Complex Systems

Publications

I divide my publications into four main types:
A. Cooperation between individuals in the framework of Evolutionary Game Theory;
B. Global Optimization (directly though not exclusively related with research in quantum systems);
C. Tumor scaling and evolutionary dynamics;
D. Dynamics of Epidemics & other interdisciplinary problems.

2025
A. 231. Evolution favours positively biased reasoning in sequential interactions with high future gains Marco Saponara, Elias Fernández Domingos, Jorge M. Pacheco, Tom Lenaerts Journal of the Royal Society Interface 22, 229 (2025) 0153
A. 230. Impact of multiple delays on the governance of risky commons Ana M. Nunes, Francisco C. Santos, Jorge M. Pacheco Physical Review E 112, 1 (2025) 014303
A. 229. A new electoral bottom-up model of institutional governance Carlos M. Garrido, Francisco C. Santos, Elias Fernández Domingos, Ana M. Nunes, Jorge M. Pacheco Nature Scientific Reports 15 (2025) 3865
2024
A. 228. Co-evolution of risk and cooperation in climate policies under wealth inequality Jorge M. Pacheco, Francisco C. Santos PNAS Nexus 3 (2024) pgae550
A. 227. Evolution of a theory of mind Tom Lenaerts, Marco Saponara, Jorge M. Pacheco, Francisco C. Santos iScience 27 (2024) 108862
2021
A. 226. The complexity of human cooperation under indirect reciprocity Fernando P. Santos, Jorge M. pacheco, Francisco C. Santos Philosophical Transactions Royal Society B376 (2021) 20200291
A. 225. Evolutionary games in cities and urban planning Sara Encarnação, Fernando P. Santos, Francisco C. Santos, Margarida Pereira, Jorge M. Pacheco, Juval Portugali Chapter 18 in "Handbook on cities and complexity" ISBN: 978 1 78990 011 8 (2021), pp 349-369
A. 224. Financial incentives to poor countries promote net emissions reductions in multilateral climate agreements Yali Dong, Shuangmei Ma, Boyu Zhang, Wen-Xu Wang, Jorge M. Pacheco One Earth 4 (2021) 1141-1149
A. 223. Social Network Interventions to Prevent Reciprocity-driven Polarization Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco, Simon A. Levin (Extended Abstract) in Proc. Int. Conf. Autonomous Agents and Multiagent Systems (AAMAS 2021) 1643-1645
A. 222. Dynamics of informal risk sharing in collective index insurance Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco, Simon A. Levin Nature Sustainability 4 (2021), 426-432
C. 221. Multistage feedback-driven compartmental dynamics of hematopoiesis Nathaniel Mon Père, Tom Lenaerts, Jorge M. Pacheco, David Dingli iScience 24 (2021) 102326
A. 220. Stable leaders pave the way for cooperation under time-dependent exploration rates Flávio P. Pinheiro, Jorge M. Pacheco, Francisco C. Santos Royal Society Open Science 8 (2021) 200910
2020
A. 219. Governance of risky public goods under graduated punishment Marta C. Couto, Jorge M. Pacheco, Francisco C. Santos Journal of Theoretical Biology 505 (2020) 110423
A. 218. Coalition-structured governance improves cooperation to provide public goods Vítor V. Vasconcelos, Phillip M. Hannam, Simon A. Levin, Jorge M. Pacheco Nature Scientific Reports 10 (2020) 9194
2019
A. 217. Reward and punishment in climate change dilemmas António R. Góis, Fernando P. Santos, Jorge M. Pacheco, Francisco C. Santos Nature Scientific Reports 9 (2019) 16193
A. 215. Evolution of collective fairness in hybrid populations of humans and agents Fernando P. Santos, Jorge M. Pacheco, Ana Paiva, Francisco C. Santos Proceedings of the AAAI Conference on Artificial Intelligence 33 (2019) 6146-6153
A. 214. Teoria de Jogos Evolutiva e Cooperação Sara Encarnação, Fernando P. Santos, Francisco C. Santos, Juval Portugali, Jorge M. Pacheco, Margarida Pereira 26th APDR Congress. Evidence-based territorial policymaking (2019)
2018
A. 213. Indirect Reciprocity and Costly Assessment in Multiagent Systems Fernando P. Santos, Jorge M. Pacheco, Francisco C. Santos 32nd AAAI Conference on Artificial Intelligence, AAAI-2018, 8149-8150 (selected as a finalist to participate in 3MT presentation contest)
A. 212. Human cooperation and the complexity of moral codes Fernando P. Santos, Jorge M. Pacheco, Francisco C. Santos Artificial Life Conference Proceedings 30 (2018) 614-615, MIT press (2018)
