ATPgroup - Application of Theoretical Physics

2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005

2018	back to top

Social Norms of Cooperation With Costly Reputation Building
Fernando P. Santos, Francisco C. Santos and Jorge M. Pacheco
Nature, vol. 555, pp. 242-245 (2018).
abstract News and Views

Social Norms of Cooperation With Costly Reputation Building
Fernando P. Santos, Jorge M. Pacheco, and Francisco C. Santos
accepted in AAAI 2018.
e-link

Engineering Pro-Sociality with Autonomous Agents
Ana Paiva, Fernando P. Santos, and Francisco C. Santos
accepted in AAAI 2018.
Recipient of the best blue sky paper award, AAAI-18 Senior Track.
e-link

Indirect Reciprocity and Costly Reputation Building in Multiagent Systems
Fernando P. Santos, Jorge M. Pacheco, and Francisco C. Santos
extended abstract accepted in the student's program of AAAI 2018.
e-link

Multiplayer ultimatum game on complex networks: the role of structural power
Fernando P. Santos, Jorge M. Pacheco, Ana Paiva and Francisco C. Santos
in Proc.of the 6th International Conference on Complex Networks and Their Applications, Studies in Computational Intelligence Series, Springer-Verlag (in press).
e-link

2017	back to top

Disease spreading in time-evolving networked communities
Jorge M. Pacheco, Sven Van Segbroeck and Francisco C. Santos
in N. Masuda and P. Holme (eds.), Temporal Network Epidemiology, Theoretical Biology, pp 291-316, Springer Nature (2017).
e-link

Environmental Impacts of Colonial Dynamics, 1400–1800: The First Global Age and the Anthropocene
Amélia Polónia and Jorge M. Pacheco,
In: Economic Development and Environmental History in the Anthropocene: Perspectives on Asia and Africa, pp. 23-49, 2017, Bloomsbury.
e-link

Structural power and the evolution of collective fairness in social networks
Fernando P. Santos, Jorge M. Pacheco, Ana Paiva and Francisco C. Santos
PLoS One 12 (4): e0175687 (2017).
e-link

Stochastic dynamics through hierarchically embedded Markov chains
Vítor V. Vasconcelos, Fernando P. Santos, Francisco C. Santos, and Jorge M. Pacheco
Physical Review Letters 118, 058301 (2017).
e-link

Incomplete cooperation and co-benefits: deepening climate cooperation with a proliferation of small agreements
Phillip M. Hannam, Vítor V. Vasconcelos, Simon A. Levin, and Jorge M. Pacheco
Climatic Change Vol. 144 (1), pp. 65–79 (2017).
e-link

Using Spark and MapReduce to Parallelize Large Scale Simulations Over Host Contact Networks
Andreia Sofia Teixeira, Pedro T. Monteiro, João Carriço, Francisco C. Santos, and Alexandre P. Francisco
In Ibrahim S., Choo KK., Yan Z., Pedrycz W. (eds). Proc. of the 17th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP 2017) Lecture Notes in Computer Science, vol 10393. pp. 591-600, 2017, Springer.
e-link

Indirect reciprocity in populations of explorative agents
Fernando P. Santos, Jorge M. Pacheco, and Francisco C. Santos
in Workshop Adaptive Learning Agents (ALA'17) at AAMAS 2017, 2017.
e-link

Emergence of social balance in signed networks
Andreia Sofia Teixeira, Francisco C. Santos, and Alexandre P. Francisco
in Goncalves B., Menezes R., Sinatra R., Zlatic V. (eds) Proc. of the 8th Workshop on Complex Networks VIII, CompleNet 2017, Springer Proceedings in Complexity, pp 185-192, Springer, 2017.
e-link

2016	back to top

Paradigm shifts and the interplay between state, business and civil sectors
Sara Encarnação, Fernando P. Santos, Francisco C. Santos, Vered Blass, Jorge M. Pacheco, Juval Portugali
Royal Society Open Science 3 (2016) 160753
e-link

About the discrete-continuous nature of a hematopoiesis model for Chronic Myeloid Leukemia
Marcos Gaudiano, Tom Lenaerts, and Jorge M. Pacheco
Mathematical biosciences Vol. 282, pp. 174-80 (2016).
e-link

Evolution of cooperation under indirect reciprocity and arbitrary exploration rates
Fernando P. Santos, Jorge M. Pacheco, Francisco C. Santos
Scientific Reports 6 (2016) 37517
e-link

An evolutionary game theoretic approach to multi-sector coordination and self-organization
Fernando P. Santos, Sara Encarnação, Francisco C. Santos, Jorge M. Pacheco
Entropy 18,2 (2016) 152
e-link

Linking Individual and Collective Behavior in Adaptive Social Networks
Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco
Physical Review Letters 116 (2016) 128702
abstract

Social Norms of Cooperation in Small-Scale Societies
Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco
PLoS Computational Biology 12 (2016) e1004709378
e-link

Evolutionary dynamics of collective index insurance
Jorge M. Pacheco, Francisco C. Santos, Simon A. Levin
Journal of Mathematical Biology 72 (2016) 997-1010
abstract

Execution Errors Enable the Evolution of Fairness in the Ultimatum Game
Fernando P. Santos, Francisco C. Santos, Ana Paiva, and Jorge M. Pacheco
in Proceedings of the 22st European Conference on Artificial Intelligence (ECAI2016), extended abstract, 1592-1593
e-link

The Role of Execution Errors in Populations of Ultimatum Bargaining Agents
Fernando P. Santos, Francisco C. Santos, Ana Paiva, and Jorge M. Pacheco
in 2nd Workshop on Conflict Resolution in Decision Making (COREDEMA 2016), Satellite Workshop at the 22st European Conference on Artificial Intelligence (ECAI2016), Amsterdam, 2016.
e-link

