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Publications of the Program for Evolutionary Dynamics at Harvard University
2003
Frank SA, Y Iwasa, MA Nowak (2003). Patterns of cell division and the risk
of cancer. Genetics 163: 1527-1532.
Frank SA, MA Nowak (2003). Developmental predisposition to cancer. Nature
422: 494.
Hudson R R, Turelli M (2003). Stochasticity overrules the "three-times
rule": Genetic drift, genetic draft, and coalescence times for nuclear
loci versus mitochondrial DNA. Evolution 57: 182-190.
Iwasa Y, F Michor, MA Nowak (2003). Evolutionary dynamics of escape from
biomedical intervention. Proc R Soc B 270: 2573-2578.
Jones AG, SJ Arnold, R Burger (2003). Stability of the G-matrix in a population experiencing pleiotropic mutation, stabilizing selection, and
genetic drift. Evolution 57: 1747-1760.
NL, MA Nowak (2003). Language dynamics in finite populations. J theor Biol 221: 445-457.
NL, MA Nowak (2003). Language, learning and evolution. In
Language Evolution, eds. MH Christiansen, S Kirby. Oxford University
Press, 317-337.
NL, A Sengupta, MA Nowak (2003). Mutation-selection networks of cancer initiation: Tumor suppressor genes and chromosomal instability. J
theor Biol 223: 433-450.
Lorenz A, J Fuchs, R Burger, J Loidl (2003). Chromosome pairing does not
contribute to nuclear architecture in vegetative yeast cells. Eukaryotic
Cell 2: 856-866.
Michor F, SA Frank, RM May, Y Iwasa, MA Nowak (2003). Somatic selection
for and against cancer. J theor Biol 225: 377-382.
Michor F, Y Iwasa, NL , MA Nowak (2003). Local regulation of homeostasis favors chromosomal instability. Curr Biol 13: 581-584.
Michor F, MA Nowak, SA Frank, Y Iwasa (2003). Stochastic elimination of
cancer cells. Proc R Soc B 270: 2017-2024.
Mitchener G, MA Nowak (2003). Competitive exclusion and coexistence of
universal grammars. B Math Biol 65: 67-93.
Nowak MA, F Michor, Y Iwasa (2003). The linear process of somatic evolution. P Natl Acad Sci USA 100: 14966-14969.
Rajagopalan H, MA Nowak, B Vogelstein, C Lengauer (2003). The significance
of unstable chromosomes in colorectal cancer. Nat Rev Cancer 3: 695-701.
Sasaki A, MA Nowak (2003). Mutation landscapes. J theor Biol 224: 241-247.
Wei X, JM Decker, S Wang, H Hui, JC Ka pes, W Xiaoyun, JF Salazar, MG
Salazar, JM Kilby, MS Saag, NL , MA Nowak, BH Hahn, PD Kwong, GM
Shaw (2003). Antibody neutralization and escape by HIV-1. Nature 422: 307-
312.
PROT3
Willensdorfer M, R Burger (2003). The two-locus model of Gaussian stabilizing selection. Theor Popul Biol 64: 101-117.
2004
Barton NH, M Turelli (2004). Effects of genetic drift on variance components under a general model of epistasis. Evolution 58: 2111-2132.
Boots M, PJ Hudson, A Sasaki (2004). Large shifts in pathogen virulence
relate to host population structure. O HYPERLINK
"http://www.sciencemag.org/cgi/content/abstract/303/5659/842" ❑ScienceD
303: 842-845.
BUrger R, A Gimelfarb (2004). The effects of intraspecific competition and
stabilizing selection on a polygenic trait. Genetics 167: 1425-1443.
BUrger R, C Krall (2004). Quantitative genetic models and changing environments. In Evolutionary Conservation Biology, eds. R Ferriere, U
Dieckmann, D Couvet. Cambridge: Cambridge University Press, 171-186.
Doebeli M, C Hauert, T Killingback (2004). The evolutionary origin of cooperators and defectors. Science 306: 859-862.
Frank SA (2004). Age-specific acceleration of cancer. Curr Biol 14: 242-
246.
