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ALIFE 2012: The Thirteenth International Conference on the Synthesis and Simulation of Living Systems

July 19–22, 2012

East Lansing, Michigan

Conference Sponsors:

The International Society for Artificial Life

ALIFE 2012: The Thirteenth International Conference on the Synthesis and Simulation of Living Systems

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ALIFE 2012: The Thirteenth International Conference on the Synthesis and Simulation of Living Systems

The Role of Standing Genetic Variation in Adaptation of Digital Organisms to a New Environment

Carlos J.R. Anderson

isal 2012; 3-10doi:https://doi.org/10.1162/978-0-262-31050-5-ch001

View Articletitled, The Role of Standing Genetic Variation in Adaptation of Digital Organisms to a New Environment

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Towards the Recapitulation of Ancient History in the Laboratory: Combining Synthetic Biology with Experimental Evolution

Betül K. Arslan, Eric A. Gaucher

isal 2012; 11-18doi:https://doi.org/10.1162/978-0-262-31050-5-ch002

View Articletitled, Towards the Recapitulation of Ancient History in the Laboratory: Combining Synthetic Biology with Experimental Evolution

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Digital Evolution Exhibits Surprising Robustness to Poor Design Decisions

David M. Bryson, Charles Ofria

isal 2012; 19-26doi:https://doi.org/10.1162/978-0-262-31050-5-ch003

View Articletitled, Digital Evolution Exhibits Surprising Robustness to Poor Design Decisions

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The role of deleterious mutations in the adaptation to a novel environment

Arthur W. Covert III, Jared Carlson-Stevermer

isal 2012; 27-31doi:https://doi.org/10.1162/978-0-262-31050-5-ch004

View Articletitled, The role of deleterious mutations in the adaptation to a novel environment

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What does sex have to do with it: tracking the fate of deleterious mutations in sexual populations.

Arthur W. Covert III, Lane Smith, Dakota Z. Derrberry, Claus O. Wilke

isal 2012; 32-36doi:https://doi.org/10.1162/978-0-262-31050-5-ch005

View Articletitled, What does sex have to do with it: tracking the fate of deleterious mutations in sexual populations.

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Heterochronous Neural Baldwinism

Keith L. Downing

isal 2012; 37-44doi:https://doi.org/10.1162/978-0-262-31050-5-ch006

View Articletitled, Heterochronous Neural Baldwinism

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A quantitative measure of non-neutral evolutionary activity for systems that exhibit intrinsic fitness

Alastair Droop, Simon Hickinbotham

isal 2012; 45-52doi:https://doi.org/10.1162/978-0-262-31050-5-ch007

View Articletitled, A quantitative measure of non-neutral evolutionary activity for systems that exhibit intrinsic fitness

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Robustness and evolvability of cooperation

Antoine Frénoy, François Taddei, Dusan Misevic

isal 2012; 53-58doi:https://doi.org/10.1162/978-0-262-31050-5-ch008

View Articletitled, Robustness and evolvability of cooperation

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Evolution of Self-Replicating Cube Conglomerations in a Simulated 3D Environment

Paul Grouchy, Hod Lipson

isal 2012; 59-66doi:https://doi.org/10.1162/978-0-262-31050-5-ch009

View Articletitled, Evolution of Self-Replicating Cube Conglomerations in a Simulated 3D Environment

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Open Ended Evolution of 3D Multicellular Development Controlled by Gene Regulatory Networks

Michal Joachimczak, Borys Wróbel

isal 2012; 67-74doi:https://doi.org/10.1162/978-0-262-31050-5-ch010

View Articletitled, Open Ended Evolution of 3D Multicellular Development Controlled by Gene Regulatory Networks

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Beyond Open-endedness: Quantifying Impressiveness

Joel Lehman, Kenneth O. Stanley

isal 2012; 75-82doi:https://doi.org/10.1162/978-0-262-31050-5-ch011

View Articletitled, Beyond Open-endedness: Quantifying Impressiveness

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Architectures for Self-reproduction: Abstractions, Realisations and a Research Program

McMullin Barry

isal 2012; 83-90doi:https://doi.org/10.1162/978-0-262-31050-5-ch012

View Articletitled, Architectures for Self-reproduction: Abstractions, Realisations and a Research Program

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Evolutionary Dynamics and Ecosystems Feedback in Two Dimensional Daisyworld

