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\begin{itemize}
\section*{Books}

\subsection*{Chapters of Books}

\item[1] ``A Model of Genetic Networks with Delayed Stochastic Dynamics'', Andre S. Ribeiro, Analysis of Microarray Data: Network based Approaches, Wiley (2007).

\item[2] ``Modeling Gene Regulatory Networks with Delayed Stochastic Dynamics'', Andre S. Ribeiro, John Grefenstette, S. A. Kauffman, Analysis of Microarray Data: Network based Approaches, Editors: Sanjoy Das, Doina Caragea, W. H. Hsu, Stephen M. Welch, Kansas State University, USA. IGI Global (2007).

\section*{Papers}

\subsection*{International Journals}

\item[3] ``Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments'', Andre S. Ribeiro, Phys. Rev. E {\bf 78(6)} (2008).

\item[4] ``Quantifying Local Structure Effects in Network Dynamics'', Andre S. Ribeiro, J. Lloyd-Price, J. Kesseli, A. Hakkinen, and O. Yli-Harja, Phys. Rev. E {\bf 78(5)}, 056108 (2008).

\item[5] ``Mutual Information in Random Boolean models of regulatory networks'', Andre S. Ribeiro, Stuart A. Kauffman, Jason Lloyd-Price, Bjorn Samuelsson, and Joshua Socolar, Physical Review E {\bf 77(1)} (2008).

\item[6] ``Mutual Information in Random Boolean models of regulatory networks'', Andre S. Ribeiro, Stuart A. Kauffman, Jason Lloyd-Price, Bjorn Samuelsson, and Joshua Socolar, Virtual Journal of Biological Physics Research (invited) {\bf 15(2)} (2008).

\item[7] ``Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions'', Andre S. Ribeiro, Physical Review E {\bf 75 (6)} (2007).

\item[8] ``Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks'', Andre S. Ribeiro, Physical Review E {\bf 76(5)} (2007).

\item[9] ``Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks'', Andre S. Ribeiro, Virtual Journal of Biological Physics Research (invited) {\bf 14} (2007).

\item[10] ``Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions'', Andre S. Ribeiro, Journal of Biological Physics Research (invited) {\bf 13 (12)} (2007).

\item[11] ``SGN Sim, a Stochastic Genetic Networks Simulator'', Andre S. Ribeiro and Jason Lloyd-Price, Bioinformatics {\bf 23(6)}, 777-779 (2007).

\item[12] ``CellLine, Cell Lineages Gene Networks Simulator'', Andre S. Ribeiro, Daniel Charlebois, Jason Lloyd-Price, Bioinformatics {\bf (in press)} (2007).

\item[13] ``Noisy Attractors and Ergodic Sets in Models of Genetic Regulatory Networks.'', Andre S. Ribeiro, Stuart A. Kauffman, Journal of Theoretical Biology {\bf 247 (4)}, 743-755 (2007).

\item[14] ``Mutual Information in Random Boolean models of regulatory networks'', Andre S. Ribeiro, Stuart A. Kauffman, Jason Lloyd-Price, Bjorn Samuelsson, and Joshua Socolar, Physical Review E {\bf (in press)} (2007).

\item[15] ``Effects of microarray noise on inference efficiency of a stochastics model of gene networks'', Daniel A. Charlebois, Andre S. Ribeiro, Antti Lehmussola, Jason Lloyd-Price, Olli Yli-Harja, Stuart A. Kauffman, WSEAS Transactions on Biology and Biomedicine {\bf 4(2)}, 15-21 (2007).

\item[16] ``Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models'', Rui Zhu, Andre S. Ribeiro, Dennis Salahub, and Stuart A. Kauffman, Journal of Theoretical Biology {\bf 246(4)}, 725-745 (2007).

\item[17] ``A proposed Model for Small-World Structural Organization of Mission Teams and Tasks in order to Optimise Efficiency and Minimize Costs'', Andre S. Ribeiro, Miguel Almeida, Acta Astronautica {\bf 59 (8-11)}, 1086-1092 (2006).

\item[18] ``Measuring Information Propagation and Retention in Boolean Networks and its Implications to a Model of Human Organizations'', Andre S. Ribeiro, Robert A. Este, Jason Lloyd-Price, S.\,A. Kauffman, WSEAS Transactions on Systems {\bf 5 (12)}, 2935-2941 (2006).

\item[19] ``A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics (extended version)'', Andre S. Ribeiro, Rui Zhu, S. A. Kauffman, Journal of Computational Biology {\bf 13 (9)} (2006).

