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  1. Mathematical Cooperation.Ralph Abraham - 1991 - World Futures 31 (2):161-167.
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  2. Ideas in Theoretical Biology.E. Ahmed - 1998 - Acta Biotheoretica 46 (2):167-168.
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  3. Abpl.Mike Ainsworth - 1993 - Acta Biotheoretica 41 (1-2):43-51.
    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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  4. Reduced Models for Unidirectional Block Conduction and Their Geometrical Setting.L. El Alaoui, J. Francoise & M. Landau - 2012 - Acta Biotheoretica 60 (1-2):131-137.
    This article revisits a reduced model of cardiac electro-physiology which was proposed to understand the genesis of unidirectional block pathology and of ectopic foci. We underline some specificities of the model from the viewpoint of dynamical systems and bifurcation theory. We point out that essentially the same properties are shared by a simpler system more accessible to analysis. With this simpler system, it becomes possible to give a new presentation of the phenomenon in a phase plane with time moving slow (...)
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  5. Robustness, Optimality, and the Handicap Principle.J. McKenzie Alexander - 2010 - Biology and Philosophy 25 (5).
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  6. Formal Methods for Hopfield-Like Networks.Hedi Amor, Fabien Corblin, Eric Fanchon, Adrien Elena & Laurent Trilling - 2013 - Acta Biotheoretica 61 (1):21-39.
    Building a meaningful model of biological regulatory network is usually done by specifying the components 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 the method to (...)
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  7. Corals and Starfish Devastation of the Great Barrier Reef: Aggregation Methods.Peter Antonelli & Pierre Auger - 1995 - Acta Biotheoretica 43 (4):481-493.
    Aggregation methods allow one to replace a large scale dynamical system (micro-system) by a reduced dynamical system (macro-system) governing a small number of global variables. This aggregation of variables can be performed when two time scales exist, a fast time scale and a slow time scale. Perturbation theory allows to obtain an approximated aggregated dynamical system which describes the behaviour of a few number of slow time varying variables which are constants of motion of the fast part of the micro-system. (...)
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  8. Practice Oriented Controversies and Borrowed Epistemic Support in Current Evolutionary Biology. The Case of Phylogeography.Alfonso Arroyo-Santos, Mark E. Olson & Francisco Vergara-Silva - 2015 - Perspectives on Science 23 (3):310-334.
    Philosophical treatments of scientific controversies usually focus on theory, excluding important practice related aspects. However, scientists in conflict often appeal to extra-theoretical and extra-empirical elements. To understand better the role that non-empirical elements play in scientific controversies, we introduce the notion of borrowed epistemic credibility, illustrating our proposal with a recent controversy in a field of evolutionary biology known as phylogeography. Our analysis shows how scientific controversies that spring from disagreements about methodological issues potentially involve deeperdebates regarding whatconstitutes good science, (...)
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  9. Validating Animal Models.Nina Atanasova - 2015 - Theoria. An International Journal for Theory, History and Foundations of Science 30 (2):163.
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  10. Modeling the Enzyme Kinetic Reaction.Abdon Atangana - 2015 - Acta Biotheoretica 63 (3):239-256.
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  11. Paradigms in Immunology and Modern, Post-Modern, Post-Post-Modern, _ Philosophy. A Review of Alfred I. Tauber, the Immune Self: Theory or Metaphor? [REVIEW]Henri Atlan - 1998 - Biology and Philosophy 13 (1):125-131.
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  12. Complex Ecological Models with Simple Dynamics: From Individuals to Populations.Pierre M. Auger & Robert Roussarie - 1994 - Acta Biotheoretica 42 (2-3):111-136.
    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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  13. Basic Reproduction Ratio for a Fishery Model in a Patchy Environment.Pierre Auger, Ali Moussaoui & Gauthier Sallet - 2012 - Acta Biotheoretica 60 (1-2):167-188.
    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 and (...)
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  14. Aggregation and Emergence in Hierarchically Organized Systems: Population Dynamics.Pierre Auger & Jean-Christophe Poggiale - 1996 - Acta Biotheoretica 44 (3-4):301-316.
    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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  15. Differentiation of Endothelial Cells: Analysis of the Constitutive and Activated Endothelial Cell Phenotypes.Hellmut G. Augustin, Detlef H. Kozian & Robert C. Johnson - 1994 - Bioessays 16 (12):901-906.
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  16. Geometry and Dynamics of Populations.Melvin Avrami - 1941 - Philosophy of Science 8 (1):115-132.
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  17. Animal Models of Polycystic Kidney Disease.Nazneen Aziz - 1995 - Bioessays 17 (8):703-712.