Evolution of Fairness in Multiplayer Ultimatum Games
Fernando P. Santos, Francisco C. Santos, Ana Paiva, and Jorge M. Pacheco
in 1st Workshop on Multidisciplinary Applications of Evolutionary Game Theory, Satellite Workshop at ALife XV, 15th International Conference on the Synthesis and Simulation of Living Systems (ALIFE XV), Mexico, July 2016.
e-link

Cooperation and Reputation in Primitive Societies
Fernando P. Santos, Francisco C. Santos, and Jorge M. Pacheco
in Proceedings of 15th International Conference on the Synthesis and Simulation of Living Systems (ALIFE XV), MIT press, July,2016.
e-link

Multiplayer ultimatum game in populations of autonomous agents
Fernando P. Santos, Francisco C. Santos, Francisco S. Melo, Ana Paiva, Jorge M. Pacheco
Adaptive and Learning Agents Workshop (ALA 2016), Int. Conf. Autonomous Agents and Multiagent Systems (AAMAS 2016), (Best paper award of ALA 2016).
e-link

Spanning Edge Betweenness in Practice
Andreia Sofia Teixeira, Francisco C. Santos, and Alexandre P. Francisco
in Complex Networks VII, Proc. of the 7th Workshop on Complex Networks (CompleNet 2016), Series Studies in Computational Intelligence, Vol. 644, pp. 3-10, Springer-Verlag, 2016.
e-link

Learning to be Fair in Multiplayer Ultimatum Games
Fernando P. Santos, Francisco C. Santos, Francisco S. Melo, Ana Paiva, and Jorge M. Pacheco
in Proceedings of the 2016 International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2016), IFAAMAS, 2016.
e-link

Modeling the socio-ecological dynamics of the first global age (1400-1800)
Amelia Polonia, Francisco C. Santos, Jorge M. Pacheco
in Proc. of the International Conference Old and New Worlds: the Global Challenges of Rural History, XV Congreso de Historia Agraria de la SEHA, Hosted by ISCTE, Lisbon, Portugal (Jan, 2016).
e-link

2015	back to top

Incomplete cooperation and co-benefits: deepening climate cooperation with a proliferation of small agreements
Phillip M. Hannam, Vítor V. Vasconcelos, Simon A. Levin, Jorge M. Pacheco
Climatic Change (2015) doi 10.1007/s10584-015-1511-2
abstract

Evolutionary dynamics of group fairness
Fernando P. Santos, Francisco C. Santos, Ana Paiva, Jorge M. Pacheco
Journal of Theoretical Biology 378 (2015) 96-102
abstract

Cooperation Dynamics of Polycentric Climate Governance
Vítor V. Vasconcelos, Francisco C. Santos and Jorge M. Pacheco
Mathematical Models and Methods in Applied Sciences (M3AS) 25 (2015) 2503
abstract

Synergy between intention recognition and commitments in cooperation dilemmas
The Anh Han, Francisco C. Santos, Tom Lenaerts and Luís Moniz Pereira
Scientific Reports 5 (2015) 9312
e-link

Co-evolutionary Dynamics of Collective Action with Signaling for a Quorum
Jorge M. Pacheco, Vítor V. Vasconcelos, Francisco C. Santos, Brian Skyrms
PLoS Computational Biology 11 (2) (2015) e1004101
e-link

Emergence of Cooperation via Intention Recognition, Commitment, and Apology - A Research Summary
The Anh Han, Luís Moniz Pereira, Francisco C. Santos, and Tom Lenaerts
AI Communications 28(4) (2015) 709-715
e-link

The Universality of Peer-Influence in Social Networks
Flavio L. Pinheiro, Marta D. Santos, Francisco C. Santos, and Jorge M. Pacheco
Proceedings of the European Conference on Artificial Life 378 ECAL 2015, Andrews, et al. (eds), pp. 149, MIT Press, 2015.
e-link

Evolutionary perks of being irrational
Fernando P. Santos, Francisco C. Santos and Ana Paiva
Proceedings of the 2015 International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2015), pp. 1847, IFAAMAS, 2015.
e-link

Teoria de Jogos Evolutiva na Modelação da Cooperação entre os Sectores Público, Privado e Civil
Sara A. Encarnação, Fernando Santos, Francisco C. Santos, Jorge M. Pacheco, and Juval Portugali
in Proc. X Congresso da Geografia Portuguesa - Os Valores da Geografia , UNL-FCSH, Lisbon, Sept (2015).
e-link

Evolution of Pairwise Commitment and Cooperation
The Anh Han, Luís Moniz Pereira, Francisco C. Santos and Tom Lenaerts Proceedings of the European Conference on Complex Systems 2014 (ECCS'14) (extended abstract).
e-link

Learning to Recognize Intentions Resolves Cooperation Dilemmas
The Anh Han, Luís Moniz Pereira, Tom Lenaerts and Francisco C. Santos
Proceedings of the 23rd annual Belgian-Dutch Conference on Machine Learning (BENELEARN 2014), Brussels, Belgium (extended abstract).

Complex Systems of Mindful Entities: on Intention Recognition and Commitment
Luís Moniz Pereira, The Anh Han and Francisco C. Santos
Book chapter in Model-Based Reasoning in Science and Technology, Series in Studies in Applied Philosophy, Epistemology and Rational Ethics, 8 (2014) 499-525
e-link

Evolution of Fairness and Conditional Cooperation in Public Goods Dilemmas
Sven Van Segbroeck, Jorge M. Pacheco, Tom Lenaerts and Francisco C. Santos
in the Proceedings of the European Conference on Complex Systems 2012 Springer Proceedings in Complexity (2014) 827-830
e-link

2014, 5 publications

Evolution of All-or-None strategies in repeated public goods dilemmas
Flávio L. Pinheiro, Vítor V. Vasconcelos, Francisco C. Santos, Jorge M. Pacheco
PLoS Computational Biology 11 (2) (2014) e1003945
e-link