Frank SA, MA Nowak (2004). Problems of somatic mutation and cancer.
Bioessays 26: 291-299.
Frankham, R (2004). Evolutionary conservation genetics. In K HYPERLINK
"http://www.uky.edu/-cfox/EvolutionaryGenetics/Index.htm" DEvolutionary
Genetics:D Concepts and Case Studies, eds. CW Fox, JB Wolf. New York:
Oxford University Press.
Frankham R, JD Ballou, DA Briscoe (2004). A Primer of Conservation
Genetics. Cambridge: D HYPERLINK
"http://www.cambridge.org/uk/catalogue/catalogue.asp?isbna0521831105"
❑Cambridge University Press❑.
Frankham R, BW Brook (2004). The importance of time scale in conservation
biology and ecology. Annales Zoologici Fennici 41: 459-463.
Frankham R, JG Kingslover (2004). Adaptation and extinction: The empirical
view. In Evolutionary Conservation Biology, eds. R Ferriere, U Dieckmann,
D Couvet. Cambridge: - HYPERLINK
"http://www.cambridge.org/us/catalogue/catalogue.asp?isbne0521827000"
❑Cambridge University Press❑.
Ganapathy G, V Ramachandran, T Warnow (2004). On contract-and-refinetransformations between phylogenetic trees. In Proceedings of the
Fifteenth ACM-SIAM Symposium on Discrete Algorithms (SODA), 893-902.
Iwasa Y, F Michor, MA Nowak (2004). Evolutionary dynamics of invasion and
escape. J theor Biol 226: 205-214.
Iwasa Y, F Michor, MA Nowak (2004). Some basic properties of immune selection. J theor Biol 229: 179-188.
Iwasa Y, F Michor, MA Nowak (2004). Stochastic tunnels in evolutionary
dynamics. Genetics 166: 1571-1579.
Jones AG, SJ Arnold, R Burger (2004). Evolution and stability of the G-
matrix on a landscape with a moving optimum. Evolution 58: 1639-1654.
Jones NA, X Wei, D Flower, M Wong, F Michor, M Saag, B Hahn, M Nowak, G
Shaw (2004). Determinants of human immunodeficiency virus type 1 escape
from the primary CD8+ cytotoxic Y lymphocyte response. J Exp Math 200:
1243-1256.
Matsen E, MA Nowak (2004). Win-stay, lose-shift in language learning from
peers. P Natl Acad Sci USA 101: 18053-18057.
Michor F, Y Iwasa, MA Nowak (2004). Dynamics of cancer progression. Nat
Rev Cancer 4: 197-205.
PROT4
Michor F, Y Iwasa, H Rajagopalan, C Lengauer, MA Nowak (2004). Linear model of colon cancer initiation. Cell Cycle 3: 358-362.
Mitchener WG, MA Nowak (2004). Chaos and language. Proc R Soc B 271: 701-
704.
Moret BME, L Nakhleh, T Warnow, CR Linder, A Tholse, A Padolina, J Sun, R
Timme (2004). Phylogenetic networks: Modeling, reconstructibility, and
accuracy. IEEE T Comput Biol Biocomp 1: 13-23.
Moret BME, U Roshan, T Warnow, TL Williams (2004). Performance of supertree methods on various dataset decompositions. In Phylogenetic
Supertrees, ed. ORP Bininda-Edmonds. Dordrecht, Netherlands: Kluwer
Academic Publishers, 301-328.
Nakhleh L, T Warnow, CR Linder (2004). Reconstructing reticulate evolution
in species -- theory and practice. In Proceedings of the Eighth Annual
International Conference on Research in Computational Molecular Biology
(RECOMB), 337-346.
Nowak MA (2004). Prisoners of the dilemma. Nature 427: 491.
Nowak MA (2004) Theory is available light. Curr Biol 14: R406-R407.
Nowak MA, F Michor, Y Iwasa (2004). Evolutionary dynamics of tumor suppressor gene inactivation. P Natl Acad Sci USA 101: 10635-10638.
Nowak MA, A Sasaki, C Taylor, D Fudenberg (2004). Emergence of cooperation
and evolutionary stability in finite populations. Nature 428: 646-650.