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  18. Causal Explanation Beyond the Gene: Manipulation and Causality in Epigenetics.Jan Baedke - 2012 - Theoria. An International Journal for Theory, History and Foundations of Science 27 (2):153-174.
    This paper deals with the interrelationship between causal explanation and methodology in a relatively young discipline in biology: epigenetics. Based on cases from molecular and ecological epigenetics, I show that James Woodward’s interventionist account of causation captures essential features about how epigeneticists using highly diverse methods, i.e. laboratory experiments and purely observational studies, think about causal explanation. I argue that interventionism thus qualifies as a useful unifying explanatory approach when it comes to cross-methodological research efforts: It can act as a (...)
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  19. Filling in the Mechanistic Details: Two-Variable Experiments as Tests for Constitutive Relevance. [REVIEW]Tudor Baetu - 2012 - 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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  20. 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]Tudor M. Baetu, Ann-Sophie Barwich, Daniel Brooks, Sébastien Dutreuil & Pierre-Luc Germain - 2013 - Biological Theory 8 (1):121 - 124.
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  21. Model Thinking in the Life Sciences: Complexity in the Making. [REVIEW]Tudor M. Baetu, Ann-Sophie Barwich, Daniel Brooks, Sébastien Dutreuil & Pierre-Luc Germain - 2013 - Biological Theory 8 (1):121-124.
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  22. A Dynamical System for Biological Development: The Case of Caenorhabditis Elegans.F. Bailly, F. Gaill & R. Mosseri - 1991 - Acta Biotheoretica 39 (3-4):167-184.
    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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  23. Ontologies: Formalising Biological Knowledge for Bioinformatics.Jonathan Bard - 2003 - Bioessays 25 (5):501-506.
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  24. Bioinformatics for Beginners.Jonathan Bard - 2002 - Bioessays 24 (9):867-868.
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  25. Incidence of Dispersion of Refractoriness and Cellular Coupling Resistance on Cardiac Reentries and Ventricular Fibrillation.A. L. Bardou, R. G. Seigneuric, J.-L. Chassé & P. M. Auger - 1999 - Acta Biotheoretica 47 (3-4):199-207.
    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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  26. Effect of Myocardial Infarction and Ischemia on Induction of Cardiac Reentries and Ventricular Fibrillation.Alain L. Bardou, Pierre M. Auger, Soumeya Achour, Philippe Dumee, Pierre J. Birkui & Marie-Claude Govaere - 1995 - Acta Biotheoretica 43 (4):363-372.
    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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  27. Theoretical Study of Cardiac Transient Conduction Blocks on Reentries Induction. Applications to Antiarrhythmic Drugs.Alain L. Bardou, Pierre M. Auger, Jean-Luc Chasse & Renaud Seigneuric - 1997 - Acta Biotheoretica 45 (3-4):227-236.
    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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  28. Preface.Alain Bardou & Pierre Auger - 1992 - Acta Biotheoretica 40 (2-3):93-93.
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  29. Entangled Life: Organism and Environment in the Biological and Social Sciences.Gillian Barker, Eric Desjardins & Trevor Pearce (eds.) - 2014 - Springer.
    Despite the burgeoning interest in new and more complex accounts of the organism-environment dyad by biologists and philosophers, little attention has been paid in the resulting discussions to the history of these ideas and to their deployment in disciplines outside biology—especially in the social sciences. Even in biology and philosophy, there is a lack of detailed conceptual models of the organism-environment relationship. This volume is designed to fill these lacunae by providing the first multidisciplinary discussion of the topic of organism-environment (...)
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  30. Towards an Ecological View of Immunity. [REVIEW]Swiatczak Bartlomiej - forthcoming - Studies in History and Philosophy of Science.
    The immune system does not just fight pathogens but also engages in interactions with beneficial microbes and non-immune cells of the body to harmonize their behavior by means of cytokines, antibodies and effector cells (Dinarello, 2007; Moticka, 2015, pp. 217e226, 261e267). However, the importance of these “housekeeping” functions has not been fully appreciated (Cohen, 2000). In his new book Immunity: The Evolution of an Idea Alfred I. Tauber traces the history of fundamental ideas in immunology and refers to recent advances (...)
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  31. Exocytosis: Post‐Receptor Events in Secretory Cells.Lindsay Bashford - 1987 - Bioessays 7 (3):133-134.
  32. Modeling the Cardiovascular-Respiratory Control System: Data, Model Analysis, and Parameter Estimation.Jerry Batzel & Mostafa Bachar - 2010 - Acta Biotheoretica 58 (4):369-380.
