complex systems 

left: a defector being wiped out in a scale-free wold of cooperators (with Franciso C. Santos, 2004)
center: stern-judging, a social normal of cooperation & punishment (with Fabio Chalub & Francisco C. Santos, 2006)

right
: virotherapy: a tumor (dark spots) is fighting a cancer (brighter spots) in a virtual 3D-organism (with Carlos L. Reis & David Dingli, 2008)

I have been working in four grand areas of research in scientific computing and complex systems, where :

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.



Publications ( updated : Dec / 2016 )


-- -- Journal Articles

  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
https://doi.org/10.1371/journal.pone.0175687

[pdf]

A. 191. 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
[pdf]

  2016

A. 190. 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
[pdf]

A. 189. 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
[pdf]

A. 188. 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
[pdf]

A. 187. Linking Individual and Collective Behavior in Adaptive Social Networks
Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco
Physical Review Letters 116 (2016) 128702
[pdf]

A. 186. 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]

A. 185. Evolutionary dynamics of collective index insurance
Jorge M. Pacheco, Francisco C. Santos, Simon A. Levin
Journal of Mathematical Biology 72 (2016) 997-1010
[pdf]

  2015

A. 184. 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
[pdf]

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

[e-link]

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
[e-link]

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
[e-link]          
                                                                                          
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
[e-link]

  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
 [e-link]

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

 [e-link]


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
 [e-link]

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
 [e-link]

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
 [e-link]

  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 
[e-link]

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
[e-link]

A. 168. Evolution of collective action in adaptive social structures
João Moreira, Jorge M. Pacheco, Francisco C. Santos
Nature Scientific Reports 3 (2013) 1521
[pdf]

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
[pdf]

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
[pdf]

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
[pdf]

  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
[pdf]

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
[e-link]

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
[e-link]

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
[e-link]

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
[pdf]

A. 147. From Local to Global Dilemmas in Social Networks
Flávio L. Pinheiro, Jorge M. Pacheco, Francisco C. Santos
PLoS-ONE 7 (2012) e32114
[e-link]

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
[pdf]

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
[e-link]

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)
[pdf]

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.
[pdf]

  2011

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.
[pdf]

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.
[e-link]

C. 139. Stochastic dynamics and the evolution of mutations in stem cells
David Dingli and Jorge M. Pacheco
BMC Biology 9 (2011) 41.
[e-link]

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.
[pdf]

A. 137. Incipient Cognition Solves the Spatial Reciprocity Conundrum of Cooperation
Jeromos Vukov, Francisco C. Santos, Jorge M. Pacheco
PLoS One 6 (2011) e17939.
[e-link]

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
[pdf] , [e-link]

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
[e-link]

  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
[e-link]

C. 131. Somatic mutations and the hierarchy of hematopoiesis
Arne Traulsen, Jorge M. Pacheco, Lucio Luzzatto,David Dingli
BioEssays 32 (2010) 1003-1008
[pdf]

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
[e-link]

C. 125. Modelling Hematopoiesis in Health and Disease
Diogo Peixoto, David Dingli, Jorge M. Pacheco
Mathematical and Computer Modelling 53 (2010) 1546-1557
[pdf]

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
[pdf]

C. 122. Reproductive fitness advantage of BCR–ABL expressing leukemia cells
Arne Traulsen, Jorge M. Pacheco, David Dingli
Cancer Letters 294 (2010) 43-48
[pdf], [e-link]

C. 121. Cyclic neutropenia in animals
Jorge M. Pacheco, Arne Traulsen, Tibor Antal, David Dingli
American Journal of Hematology 84 (2009) 258
[pdf], [e-link]

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
[pdf] , [e-link]

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
[pdf] , [e-link]

  2009

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
[e-link]

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
[pdf] , [press]

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
[pdf] , [e-link] [press]

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
[pdf] , [e-link] , [press]

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
[pdf] , [e-link]

C. 107. The allometry of chronic myeloid leukemia
Jorge M. Pacheco, Arne Traulsen, David Dingli
Journal of Theoretical Biology 259 (2009) 635-640
[pdf] , [e-link]