\item[20] ``A General Model for Gene Regulatory Networks with Stochastic Dynamics'', Andre S. Ribeiro, Rui Zhu, S. A. Kauffman, WSEAS Transactions on Biology and Biomedicine {\bf 3} (2006).

\item[21] ``Effects of lattice structure in the dynamics of coupled elements'', Andre S. Ribeiro, P.\,G. Lind, Physica Scripta {\bf 71} (2005).

\item[22] ``A Proposed Model for Small-World Structural Organization of Mission Teams and Tasks in order to Optimise Efficiency and Minimize Costs'', Andre S. Ribeiro, Miguel Almeida, Esa Bulletin Magazine {\bf Special Issue} (2003).

\subsection*{Portuguese Journals}

\item[23] ``Emergência de Inteligência nos Sistemas'', F. Carvalho Rodrigues, Andre S. Ribeiro, Revista da Academia das Ciências de Lisboa (2004).

\item[24] ``Humanidade: do local ao planetário. 
Resultados da aplicação da Teoria dos Sistemas Complexos à descoberta das estradas do mar pelos portugueses'', Andre S. Ribeiro, F. Carvalho Rodrigues, Revista da Academia da Marinha de Portugal (2003).

\item[25] ``The Cost in Energy and in Time of the Intelligence'', Andre S. Ribeiro, F. Carvalho Rodrigues, Scientific Annals of UnI {\bf 2} (2001).

\item[26] ``The Limitations of the Science: concerning the Recent Presidential elections in the USA'', F. Carvalho Rodrigues, Andre S. Ribeiro, Scientific Annals of UnI {\bf 2} (2001).

\item[27] ``Quantity of Information in Portuguese Architecture'', F. Carvalho Rodrigues, Carlos A. M. Duarte, Andre S. Ribeiro, Tessaleno C. Devezas, Idade da Imagem {\bf 2} (2001).

\item[28] ``The Loss of Societal Cohesion due to HIV/AIDS Epidemics'', F.Carvalho Rodrigues, Andre S. Ribeiro, Scientific Annals of UnI {\bf 2} (2001).

\item[29] ``Quantidade de Informação na Arquitectura Portuguesa'', F.Carvalho-Rodrigues, C.\,A.\,M. Duarte, Andre S. Ribeiro, T.\,C. Devezas and E. Côrte-Real, Revista da Academia de Ciencias de Lisboa (2001).

\section*{Proceedings}

\subsection*{International Conferences}

\item[30] ``Selective Advantages of Stochastic Phenotypic determination in unpredictable Environments'', Andre S. Ribeiro, John J. Grefenstette, Daniel Cloud, Antti Hakkinen, Tiina Rajala and Olli Yli-Harja, Fifth International Workshop on Computational Systems Biology, WCSB 2008, June 11-13, 2008, Leipzig, Germany (2008).

\item[31] ``Optimize Observational Time Points to
Maximize the Inferability of Gene Networks'', Frank Emmert-Streib and Andre S. Ribeiro, ICANN, 2008 (2008).

\item[32] ``Mutual Information in Random Boolean models of regulatory networks'', Josh Socolar, Andre S. Ribeiro, Bjorn Samuelsson, Jason Lloyd-Price, and Stuart A. Kauffman, APS March Meeting, March 10–14, 2008, New Orleans, Louisiana, USA (2008).

\item[33] ``Reverse Engineering of Firefly Luciferase Pathway Model'', Tiina Manninen, Andre S. Ribeiro, Jason Lloyd-Price, Marja-Leena Linne, Keijo Ruohonen, Olli Yli-Harja, Stuart A. Kauffman, Gensips 2007, Finland (2007).

\item[34] ``Models of Gene Regulatory Networks'', Andre S. Ribeiro, J. Lloyd-Price, M. Bratland, W. Chan, S. Noskov, D. Charlebois and S. A. Kauffman, Progress in Systems Biology, Ottawa, Nov 9-10 (2006).

\item[35] ``Measuring Information Propagation and Retention in Boolean Networks and its Implications to a Model of Human Organizations.'', Andre S. Ribeiro, R. A. Este, J. Lloyd-Price, S. A. Kauffman, 6th WSEAS Int. Conf. on Simulation, Modeling and Optimization (SMO '06), Lisbon, Portugal, Sept. 22-24, 2006. (2006).

