays 17 (8):703-712.
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  11. Mostafa Bachar (forthcoming). Modeling the Cardiovascular-Respiratory Control System: Data, Model Analysis, and Parameter Estimation. Acta Biotheoretica.
    Several key areas in modeling the cardiovascular and respiratory control systems are reviewed and examples are given which reflect the research state of the art in these areas. Attention is given to the interrelated issues of data collection, experimental design, and model application including model development and analysis. Examples are given of current clinical problems which can be examined via modeling, and important issues related to model adaptation to the clinical setting.
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  12. Tudor Baetu (2012). Filling in the Mechanistic Details: Two-Variable Experiments as Tests for Constitutive Relevance. [REVIEW] European Journal for Philosophy of Science 2 (3):337-353.
    This paper provides an account of the experimental conditions required for establishing whether correlating or causally relevant factors are constitutive components of a mechanism connecting input (start) and output (finish) conditions. I argue that two-variable experiments, where both the initial conditions and a component postulated by the mechanism are simultaneously manipulated on an independent basis, are usually required in order to differentiate between correlating or causally relevant factors and constitutively relevant ones. Based on a typical research project molecular biology, a (...)
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  13. Tudor M. Baetu, Ann-Sophie Barwich, Daniel Brooks, Sébastien Dutreuil & Pierre-Luc Germain (2013). Model Thinking in the Life Sciences: Complexity in the Making: Second European Advanced Seminar in the Philosophy of the Life Sciences,“In Vivo, Ex Vivo, in Vitro, in Silico: Models in the Life Sciences” Hermance, Switzerland, 10–14 September 2012.(Meeting Report). [REVIEW] Biological Theory 8 (1):121 - 124.
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  14. Tudor M. Baetu, Ann-Sophie Barwich, Daniel Brooks, Sébastien Dutreuil & Pierre-Luc Germain (2013). Model Thinking in the Life Sciences: Complexity in the Making. [REVIEW] Biological Theory 8 (1):121-124.
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  15. F. Bailly, F. Gaill & R. Mosseri (1991). A Dynamical System for Biological Development: The Case of Caenorhabditis Elegans. Acta Biotheoretica 39 (3-4).
    We show how a simple nonlinear dynamical system (the discrete quadratic iteration on the unit segment) can be the basis for modelling the embryogenesis process. Such an approach, even though being crude, can nevertheless prove to be useful when looking with the two main involved processes:i) on one hand the cell proliferation under successive divisions ii) on the other hand, the differentiation between cell lineages. We illustrate this new approach in the case of Caenorhabditis elegans by looking at the early (...)
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  16. Jonathan Bard (2003). Ontologies: Formalising Biological Knowledge for Bioinformatics. Bioessays 25 (5):501-506.
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  17. Jonathan Bard (2002). Bioinformatics for Beginners. Bioessays 24 (9):867-868.
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  18. A. L. Bardou, R. G. Seigneuric, J.-L. Chassé & P. M. Auger (1999). Incidence of Dispersion of Refractoriness and Cellular Coupling Resistance on Cardiac Reentries and Ventricular Fibrillation. Acta Biotheoretica 47 (3-4).
    We used computer simulations to study the possible role of the dispersion of cellular coupling, refractoriness or both, in the mechanisms underlying cardiac arrhythmias. Local ischemia was first assumed to induce cell to cell dispersion of the coupling resistance (Case 1), refractory period (Case 2), or both of them (Case 3). Our numerical experiments based on the van Capelle and Durrer model showed that vortices could not be induced by cell to cell variations. With cellular properties dispersed in a patchy (...)
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  19. Alain L. Bardou, Pierre M. Auger, Soumeya Achour, Philippe Dumee, Pierre J. Birkui & Marie-Claude Govaere (1995). Effect of Myocardial Infarction and Ischemia on Induction of Cardiac Reentries and Ventricular Fibrillation. Acta Biotheoretica 43 (4).
    The present work is aimed at investigating the effects of myocardial infarction and ischemia on induction of ventricular fibrillation. Electrophysiologic effects of global and local ischemia (variation of the dispersion of refractory periods as well as conduction velocity) on initiation of reentry mechanisms was studied by means of computer simulations based on a cellular automata model of propagation of activation wave through a ventricular surface element. A local area of ischemia where effects of the dispersion of refractory periods are investigated (...)
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  20. Alain L. Bardou, Pierre M. Auger, Jean-Luc Chasse & Renaud Seigneuric (1997). Theoretical Study of Cardiac Transient Conduction Blocks on Reentries Induction. Applications to Antiarrhythmic Drugs. Acta Biotheoretica 45 (3-4).