Nowak MA, K Sigmund (2004). Evolutionary dynamics of biological games.
Science 303: 793-799.
Nowak MA, K Sigmund (2004). Population dynamics in evolutionary ecology.
In
HYPERLINK "http://www.wiley.com/WileyCDA/WileyTitle/productCd-
3527305882.html" OLife Sciences for the 21st CenturyO, eds. E Keinan, I
Schechter, M Sela. Weinheim: Wiley-VCH Verlag GmbH & Co.
O'Grady JJ, MA Burgman, DA Keith, LL Master, SJ Andelman, BW Brook, GA
Hammerson, T Regan, R Frankham (2004). Correlations among extinction risks
assessed by different systems of threatened species categorization.
Consery Biol 18: 1624-1635.
O'Grady JJ, DH Reed, BW Brook, R Frankham (2004). What are the best correlates of predicted extinction risk? Biol Consery 118: 513-520.
Reed DH, JJ O'Grady, BW Brook, JD Ballou, R Frankham (2004). Large estimates of minimum viable population sizes. Consery Biol 18: 1179.
Roshan U, BME Moret, TL Williams, T Warnow (2004). Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees. In
Proc. IEEE Computer Society Bioinformatics Conference CSB 2004. Stanford:
Stanford University Press.
Spielman D, BW Brook, R Frankham (2004). Does inbreeding and loss of genetic diversity decrease disease resistance? Consery Gen 5: 439-448.
Spielman D, BW Brook, R Frankham (2004). Most species are not driven to
extinction before genetic factors impact them. P Natl Acad Sci USA 101:
15261-15264. O HYPERLINK
"http://www.fas.harvard.edu/-ped/research/publications/2004/Spielman04.pdf
IT O❑
Taylor C, D Fudenberg, A Sasaki, MA Nowak (2004). Evolutionary game dynamics in finite populations. B Math Biol 66: 1621-1644.
Turelli M, NH Barton (2004). Polygenic variation maintained by balancing
selection: Pleiotropy, sex-dependent allelic effects and G x E interactions. Genetics 166: 1053-1079.
Wang L, T Warnow (2004). Distance-based genome rearrangement phylogeny. In
Mathematics of Evolution and Phylogeny, ed. O Gascuel. Oxford: Oxford
University Press.
PROT5
Warnow T, SN Evans, D Ringe, L Nakhleh (2004). Stochastic models of language evolution and an application to the Indo-European family of
languages. In Proceedings of the Conference on Phylogenetic Methods and
the Prehistory of Languages. Cambridge: Cambridge University Press.
Whitlock MC, R Burger (2004). The good, the bad, and the ugly: Fixation of
new mutations in small populations. In Evolutionary Conservation Biology,
eds. R Ferriere, U Dieckmann, D Couvet. Cambridge: K HYPERLINK
"http://www.cambridge.org/us/catalogue/catalogue.asp?isbn•0521827000"
❑Cambridge University PressO.
Wodarz D, N , Y Iwasa (2004). On the emergence of multifocal cancers. J Carcinogenesis 3: 13.
2005
Burger R (2005). A multilocus analysis of intraspecific competition and
stabilizing selection on a quantitative trait. J Math Biol 50: 355-396.
Boeckx C, M Piattelli-Palmarini (2005). Language as a natural object, linguistics as a natural science. Linguist Rev 22: 351-370.
63.Brown WM, L Cronk, K Grochow, A Jacobson, CK Liu, Z Popovik, R Trivers
(2005). Dance reveals symmetry especially in young men. Nature 438: T148-
T150.
Claussen J, Traulsen A (2005). Nongaussian fluctuations arising from finite populations: Exact results for the evolutionary Moran process. Phys
Rev E 71: 025101.
Doebeli M, C Hauert (2005). Models of cooperation based on the Prisoner's
Dilemma and the Snowdrift game. Ecol Lett 8: 748-766.
Feugier FG, A Mochizuki, Y Iwasa (2005). Self-organizing formation of vascular system of plant leaves: Co-orientation between auxin flux and
pump proteins. K HYPERLINK "http://dx.doi.org" ❑J theor BiolD 236: 366-
375.