The ecology of cancer from an evolutionary game theory perspective
Jorge M. Pacheco, Francisco C. Santos, David Dingli
Interface focus 4 (2014) 20140019
e-link

The Origin of peer influence in social networks
Flávio L. Pinheiro, Marta D. Santos, Francisco C. Santos and Jorge M. Pacheco
Physical Review Letters 112, 9 (2014) 098702
abstract

Climate Change Governance, Cooperation and Self-organization
Jorge M. Pacheco, Vítor V. Vasconcelos and Francisco C. Santos
Physics of Life Review Physics of Life Reviews 11, 4 (2014) 573-586

Climate policies under wealth inequality
Vítor V. Vasconcelos, Francisco C. Santos, Jorge M. Pacheco and Simon A. Levin
Proceedings of the National Academy of Sciences (USA) 111 (6) (2014) 2212-2216
(doi:10.1073/pnas.1323479111)
e-link

2013, 9 publications

A bottom-up institutional approach to cooperative governance of risky commons
Vítor V. Vasconcelos, Francisco C. Santos and Jorge M. Pacheco
Nature Climate Change 3 (2013) 797-801
e-link News&Views

Urban Dynamics, Fractals and Generalized Entropy
Sara Encarnação, Marcos Gaudiano, Francisco C. Santos, José A. Tenedório, Jorge M. Pacheco
Entropy 15 (2013) 2679-2697
e-link

Evolution of collective action in adaptive social structuress
João Moreira, Jorge M. Pacheco and Francisco C. Santos
Scientific Reports 3 (2013) 1521
e-link

Reward from Punishment Does Not Emerge at All Costs
Jeromos Vukov, Flávio L. Pinheiro, Francisco C. Santos and Jorge M. Pacheco
PLoS Computational Biology 9(1) (2013) e1002868
e-link

On the dynamics of neutral mutations in a mathematical model for a homogeneous stem cell population
Arne Traulsen, Tom Lenaerts, Jorge M. Pacheco and David Dingli
Journal of the Royal Society Interface 10, 79 (2013) 20120810
e-link

Individual memory and the emergence of cooperation
João Moreira, Jeromos Vukov, Cláudia Sousa, Francisco C Santos, André F. Almeida, Marta D Santos, Jorge M. Pacheco
Animal Behaviour 85 (1) (2013) 233-239

Behavioral dynamics under climate change dilemmas
Francisco C. Santos and Jorge M. Pacheco
book chapter in New Challenges to Philosophy of Science, The Philosophy of Science in a European Perspective Series (Volume 4) , edited by Hanne Andersen, Dennis Dieks, Wenceslao J. Gonzalez, Marcel Weber, Gregory Wheeler, (2013) 113-124, Springer

Self-organized game dynamics in complex networks
Flávio L. Pinheiro, Vítor V. Vasconcelos, Francisco C. Santos and Jorge M. Pacheco
in Advances in Artificial Life, ECAL 2013: Proceedings of the 12th European Conference on the Synthesis and Simulation of Living Systems, MIT Press, 2013

Bootstrapping back the climate with self-organization
Vítor V. Vasconcelos, Flávio L. Pinheiro,Francisco C. Santos and Jorge M. Pacheco
in Advances in Artificial Life, ECAL 2013: Proceedings of the 12th European Conference on the Synthesis and Simulation of Living Systems, MIT Press, 2013

2012, 16 publications

Dynamics of N-Person Snowdrift Games in Structured Populations
Marta D. Santos, Flávio L. Pinheiro, Francisco C. Santos and Jorge M. Pacheco
Journal of Theoretical Biology 315 (2012) 81-86
Science Direct

Fractal cartography of urban areas
Sara Encarnação, Marcos Gaudiano, Francisco C. Santos, José Tenedório and Jorge M. Pacheco
Nature Scientific Reports, 2 (2012) 527
e-link

How selection pressure changes the nature of social dilemmas in structured populations
Flávio L. Pinheiro, Francisco C. Santos and Jorge M. Pacheco
New Journal of Physics, 14 (2012) 073035
e-link

Cognitive strategies take advantage of the cooperative potential of heterogeneous networks
Jeromos Vukov, Francisco C. Santos and Jorge M. Pacheco
New Journal of Physics, 14 (2012) 063031
e-link

Emergence of Fairness in Repeated Group Interactions
Sven Van Segbroeck, Jorge M. Pacheco Tom Leanerts and Francisco C. Santos
Physical Review Letters 108 (2012) 158104
e-link pdf

Corpus-based Intention Recognition in Cooperation Dilemmas
Han The Anh, Luís Moniz Pereira and Francisco C. Santos
Artificial Life, 18-4 (2012) 365-383
e-link

From Local to Global Dilemmas in Social Networks
Flávio L. Pinheiro, Jorge M. Pacheco and Francisco C. Santos
PLoS ONE 7(2) (2012) e32114
e-link pdf

Evolutionary dynamics of climate change under collective-risk dilemmas
Francisco C. Santos, Vitor Vasconcelos, Marta D. Santos, Pedro Neves and Jorge M. Pacheco
Mathematical Models and Methods in Applied Sciences Vol. 22, Supp. Issue (1) (2012) 1140004

The Role of Diversity in the Evolution of Cooperation
Francisco C. Santos, Flávio L. Pinheiro, T. Lenaerts and Jorge M. Pacheco
Journal of Theoretical Biology, 299 (2012) 88-96
e-link

Evolutionary dynamics of collective action when individual fitness derives from group decisions taken in the past
João A. Moreira, Flávio L. Pinheiro, Ana Nunes and Jorge M. Pacheco
Journal of Theoretical Biology 298 (2012) 8–15
e-link preprint

Tracking the evolution of cooperation in complex networked populations
Flávio L. Pinheiro, Francisco C. Santos and Jorge M. Pacheco
Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBio 2012), Lecture Notes in Computer Science Volume 7246/2012 (2012) 86-96 by Springer Berlin/Heidelberg
e-link