A. 211. Multiplayer Ultimatum Games and Collective Fairness in Networked Communities Fernando P. Santos, Jorge M. Pacheco, Ana Paiva, Francisco C. Santos Artificial Life Conference Proceedings 30 (2018), 286-287, MIT press (2018)
D. 210. Structural and temporal patterns of the first global trading market Ana Sofia Ribeiro, Flávio L. Pinheiro, Francisco C. Santos, Amélia Polónia, Jorge M. Pacheco Royal Society Open Science 5 (2018) 180577 (Supplementary Material)
C. 209. Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria Nathaniel mon Père, Tom Lenaerts, Jorge M. Pacheco, David Dingli PLoS Computational Biology 14,6 (2018) e1006133
A. 208. Paths to the adoption of electric vehicles: An evolutionary game theoretical approach Sara Encarnação, Fernando P. Santos, Francisco C. Santos, Vered Blass, Jorge M. Pacheco, Juval Portugali Transportation Research B113 (2018) 24-33
A. 207. Social norm complexity and past reputations in the evolution of cooperation Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco Nature 555 (2018) 242-245 Supplementary Information / News and Views / blog@Nature
A. 206. Social Norms of Cooperation With Costly Reputation Building Fernando P. Santos, Jorge M. Pacheco, Francisco C. Santos 32nd AAAI Conference on Artificial Intelligence, AAAI-2018, 4727-4734
2017
A. 205. Indirect reciprocity in finite populations of explorative agents Fernando P. Santos, Jorge M. Pacheco, Francisco C. Santos Adaptive Learning Agents (ALA) Workshop at AAMAS 2017
A. 204. Multiplayer ultimatum game on complex networks: the role of structural power Fernando P. Santos, Jorge M. Pacheco, Ana Paiva, Francisco C. Santos Book of Abstracts - 6th International Conference on Complex Networks and Their Applications (2017)
A. 203. Information as the New Oil: The Smart Cities Dilemma (Extended Abstract) Sara Encarnação, Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco, Juval Portugali Smart Cities Conference: Potentials, Prospects and Discontents (2017)
A. 202. Untangling multi-sector governance strategies with evolutionary game theory (Extended Abstract) Sara Encarnação, Fernando P. Santos, Francisco C. Santos, Vered Blass, Jorge M. Pacheco, Juval Portugali Proceedings of the AESOP Annual Conference 2017
C. 201. Disease spreading in time-evolving networked communities Jorge M. Pacheco, Sven van Segbroeck, Francisco C. Santos in Temporal Network Epidemiology (N. Masuda and P. Holme, Edts), Ch. 13 pp 291-316, Springer Nature (2017)
A. 200. Structural power and the evolution of collective fairness in social networks Fernando P. Santos, Jorge M. Pacheco, Ana Paiva, Francisco C. Santos PLoS-ONE 12(4) (2017) e0175687
D. 199. Environmental Impacts of Colonial Dynamics in the First Global Age and the Anthropocene Amélia Polónia, Jorge M. Pacheco in Economic Development and Environmental History in the Anthropocene (Bloomsbury 2017)
A. 198. Stochastic dynamics through hierarchically embedded Markov chains Vítor V. Vasconcelos, Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco Physical Review Letters 118 (2017) 058301
A. 197. 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 144 (1), 65-79
2016
A. 196. The Role of Execution Errors in Populations of Ultimatum Bargaining Agents Fernando P. Santos, Francisco C. Santos, Ana Paiva, Jorge M. Pacheco International Workshop on Conflict Resolution in Decision Making (2016) 36-50
A. 195. Multiplayer ultimatum game in populations of autonomous agents Fernando P. Santos, Francisco C. Santos, Francisco S. Melo, Ana Paiva, Jorge M. Pacheco Proceedings of Adaptive and Learning Agents Workshop (ALA 2016), part of 2016 Int. Conf. Autonomous Agents and Multiagent Systems (AAMAS 2016)
A. 194. Learning to be Fair in Multiplayer Ultimatum Games (Extended Abstract) Fernando P. Santos, Francisco C. Santos, Francisco S. Melo, Ana Paiva, Jorge M. Pacheco Proceedings of the 2016 International Conference on Autonomous Agents & Multiagent Systems AAMAS (2016) 1381-1382
A. 193. Execution Errors Enable the Evolution of Fairness in the Ultimatum Game Fernando P. Santos, Francisco C. Santos, Ana Paiva, Jorge M. Pacheco Proceedings of the 22st European Conference on Artificial Intelligence (ECAI2016) 285 (2016) 1592-1593 (IOS Press)