\item[36] ``A General Model for Gene Regulatory Networks with Stochastic Dynamics'', Andre S. Ribeiro, Rui Zhu, S. A. Kauffman, WSEAS International Conference on Mathematical Biology and Ecology (MABE ‘06) (2006).

\item[37] ``How the individual, society and space become structurally coupled over time'', E. Corte-Real, Andre S. Ribeiro, S. Andre, S. Batel, C. Lisboa, C. Rosa, 5th Space Syntax Symposium (2005).

\item[38] ``Pre-design of signage and orientation systems in Portuguese hospitals'', E. Corte-Real, Andre S. Ribeiro, S. Andre, S. Batel, C. Lisboa, C. Rosa, 5th International Space Syntax Symposium (2005).

\item[39] ``Inferring Dynamical Gene Regulatory Networks Subject to Noise'', Stuart A. Kauffman, Andre S. Ribeiro, Jason Lloyd-Price, Third Annual Rocky Mountain Regional Bioinformatics (2005).

\item[40] ``A proposed Model for Small-World Structural Organization of Mission Teams and Tasks in order to Optimise Efficiency and Minimize Costs'', Andre S. Ribeiro, Miguel Almeida, Fifth IAA International Conference on Low-Cost Planetary Missions, ESA (2003).

\item[41] ``Geometry Effects on synchronization between Coupled Elements'', Andre S. Ribeiro, P.\,G. Lind, APHYS2003, 1st International Meeting on Applied Physics, Spain (2003).

\item[42] ``Interdisciplinary analysis of Sign Systems and Guidance Systems in Hospitals'', André, Sónia, Corte-Real, Eduardo, Andre S. Ribeiro, Rosa, Carlos, Simões, Vitor, proceedings of Fourth International Space Syntax Symposium (2003).

\subsection*{Portuguese Conferences}

\item[43] ``Is Extra-terrestrial intelligence possible? An approach using complex systems theory on the computation of the probability for the emergence of intelligence'', Andre S. Ribeiro, Advanced School and Workshop on Soft Computing and Complex Systems (2003).

\item[44] ``Humanity, Transition of the local to the planetarium. The importance of Portugal in the emergence of a global village'', Andre S. Ribeiro, F. Carvalho Rodrigues, Pedro Nunes - Novos Saberes na Rota do Futuro, Portugal (2002).

\item[45] ``Calculation of the Energy Consumption and Capacity of Storage of Information in Complex Systems'', F. Carvalho Rodrigues, Andre S. Ribeiro, Proceedings of the National Conference of Physics,  Portugal (2002).

\section*{Communications}

\subsection*{Invited}

\item[46] ``Modeling Strategies of Gene Regulatory Networks, IBI / IBM Systems Biology Workshop, Hawthorne Industry Solutions Lab, NY, USA, Sep. 18-20, 2006.'', Andre S. Ribeiro, S. A. Kauffman, IBI / IBM Systems Biology Workshop, Hawthorne Industry Solutions Lab, NY, USA (2006).

\item[47] ``A flux based self regulated traffic lights control system'', Andre S. Ribeiro, UECE, Unidade de Estudos sobre a Complexidade na Economia, at Complexo Interdisciplinar da Universidade de Lisboa (2005).

\item[48] ``Inference Algorithm for Dynamical Gene Regulatory Networks'', Andre S. Ribeiro, S. A. Kauffman, Indiana University, The Biocomplexity Institute, Seminars (2005).

\item[49] ``JAS-ARACNE Inference Engine of Gene Regulatory Networks'', Andre S. Ribeiro, S. A. Kauffman, Jason Lloyd Price, 1st Conference on Biocomplexity of the Institute for Biocomplexity and Informatics (2005).

\item[50] ``Characterizing the evolution of biological neural networks'', Andre S. Ribeiro, Seminar organized by LIP, Laboratório de Instrumentação e Física Experimental de Partículas (2004).

\item[51] ``Intelligence Emergence in Systems'', Andre S. Ribeiro, F. Carvalho Rodrigues, Sciences Academy of Lisbon (2004).

\item[52] ``Using Complex Systems Theory on the Computation of the Probability for the Emergence of Intelligence'', Andre S. Ribeiro, 4ª Série dos Seminários sobre Complexidade”, organized by UECE, Unidade de Estudos sobre a Complexidade na Economia (2003).

\section*{Thesis}

\item[53] ``Prone States for Intelligence Emergence in Systems'', Andre S. Ribeiro, Instituto Superior Tecnico, Universidade Tecnica de Lisboa, Portugal (2004).

\end{itemize}
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