Intention recognition, commitment and the evolution of cooperation
Han The Anh, Luís Moniz Pereira and Francisco C. Santos
forthcoming in 2012 IEEE World Congress on Computational Intelligence (IEEE WCCI 2012), Congress on Evolutionary Computation (IEEE CEC 2012), June 10-15, Brisbane, Australia

The emergence of commitments and cooperation
Han The Anh, Luís Moniz Pereira and Francisco C. Santos
in Proceedings of the 11th International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2012), Conitzer, Winikoff, Padgham, and van der Hoek (eds.), pp. 559-566, IFAAMAS (2012)

Evolving the asymmetry of the Prisoner's dilemma game in adaptive social structures
Joao Moreira, Jorge M. Pacheco, Francisco C. Santos
in Bio-Inspired Models of Network, Information and Computing Systems (BIONETICS 2010), Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering 87 (2012) 205-212

Evolutionary Dynamics of Cooperation Under the Distributed Prisoner's Dilemma
Flavio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco
in Bio-Inspired Models of Network, Information and Computing Systems (BIONETICS 2010), Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering 87 (2012) 523-532

Collective Evolutionary Dynamics and Spatial Reciprocity under the N-Person Snowdrift Game
Marta D. Santos, Francisco C. Santos, Jorge M. Pacheco
in Bio-Inspired Models of Network, Information and Computing Systems (BIONETICS 2010), Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering 87 (2012) 178-188

2011, 21 publications

Dynamics of mutant cells in hierarchical organized tissues
Benjamin Werner, David Dingli, Tom Lenaerts, Jorge M. Pacheco, Arne Traulsen
PLoS-Computational Biology 7(12) (2011) e1002290
e-link

Evolutionary Dynamics of Mutations in Hematopoietic Stem Cells and Beyond
David Dingli, Arne Traulsen and Jorge M. Pacheco
Stem Cells and Cancer Stem Cells, 3(11) (2011) 115-123

Escaping the tragedy of the commons via directed investments
Jeromos Vukov, Francisco C. Santos and Jorge M. Pacheco
Journal of Theoretical Biology 287 (2011) 37-41
e-link

Risk of collective failure provides an escape from the tragedy of the commons
Francisco C. Santos and Jorge M. Pacheco
Proceedings of the National Academy of Sciences (USA) 108 (26) (2011) 10421-10425
pre-print abstract

Stochastic dynamics and the evolution of mutations in stem cells
David Dingli & Jorge M. Pacheco
BMC Biology 9:41 (2011)
e-link

Explaining the in vivo and in vitro differences in leukemia therapy
T. Lenaerts, F. Castagnetti, A. Traulsen, J.M. Pacheco, G. Rosti and D. Dingli
Cell Cycle 10 (2011) 1540-1544
abstract

Incipient Cognition Solves the Spatial Reciprocity Conundrum of Cooperationn
Jeromos Vukov, Francisco C. Santos, Jorge M. Pacheco
PLoS One 6(3) (2011) e17939
abstract pdf supporting information

Co-evolution of pre-play signaling and cooperation
Francisco C. Santos, Jorge M. Pacheco and Brian Skyrms
Journal of Theoretical Biology 274 (1) (2011) 30-35
Abstract PDF

Selection pressure transforms the nature of social dilemmas in adaptive networks
Sven Van Segbroeck, Francisco C. Santos, Tom Lenaerts and Jorge M. Pacheco
New Journal of Physics 13 (2011) 013007
Abstract PDF

The messianic effect of pathological altruism
Jorge M. Pacheco and Francisco C. Santos
Pathological Altruism, Oxford University Press, USA (1st edition, July 25, 2011)
Edited by Barbara Oakley, Ariel Knafo, Guruprasad Madhavan and David Sloan Wilson.
reviews cover OUP Amazon.com New York Times

Evolutionary dynamics of collective action
Jorge M. Pacheco, Francisco C. Santos,Max O. Souza, Brian Skyrms
in The Mathematics of Darwin's Legacy, series on Mathematics and Biosciences in Interaction, Chalub and Rodrigues (eds), p.119, Birkhauser Basel (1st Edition., 2011, Hardcover, ISBN: 978-3-0348-0121-8).
pdf

Modelling Hematopoiesis in Health and Disease
Diogo Peixoto, David Dingli, Jorge M. Pacheco
Mathematical and Computer Modelling Volume 53, Issues 7-8, (2011) 1546-1557

Evolutionary Dynamics of Cooperation in Multiplayer Games
João Moreira
Msc. Thesis at the University of Lisbon
supervised by Jorge M. Pacheco and co-supervision of Francisco C. Santos

The impact of diversity on the emergence of cooperation
Flávo L. Pinheiro
Msc. Thesis at the University of Lisbon
supervised by Jorge M. Pacheco and co-supervision of Francisco C. Santos

Ab-initio Design of Bulk Materials Assembled With Silicon Clusters
Carlos L. Reis
PhD. Thesis at the University of Lisbon
supervised by Jorge M. Pacheco

Evolutionary dynamics of collective action
Jorge M. Pacheco, Francisco C. Santos,Max O. Souza, Brian Skyrms
in Advances in Artificial Life, ECAL 2011: Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems , T. Lenaerts, M. Giacobini, H. Bersini, P. Bourgine, M. Dorigo and R. Doursat, eds. MIT Press, 2011

Co-evolution of pre-play signaling and cooperation
Francisco C. Santos, Jorge M. Pacheco and Brian Skyrms
in Advances in Artificial Life, ECAL 2011: Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems , T. Lenaerts, M. Giacobini, H. Bersini, P. Bourgine, M. Dorigo and R. Doursat, eds. MIT Press, 2011

Intention Recognition Promotes The Emergence of Cooperation
Han The Anh, Luís Moniz Pereira, Francisco C. Santos
Adaptive Behavior 19 (4) 264-279 (2011)

The role of intention recognition in the evolution of cooperative behavior
Han The Anh, Luís Moniz Pereira, Francisco C. Santos
Proceedings of the 22nd International Joint Conference on Artificial Intelligence, July 2011, Barcelona, Spain (IJCAI 2011), pp. 1684-1689, AAAI / MIT press.