A. 192. Evolution of Fairness in Multiplayer Ultimatum Games Fernando P. Santos, Francisco C. Santos, Ana Paiva, Jorge M. Pacheco Multidisciplinary Applications of Evolutionary Game Theory, Satellite Workshop at ALife XV (2016)
A. 191. Cooperation and Reputation in Primitive Societies Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco Proceedings of The Fifteenth International Conference on the Synthesis and Simulation of Living Systems - ALIFE XV (2016) 470-471 (Tom Froese Ed., MIT press)
A. 190. Dynamics of Fairness in Groups of Autonomous Learning Agents Fernando P. Santos, Francisco C. Santos, Francisco S. Melo, Ana Paiva, Jorge M. Pacheco Autonomous Agents and Multiagent Systems, Lecture Notes in Computer Science 10002 (2016) 107-126 (Springer International Publishing) Best Paper Award at ALA 2016
A. 189. 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
A. 188. Evolution of cooperation under indirect reciprocity and arbitrary exploration rates Fernando P. Santos, Jorge M. Pacheco, Francisco C. Santos Nature Scientific Reports 6 (2016) 37517
A. 187. An evolutionary game theoretic approach to multi-sector coordination and self-organization Fernando P. Santos, Sara Encarnação, Francisco C. Santos, Juval Portugali, Jorge M. Pacheco Entropy 18,2 (2016) 152
A. 186. Linking Individual and Collective Behavior in Adaptive Social Networks Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco Physical Review Letters 116 (2016) 128702
A. 185. Social Norms of Cooperation in Small-Scale Societies Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco PLoS-Computational Biology 12 (2016) e1004709378
A. 184. Evolutionary dynamics of collective index insurance Jorge M. Pacheco, Francisco C. Santos, Simon A. Levin Journal of Mathematical Biology 72 (2016) 997-1010
2015
A. 183. The Universality of Peer-Influence in Social Networks Flávio L. Pinheiro, Marta D. Santos, Francisco C. Santos, Jorge M. Pacheco Proceedings of the European Conference on Artificial Life 2015 ECAL 2015, Andrews, et al. (eds), pp. 149, MIT Press, 2015
A. 182. Evolutionary dynamics of group fairness Fernando P. Santos, Francisco C. Santos, Ana Paiva, Jorge M. Pacheco Journal of Theoretical Biology 378 (2015) 96-102
A. 181. Cooperation Dynamics of Polycentric Climate Governance Vítor V. Vasconcelos, Francisco C. Santos, Jorge M. Pacheco Mathematical Models and Methods in Applied Sciences (M3AS) 25 (2015) 2503
D. 180. Crime as a complex system: Comment on "Statistical physics of crime: A review" by MR D'Orsogna and M. Perc Jorge M. Pacheco Physics of Life Reviews 12 (2015) 32
A. 179. 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
2014
A. 178. 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
C. 177. The ecology of cancer from an evolutionary game theory perspective Jorge M. Pacheco, Francisco C. Santos, David Dingli Interface focus 4, 4 (2014) 20140019
A & D. 176. Origin of Peer Influence in Social Networks Flávio L. Pinheiro, Marta D. Santos, Francisco C. Santos, Jorge M. Pacheco Physical Review Letters 112, 9 (2014) 098702
A. 175. Climate Change Governance, Cooperation and Self-organization Jorge M. Pacheco, Vítor V. Vasconcelos, Francisco C. Santos Physics of Life Reviews 11, 4 (2014) 573-586
A. 174. Climate Policies under Wealth Inequality Vítor V. Vasconcelos, Francisco C. Santos, Jorge M. Pacheco, Simon A. Levin Proceedings of the National Academy of Sciences (USA) 111 (6) (2014) 2212-2216
A. 171. Evolution of Fairness and Conditional Cooperation in Public Goods Dilemmas Sven Van Segbroeck, Jorge M. Pacheco, Tom Lenaerts, Francisco C. Santos Proceedings of the European Conference on Complex Systems 2012 Springer Proceedings in Complexity 2014, pp 827-830
2013
A. 173. Bootstrapping back the climate with self-organisation Vítor V. Vasconcelos, Flávio L. Pinheiro,Francisco C. Santos, 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)
A. 172. Self-organized game dynamics in complex networks Flávio L. Pinheiro, Vítor V. Vasconcelos, Francisco C. Santos, 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)
D. 170. Urban Dynamics, Fractals and Generalized Entropy Sara Encarnação, Marcos Gaudiano, Francisco C. Santos, José A. Tenedório, Jorge M. Pacheco Entropy 15 (2013) 2679-2697