Punithan Dharani, RI (Bob) McKay

isal 2012; 91-98doi:https://doi.org/10.1162/978-0-262-31050-5-ch013

View Articletitled, Evolutionary Dynamics and Ecosystems Feedback in Two Dimensional Daisyworld

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Adaptation and Divergence during Experimental Evolution of Multicellular Saccharomyces cerevisiae

Maria Rebolleda-Gomez, William Ratcliff, Michael Travisano

isal 2012; 99-104doi:https://doi.org/10.1162/978-0-262-31050-5-ch014

View Articletitled, Adaptation and Divergence during Experimental Evolution of Multicellular Saccharomyces cerevisiae

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Comparing Distance-Based Phylogenetic Tree Construction Methods Using An Individual-Based Ecosystem Simulation, EcoSim

Ryan Scott, Robin Gras

isal 2012; 105-110doi:https://doi.org/10.1162/978-0-262-31050-5-ch015

View Articletitled, Comparing Distance-Based Phylogenetic Tree Construction Methods Using An Individual-Based Ecosystem Simulation, EcoSim

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Evolved Modular Epistasis in Artificial Organisms

Sergi Valverde, Ricard V. Solé

isal 2012; 111-115doi:https://doi.org/10.1162/978-0-262-31050-5-ch016

View Articletitled, Evolved Modular Epistasis in Artificial Organisms

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Evolutionary Potential is Maximized at Intermediate Diversity Levels

Bess L. Walker, Charles Ofria

isal 2012; 116-120doi:https://doi.org/10.1162/978-0-262-31050-5-ch017

View Articletitled, Evolutionary Potential is Maximized at Intermediate Diversity Levels

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Is Evolution by Natural Selection the Algorithm of Biological Evolution?

Richard A. Watson

isal 2012; 121-128doi:https://doi.org/10.1162/978-0-262-31050-5-ch018

View Articletitled, Is Evolution by Natural Selection the Algorithm of Biological Evolution?

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Coevolving parasites improve host evolutionary search on structured fitness landscapes

Hywel T. P. Williams

isal 2012; 129-136doi:https://doi.org/10.1162/978-0-262-31050-5-ch019

View Articletitled, Coevolving parasites improve host evolutionary search on structured fitness landscapes

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Sexual Selection, Resource Distribution, and Population Size in Synthetic Sympatric Speciation

Mark Woehrer, Dean Hougen, Ingo Schlupp

isal 2012; 137-144doi:https://doi.org/10.1162/978-0-262-31050-5-ch020

View Articletitled, Sexual Selection, Resource Distribution, and Population Size in Synthetic Sympatric Speciation

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Contextual Geometric Structures: modeling the fundamental components of cultural behavior

Bradly Alicea

isal 2012; 147-154doi:https://doi.org/10.1162/978-0-262-31050-5-ch021

View Articletitled, Contextual Geometric Structures: modeling the fundamental components of cultural behavior

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Effects of Local Communication and Topology on Collective Movement Initiation

Brent E. Eskridge

isal 2012; 155-162doi:https://doi.org/10.1162/978-0-262-31050-5-ch022

View Articletitled, Effects of Local Communication and Topology on Collective Movement Initiation

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Evolving a Follower in the Presence of a Potential Leader

Brent E. Eskridge

isal 2012; 163-170doi:https://doi.org/10.1162/978-0-262-31050-5-ch023

View Articletitled, Evolving a Follower in the Presence of a Potential Leader

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An ecology-based evolutionary algorithm to evolve solutions to complex problems

Sherri Goings, Heather Goldsby, Betty H.C. Cheng, Charles Ofria

isal 2012; 171-177doi:https://doi.org/10.1162/978-0-262-31050-5-ch024

View Articletitled, An ecology-based evolutionary algorithm to evolve solutions to complex problems

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The Evolution of Temporal Polyethism

Heather J. Goldsby, Neem Serra, Fred Dyer, Benjamin Kerr, Charles Ofria

isal 2012; 178-185doi:https://doi.org/10.1162/978-0-262-31050-5-ch025

View Articletitled, The Evolution of Temporal Polyethism

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Polarization and Belief Dynamics in the Black and White Communities: An Agent-Based Network Model from the Data

Patrick Grim, Stephen B. Thomas, Steven Fisher, Christopher Reade, Daniel J. Singer, Mary A. Garza, Craig S. Fryer, Jamie Chatman

isal 2012; 186-193doi:https://doi.org/10.1162/978-0-262-31050-5-ch026

View Articletitled, Polarization and Belief Dynamics in the Black and White Communities: An Agent-Based Network Model from the Data