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
Selected for the Virtual Journal of Biological Physics Research 17, 4 (2009) February 15th
[pdf] , [e-link] , [press]

  2008

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
[e-link]

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)
[e-link]

C. 100. Cyclic neutropenia in mammals
Jorge M. Pacheco, Arne Traulsen, Tibor Antal, David Dingli
American Journal of Hematology 83 (2008) 920
[pdf] , [e-link]

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
[pdf] , [pdf-SI] , [e-link]

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
[pdf] , [e-link]

C. 097. Progenitor Cell Self-renewal and Cyclic Neutropenia
David Dingli, Tibor Antal, Arne Traulsen, Jorge M. Pacheco
Cell Proliferation 42 (2009) 330-338
[pdf] , [e-link]

C. 096. Dynamics of Hematpoiesis across Mammals
David Dingli, Arne Traulsen, Jorge M. Pacheco
Proceedings Royal Society London B275 (2008) 2389-2392
[pdf] , [e-link] , [press]

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
[pdf] , [e-link

C. 094. Multiple mutant clones in blood rarely coexist
David Dingli, Jorge M. Pacheco, Arne Traulsen
Physical Review E 77(2008) 021915
[pdf] , [e-link]

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
[pdf] , [e-link

  2007

C. 088. Acquired hematopoietic stem cell disorders and mammalian size
J. Viana Lopes, Jorge M. Pacheco, David Dingli
Blood 110 (2007) 4120-4122
[pdf] , [e-link

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
[pdf] , [e-link]

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
[pdf] , [e-link]

C. 085. Ontogenic growth of the haematopoietic stem cell pool in humans
David Dingli, Jorge M. Pacheco,
Proceedings Royal Society London B274 (2007) 2479
[pdf] , [e-link]

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
[pdf] , [e-link]

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
[pdf] , [e-link]

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
[pdf] , [e-link]

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
Selected for the Virtual Journal of Biological Physics Research 13, 6 (2007) March 15th
[pdf] , [e-link

C. 075. Compartmental Architecture and Dynamics of Hematopoiesis (
David Dingli, Arne Traulsen, Jorge M. Pacheco
PLoS ONE 2(4) (2007) e345
[e-link]

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
[pdf] , [e-link

C. 072. Stochastic dynamics of hematopoietic tumor stem cells
David Dingli, Arne Traulsen, Jorge M. Pacheco
Cell Cycle 6 (4) (2007) 461-466
[pdf] , [e-link] , [issue cover]

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
[pdf] , [e-link]

C. 070. The Emergence of Tumor Metastases
David Dingli, Franziska Michor, Tibor Antal, Jorge M. Pacheco
Cancer Biology & Therapy 6,3 (2007) 522-529
[pdf] , [e-link

  2006

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
[e-link]

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
Selected for the Virtual Journal of Biological Physics Research 13, 1 (2007) January 1st
[pdf] , [e-link]

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
[e-link

C. 066. Allometric scaling of the hematopoietic stem cell pool accross mammals (open access)
David Dingli, Jorge M. Pacheco
PLoS ONE 1 (2006) e2
[e-link]

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
[pdf] , [e-link

A. 063. Active linking in evolutionary games
Jorge M. Pacheco, Arne Traulsen, Martin A. Nowak
Journal of Theoretical Biology 243 (2006) 437-443
[pdf] , [e-link

A. 062. Stochasticicy and Evolutionary Stability
Arne Traulsen, Jorge M. Pacheco, Lorens Imhof
Physical Review E 74 (2006) 021905
[pdf] , [e-link

A. 061. Stochastic dynamics of invasion and fixation
Arne Traulsen, Martin A. Nowak, Jorge 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]

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)
[e-link] , [press]

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)
[pdf] , [e-link]

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
[pdf] , [e-link

  2005

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
Selected for the Virtual Journal of Biological Physics Research 10 (2005) December 1st
[pdf] , [e-link]

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)
[pdf] , [e-link]