A. 169. A bottom-up institutional approach to cooperative governance of risky commons Vítor V. Vasconcelos, Francisco C. Santos, Jorge M. Pacheco Nature Climate Change 3 (2013) 797–801
A. 168. Evolution of collective action in adaptive social structures João Moreira, Jorge M. Pacheco, Francisco C. Santos Nature Scientific Reports 3 (2013) 1521
A. 167. Reward from punishment does not emerge at all costs Jeromos Vukov, Flávio P. Pinheiro, Francisco C. Santos, Jorge M. Pacheco PLoS-Comp. Biol. 9 (2013) e1002868
A. 166. 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 (2013) 233
D. 165. 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 (2013) 20120810
A. 160. Behavioral dynamics under climate change dilemmas Francisco C. Santos, Jorge M. Pacheco 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, Springer, pp. 113-124, Springer. 2013.
2012
A. 164. Dynamics of N-Person Snowdrift Games in Structured Populations Marta D. Santos, Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco Journal of Theoretical Biology 315 (2012) 81-86
D. 163. Fractal cartography of urban areas Sara Encarnação, Marcos Gaudiano, Francisco C. Santos, José A. Tenedório, Jorge M. Pacheco Nature Scientific Reports 2 (2012) 527
A. 162. How selection pressure changes the nature of social dilemmas in structured populations Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco New Journal of Physics 14 (2012) 073035
A. 161. Cognitive strategies take advantage of the cooperative potential of heterogeneous networks Jeromos Vukov, Francisco C. Santos, Jorge M. Pacheco New Journal of Physics 14 (2012) 063031
A. 159. Evolution of social diversity under the distributed prisoners dilemma Flávio L. Pinheiro, João A. Moreira, Marta D. Santos, Francisco C. Santos, Jorge M. Pacheco in Bio-Inspired Models of Network, Information, and Computing Systems Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering Volume 87, 2012, pp 523-532
A. 156. Evolving the asymmetry of the Prisoner's dilemma game in adaptive social structures João Moreira, Jorge M. Pacheco, Francisco C. Santos Bio-Inspired Models of Network, Information, and Computing Systems Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering Volume 87, 2012, pp 205-212
A. 155. Evolutionary Dynamics of Cooperation Under the Distributed Prisoner's Dilemma Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco Bio-Inspired Models of Network, Information, and Computing Systems Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering Volume 87, 2012, pp 523-532
A. 154. Collective Evolutionary Dynamics and Spatial Reciprocity under the N-Person Snowdrift Game Marta D. Santos, Francisco C. Santos and Jorge M. Pacheco, Bio-Inspired Models of Network, Information, and Computing Systems Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering Volume 87, 2012, pp 178-188
A. 151. Tracking the Evolution of Cooperation in Complex Networked Populations Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco Lecture Notes in Computer Science 7246 (2012) 86
A. 150. The emergence of fairness in repeated group interactions Sven Van Segbroeck, Jorge M. Pacheco, Tom Lenaerts, Francisco C. Santos Physical Review Letters 108 (2012) 158104
A. 147. From Local to Global Dilemmas in Social Networks Flávio L. Pinheiro, Jorge M. Pacheco, Francisco C. Santos PLoS-ONE 7 (2012) e32114
A. 146. Evolutionary dynamics of collective action when individual fitness derives from group decisions taken in the past João A. Moreira, Flávio L. Pinheiro, Ana Nunes, Jorge M. Pacheco Journal of Theoretical Biology 298 (2012) 8–15
A. 144. Evolutionary Dynamics of Climate Change under Collective-Risk Dilemmas Francisco C. Santos, Victor V. Vasconcelos, Marta D. Santos, Pedro B. Neves, and Jorge M. Pacheco M3AS: Mathematical Models and Methods in Applied Sciences (2012, Special Issue on Mathematics and Complexity in Human and Life Sciences)
C. 143. Evolutionary Dynamics of Mutations in Hematopoietic Stem Cells and Beyond David Dingli, Arne Traulsen and Jorge M. Pacheco in Stem Cells and Cancer Stem Cells, Volume 3, Chapter 11 (2012) (Springer Science)
A. 142. Role of diversity in the evolution of cooperation Francisco C. Santos, Flávio L. Pinheiro, Tom Lenaerts and Jorge M. Pacheco Journal of Theoretical Biology 299 (2012) 88-96.
