Computing with Artificial Gene Regulatory Networks

[1]  Martin Trefzer,et al.  Evolution and Analysis of a Robot Controller Based on a Gene Regulatory Network , 2010, ICES.

[2]  Dario Floreano,et al.  Analog Genetic Encoding for the Evolution of Circuits and Networks , 2007, IEEE Transactions on Evolutionary Computation.

[3]  Torsten Reil,et al.  Dynamics of Gene Expression in an Artificial Genome - Implications for Biological and Artificial Ontogeny , 1999, ECAL.

[4]  Yves Duthen,et al.  Controlling cooperative and conflicting continuous actions with a Gene Regulatory Network , 2012, 2012 IEEE Conference on Computational Intelligence and Games (CIG).

[5]  Sylvain Cussat-Blanc,et al.  Gene regulated car driving: using a gene regulatory network to drive a virtual car , 2014, Genetic Programming and Evolvable Machines.

[6]  Larry Bull,et al.  On Dynamical Genetic Programming: Random Boolean Networks in Learning Classifier Systems , 2009, EuroGP.

[7]  Christodoulos A. Floudas,et al.  Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database , 2011, Scientific reports.

[8]  Barbara Drossel.  Number of attractors in random Boolean networks. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[9]  D. Taatjes,et al.  The human Mediator complex: a versatile, genome-wide regulator of transcription. , 2010, Trends in biochemical sciences.

[10]  R. Beer,et al.  20 – A developmental model for the evolution of complete autonomous agents , 2003 .

[11]  Robert A. Martienssen,et al.  RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond , 2013, Nature Reviews Genetics.

[12]  R. Stewart,et al.  Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells , 2011, Nature.

[13]  Tao Pan,et al.  Tissue-Specific Differences in Human Transfer RNA Expression , 2006, PLoS genetics.

[14]  Susan Stepney,et al.  The artificial epigenetic network , 2013, 2013 IEEE International Conference on Evolvable Systems (ICES).

[15]  T. Glisovic,et al.  RNA‐binding proteins and post‐transcriptional gene regulation , 2008, FEBS letters.

[16]  J. Lis,et al.  Control of transcriptional elongation. , 2013, Annual review of genetics.

[17]  Wolfgang Banzhaf,et al.  Artificial ChemistriesA Review , 2001, Artificial Life.

[18]  Sui Huang,et al.  Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability , 2012, PLoS Comput. Biol..

[19]  Peter J. Bentley.  Evolving Fractal Gene Regulatory Networks for Graceful Degradation of Software , 2005, Self-star Properties in Complex Information Systems.

[20]  Eric Goles Ch.,et al.  On the robustness of update schedules in Boolean networks , 2009, Biosyst..

[21]  Y. Benenson.  Biomolecular computing systems: principles, progress and potential , 2012, Nature Reviews Genetics.

[22]  Mauro Birattari,et al.  On the Design of Boolean Network Robots , 2011, EvoApplications.

[23]  S. Kauffman,et al.  Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective. , 2009, Seminars in cell & developmental biology.

[24]  Michael A. Savageau,et al.  Introduction to S-systems and the underlying power-law formalism , 1988 .

[25]  Wolfgang Banzhaf.  On the Dynamics of an Artificial Regulatory Network , 2003, ECAL.

[26]  J. Mallm,et al.  Genome-wide nucleosome positioning during embryonic stem cell development , 2012, Nature Structural &Molecular Biology.

[27]  W. Banzhaf.  Artificial Regulatory Networks and Genetic Programming , 2003 .

[28]  Y. van de Peer,et al.  Improving the Adaptability of Simulated Evolutionary Swarm Robots in Dynamically Changing Environments , 2014, PloS one.

[29]  Richard I. Kitney,et al.  Synthetic Biology — A Primer , 2012 .

[30]  Stéphane Doncieux,et al.  The Transferability Approach: Crossing the Reality Gap in Evolutionary Robotics , 2013, IEEE Transactions on Evolutionary Computation.

[31]  Borys Wróbel,et al.  Evolving morphologies and controllers for soft-bodied multicellular animats using gene regulatory networks and artificial embryogenesis , 2012, GECCO '12.