Emergence of cooperation in adaptive social networks with behavioral diversity
Sven Van Segbroeck, Francisco C. Santos, Tom Lenaerts and Jorge M. Pacheco
in Proceedings of the 10th European Conference on Artifical Life, ECAL 2009, Budapest, Hungary Kampis, G.; Karsai, I.; Szathmary, E. (Eds.).
Advances in Artificial Life: Darwin Meets von Neumann, Lecture Notes in Computer Science,, vol. 5777, pp.434-441, Springer-Verlag, Berlin, Germany, 2011

To grip or not to grip? Evolving role allocation and internal conflict in autonomous robots
Christos Ampatzis, Francisco C. Santos, Vito Trianni and Elio Tuci
in Proceedings of the 10th European Conference on Artifical Life, ECAL 2009, Budapest, Hungary Kampis, G.; Karsai, I.; Szathmary, E. (Eds.).
Advances in Artificial Life: Darwin Meets von Neumann, Lecture Notes in Computer Science,, vol. 5777, pp.434-441, Springer-Verlag, Berlin, Germany, 2011

2010, 18 publications

Mechanisms Supporting Cooperation for the Evolutionary Prisoner's Dilemma Games
György Szabó, Attila Szolnoki and Jeromos Vukov
in Econophysics and Economics of Games, Social Choices and Quantitative Techniques, New Economic Windows Springer (2010), Part I, 24-31, DOI: 10.1007/978-88-470-1501-2_4
e-link

Coordinating towards a Common Good
Francisco C. Santos, Jorge M Pacheco
AIP Conf. Proc 1281 (2010) 1540
e-link

Vibrational spectra of silicon cage clusters doped with Ti, Zr, or Hf
Carlos L. Reis, Jorge M Pacheco
Physical Review B 82 (2010) 155440
pdf e-link

Somatic mutations and the hierarchy of hematopoiesis
Arne Traulsen, Jorge M. Pacheco, Lucio Luzzatto, David Dingli
BioEssays 32(11) (2010) 1003-8

Creating metamaterials at the nano-scale
Jorge M. Pacheco, Carlos L. Reis
Actas da Academia de Ciências de Lisboa (2010) in press

Minimizing CO2 Emissions in a Computing World
Carlos L. Reis, Jorge M. Pacheco
Fifth International Conference on Software Engineering Advances (ICSEA), 2010, pages 395 - 399 (DOI:10.1109/ICSEA.2010.67)

Sistemas Territoriais Complexos – da não linearidade das dinâmicas territoriais à emergência de territórios auto-organizados
Sara A. Encarnacao, Sergio Serafim, Marcos Gaudiano, Francisco C. Santos, Jorge M. Pacheco and Jose A. Tenedorio
Proceedings of the XII Coloquio Iberico de Geografia (2010).

Co-evolution of cooperation, response to adverse social ties and network structure
Sven Van Segbroeck, Francisco C. Santos, Jorge M. Pacheco and Tom Lenaerts
Games 1:3 (2010) 317-337
abstract pdf

Adaptive contact networks change effective disease infectiousness and dynamics
Sven Van Segbroeck, Francisco C. Santos and Jorge M. Pacheco
PLoS Computational Biology 6:8 (2010) e1000895
abstract pdf supporting information Press Coverage

Learning to coordinate in complex networks
Sven Van Segbroeck,Steven de Jong, Ann Nowe, Francisco C. Santos and Tom Lenaerts
Adaptive Behavior 18:5 (2010) 416-427
abstract pdf

Hierarchically constrained dynamics and emergence of complex behaviour in nano-hybrids
Luís D. Carlos, Jorge M. Pacheco, Rute A. S. Ferreira, António L. L. Videira
SMALL 6 (2010) 386-390

Tyrosine kinase inhibitor therapy can cure chronic myeloid leukemia without hitting leukemic stem cells
Tom Lenaerts, Jorge M. Pacheco, Arne Traulsen, David Dingli
Haematologica 95 (2010) 900-907

In silico evolutionary dynamics of tumor virotherapy
Carlos L. Reis, Jorge M. Pacheco, Matthews K. Ennis, David Dingli
Integrative Biology (2010) 41-45
abstract html article press coverage

Emergence of collective action under coordination dilemmas
Francisco C. Santos, Brian Skyrms, Max O. Souza and Jorge M. Pacheco forthcoming in Proceedings of the European Conference on Complex Systems 2010

Coordinating towards a common good
Jorge M. Pacheco, Francisco C. Santos,Max O. Souza, Brian Skyrms
Book Chapter in Dynamics and Games in Science, in Honour of Mauricio Peixoto and David Rand, DYNA2008, Springer-Verlag, (2010, in press)

Evolutionary Dynamics of Chronic Myeloid Leukemia
David Dingli, Arne Traulsen, Tom Lenaerts, Jorge M. Pacheco
Genes and Cancer 1, 4 (2010) 309-315

Modeling the architecture and dynamics of hematopoiesis
David Dingli, Jorge M. Pacheco
Wiley Intedisciplinary Reviews : Systems Biology (2010) 2(2):235-44

Hematopoietic stem cells and their dynamics
David Dingli, Arne Traulsen, Jorge M. Pacheco
in "Stem Cells: Basics and Applications" K. D. Deb and S. M. Totey (Edts) (McGraw-Hill, New Delhi, 2010) in press

Reproductive fitness advantage of BCR–ABL expressing leukemia cells
Arne Traulsen, Jorge M. Pacheco, David Dingli
Cancer Letters 1;294(1) (2010) 43–48