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The Effects of Finite Populations and Selection on the Emergence of Signaling

Kyle I. Harrington, A. Pinar Ozisik, Jordan B. Pollack

isal 2012; 194-201doi:https://doi.org/10.1162/978-0-262-31050-5-ch027

View Articletitled, The Effects of Finite Populations and Selection on the Emergence of Signaling

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App Epidemics: Modelling the Effects of Publicity in a Mobile App Ecosystem

Soo Ling Lim, Peter J. Bentley

isal 2012; 202-209doi:https://doi.org/10.1162/978-0-262-31050-5-ch028

View Articletitled, App Epidemics: Modelling the Effects of Publicity in a Mobile App Ecosystem

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An Ant-Based Computer Simulator

Loizos Michael, Anastasios Yiannakides

isal 2012; 210-217doi:https://doi.org/10.1162/978-0-262-31050-5-ch029

View Articletitled, An Ant-Based Computer Simulator

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Effects of public good properties on the evolution of cooperation

Dusan Misevic, Antoine Frénoy, David P. Parsons, François Taddei

isal 2012; 218-225doi:https://doi.org/10.1162/978-0-262-31050-5-ch030

View Articletitled, Effects of public good properties on the evolution of cooperation

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Coevolutionary Dynamics between Roles and Social Sensitivity in an Extended Minority Game

Keita Nishimoto, Ivan Tanev, Katsunori Shimohara, Reiji Suzuki, Takaya Arita

isal 2012; 226-233doi:https://doi.org/10.1162/978-0-262-31050-5-ch031

View Articletitled, Coevolutionary Dynamics between Roles and Social Sensitivity in an Extended Minority Game

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Characterizing Autonomy in the Web via Transfer Entropy Network

Mizuki Oka, Takashi Ikegami

isal 2012; 234-242doi:https://doi.org/10.1162/978-0-262-31050-5-ch032

View Articletitled, Characterizing Autonomy in the Web via Transfer Entropy Network

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Evolution of a Communication Code in Cooperative Tasks

Aditya Rawal, Padmini Rajagopalan, Risto Miikkulainen, Kay Holekamp

isal 2012; 243-250doi:https://doi.org/10.1162/978-0-262-31050-5-ch033

View Articletitled, Evolution of a Communication Code in Cooperative Tasks

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odNEAT: An Algorithm for Distributed Online, Onboard Evolution of Robot Behaviours

Fernando Silva, Paulo Urbano, Sancho Oliveira, Anders Lyhne Christensen

isal 2012; 251-258doi:https://doi.org/10.1162/978-0-262-31050-5-ch034

View Articletitled, odNEAT: An Algorithm for Distributed Online, Onboard Evolution of Robot Behaviours

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Finding Optimal Random Boolean Networks for Reservoir Computing

David Snyder, Alireza Goudarzi, Christof Teuscher

isal 2012; 259-266doi:https://doi.org/10.1162/978-0-262-31050-5-ch035

View Articletitled, Finding Optimal Random Boolean Networks for Reservoir Computing

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Representational Momentum May Explain Aspects of Vowel Shifts

Samarth Swarup, Corrine McCarthy

isal 2012; 267-274doi:https://doi.org/10.1162/978-0-262-31050-5-ch036

View Articletitled, Representational Momentum May Explain Aspects of Vowel Shifts

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Environment classification in multiagent systems inspired by the adaptive immune system

Danesh Tarapore, Anders Lyhne Christensen, Pedro U Lima, Jorge Carneiro

isal 2012; 275-282doi:https://doi.org/10.1162/978-0-262-31050-5-ch037

View Articletitled, Environment classification in multiagent systems inspired by the adaptive immune system

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Evolutionary Transitions and Top-Down Causation

Sara Imari Walker

isal 2012; 283-290doi:https://doi.org/10.1162/978-0-262-31050-5-ch038

View Articletitled, Evolutionary Transitions and Top-Down Causation

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The Role of Working Memory in an Urban Pursuit Scenario

Ransom K. Winder, James A Reggia

isal 2012; 291-298doi:https://doi.org/10.1162/978-0-262-31050-5-ch039

View Articletitled, The Role of Working Memory in an Urban Pursuit Scenario

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Second Order Learning and the Evolution of Mental Representation