2011
A. 149. Co-evolution of pre-play signaling and cooperation Francisco C. Santos, Jorge M. Pacheco, Brian Skyrms in Advances in Artificial Life, ECAL 2011: Proceedings of the 11th 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
A. 148. 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 11th 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
C. 145. Dynamics of mutant cells in hierarchical organized tissues Benjamin Werner, David Dingli, Tom Lenaerts, Jorge M. Pacheco, Arne Traulsen PLoS-Computational Biology 7 (2011) 10022900
A. 141. 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.
A. 140. 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 (2011) 10421-10425.
C. 139. Stochastic dynamics and the evolution of mutations in stem cells David Dingli and Jorge M. Pacheco BMC Biology 9 (2011) 41.
C. 138. 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.
A. 137. Incipient Cognition Solves the Spatial Reciprocity Conundrum of Cooperation Jeromos Vukov, Francisco C. Santos, Jorge M. Pacheco PLoS One 6 (2011) e17939.
A. 136. Co-evolution of pre-play signaling and cooperation Francisco C Santos, Jorge M Pacheco, Brian Skyrms Journal of Theoretical Biology 274 (2011) 30-35
A. 135. Selection pressure transforms the nature of social dilemmas in adaptive networks Sven Van Segbroeck, Francisco C Santos, Tom Lenaerts, Jorge M Pacheco New Journal of Physics 13 (2011) 013007
A. 134. The Messianic Effect of Pathological Altruism Jorge M. Pacheco, Francisco C. Santos in "Pathlogical Altruism" (B. Oakley, A. Knafo, G. Madhavan, David S. Wilson, Edts, Oxford U. Press, 2011)
D. 129. Creating metamaterials at the nano-scale Jorge M. Pacheco, Carlos L. Reis in "Quantal Aspects in Physics and Chemistry", (J. S. Redinha, J. da Providência, A. J. C. Varandas, Edts.) Coimbra University Press, (Coimbra, Portugal, 2011)
A. 118. Emergence of cooperation in adaptive social networks with behavioral diversity S. 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
2010
A. 157. Emergence of collective action under coordination dilemmas Francisco C. Santos, Brian Skyrms, Max O. Souza, Jorge M. Pacheco Proceedings of the European Conference on Complex Systems (2010)
A. 152. 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 in Proceedings of the XII Coloquio Iberico de Geografia (2010).