Bulk materials made of silicon cage clusters doped with Ti, Zr, or Hf
Carlos L. Reis, J. M. Pacheco
in J. Physics Condensed Matter 22 (2010) 035501
pdf e-link

2009, 19 publications

Cyclic neutropenia in animals
Jorge M. Pacheco, Arne Traulsen, Tibor Antal, David Dingli
American Journal of Hematology 84 (2009) 258

Social diversity favors the emergence of cooperative behavior
Francisco C. Santos, Marta D. Santos, Sven Van Segbroeck and Jorge M. Pacheco
Proceedings of the Benelux Conference on Artificial Intelligence (2009)

Behavioral differences and the evolution of cooperation in adaptive social networks
S. Van Segbroeck, Francisco C. Santos, Tom Lenaerts and Jorge M. Pacheco
Proceedings of the Benelux Conference on Artificial Intelligence (2009)

Evolution of Cooperation in Adaptive Social Networks
S. Van Segbroeck, Francisco C. Santos, Arne Traulsen, Tom Lenaerts, Jorge M. Pacheco
in Handbook on Biological Networks World Scientific Publishing Company, Singapore 2009 Edited by S. Boccaletti, V. Latora, and Y. Moreno

Reply: Evolutionary game theory: lessons and limitations, a cancer perspective
D. Dingli, F. A. C. C. Chalub, F. C. Santos, S. Van Segbroeck, J. M. Pacheco
British Journal of Cancer 101, (2009) 2062-2063

Population structure induces a symmetry breaking favoring the emergence of cooperation
Jorge M. Pacheco, Flávio L. Pinheiro, Francisco C. Santos
PLoS Computational Biology 5(12) (2009) e1000596
pdf

Cancer phenotype as the outcome of an evolutionary game between normal and malignant cells
D. Dingli, F.A.C.C. Chalub, F. C. Santos, S. Van Segbroeck, J. M. Pacheco
British Journal of Cancer 101 (2009) 1130-1136
pdf

Selection of noise level in strategy adoption for spatial social dilemmas
Attila Szolnoki, Jeromos Vukov, Gyorgy Szabó
Phys Rev E 80 (2009) 056112
pdf

The evolution of cooperation under n-person snowdrift games
Max O. Souza, Jorge M. Pacheco, Francisco C. Santos
Journal of Theoretical Biology 260 (4) (2009) 581-588
pdf

The allometry of chronic myeloid leukemia
Jorge M. Pacheco, Arne Traulsen, David Dingli
Journal of Theoretical Biology 259 (2009) 635-640
pdf

Progenitor Cell Self-renewal and Cyclic Neutropenia
David Dingli, Arne Traulsen, Jorge M. Pacheco
Cell Proliferation 42 (2009) 330–33
pdf e-link

Evolutionary dynamics of collective action in N-person stag hunt dilemmas
Jorge M. Pacheco, Francisco C. Santos, Max O. Souza, Brian Skyrms
Proceedings Royal Society B 276 1655 (2009) (Online 25-Sept-2008)
pdf e-link

Reacting differently to adverse ties promotes cooperation in social networks
Sven Van Segbroeck, Francisco C. Santos, Tom Lenaerts, Jorge M. Pacheco
Physical Review Letters 102, 058105 (2009) Selected for the Virtual Journal of Biological Physics Research 17:4 (2009)
pdf press

The coevolution of loyalty and cooperation
Sven Van Segbroeck, Francisco C. Santos, Ann Nowé, Jorge M. Pacheco, Tom Lenaerts
in Proceedings of the IEEE Congress on Evolutionary Computation 2009, Trondheim (2009)

Evolution of cooperation in adaptive social networks.
Sven Van Segbroeck, Francisco C. Santos, Arne Traulsen, Tom Lenaerts and Jorge M. Pacheco
in "Handbook on Biological Networks" S. Boccaletti, V. Latora, and Y. Moreno (Edts.) World Scientific Publishing Company, Singapore (2009)

Evolutionary games in self-organizing populations
Arne Traulsen, Francisco C. Santos, Jorge M. Pacheco
"Adaptive Networks: Theory, Models and Applications"
Thilo Gross & Hiroki Sayama (Edts.)
New England Complex Systems Institute Book Series on Complexity
(Springer N.Y., 2009)
pdf e-link

2008, 11 publications

Neutral evolution in paroxysmal nocturnal hemoglobinuria
David Dingli, Lucio Luzzatto, Jorge M. Pacheco
Proceedings of the National Academy of Sciences (USA) 105 (2008) 18496
pdf e-link

Successful Cancer Treatment: Eradication of Cancer Stem Cells
David Dingli, Jorge M. Pacheco
in "Methods of Cancer Diagnosis, Therapy and Prognosis", Vol. 2, 179-191
M. A. Hayat (Editor)
Springer Netherlands (2008)
pdf e-link

The evolution of prompt reaction to adverse ties
Sven Van Segbroeck, Francisco C. Santos, Ann Nowé, Jorge M. Pacheco, Tom Lenaerts
BMC Evolutionary Biology 8 (2008) 287
e-link

Cyclic neutropenia in mammals
Jorge M. Pacheco, Arne Traulsen, Tibor Antal, David Dingli
American Journal of Hematology 83 (2008) 920
pdf e-link

Social diversity promotes the emergence of cooperation in public goods games
Francisco C. Santos, Marta D. Santos, Jorge M. Pacheco
Nature 454 (2008) 213-216
pdf e-link press

Dynamics of haemopoiesis across mammals
David Dingli, Arne Traulsen, Jorge M. Pacheco
Proc Biol Sci. 275(1649) (2008) 2389–2392
pdf e-link press

Chronic Myeloid Leukemia: Origin, Development, Response To Therapy, And Relapse
David Dingli, Arne Traulsen, Jorge M. Pacheco
Clinical Leukemia 2 (2008) 133-139
pdf e-link