    Limitations of antiarrhythmic drugs on cardiac sudden death prevention appeared since the early 80's. The "Cardiac Arrhythmia Suppression Trial"(CAST) showed more recently that mortality was significantly higher inpatients treated with some particular antiarrhythmic drugs than in non-treated patients. In this field, our group recently demonstrated that a bolus of a Class 1B antiarrhythmic drug was able to trigger a ventricular fibrillation due to transient blocks induction. The aim of the present work was to systematically study, by use of the van (...)
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  21. Alain Bardou & Pierre Auger (1992). Preface. Acta Biotheoretica 40 (2-3).
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  22. Gillian Barker, Eric Desjardins & Trevor Pearce (eds.) (2013). Entangled Life: Organism and Environment in the Biological and Social Sciences. Springer.
  23. William Bechtel, Some Virtues of Modeling with Both Hands.
    Webb distinguishes two endeavors she calls animal modeling and animat modeling and advocates for the former. I share her preference and point to additional virtues of modeling actual biological mechanisms (animal modeling). As Webb argues, animat modeling should be regarded as modeling of specific, but madeup, biological mechanisms. I contend that modeling made-up mechanisms in situations in which we have some knowledge of the actual mechanisms involved is modeling with one hand—the good one—tied behind one’s back.1 The hand that is (...)
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  24. Gila Benchetrit (unknown). A Simple Dynamic Model of Respiratory Pump. Acta Biotheoretica.
    To study the interaction of forces that produce chest wall motion, we propose a model based on the lever system of Hillman and Finucane (J Appl Physiol 63(3):951–961, 1987 ) and introduce some dynamic properties of the respiratory system. The passive elements (rib cage and abdomen) are considered as elastic compartments linked to the open air via a resistive tube, an image of airways. The respiratory muscles (active) force is applied to both compartments. Parameters of the model are identified in (...)
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  25. Cora Bergantiños, Xavier Vilana, Montserrat Corominas & Florenci Serras (2010). Imaginal Discs: Renaissance of a Model for Regenerative Biology. Bioessays 32 (3):207-217.
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  26. Andre Bergholz, Stephan Heymann, Jörg A. Schenk & JohannChristoph Freytag (2001). Biological Sequences Integrated: A Relational Database Approach. Acta Biotheoretica 49 (3).
    Over the last decade the modeling and the storage of biological data has been a topic of wide interest for scientists dealing with biological and biomedical research. Currently most data is still stored in text files which leads to data redundancies and file chaos.In this paper we show how to use relational modeling techniques and relational database technology for modeling and storing biological sequence data, i.e. for data maintained in collections like EMBL or SWISS-PROT to better serve the needs for (...)
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  27. Marta Bertolaso (2011). Hierarchies and Causal Relationships in Interpretative Models of the Neoplastic Process. History and Philosophy of the Life Sciences 33 (4).
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  28. R. Betabert, T. B. Sherer & J. T. Greenamyre (2002). Animal Models of Parkinson's Diseases. Bioessays 24:308-318.
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  29. Ranjita Betarbet, Todd B. Sherer & J. Timothy Greenamyre (2002). Animal Models of Parkinson's Disease. Bioessays 24 (4):308-318.
  30. Jonathan Birch (2014). Gene Mobility and the Concept of Relatedness. Biology and Philosophy 29 (4):445-476.
    Cooperation is rife in the microbial world, yet our best current theories of the evolution of cooperation were developed with multicellular animals in mind. Hamilton’s theory of inclusive fitness is an important case in point: applying the theory in a microbial setting is far from straightforward, as social evolution in microbes has a number of distinctive features that the theory was never intended to capture. In this article, I focus on the conceptual challenges posed by the project of extending Hamilton’s (...)
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  31. Ángel Blasco, Luis Sanz, Pierre Auger & Rafael Bravo de la Parra (2002). Linear Discrete Population Models with Two Time Scales in Fast Changing Environments II: Non-Autonomous Case. Acta Biotheoretica 50 (1).
    As the result of the complexity inherent in nature, mathematical models employed in ecology are often governed by a large number of variables. For instance, in the study of population dynamics we often deal with models for structured populations in which individuals are classified regarding their age, size, activity or location, and this structuring of the population leads to high dimensional systems. In many instances, the dynamics of the system is controlled by processes whose time scales are very different from (...)
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  32. G. J. Boender, A. A. De Koeijer & E. A. J. Fischer (2012). Derivation of a Floquet Formalism Within a Natural Framework. Acta Biotheoretica 60 (3):303-317.
