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Lineage grammars: describing, simulating and analyzing population dynamics

Adam Spiro, Luca Cardelli, Ehud Shapiro
2014 BMC Bioinformatics  
Results: We show that eSTGs conveniently describe population dynamics at multiple levels including cellular dynamics, tissue development and niches of organisms.  ...  Conclusions: We conclude that our suggested formalism can be used to easily specify, simulate and analyze complex biological systems, and supports modular description of local biological dynamics that  ...  Acknowledgements This research was supported by The European Union FP7-ERC-AdG Foundation and by the Kenneth and Sally Leafman Appelbaum Discovery Fund.  ... 
doi:10.1186/1471-2105-15-249 pmid:25047682 pmcid:PMC4223406 fatcat:k7w6b774z5eg3huh6uec7oipcy

An Empirical Study of Graph Grammar Evolution [chapter]

Martin Luerssen, David Powers
2009 Evolutionary Computation  
Pole balancing setup and simulation, see Stanley & Miikkulainen (2002) 10 randomly pregenerated unit/ data stream configurations Binomial-3 Regression Simulation Graph relaxed for 10 cycles Simulation  ...  Each solution graph is described by its own individual grammar, referred to as an i-grammar, which is composed of a set of productions from which this graph (and only this graph) can be derived.  ... 
doi:10.5772/9614 fatcat:f4ct3vcibjg67lyyb3cy5q7um4

Accuracy of Answers to Cell Lineage Questions Depends on Single-Cell Genomics Data Quality and Quantity

Adam Spiro, Ehud Shapiro, Roger Dimitri Kouyos
2016 PLoS Computational Biology  
Author Summary A human cell lineage tree describes the entire developmental dynamics of a person starting from the zygote and ending with each and every extant cell.  ...  Fundamental open problems in biology and medicine are in fact questions about the human cell lineage tree: its structure and its dynamics in development, growth, renewal, aging, and disease.  ...  Acknowledgments We would like to thank Tamir Biezuner for performing the ex-vivo experiments and helping in calibrating the different models parameters, and Yoni Herzog for helping in the writing of the  ... 
doi:10.1371/journal.pcbi.1004983 pmid:27295404 pmcid:PMC4905655 fatcat:qyqon7xaqfcylpyhls2daqdtlu

A generic, cost-effective, and scalable cell lineage analysis platform

Tamir Biezuner, Adam Spiro, Ofir Raz, Shiran Amir, Lilach Milo, Rivka Adar, Noa Chapal-Ilani, Veronika Berman, Yael Fried, Elena Ainbinder, Galit Cohen, Haim M. Barr (+2 others)
2016 Genome Research  
We validated the platform by applying it to cells sampled from an ex vivo grown tree and analyzed its feasibility landscape by computer simulations.  ...  We conclude that the platform may serve as a generic tool for lineage analysis and thus pave the way toward large-scale human cell lineage discovery.  ...  Wu at the Broad Institute, and Professor C. Klein at Regensburg University for providing us with SC genomic DNA samples, thus supporting the individual's cell lineage tree experiment (Fig. 4) .  ... 
doi:10.1101/gr.202903.115 pmid:27558250 pmcid:PMC5088600 fatcat:rp73zd2fvnawte2e2rga3i3md4

Listening to Viral Tongues: Comparing Viral Trees Using a Stochastic Context-Free Grammar

A. Rzhetsky
2005 Molecular biology and evolution  
Using this method, we demonstrate that a stochastic grammar can generate three influenza-subtype (A H1, A H3, and B) hemagglutinin trees used in an earlier study, with statistically similar parameters.  ...  Ferguson for providing us with the three sets of aligned hemagglutinin sequences of human influenza, two anonymous referees, and Ms.  ...  Acknowledgments This study was supported by grants from the National Institutes of Health, the National Science Foundation, the Department of Energy, and the Defense Advanced Research Projects Agency to  ... 
doi:10.1093/molbev/msi074 pmid:15626684 fatcat:bfg2em22uvc7vd2oxpl7765dm4

Précis of Foundations of language: brain, meaning, grammar, evolution

Ray Jackendoff
2003 Behavioral and Brain Sciences  
However, generative grammar was mistaken in assuming that the syntactic component is the sole course of combinatoriality, and that everything else is "interpretive."  ...  Generative grammar was right to focus on the child's acquisition of language as its central problem, leading to the hypothesis of an innate Universal Grammar.  ...  At least from the perspective of integrative approaches, it is interesting to see how model frameworks of population dynamics and evolutionary game theory can be extended to describe language evolution  ... 
pmid:15377127 fatcat:bzensiywbngxjlsooeenx3czpm

Précis of Foundations of Language: Brain, Meaning, Grammar, Evolution,

Ray Jackendoff
2003 Behavioral and Brain Sciences  
However, generative grammar was mistaken in assuming that the syntactic component is the sole course of combinatoriality, and that everything else is "interpretive."  ...  Generative grammar was right to focus on the child's acquisition of language as its central problem, leading to the hypothesis of an innate Universal Grammar.  ...  At least from the perspective of integrative approaches, it is interesting to see how model frameworks of population dynamics and evolutionary game theory can be extended to describe language evolution  ... 
doi:10.1017/s0140525x03000153 fatcat:eewzkvv7wjc4tnn4okt7cbui64

eSTGt: a programming and simulation environment for population dynamics

Adam Spiro, Ehud Shapiro
2016 BMC Bioinformatics  
We have previously presented a formal language for describing population dynamics based on environment-dependent Stochastic Tree Grammars (eSTG).  ...  Simulated lineage trees can be used to validate various hypotheses in silico and to predict the behavior of dynamical systems under various conditions.  ...  Acknowledgements We thank Tamir Biezuner for performing the ex vivo experiment and helping to calibrate the simulation parameters.  ... 
doi:10.1186/s12859-016-1004-y pmid:27117841 pmcid:PMC4847376 fatcat:xapmtghhfndtfkoujj2y7fturi