Multiple mutant clones in blood rarely coexist
David Dingli, Jorge M. Pacheco, Arne Traulsen
Physical Review E 77(2008) 021915
pdf e-link

Some dynamic aspects of hematopoietic stem-cells
David Dingli, Jorge M. Pacheco
Stem Cell Reviews 4(1) (2008) 57-64
pdf e-link

Repeated games and direct reciprocity under active linking
Jorge M. Pacheco, Arne Traulse, Hisashi Ohtsuki, Martin A. Nowak
Journal of Theoretical Biology 250 (2008) 723
pdf e-link

Social Odometry in Populations of Autonomous Robots
Álvaro Gutiérrez, Alexandre Campo, Francisco C. Santos, Carlo Pinciroli and Marco Dorigo
Lecture Notes in Computer Science 5217 (2008) 371-378, Springer
abstract pdf

2007, 25 publications

Stability analysis of a bulk material built from silicon cage clusters: A first principles approach
Carlos L. Reis, José Luís Martins, J. M. Pacheco
in Physics Review B 76 (2007) 233406
pdf e-link

Acquired hematopoietic stem cell disorders and mammalian size
J. Viana Lopes, Jorge M. Pacheco, David Dingli
Blood 110 (2007) 4120-4122.
pdf e-link

On the origin of multiple mutant clones in paroxysmal nocturnal hemoglobinuria
Arne Traulsen, J. M. Pacheco, David Dingli
Stem Cells 25 (2007) 3081-3084
pdf e-link

A Multi-Level Selection Model for the Emergence of Social Norms
Francisco C. Santos, Fabio A. C. C. Chalub, Jorge M. Pacheco
Lecture Notes in Computer Science 4648 (2007) 525-534
pdf e-link

Depth of response and outcome in multiple myeloma
David Dingli, J. M. Pacheco, Grzegorz S. Nowakowski, Shaji Kumar, Angela Dispenzieri, Suzanne Hayman, Martha Lacy, Dennis Gastineau, Morie Gertz
Journal of Clinical Oncology 25 (2007) 4933-4937
pdf e-link

Ontogenic growth of the haematopoietic stem cell pool in humans
David Dingli, J. M. Pacheco
Proceedings Royal Society B274 (2007) 2479
pdf e-link

Single versus multiple transplants for multiple myeloma: Insights from in vivo and in silicostudies
David Dingli, J. M. Pacheco, M. A. Gertz
Blood 108 (2006) 458
e-link

The serum M-spike and transplant outcome in patients with multiple myeloma
David Dingli, J. M. Pacheco, Angela Dispenzieri, Suzanne Hayman, Shaji Kumar, Martha Lacy, Dennis Gastineau, Morie Gertz
Blood 108 (2006) 455
e-link

From stem cells to blood: dynamic and architectural aspects of hematopoiesis
David Dingli, A. Traulsen, J. M. Pacheco
Haematologica 92 (2007) 454
e-link

The size of the human active hematopoietic stem cell pool from birth to adulthood
David Dingli, J. M. Pacheco
Haematologica 92 (2007) 369
e-link

Impact of stochastic dynamics on the active hematopoietic stem cell pool
David Dingli, A. Traulsen, J. M. Pacheco
Haematologica 92 (2007) 161
e-link

Evolution of norms in a multi-level selection model of conflict and cooperation
Jorge M. Pacheco, Francisco C. Santos, Chalub, F. A. C. C.
Electronic Journal of Theoretical Physics 4 16 (2) (2007) 157-172

Evolutionary Graph Theory: Breaking the symmetry between interaction and replacement
Hisashi Ohtsuki, J. M. Pacheco, Martin A. Nowak
Journal of Theoretical Biology 246 (4) (2007) 681-694
pdf e-link

Breaking the symmetry between interaction and replacement in evolutionary dynamics on graphs
Hisashi Ohtsuki, Martin A. Nowak, J. M. Pacheco
Physical Review Letters 98 (2007) 108106
Selected for the Virtual Journal of Biological Physics Research 13, 6 (2007) March 15th
pdf e-link

Compartmental Architecture and Dynamics of Hematopoiesis (open access)
David Dingli, Arne Traulsen, J. M. Pacheco
PLoS ONE 2(4) (2007) e345
e-link

In vivo and in silico studies on single versus multiple transplants for multiple myeloma
David Dingli, J. M. Pacheco, Angela Dispenzieri, Suzanne Hayman, Shaji Kumar, Martha Lacy, Dennis Gastineau, Morie Gertz
Cancer Science 98 (5) (2007) 734–739
pdf e-link

Stochastic dynamics of hematopoietic tumor stem cells
David Dingli, Arne Traulsen, J. M. Pacheco
Cell Cycle 6 (4) (2007) 461-466
pdf e-link issue cover

Pairwise Comparison and selection temperature in evolutionary game dynamics
Arne Traulsen, Martin A. Nowak, J. M. Pacheco
Journal of Theoretical Biology 246 ( 2007) 522-529
pdf e-link

The Emergence of Tumor Metastases
David Dingli, Franziska Michor, Tibor Antal, J. M. Pacheco
Cancer Biology & Therapy 6,3 (2007) 522-529
pdf e-link

Evolution of cooperation in a population of selfish adaptive agents
Jorge M. Pacheco, Tom Lenaerts, Francisco C. Santos
Lecture Notes in Computer Science 4648 (2007) 535-544
pdf e-link

Types, instances and high-level constraints in growing networks
Hugues Bersini, Francisco C. Santos, Tom Lenaerts
In Proc. of the European Conference on Complex Systems 2007, Dresden 2007.
(ECCS'07).

Cooperation prevails when individuals adjust their social ties
Francisco C. Santos, Jorge M. Pacheco and Tom Lenaerts
In Proc. of the European Conference on Complex Systems 2007, Dresden 2007.
(ECCS'07).