    Many biological systems experience a periodic environment. Floquet theory is a mathematical tool to deal with such time periodic systems. It is not often applied in biology, because linkage between the mathematics and the biology is not available. To create this linkage, we derive the Floquet theory for natural systems. We construct a framework, where the rotation of the Earth is causing the periodicity. Within this framework the angular momentum operator is introduced to describe the Earth’s rotation. The Fourier operators (...)
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  33. J. Bogaert (2001). Size Dependence of Interior-to-Edge Ratios: Size Predominates Shape. Acta Biotheoretica 49 (2).
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  34. Jean-Sébastien Bolduc & Frank Cézilly (2012). Optimality Modelling in the Real World. Biology and Philosophy 27 (6):851-869.
    In a recent paper, Potochnik (Biol Philos 24(2):183–197, 2009) analyses some uses of optimality modelling in light of the anti-adaptationism criticism. She distinguishes two broad classes of such uses (weak and strong) on the basis of assumptions held by biologists about the role and the importance of natural selection. This is an interesting proposal that could help in the epistemological characterisation of some biological practices. However, Potochnik’s distinction also rests on the assumption that all optimality modelling represent the selection dynamic (...)
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  35. Jessica A. Bolker (2009). Exemplary and Surrogate Models: Two Modes of Representation in Biology. Perspectives in Biology and Medicine 52 (4):485-499.
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  36. Jessica A. Bolker (1995). Model Systems in Developmental Biology. Bioessays 17 (5):451-455.
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  37. Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.) (2007). Systems Biology: Philosophical Foundations. Elsevier.
    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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  38. Fred L. Bookstein (2013). Allometry for the Twenty-First Century. Biological Theory 7 (1):10-25.
    The current literature that attempts to bridge between geometric morphometrics (GMM) and finite element analyses (FEA) of CT-derived data from bones of living animals and fossils appears to lack a sound biotheoretical foundation. To supply the missing rigor, the present article demonstrates a new rhetoric of quantitative inference across the GMM–FEA bridge—a rhetoric bridging form to function when both have been quantified so stringently. The suggested approach is founded on diverse standard textbook examples of the relation between forms and the (...)
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  39. Fred L. Bookstein (2009). How Quantification Persuades When It Persuades. Biological Theory 4 (2):132-147.
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  40. Fred L. Bookstein (2009). Was There Information in My Data? Really?Model Based Inference in the Life Sciences: A Primer on EvidenceDavid R. Anderson New York: Springer, 2008 (Xxiv+184 Pp.; $39.95 Pbk; ISBN 978-0-387-74073-7). [REVIEW] Biological Theory 4 (3):302-308.
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  41. Sabine Brauckmann (2006). Seeing with Hands and Talking Without Words: On Models and Images in the Sciences. Biological Theory 1 (2):199-202.
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  42. Stephanie Brewer & Trevor Williams (2004). Finally, a Sense of Closure? Animal Models of Human Ventral Body Wall Defects. Bioessays 26 (12):1307-1321.
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  43. 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.
    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 their qualitative interactions) have (...)
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  44. Jennifer A. Brisson & David L. Stern (2006). The Pea Aphid, Acyrthosiphon Pisum: An Emerging Genomic Model System for Ecological, Developmental and Evolutionary Studies. Bioessays 28 (7):747-755.
  45. Taraz E. Buck, Jieyue Li, Gustavo K. Rohde & Robert F. Murphy (2012). Toward the Virtual Cell: Automated Approaches to Building Models of Subcellular Organization “Learned” From Microscopy Images. Bioessays 34 (9):791-799.
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  46. Brett Calcott (2009). Manfred D. Laubichler and Gerd B. Müller (Eds): Modeling Biology: Structures, Behaviors, Evolution (Vienna Series in Theoretical Biology). Acta Biotheoretica 57 (3).
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  47. Allan M. Campbell (1986). Bacteriophage Lambda as a Model System. Bioessays 5 (6):277-280.
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  48. John Casti, Anders Karlqvist & Giorgio Israel (1995). Newton to Aristotle, Toward a Theory of Models For Living Systems. History and Philosophy of the Life Sciences 17 (1):173.
  49. Francesco Catania & Michael Lynch (2013). A Simple Model to Explain Evolutionary Trends of Eukaryotic Gene Architecture and Expression. Bioessays 35 (6):561-570.
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  50. Daniel Chessel (1971). Modèles de la Relation Hôte-Parasite. Acta Biotheoretica 20 (1-2).
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