A. 132. Coevolution of Cooperation, Response to Adverse Social Ties and Network Structure Sven Van Segbroeck, Francisco C. Santos, Jorge M. Pacheco, Tom Lenaerts Games 1(3) (2010) 317-337
C. 131. Somatic mutations and the hierarchy of hematopoiesis Arne Traulsen, Jorge M. Pacheco, Lucio Luzzatto,David Dingli BioEssays 32 (2010) 1003-1008
A. 130. Evolutionary dynamics of collective action Jorge M. Pacheco, Francisco C. Santos, Max O. Souza, Brian Skyrms in "The Mathematics of Darwin Legacy" (José Francisco Rodrigues, Fábio Chalub, edts, 2010)
D. 127. Adaptive contact networks change disease infectiousness and dynamics Sven Van Segbroeck, Francisco C. Santos, Jorge M. Pacheco PLoS Computational Biology 6(8)(2010) e1000895
C. 126. Darwin and the Somatic Evolution of Cancer Jorge M. Pacheco, David Dingli Actas da Academia de Ciências de Lisboa (2010)
C. 125. Modelling Hematopoiesis in Health and Disease Diogo Peixoto, David Dingli, Jorge M. Pacheco Mathematical and Computer Modelling 53 (2010) 1546-1557
C. 124. Evolutionary Dynamics of Chronic Myeloid Leukemia David Dingli, Arne Traulsen, Tom Lenaerts, Jorge M. Pacheco Genes and Cancer 1, 4 (2010) 309-315
C. 122. Reproductive fitness advantage of BCR–ABL expressing leukemia cells Arne Traulsen, Jorge M. Pacheco, David Dingli Cancer Letters 294 (2010) 43-48
A. 117x. Coordinating towards a Common Good Francisco C. Santos and Jorge M. Pacheco in Proc. of ICNAAM 2010: International Conference of Numerical Analysis and Applied Mathematics 2010 AIP Conference Proceedings Vol. 1281, p. 1540 (2010)
D. 115. 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
C. 113. 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
C. 110. In silico evolutionary dynamics of tumor virotherapy Carlos L. Reis, Jorge M. Pacheco, Matthews K. Ennis, David Dingli Integrative Biology 2 (2010) 41-45
2009
C. 123. Hematotpoietic 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, 2009)
C. 121. Cyclic neutropenia in animals Jorge M. Pacheco, Arne Traulsen, Tibor Antal, David Dingli American Journal of Hematology 84 (2009) 258
A. 120. 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)
A. 119. 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)
A. 117. The coevolution of loyalty and cooperation S. Van Segbroeck, Francisco C. Santos, Ann Nowé, Tom Lenaerts and Jorge M. Pacheco Proceedings of the IEEE Congress on Evolutionary Computation (2009) 500-505
A. 116. 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
A. 112. Population structure induces a symmetry breaking favoring the emergence of cooperation (open access) Jorge M. Pacheco, Flávio L. Pinheiro, Francisco C. Santos PLoS-Computational Biology 5(12) (2009) e1000596
C. 111. Reply. . . Evolutionary game theory: lessons and limitations, a cancer perspective David Dingli, F. A. Chalub, F. C. Santos, S. Van Segbroeck, Jorge M. Pacheco British Journal of Cancer 101 (2009) 2062-2063
C. 109. Cancer phenotype as the outcome of an evolutionary game between normal and malignant cells David Dingli, F. A. Chalub, F. C. Santos, S. Van Segbroeck, Jorge M. Pacheco British Journal of Cancer 101 (2009) 1130–1136
A. 108. Evolution of Cooperation under N-person Snowdrift Games Max O. Souza, Jorge M. Pacheco, Francisco C. Santos Journal of Theoretical Biology 260 (2009) 581-588
C. 107. The allometry of chronic myeloid leukemia Jorge M. Pacheco, Arne Traulsen, David Dingli Journal of Theoretical Biology 259 (2009) 635-640
C. 106. Modeling the architecture and dynamics of hematopoiesis David Dingli, Jorge M. Pacheco in Wiley Interdisciplinary Reviews : Systems Biology (2009)
A. 104. 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 (2009) 058105
C. 103. Neutral evolution in paroxysmal nocturnal hemoglobinuria David Dingli, Lucio Luzzatto, Jorge M. Pacheco Proceedings of the National Academy of Sciences (USA) 105 (2008) 18496
A. 102. Evolutionary games in self-organizing populations Arne Traulsen, Francisco C. Santos, Jorge M. Pacheco in "Adaptive Networks: Theory, Models and Applications" Thilo Gross & Hiroki Sayama (Edts.) New England Complex Systems Institute Book Series on Complexity Springer Series “Understanding Complex Systems”, vol. 51, pp. 253-267 (Springer Berlin / Heidelberg, 2009)
A. 099. 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 London B276 (2009) 315-321
C. 097. Progenitor Cell Self-renewal and Cyclic Neutropenia David Dingli, Tibor Antal, Arne Traulsen, Jorge M. Pacheco Cell Proliferation 42 (2009) 330-338
2008
A. 153. Coordinating towards a common good Jorge M. Pacheco, Francisco C. Santos, Max O. Souza, Brian Skyrms in Dynamics and Games in Science, (in Honour of Mauricio Peixoto and David Rand, DYNA2008) Springer-Verlag, (2008).