How Affinity Influences Tolerance in an Idiotypic Network
Emma Hart, Hugues Bersini and Francisco C. Santos
Journal of Theoretical Biology 249 (2007) 422-436.

Networks regulating networks: The effects of constraints on topological evolution
Francisco C. Santos, Hugues Bersini and Tom Lenaerts
Lecture Notes in Computer Science 4648 (2007), 956-965, Springer.

2006, 19 publications

Silicon-metal clusters: nano-templates for cluster assembled materials
G. K. Gueorguiev, J. M. Pacheco, S. Stafström
in Thin Solid Films 515 (2006) 1192-1196
pdf e-link

Stern-judging : A simple, successful norm which promotes cooperation under indirect reciprocity (open access)
J. M. Pacheco, F. C. Santos, Fabio A. C. C. Chalub
PLoS Computational Biology 2(12) (2006) e178
e-link

Coevolution of strategy and structure in complex networks with dynamical linking
J. M. Pacheco, Arne Traulsen, Martin A. Nowak
Physical Review Letters 97 (2006) 258103
Selected for the Virtual Journal of Biological Physics Research 13, 1 (2007) January 1st
pdf e-link

Cooperation Prevails when individuals adjust their social ties (open access)
F. C. Santos, J. M. Pacheco, Tom Lenaerts
PLoS Computational Biology 2(10) (2006) 1284
e-link

Allometric scaling of the hematopoietic stem cell pool accross mammals (open access)
David Dingli, J. M. Pacheco
PLoS ONE 1 (2006) e2
e-link

Stochastic payoff evaluation increases the temperature of selection
Arne Traulsen, Martin A. Nowak, J. M. Pacheco
Journal of Theoretical Biology 244 (2006) 349-356
pdf e-link

Emergence of Cooperation in Heterogeneous Structured Populations
F. C. Santos, J. M. Pacheco, Tom Lenaerts
Proceedings of the 10th Conference on the Simulation and Synthesis of Living Systems
(L. M. Rocha et al., Edts.) MIT Press (2006) 432-437
pdf e-link

Active linking in evolutionary games
J. M. Pacheco, Arne Traulsen, Martin A. Nowak
Journal of Theoretical Biology 243 (2006) 437-443
pdf e-link

Stochasticicy and Evolutionary Stability
Arne Traulsen, J. M. Pacheco, Lorens Imhof
Physical Review E 74 (2006) 021905
Selected for the Virtual Journal of Biological Physics Research 12, 4 (2006) August 15th
pdf e-link

Stochastic dynamics of invasion and fixation
Arne Traulsen, Martin A. Nowak, J. M. Pacheco
Physical Review E 74 (2006) 011909
Selected for the Virtual Journal of Biological Physics Research 12, 3 (2006) August 1st
pdf e-link

Evolutionary Dynamics of Social Dilemmas in Structured Heterogeneous Populations (open access)
Francisco C. Santos, J. M. Pacheco, Tom Lenaerts
Proceedings of the National Academy of Sciences, USA103 (2006) 3490-3494 (Online 16-Feb-2006)
e-link press

The Evolution of Norms
Fabio A. C. C. Chalub, Francisco C. Santos, J. M. Pacheco
Journal of Theoretical Biology 241(2) (2006) 233-240 (Online 04-Jan-2006)
pdf e-link

A new route to the evolution of cooperation
Francisco C. Santos, J. M. Pacheco
Journal of Evolutionary Biology 19(3) (2006) 726-733
pdf e-link

Tolerance vs Intolerance: How Affinity Defines Topology in an Idiotypic Network
Emma Hart, Hugues Bersini and Francisco C. Santos
Lecture Notes in Computer Science 4163 (2006) 109-121, Springer.
PDF

Games on graphs.
Francisco C. Santos
MSc Thesis, (co-supervised by J. M. Pacheco) Université Libre de Bruxelles, TR/IRIDIA/2006-24.

How scale-free type-based networks emerge from instance-based dynamics
Tom Lenaerts, Hugues Bersini and Francisco C. Santos
Proceedings of the 10th International Conference on the Simulation and Synthesis of Living Systems (Alife X), (Rocha et al.,Editors), p.8-15, MIT Press (2006)

Growing Biological networks:Beyond the gene-duplication model
Hugues Bersini, Tom Lenaerts and Francisco C. Santos
Journal of Theoretical Biology 241 (3) (2006) (Online 25-Jan-2006).
pdf

Epidemics spreading and cooperation dynamics on homogeneous small-world networks
Francisco C. Santos, João F. Rodrigues, J. M. Pacheco
Physical Review E 72 (2005) 056128
Selected for the Virtual Journal of Biological Physics Research 10 (2005) December 1st
pdf e-link

Graph topology plays a determinant role in the evolution of cooperation
Francisco C. Santos, João F. Rodrigues, J. M. Pacheco
Proc. Royal Soc. London B273 (2006) 51-55 (online October 2005)
pdf e-link

2005, 4 publications

Scale-Free networks provide a unifying framework for the Emergence of Cooperation
Francisco C. Santos, J. M. Pacheco
Physical Review Letters 95 (2005) 098104
Selected for the Virtual Journal of Biological Physics Research 10 (2005) September 1st
pdf e-link

Network dependence of the dilemmas of cooperation
J. M. Pacheco, Francisco C. Santos
Science of Complex Networks: from Biology to the Internet and WWW
AIP Conference Proceedings 776 (2005) pp 90-100 (J. F. F. Mendes, Editor)
pdf

Recurrent epidemics in small world networks
J. Verdasca, M. M. Telo da Gama, A. Nunes, N. R. Bernardino, J. M. Pacheco, M. C. Gomes
Journal of Theoretical Biology 233 (2005) 553-561
pdf e-link

Growing Biochemical Networks: Identifying the Intrinsic Properties
Hugues Bersini, Tom Lenaerts and Francisco C. Santos
Lecture Notes in Artificial Intelligence 3630 : 864-873(2005) Springer