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
Selected for the Virtual Journal of Biological Physics Research 10 (2005) September 1st
[pdf] , [e-link]

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
[pdf] , [e-link]


-- -- Book Chapters

A. 199. The Role of Execution Errors in Populations of Ultimatum Bargaining Agents
Fernando P. Santos, Francisco C. Santos, Ana Paiva, Jorge M. Pacheco
in
2nd Workshop on Conflict Resolution in Decision Making (COREDEMA 2016),
Satellite Workshop at ECAI 2016, Den Haag, The Netherlands, August, 2016
[pdf]

D. 192. 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)
[pdf]

A. 160. Behavioral dynamics under climate change dilemmas
Francisco C. Santos, 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, Springer, pp. 113-124, Springer. 2013.
[pdf]

A. 153. 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, (in press).
[pdf]

C. 143. Evolutionary Dynamics of Mutations in Hematopoietic Stem Cells and Beyond
David Dingli, Arne Traulsen and Jorge M. Pacheco
Stem Cells and Cancer Stem Cells, Volume 3, Chapter 11 (2012, accepted)(Springer Science)
[pdf]

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)
[pdf]

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)
[pdf]

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) in press
[pdf]

A. 116. Evolution of Cooperation in Adaptive Social Networks
S. Van Segbroeck, Francisco C. Santos, Arne Traulsen, Tom Lenaerts, Jorge M. Pacheco
n Handbook on Biological Networks
World Scientific Publishing Company, Singapore 2009
Edited by S. Boccaletti, V. Latora, and Y. Moreno
[pdf] , [e-link]

C. 106. Modeling the architecture and dynamics of hematopoiesis
David Dingli, Jorge M. Pacheco
Wiley Interdisciplinary Reviews : Systems Biology (2009, accepted)
[pdf] , [e-link]

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)
[pdf] , [e-link]

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)
[pdf] , [e-link]

C. 093. Some dynamic aspects of hematopoietic stem-cells
David Dingli, Jorge M. Pacheco
Stem Cell Reviews 4 (2008) 57-64
[pdf] , [e-link]


-- -- Conference Proceedings

A. 198. 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), (Best paper award)

[pdf]

A. 197. 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
IFAAMAS (2016) 1381-1382
[pdf]

A. 196. 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) (2016) 1592-1593 (IOS Press)

[pdf]

A. 195. 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)
[pdf]

A. 194. 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 (2016) 470-471
(Tom Froese Ed., MIT press)
[pdf]

A. 193. 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,
AAMAS 2016 Workshops Best Papers 10002 (2016) 107-126
(Springer International Publishing)
[pdf]


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

[pdf]

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 (in press, 2013)
[pdf]

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 (in press, 2013)
[pdf]

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
[e-link]

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
[pdf]

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 (in Press) 
[pdf]

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
[pdf]

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
[pdf]

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 
[pdf]

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).
[pdf]

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
[pdf]

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
[e-link]

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
[e-link]

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)
[pdf]

C. 126. Darwin and the Somatic Evolution of Cancer
Jorge M. Pacheco, David Dingli
Actas da Academia de Ciências de Lisboa (2010) in press
[pdf]

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)
[pdf], [e-link]

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)
[pdf], [e-link]

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
[pdf], [e-link]

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)
[pdf]

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
[pdf] , [e-link]

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
[pdf] , [e-link]

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
[pdf] , [e-link]

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
[pdf] , [e-link

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
[pdf] , [e-link

C. 082. From stem cells to blood: dynamic and architectural aspects of hematopoiesis
David Dingli, A. Traulsen, Jorge M. Pacheco,
Haematologica 92 (2007) 454.
[pdf] , [e-link]

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
[pdf] , [e-link]

C. 080. Impact of stochastic dynamics on the active hematopoietic stem cell pool
David Dingli, A. Traulsen, Jorge M. Pacheco
Haematologica 92 (2007) 161
[pdf] , [e-link]

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)
[pdf] ,

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
[pdf] , [e-link]

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)
[pdf] , [e-link]

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.)
[pdf] , [e-link]

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
[pdf] , [e-link]