C. 105. 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)
A. 101. The evolution of prompt reaction to adverse ties Sven Van Segbroeck, Francisco C. Santos, Ann Nowé, Jorge M. Pacheco, Tom Lenaerts BMC Evolutionary Biology 8:287 (2008)
C. 100. Cyclic neutropenia in mammals Jorge M. Pacheco, Arne Traulsen, Tibor Antal, David Dingli American Journal of Hematology 83 (2008) 920
A. 098. 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
C. 096. Dynamics of Hematpoiesis across Mammals David Dingli, Arne Traulsen, Jorge M. Pacheco Proceedings Royal Society London B275 (2008) 2389-2392
C. 095. Chronic Myeloid Leukemia: Origin, Development, Response To Therapy, And Relapse David Dingli, Arne Traulsen, Jorge M. Pacheco Clinical Leukemia 2 (2008) 133-139
C. 094. Multiple mutant clones in blood rarely coexist David Dingli, Jorge M. Pacheco, Arne Traulsen Physical Review E 77(2008) 021915
C. 093. Some dynamic aspects of hematopoietic stem-cells David Dingli, Jorge M. Pacheco in Stem Cell Reviews 4 (2008) 57-64
A. 089. 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
2007
A. 091. 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
A. 090. 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
C. 088. Acquired hematopoietic stem cell disorders and mammalian size J. Viana Lopes, Jorge M. Pacheco, David Dingli Blood 110 (2007) 4120-4122
C. 087. On the origin of multiple mutant clones in paroxysmal nocturnal hemoglobinuria Arne Traulsen, Jorge M. Pacheco, David Dingli Stem Cells 25 (2007) 3081-3084
C. 086. Depth of response and outcome in multiple myeloma David Dingli, Jorge 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
C. 085. Ontogenic growth of the haematopoietic stem cell pool in humans David Dingli, Jorge M. Pacheco, Proceedings Royal Society London B274 (2007) 2479
C. 082. From stem cells to blood: dynamic and architectural aspects of hematopoiesis David Dingli, A. Traulsen, Jorge M. Pacheco, Haematologica 92 (2007) 454.
C. 081. The size of the human active hematopoietic stem cell pool from birth to adulthood David Dingli, Jorge M. Pacheco Haematologica 92 (2007) 369
C. 080. Impact of stochastic dynamics on the active hematopoietic stem cell pool David Dingli, A. Traulsen, Jorge M. Pacheco Haematologica 92 (2007) 161
A. 079. Evolution of norms in a multi-level selection model of conflict and cooperation Jorge M. Pacheco, F. C. Santos, Fabio A. C. C. Chalub Electronic Journal of Theoretical Physics 4 (2007) 157
C. 078. The serum M-spike and transplant outcome in patients with multiple myeloma David Dingli, Jorge M. Pacheco, Angela Dispenzieri, Suzanne Hayman, Shaji Kumar, Martha Lacy, Dennis Gastineau, Morie Gertz Cancer Science 98 (7) (2007) 1035–1040
A. 077. Evolutionary Graph Theory: Breaking the symmetry between interaction and replacement Hisashi Ohtsuki, Jorge M. Pacheco, Martin A. Nowak Journal of Theoretical Biology 246 (4) (2007) 681-694
A. 076. Breaking the symmetry between interaction and replacement in evolutionary dynamics on graphs Hisashi Ohtsuki, Martin A. Nowak, Jorge M. Pacheco Physical Review Letters 98 (2007) 108106
C. 075. Compartmental Architecture and Dynamics of Hematopoiesis ( David Dingli, Arne Traulsen, Jorge M. Pacheco PLoS ONE 2(4) (2007) e345
C. 073. In vivo and in silico studies on single versus multiple transplants for multiple myeloma David Dingli, Jorge M. Pacheco, Angela Dispenzieri, Suzanne Hayman, Shaji Kumar, Martha Lacy, Dennis Gastineau, Morie Gertz Cancer Science 98 (5) (2007) 734–739
C. 072. Stochastic dynamics of hematopoietic tumor stem cells David Dingli, Arne Traulsen, Jorge M. Pacheco Cell Cycle 6 (4) (2007) 461-466
A. 071. Pairwise Comparison and selection temperature in evolutionary game dynamics Arne Traulsen, Martin A. Nowak, Jorge M. Pacheco Journal of Theoretical Biology 246 ( 2007) 522-529
C. 070. The Emergence of Tumor Metastases David Dingli, Franziska Michor, Tibor Antal, Jorge M. Pacheco Cancer Biology & Therapy 6,3 (2007) 522-529