[32]  Hannu Tenhunen,et al.  A Computational Scheme Based on Random Boolean Networks , 2007, Trans. Comp. Sys. Biology.

[33]  Yan Meng,et al.  A Hierarchical Gene Regulatory Network for Adaptive Multirobot Pattern Formation , 2012, IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics).

[34]  Jorge G. T. Zañudo,et al.  Boolean Threshold Networks: Virtues and Limitations for Biological Modeling , 2010, 1011.3848.

[35]  Christof Teuscher,et al.  Deducing local rules for solving global tasks with random Boolean networks , 2005 .

[36]  Chrystopher L. Nehaniv,et al.  Evolving Embodied Genetic Regulatory Network-Driven Control Systems , 2003, ECAL.

[37]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[38]  Susan Stepney,et al.  Artificial Biochemical Networks: Evolving Dynamical Systems to Control Dynamical Systems , 2014, IEEE Transactions on Evolutionary Computation.

[39]  Susan Stepney,et al.  Controlling Complex Dynamics with Artificial Biochemical Networks , 2010, EuroGP.

[40]  Andrew M. Tyrrell,et al.  Characterising neurological time series data using biologically motivated networks of coupled discrete maps , 2013, Biosyst..

[41]  Jonathan Timmis,et al.  A Developmental and Immune-Inspired Dynamic Task Allocation Algorithm for Microprocessor Array Systems , 2010, ICARIS.

[42]  Susan Stepney,et al.  Adaptive robotic gait control using coupled artificial signalling networks, hopf oscillators and inverse kinematics , 2013, 2013 IEEE Congress on Evolutionary Computation.

[43]  M. Aldana.  Boolean dynamics of networks with scale-free topology , 2003 .

[44]  Marc Schoenauer,et al.  Evolving Genes to Balance a Pole , 2010, EuroGP.

[45]  Susan Stepney,et al.  The incorporation of epigenetics in artificial gene regulatory networks , 2013, Biosyst..

[46]  David Johan Christensen,et al.  Fractal Gene Regulatory Networks for Robust Locomotion Control of Modular Robots , 2010, SAB.

[47]  Martin Trefzer,et al.  Image compression of natural images using artificial gene regulatory networks , 2010, GECCO '10.

[48]  Cuauhtémoc López Martín,et al.  Use of evolved artificial regulatory networks to simulate 3D cell differentiation , 2010, Biosyst..

[49]  Julian Francis Miller,et al.  An evolutionary system using development and artificial Genetic Regulatory Networks for electronic circuit design , 2009, Biosyst..

[50]  Mikhail Prokopenko,et al.  Information Dynamics in Small-World Boolean Networks , 2011, Artificial Life.

[51]  A. Bird,et al.  Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals , 2003, Nature Genetics.

[52]  T.G.W. Gordon,et al.  Exploring models of development for evolutionary circuit design , 2003, The 2003 Congress on Evolutionary Computation, 2003. CEC '03..

[53]  S. Kauffman.  Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[54]  Andreas Bracher,et al.  Molecular chaperones in protein folding and proteostasis , 2011, Nature.

[55]  Tsung-Hsien Yang,et al.  Combining GRN Modeling and Demonstration-Based Programming for Robot Control , 2009, EANN.

[56]  W. Banzhaf,et al.  Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence. , 2006, Bio Systems.

[57]  John T. Lis,et al.  Defining mechanisms that regulate RNA polymerase II transcription in vivo , 2009, Nature.

[58]  Susan Stepney,et al.  Biochemical connectionism , 2013, Natural Computing.

[59]  R. Albert,et al.  Boolean Modelingof Genetic Regulatory Networks , 2004 .

[60]  Susan Stepney,et al.  Computational models of signalling networks for non-linear control , 2013, Biosyst..

[61]  Peter J. Bentley,et al.  Development brings scalability to hardware evolution , 2005, 2005 NASA/DoD Conference on Evolvable Hardware (EH'05).

[62]  Christof Teuscher,et al.  Emergent Criticality Through Adaptive Information Processing in Boolean Networks , 2011, Physical review letters.

[63]  Jordan B. Pollack,et al.  Using Pictures to Visualize the Complexity of Gene Regulatory Networks , 2012, ALIFE.