Gerhart J, C Lowe, M Kirschner (2005). Hemichordates and the origin of
chordates. Curr Opin Genet Dev 15: 461-467. Gilligan DM, DA Briscoe, R
Frankham (2005). Comparative losses of quantitative and molecular genetic
variation in finite populations of Drosophila melanogaster. Genet Res 85:
47-55.
Gilligan DM, DA Briscoe, R Frankham (2005). Comparative losses of quantitative and molecular genetic variation in finite populations of
Drosophila melanogaster. Genet Res 85: 47-55.
Hale J, EP Stabler (2005). Strict deterministic aspects of minimalist grammars. In Logical Aspects of Computational Linguistics, ed. P Blache et
al. Springer LNCS-3492, 162-176.
Hauert C, G Szabo (2005). Game theory and physics. Am J Phys 73: 405-414.
Imhof LA (2005). Evolutionary game dynamics under stochastic influences.
Jahresbericht der DMV 107: 197-213.
Imhof LA (2005). The long-run behavior of the stochastic replicator dynamics. Ann Appl Probab 15: 1019-1045.
Imhof LA, D Fudenberg, MA Nowak (2005). Evolutionary cycles of cooperation
and defection. P Natl Acad Sci USA 102: 10797-10800.
Imhof LA, S Walcher (2005). Exclusion and persistence in deterministic and
stochastic chemostat models. K HYPERLINK "http://dx.doi.org" ❑J Differ
Equations' 217: 26-53.
Iwasa Y, F Michor, NL , MA Nowak (2005). Population genetics of tumor suppressor genes. J theor Biol 233: 15-23.
Iwasa Y, F Michor, MA Nowak (2005). Virus evolution within patients increases pathogenicity. J theor Biol 232: 17-26.
PROT6
Keenan EL, EP Stabler (2005). Linguistic invariants and language variation. In Logic, Methodology and Philosophy of Science, ed. P Hajek et
al. London: Kings College Publications, 395-411.
Lee Y, T Collier, C Taylor, EP Stabler (2005). The role of population structure in language evolution. In Proceedings of the 10th International
Symposium on Artificial Life and Robotics.
Lee Y, T Collier, EP Stabler, C Taylor (2005). Grammar structure and the
dynamics of language evolution. In Proceedings of the 8th European
Conference on Artificial Life.
Lieberman E, C Hauert, MA Nowak (2005). Evolutionary dynamics on graphs.
Nature 433: 312-316.
Lieberman E, C Hauert, MA Nowak (2005). Evolutionary dynamics on graphs.
Nature 433: 312-316.
Michor F (2005). Chromosomal instability and human cancer. Proc R Soc B
360: 631-635.
Michor F, TP Hughes, Y Iwasa, S Branford, NP Shah, CL Sawyers, MA Nowak
(2005). Dynamics of chronic myeloid leukemia. Nature 435: 1267-1270.
Michor F, Y Iwasa, C Lengauer, MA Nowak (2005). Dynamics of colorectal
cancer. Semin Cancer Biol 15: 484-493.
Michor F, Y Iwasa, C Lengauer, B Vogelstein, MA Nowak (2005). Can chromosomal instability initiate tumorigenesis? Semin Cancer Biol 15: 43-
49.
Michor PW, D Mumford (2005). Vanishing geodesic distance on spaces of submanifolds and diffeomorphisms. Documenta Math 10: 217-245.
Moret BME, J Tang, T Warnow (2005). Reconstructing phylogenies from gene-
content and gene-order data. In Mathematics of Evolution and Phylogeny,
ed. O Gascuel. Oxford: Oxford University Press, 321-352.
Nakamaru M, Y Iwasa (2005). The evolution of altruism by costly punishment
in the lattice structured population: Score-dependent viability versus
score-dependent fertility. Evol Ecol Rev 7: 853-870.
Nakhleh L, D Ringe, T Warnow (2005). Perfect phylogenetic networks: A new
methodology for reconstructing the evolutionary history of natural languages. Language 81: 382-420.