Solvi Arnold, Reiji Suzuki, Takaya Arita

isal 2012; 301-308doi:https://doi.org/10.1162/978-0-262-31050-5-ch040

View Articletitled, Second Order Learning and the Evolution of Mental Representation

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On the Relationship Between Environmental and Mechanical Complexity in Evolved Robots

Joshua E Auerbach, Josh C. Bongard

isal 2012; 309-316doi:https://doi.org/10.1162/978-0-262-31050-5-ch041

View Articletitled, On the Relationship Between Environmental and Mechanical Complexity in Evolved Robots

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Testing the Variability Selection Hypothesis: The Adoption of Social Learning in Increasingly Variable Environments

James M. Borg, Alastair Channon

isal 2012; 317-324doi:https://doi.org/10.1162/978-0-262-31050-5-ch042

View Articletitled, Testing the Variability Selection Hypothesis: The Adoption of Social Learning in Increasingly Variable Environments

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Evolutionary Design and Experimental Validation of a Flexible Caudal Fin for Robotic Fish

Anthony J. Clark, Jared M. Moore, Jianxun Wang, Xiaobo Tan, Philip K. McKinley

isal 2012; 325-332doi:https://doi.org/10.1162/978-0-262-31050-5-ch043

View Articletitled, Evolutionary Design and Experimental Validation of a Flexible Caudal Fin for Robotic Fish

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Informational Drives for Sensor Evolution

Sander G. van Dijk, Daniel Polani

isal 2012; 333-340doi:https://doi.org/10.1162/978-0-262-31050-5-ch044

View Articletitled, Informational Drives for Sensor Evolution

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Task decomposition with neuroevolution in extended predator-prey domain

Ashish Jain, Anand Subramoney, Risto Miikulainen

isal 2012; 341-348doi:https://doi.org/10.1162/978-0-262-31050-5-ch045

View Articletitled, Task decomposition with neuroevolution in extended predator-prey domain

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Brainless Bodies: Controlling the Development and Behavior of Multicellular Animats by Gene Regulation and Diffusive Signals

M. Joachimczak, T. Kowaliw, R. Doursat, B. Wróbel

isal 2012; 349-356doi:https://doi.org/10.1162/978-0-262-31050-5-ch046

View Articletitled, Brainless Bodies: Controlling the Development and Behavior of Multicellular Animats by Gene Regulation and Diffusive Signals

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The Minimal Complexity of Adapting Agents Increases with Fitness

Nikhil J Joshi, Giulio Tononi, Christof Koch

isal 2012; 357-363doi:https://doi.org/10.1162/978-0-262-31050-5-ch047

View Articletitled, The Minimal Complexity of Adapting Agents Increases with Fitness

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On the Emergent Behaviors of a Robot Controlled by a Real-Time Evolving Neural Network

Walter O. Krawec

isal 2012; 364-371doi:https://doi.org/10.1162/978-0-262-31050-5-ch048

View Articletitled, On the Emergent Behaviors of a Robot Controlled by a Real-Time Evolving Neural Network

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Automatically Designing and Printing 3-D Objects with EvoFab 0.2

Tim Kuehn, John Rieffel

isal 2012; 372-378doi:https://doi.org/10.1162/978-0-262-31050-5-ch049

View Articletitled, Automatically Designing and Printing 3-D Objects with EvoFab 0.2

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Rewarding Reactivity to Evolve Robust Controllers without Multiple Trials or Noise

Joel Lehman, Sebastian Risi, David B. D’Ambrosio, Kenneth O. Stanley

isal 2012; 379-386doi:https://doi.org/10.1162/978-0-262-31050-5-ch050

View Articletitled, Rewarding Reactivity to Evolve Robust Controllers without Multiple Trials or Noise

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Aracna: An Open-Source Quadruped Platform for Evolutionary Robotics

Sara Lohmann, Jason Yosinski, Eric Gold, Jeff Clune, Jeremy Blum, Hod Lipson

isal 2012; 387-392doi:https://doi.org/10.1162/978-0-262-31050-5-ch051

View Articletitled, Aracna: An Open-Source Quadruped Platform for Evolutionary Robotics

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Analysis of Evolved Agents Performing Referential Communication

Santosh Manicka

isal 2012; 393-400doi:https://doi.org/10.1162/978-0-262-31050-5-ch052

View Articletitled, Analysis of Evolved Agents Performing Referential Communication

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Effects of Individual Differences on Knowledge and Wisdom of Society: A Social Modeling Approach