2006
C. 084. Single versus multiple transplants for multiple myeloma: Insights from in vivo and in silico studies David Dingli, Jorge M. Pacheco, M. A. Gertz, Blood 108 (2006) 458
C. 083. The serum M-spike and transplant outcome in patients with multiple myeloma David Dingli, Jorge M. Pacheco, Angela Dispenzieri, Suzanne Hayman, Shaji Kumar, Martha Lacy, Dennis Gastineau, Morie Gertz Blood 108 (2006) 455
A. 069. Stern-judging : A simple, successful norm which promotes cooperation under indirect reciprocity Jorge M. Pacheco, F. C. Santos, Fabio A. C. C. Chalub PLoS Computational Biology 2(12) (2006) e178
A. 068. Coevolution of strategy and structure in complex networks with dynamical linking Jorge M. Pacheco, Arne Traulsen, Martin A. Nowak Physical Review Letters 97 (2006) 258103
A. 067. Cooperation Prevails when individuals adjust their social ties (open access) F. C. Santos, Jorge M. Pacheco, Tom Lenaerts PLoS Computational Biology 2(10) (2006) 1284
C. 066. Allometric scaling of the hematopoietic stem cell pool accross mammals (open access) David Dingli, Jorge M. Pacheco PLoS ONE 1 (2006) e2
A. 065. Stochastic payoff evaluation increases the temperature of selection Arne Traulsen, Martin A. Nowak, Jorge M. Pacheco Journal of Theoretical Biology 244 (2006) 349-356
A. 064. Emergence of Cooperation in Heterogeneous Structured Populations F. C. Santos, Jorge 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
A. 063. Active linking in evolutionary games Jorge M. Pacheco, Arne Traulsen, Martin A. Nowak Journal of Theoretical Biology 243 (2006) 437-443
A. 062. Stochasticicy and Evolutionary Stability Arne Traulsen, Jorge M. Pacheco, Lorens Imhof Physical Review E 74 (2006) 021905
A. 061. Stochastic dynamics of invasion and fixation Arne Traulsen, Martin A. Nowak, Jorge M. Pacheco Physical Review E 74 (2006) 011909
A. 060. Evolutionary Dynamics of Social Dilemmas in Structured Heterogeneous Populations (open access) Francisco C. Santos, Jorge M. Pacheco, Tom Lenaerts Proceedings of the National Academy of Sciences (USA) 103 (2006) 3490-3494 (Online 16-Feb-2006)
A. 059. The Evolution of Norms Fabio A. C. C. Chalub, Francisco C. Santos, Jorge M. Pacheco Journal of Theoretical Biology 241(2) (2006) 233-240 (Online 04-Jan-2006)
A. 058. A new route to the evolution of cooperation Francisco C. Santos, Jorge M. Pacheco Journal of Evolutionary Biology 19(3) (2006) 726-733
A. 056. Graph topology plays a determinant role in the evolution of cooperation Francisco C. Santos, João F. Rodrigues, Jorge M. Pacheco Proceedings Royal Society London B273 (2006) 51-55 (online October 2005)
2005
A. 074. Darwin, Evolution and Cooperation Jorge M. Pacheco Proceedings of the International Conference Advances in Physical Science, Aveiro, Portugal, September 2005 (L. D. Carlos, editor)
A&D. 057. Epidemics spreading and cooperation dynamics on homogeneous small-world networks Francisco C. Santos, João F. Rodrigues, Jorge M. Pacheco Physical Review E 72 (2005) 056128
A. 055. Scale-Free networks provide a unifying framework for the Emergence of Cooperation Francisco C. Santos, Jorge M. Pacheco Physical Review Letters 95 (2005) 098104
A. 054. Network dependence of the dilemmas of cooperation Jorge 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)
D. 053. Recurrent epidemics in small world networks J. Verdasca, M. M. Telo da Gama, A. Nunes, N. R. Bernardino, Jorge M. Pacheco, M. C. Gomes Journal of Theoretical Biology 233 (2005) 553-561
BEFORE
B. 041. Monte Carlo simulations with first-principles energies Jorge M. Pacheco, José Luís Martins Density Functional Theory and its Applications to Materials, AIP Conference Proceedings 571 (2001) 166 (V. E. van Doren, K. van Alsenoy, P. Geerlings, Edts.)
B. 040. Highly efficient implementation of a Gaussian program to computing total energy of giant molecules Jorge M. Pacheco, José Luís Martins Lecture Notes in Computer Science 1981 (2001) 230