Nowak MA, NL
(2005). The evolution of altruism: From game theory
to human language. In Spiritual Information, ed. CL Harper. - HYPERLINK
"http://www.templetonpress.org/book.asp?book_ic*78" ❑Templeton Foundation
PressO, 308-314.
Nowak MA, K Sigmund (2005). Evolution of indirect reciprocity. Nature 427:
1291-1298.
Satake A, ON Bjornstad, Y Iwasa (2005). Invasibility of seed predators on
synchronized and intermittent seed production of host plants. In K
HYPERLINK lihttp://www.springer.com/cda/content/document/cda_downloaddocument/Life%20
Sciences.pdf?SGWID-0-0-45-281298-0" Conceptual Ecology and Invasions
Biology: Reciprocal Approaches to Nature, ed. MW Cadotte, SM McMahon, T
Fukami. Kluwer, Netherlands: Kluwer Academic Press, 281-298.
Slade P, J Wakeley (2005). The structured ancestral selection graph and
the many-demes limit. Genetics 169: 1117-1131.
Traulsen A, JC Claussen, C Hauert (2005). Coevolutionary dynamics: From
finite to infinite populations. Phys Rev Lett 95: 238701.
Traulsen A, AM Sengupta, MA Nowak (2005). Stochastic evolutionary dynamics
on two levels. J theor Biol 235: 393-401.
Trivers R (2005). Reciprocal altruism: 30 years later. In K HYPERLINK
"http://www.springer.com/west/home/life+sci/behavioural?SGWID•4-10029-22-
PROT7
67933787-0" ❑Cooperation in Primates and Humans:E Mechanisms and
Evolution, ed. CP van Schaik, PM Kappeler. Berlin: Springer-Verlag, 67-83.
Wakeley J (2005). The limits of theoretical population genetics. Genetics
169: 1-7.
Wedekind C, R Miller (2005). Risk-induced hatching in salmonids. Ecology
86: 2525-2529.
Wedekind C, R Miller (2005). The hatchery. B Ecol Soc USA 86: 124-125.
Wedekind C, M Walker, TJ Little (2005). The course of malaria in mice: MHC
effects, but no general MHC heterozygote advantage in single-strain infections. Genetics 170: 1427-1430.
Willensdorfer M, MA Nowak (2005). Mutation in evolutionary games can increase average fitness at equilibrium. J theor Biol 237: 355-362.
2006
Abbott LH, F Michor (2006). Mathematical models of targeted cancer therapy. Brit J Cancer 95: 1136-1141.
Antal T, PL Krapivsky (2006). Flows on graphs with random capacities. Phys
Rev E 74: 051110.
Brandt H, C Hauert, K Sigmund (2006). Punishing and abstaining for public
goods. P Natl Acad Sci USA 103: 495-497.
Burger R, KA Schneider (2006). Intraspecific competitive divergence and
convergence under assortative mating. Am Nat 167: 190-205.
BUrger R, KA Schneider, M Willensdorfer (2006). The conditions for speciation through intraspecific competition. Evolution 60: 2185-2206.
BUrger R, M Willensdorfer, MA Nowak (2006). Why are phenotypic mutation
rates much higher than genotypic mutation rates? Genetics 172: 197-206.
Boeckx C (2006). Linguistic Minimalism: Origins, Concepts, Methods, and
Aims. Oxford/New York: Oxford University Press.
Burt A, R Trivers (2006). Genes in Conflict: The Biology of Selfish
Genetic Elements. Cambridge, MA: Harvard University Press.
Dingli D, F Michor (2006). Successful therapy must eradicate cancer stem
cells. K HYPERLINK
"http://stemcells.alphamedpress.org/cgi/content/abstract/2006-0136v1"
-Stem CellsO 24: 2603-2610.
Dingli D, MA Nowak (2006). Infectious tumor cells. Nature 443: 35-36.
Dingli D, JM Pacheco (2006). Allometric scaling of the active hematopoietic stem cell pool across mammals. PLoS ONE 1: e2.
Doebeli M, C Hauert (2006). The limits of Hamilton's rule. J Evol Biol 19:
1386-1388.