Toshihiko Matsuka, Hidehito Honda

isal 2012; 401-406doi:https://doi.org/10.1162/978-0-262-31050-5-ch053

View Articletitled, Effects of Individual Differences on Knowledge and Wisdom of Society: A Social Modeling Approach

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With a little help from selection pressures: evolution of memory in robot controllers

Charles Ollion, Tony Pinville, Stéphane Doncieux

isal 2012; 407-414doi:https://doi.org/10.1162/978-0-262-31050-5-ch054

View Articletitled, With a little help from selection pressures: evolution of memory in robot controllers

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Evolved neural network controllers for physically simulated robots that hunt with an artificial visual cortex

Michael E. Palmer, Andrew Chou

isal 2012; 415-422doi:https://doi.org/10.1162/978-0-262-31050-5-ch055

View Articletitled, Evolved neural network controllers for physically simulated robots that hunt with an artificial visual cortex

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Evolution of Virtual Creature Foraging in a Physical Environment

Marcin L. Pilat, Takashi Ito, Reiji Suzuki, Takaya Arita

isal 2012; 423-430doi:https://doi.org/10.1162/978-0-262-31050-5-ch056

View Articletitled, Evolution of Virtual Creature Foraging in a Physical Environment

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Deformable Octahedron Burrowing Robot

Juan Cristobal Zagal, Cristobal Armstrong, Shuguang Li

isal 2012; 431-438doi:https://doi.org/10.1162/978-0-262-31050-5-ch057

View Articletitled, Deformable Octahedron Burrowing Robot

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Modeling Scalable Pattern Generation in DNA Reaction Networks

Peter B. Allen, Xi Chen, Zack B. Simpson, Andrew D. Ellington

isal 2012; 441-448doi:https://doi.org/10.1162/978-0-262-31050-5-ch058

View Articletitled, Modeling Scalable Pattern Generation in DNA Reaction Networks

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Energy-based Artificial Chemistry Simulator

Vincent Ducharme, Richard Egli, Claude Y. Legault

isal 2012; 449-456doi:https://doi.org/10.1162/978-0-262-31050-5-ch059

View Articletitled, Energy-based Artificial Chemistry Simulator

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The Behavior-Based Hypercycle: From Parasitic Reaction to Symbiotic Behavior

Tom Froese, Takashi Ikegami, Nathaniel Virgo

isal 2012; 457-464doi:https://doi.org/10.1162/978-0-262-31050-5-ch060

View Articletitled, The Behavior-Based Hypercycle: From Parasitic Reaction to Symbiotic Behavior

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Checkpoint Orientated Cell Cycle Modeling Issues in Simulation of Synchronized Situation

Jonathan Pascalie, Valérie Lobjois, Hervé Luga, Bernard Ducommun, Yves Duthen

isal 2012; 465-472doi:https://doi.org/10.1162/978-0-262-31050-5-ch061

View Articletitled, Checkpoint Orientated Cell Cycle Modeling Issues in Simulation of Synchronized Situation

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Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection

Aaron Reba, Austin G. Meyer, Jeffrey E. Barrick

isal 2012; 473-480doi:https://doi.org/10.1162/978-0-262-31050-5-ch062

View Articletitled, Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection

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Design and construction of a prototype CMY (Cyan-Magenta-Yellow) genetic circuit as a mutational readout device to measure evolutionary stability dynamics and determine design principles for robust synthetic systems

Sean C. Sleight, Herbert M Sauro

isal 2012; 481-488doi:https://doi.org/10.1162/978-0-262-31050-5-ch063

View Articletitled, Design and construction of a prototype CMY (Cyan-Magenta-Yellow) genetic circuit as a mutational readout device to measure evolutionary stability dynamics and determine design principles for robust synthetic systems

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Using Pictures to Visualize the Complexity of Gene Regulatory Networks

Sylvain Cussat-Blanc, Jordan Pollack

isal 2012; 491-498doi:https://doi.org/10.1162/978-0-262-31050-5-ch064

View Articletitled, Using Pictures to Visualize the Complexity of Gene Regulatory Networks

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Finger-painting Fitness Landscapes: An Interactive Tool for Exploring Complex Evolutionary Dynamics.

Luis Zaman, Charles Ofria, Richard E. Lenski

isal 2012; 499-505doi:https://doi.org/10.1162/978-0-262-31050-5-ch065

View Articletitled, Finger-painting Fitness Landscapes: An Interactive Tool for Exploring Complex Evolutionary Dynamics.

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