Abstracting grammar from social–cognitive foundations: A developmental sketch of learning

Paul Ibbotson
2011 Review of General Psychology  
interacts with and constrains emerging syntactic representations.  ...  Second, I focus on building layers of abstractions on top of this foundation and the kind of cognitive processes that are involved.  ...  These image schemas are a kind of perceptual redescription of an event that is analyzed within the infant's attention.  ... 
doi:10.1037/a0025609 fatcat:d6nkbosqlbel3lqzwaz5kjltty

Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees

Wuming Gong, Alejandro A. Granados, Jingyuan Hu, Matthew G. Jones, Ofir Raz, Irepan Salvador-Martínez, Hanrui Zhang, Ke-Huan K. Chow, Il-Youp Kwak, Renata Retkute, Alidivinas Prusokas, Augustinas Prusokas (+25 others)
2021 Cell Systems  
The simulation and reconstruction methods here generated delineate a potential way forward for solving larger cell lineage trees such as in mouse.  ...  To date, no lineage reconstruction algorithms have been rigorously examined for their performance and robustness across dataset types and number of cells.  ...  Simulating such a large tree was made possible by applying the environment-dependent stochastic tree grammars (eSTGt), a programing and simulation environment for population dynamics (Spiro and Shapiro  ... 
doi:10.1016/j.cels.2021.05.008 pmid:34146472 fatcat:o7bpdmqjl5cwhpjw6r2cckroiy

With diversity in mind: Freeing the language sciences from Universal Grammar

Nicholas Evans, Stephen C. Levinson
2009 Behavioral and Brain Sciences  
of recursion, constituency, and grammatical relations.  ...  This target article summarizes decades of cross-linguistic work by typologists and descriptive linguists, showing just how few and unprofound the universal characteristics of language are, once we honestly  ...  and generative grammar.  ... 
doi:10.1017/s0140525x09990525 fatcat:pqieza6vancijg4vfnu7humrli

Devil in the details: Analysis of a coevolutionary model of language evolution via relaxation of selection

Luke McCrohon, Olaf Witkowski
2011 European Conference on Artificial Life  
Specifically, we show that the model's population size setting and agent "geography" place strong limits on both cultural and biological diversity in the model.  ...  It is not only used to test hypotheses, but also as a source of data on difficult to observe evolutionary dynamics.  ...  Acknowledgements We would like to thank Hajime Yamauchi for permission to reproduce the charts from (Yamauchi and Hashimoto, 2010) .  ... 
dblp:conf/ecal/McCrohonW11 fatcat:gwldbmixljfetj4qgbonwqmlom

Coupled map lattices dynamics on a variable space for the study of development: A general discussion on Caenorhabditis elegans

Franco A. Bignone
1999 Theoretical Computer Science  
The implementation of models to simulate dynamical aspects of biological systems, particularly in the study of replication and development, has to take into account that gene-gene interactions and cell-cell  ...  In this paper, we discuss the possibility of a detailed reconstruction of cellular dynamics during early stages of development with coupled map lattices or formalizations of Lindenmayer grammars.  ...  Acknowledgements The author wishes to thank Roberto Livi, Antonio Politi, Salvatore Di Gregorio, Ralf and Heinke Schnabel for helpful discussions. Thanks to Ralf Schnabel for  ... 
doi:10.1016/s0304-3975(98)00155-8 fatcat:3kkbzmfpp5dqdpbgcvfncojjym

Towards an evolutionary theory of language

Martin A Nowak, Natalia L Komarova
2001 Trends in Cognitive Sciences  
Finally, we present a framework for the population dynamics of grammar acquisition, which allows us to study the cultural evolution of grammar and the biological evolution of universal grammar.  ...  Here we discuss how natural selection can guide the emergence of some basic features of human language, including arbitrary signs, words, syntactic communication and grammar.  ...  Sloan Foundation and NSF is gratefully acknowledged.  ... 
doi:10.1016/s1364-6613(00)01683-1 pmid:11425617 fatcat:t2naftm6ireangsvjej5uya5di

What Can Mathematical, Computational, and Robotic Models Tell Us about the Origins of Syntax? [chapter]

2009 Biological Foundations and Origin of Syntax  
Paradigms for Studying Language Evolution 15 The discussions in the group arose from the multi-faceted experience of the participants with 16 computer-based simulations of language dynamics, robotic experiments  ...  social processes that could give rise to forms of language, and macroscopic 32 models, that aggregate the behavior of a population and then formulate equations defining the 33 evolution over time among  ...  Evolutionary dynamics of grammar 25 acquisition. Jour. Theor. Biol, 209(1), pp. 43-59. 26 Komarova, N.L. and Nowak, M.A. (2001). Population dynamics of grammar acquisition, in A. 27 Cangelosi & D.  ... 
doi:10.7551/mitpress/8468.003.0026 fatcat:ctkeihiosnh2fiexb3ow6re7dq
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