Publications [LaTeX]
Books
Chapters of Books
1 - A Model of Genetic Networks with Delayed Stochastic Dynamics
Andre S. Ribeiro
Analysis of Microarray Data: Network based Approaches, Wiley (2007)
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)
Papers
International Journals
3 - Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments
Andre S. Ribeiro
Phys. Rev. E 78(6) (2008)
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 78(5), 056108 (2008)
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 77(1) (2008)
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) 15(2) (2008)
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 75 (6) (2007)
8 - Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks
Andre S. Ribeiro
Physical Review E 76(5) (2007)
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) 14 (2007)
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) 13 (12) (2007)
11 - SGN Sim, a Stochastic Genetic Networks Simulator
Andre S. Ribeiro and Jason Lloyd-Price
Bioinformatics 23(6), 777-779 (2007)
12 - CellLine, Cell Lineages Gene Networks Simulator
Andre S. Ribeiro, Daniel Charlebois, Jason Lloyd-Price
Bioinformatics (in press) (2007)
13 - Noisy Attractors and Ergodic Sets in Models of Genetic Regulatory Networks.
Andre S. Ribeiro, Stuart A. Kauffman
Journal of Theoretical Biology 247 (4), 743-755 (2007)
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 (in press) (2007)
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 4(2), 15-21 (2007)
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 246(4), 725-745 (2007)
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 59 (8-11), 1086-1092 (2006)
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 5 (12), 2935-2941 (2006)
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 13 (9) (2006)
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 3 (2006)
21 - Effects of lattice structure in the dynamics of coupled elements
Andre S. Ribeiro, P.G. Lind
Physica Scripta 71 (2005)
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 Special Issue (2003)
Portuguese Journals
23 - Emergência de Inteligência nos Sistemas
F. Carvalho Rodrigues, Andre S. Ribeiro
Revista da Academia das Ciências de Lisboa (2004)
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)
25 - The Cost in Energy and in Time of the Intelligence
Andre S. Ribeiro, F. Carvalho Rodrigues
Scientific Annals of UnI 2 (2001)
26 - The Limitations of the Science: concerning the Recent Presidential elections in the USA
F. Carvalho Rodrigues, Andre S. Ribeiro
Scientific Annals of UnI 2 (2001)
27 - Quantity of Information in Portuguese Architecture
F. Carvalho Rodrigues, Carlos A. M. Duarte, Andre S. Ribeiro, Tessaleno C. Devezas
Idade da Imagem 2 (2001)
28 - The Loss of Societal Cohesion due to HIV/AIDS Epidemics
F.Carvalho Rodrigues, Andre S. Ribeiro
Scientific Annals of UnI 2 (2001)
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)
Proceedings
International Conferences
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)
31 - Optimize Observational Time Points to
Maximize the Inferability of Gene Networks
Frank Emmert-Streib and Andre S. Ribeiro
ICANN, 2008 (2008)
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 1014, 2008, New Orleans, Louisiana, USA (2008)
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)
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)
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)
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)
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)
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)
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)
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)
41 - Geometry Effects on synchronization between Coupled Elements
Andre S. Ribeiro, P.G. Lind
APHYS2003, 1st International Meeting on Applied Physics, Spain (2003)
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)
Portuguese Conferences
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)
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)
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)
Communications
Invited
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)
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)
48 - Inference Algorithm for Dynamical Gene Regulatory Networks
Andre S. Ribeiro, S. A. Kauffman
Indiana University, The Biocomplexity Institute, Seminars (2005)
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)
50 - Characterizing the evolution of biological neural networks
Andre S. Ribeiro
Seminar organized by LIP, Laboratório de Instrumentação e Física Experimental de Partículas (2004)
51 - Intelligence Emergence in Systems
Andre S. Ribeiro, F. Carvalho Rodrigues
Sciences Academy of Lisbon (2004)
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)
Thesis
53 - Prone States for Intelligence Emergence in Systems
Andre S. Ribeiro
Instituto Superior Tecnico, Universidade Tecnica de Lisboa, Portugal (2004)