    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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  33. Some Virtues of Modeling with Both Hands.William Bechtel - unknown
    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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  34. Imaginal Discs: Renaissance of a Model for Regenerative Biology.Cora Bergantiños, Xavier Vilana, Montserrat Corominas & Florenci Serras - 2010 - Bioessays 32 (3):207-217.
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  35. Biological Sequences Integrated: A Relational Database Approach.Andre Bergholz, Stephan Heymann, Jörg A. Schenk & JohannChristoph Freytag - 2001 - 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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  36. How to Build a Multiscale Model in Biology.Samuel Bernard - 2013 - Acta Biotheoretica 61 (3):291-303.
    Biological processes span several scales in space, from the single molecules to organisms and ecosystems. Multiscale modelling approaches in biology are useful to take into account the complex interactions between different organisation levels in those systems. We review several single- and multiscale models, from the most simple to the complex ones, and discuss their properties from a multiscale point of view. Approaches based on master equations for stochastic processes, individual-based models, hybrid continuous-discrete models and structured PDE models are presented.
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  37. Hierarchies and Causal Relationships in Interpretative Models of the Neoplastic Process.Marta Bertolaso - 2011 - History and Philosophy of the Life Sciences 33 (4).
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  38. Systems Biology Reveals Biology of Systems.Marta Bertolaso, Alessandro Giuliani & Laura De Gara - 2011 - Complexity 16 (6):10-16.
  39. Animal Models of Parkinson's Diseases.R. Betabert, T. B. Sherer & J. T. Greenamyre - 2002 - Bioessays 24:308-318.
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  40. Animal Models of Parkinson's Disease.Ranjita Betarbet, Todd B. Sherer & J. Timothy Greenamyre - 2002 - Bioessays 24 (4):308-318.
  41. Mathematical Analysis of a Two Strain Hiv/Aids Model with Antiretroviral Treatment.C. P. Bhunu, W. Garira & G. Magombedze - 2009 - Acta Biotheoretica 57 (3):361-381.
    A two strain HIV/AIDS model with treatment which allows AIDS patients with sensitive HIV-strain to undergo amelioration is presented as a system of non-linear ordinary differential equations. The disease-free equilibrium is shown to be globally asymptotically stable when the associated epidemic threshold known as the basic reproduction number for the model is less than unity. The centre manifold theory is used to show that the sensitive HIV-strain only and resistant HIV-strain only endemic equilibria are locally asymptotically stable when the associated (...)
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  42. Is Defining Life Pointless? Operational Definitions at the Frontiers of Biology.Leonardo Bich & Sara Green - 2017 - Synthese:1-28.
    Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different research practices. This paper examines the possible (...)
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  43. Gene Mobility and the Concept of Relatedness.Jonathan Birch - 2014 - 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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  44. Linear Discrete Population Models with Two Time Scales in Fast Changing Environments II: Non-Autonomous Case.Ángel Blasco, Luis Sanz, Pierre Auger & Rafael Bravo de la Parra - 2002 - Acta Biotheoretica 50 (1):15-38.
    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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  45. Derivation of a Floquet Formalism Within a Natural Framework.G. J. Boender, A. A. De Koeijer & E. A. J. Fischer - 2012 - 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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  46. Size Dependence of Interior-to-Edge Ratios: Size Predominates Shape.J. Bogaert - 2001 - Acta Biotheoretica 49 (2):121-123.
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  47. In Silico Study of the Influence of Intensity and Duration of Blood Flow Reduction on Cell Death Through Necrosis or Apoptosis During Acute Ischemic Stroke.Jean-Pierre Boissel - 2010 - Acta Biotheoretica 58 (2):171-190.
    Ischemic stroke involves numerous and complex pathophysiological mechanisms including blood flow reduction, ionic exchanges, spreading depressions and cell death through necrosis or apoptosis. We used a mathematical model based on these phenomena to study the influences of intensity and duration of ischemia on the final size of the infarcted area. This model relies on a set of ordinary and partial differential equations. After a sensibility study, the model was used to carry out in silico experiments in various ischemic conditions. The (...)
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  48. Optimality Modelling in the Real World.Jean-Sébastien Bolduc & Frank Cézilly - 2012 - 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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  49. Exemplary and Surrogate Models: Two Modes of Representation in Biology.Jessica A. Bolker - 2009 - Perspectives in Biology and Medicine 52 (4):485-499.
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  50. Model Systems in Developmental Biology.Jessica A. Bolker - 1995 - Bioessays 17 (5):451-455.
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