Eldon B, J Wakeley (2006). Coalescent processes when the distribution of
offspring number among individuals is highly skewed. Genetics 172: 2621-
2633
Evans SN, D Ringe, T Warnow (2006). Inference of divergence times as a
statistical inverse problem. In Phylogenetic Methods and the Prehistory of
Languages, ed.. P Forster, C Renfrew. Series eds. C Scarre, DA Kemp.
McDonald Institute for Archaeological Research/University of Cambridge,
119-129.
Foster KR (2006). The Phoenix effect. Nature 441: 291-292.
Fudenberg D, LA Imhof (2006). Imitation processes with small mutations. J
Econ Theory 131: 251-262.
Fudenberg D, MA Nowak, C Taylor, LA Imhof (2006). Evolutionary game dynamics in finite populations with strong selection and weak mutation. K
HYPERLINK
"http://www.elsevier.com/wps/find/journaldescription.cws_home/622950/descr
iption" \l "description" ❑Theor Popul BiolD 70: 352-363.
PROT8
Ghirlanda S, M Enquist, M Nakamaru (2006). Cultural evolution develops its
own rules: The rise of conservatism and persuasion. Curr Anthro 47: 1027-
1034.
Haig D (2006). Intragenomic politics. Cytogenet Genome Res 113: 68-74.
Haig D (2006). Self-imposed silence: Parental antagonism and the evolution
of X-chromosome inactivation. Evolution 60: 440-447.
Hauert C (2006). Spatial effects in social dilemmas. J theor Biol 240:
627-636.
Hauert C, M Holmes, M Doebeli (2006). Evolutionary games and population
dynamics: Maintenance of cooperation in public goods games. Proc R Soc B
273: 2565-2570.
Hauert C, F Michor, MA Nowak, M Doebeli (2006). Synergy and discounting of
cooperation in social dilemmas. J theor Biol 239: 195-202.
Imhof LA, MA Nowak (2006). Evolutionary game dynamics in a Wright-Fisher
process. J Math Biol 52: 667-681.
Iwasa Y, MA Nowak, F Michor (2006). Evolution of resistance during clonal
expansion. Genetics 172: 2557-2566.
Matsen FA, J Wakeley (2006). Convergence to the island-model coalescent
process in populations with restricted migration. Genetics 172: 701-708.
Michor F, Y Iwasa, MA Nowak (2006). The age incidence of chronic myeloid
leukemia can be explained by a one-mutation model. P Natl Acad Sci USA
103: 14931-14934.
Michor F, MA Nowak, Y Iwasa (2006). Evolution of resistance to cancer therapy. Curr Pharm Design 12: 261-271.
Michor F, MA Nowak, Y Iwasa (2006). Stochastic dynamics of metastasis formation. J theor Biol 240: 521-530.
Michor PW, D Mumford (2006). Riemannian geometries on spaces of plane curves. J Eur Math Soc 8: 1-48.
Nowak MA (2006). Evolutionary Dynamics. Cambridge, MA: Harvard University
Press.
Nowak MA (2006). Five rules for the evolution of cooperation. Science 314:
1560-1563.
Nowak MA, F Michor, Y Iwasa (2006). Genetic instability and clonal expansion. J theor Biol 241: 26-32.
Ohtsuki H, C Hauert, E Lieberman, MA Nowak (2006). A simple rule for the
evolution of cooperation on graphs and social networks. K HYPERLINK lihttp://www.nature.cominature/journal/v441/n7092/absinature04605.html"
ONature I 441: 502-505.
Ohtsuki H, Y Iwasa (2006). The leading eight: Social norms that can maintain cooperation by indirect reciprocity. J theor Biol 239: 435-444.
Ohtsuki H, MA Nowak (2006). Evolutionary games on cycles. Proc R Soc B
273: 2249-2256.
Ohtsuki H, MA Nowak (2006). The replicator equation on graphs. J theor
Biol 243: 86-97.
Pacheco JM, A Traulsen, MA Nowak (2006). Active linking in evolutionary
games. J theor Biol 243: 437-443.
Pacheco JM, A Traulsen, MA Nowak (2006). Coevolution of strategy and structure in complex networks with dynamical linking. Phys Rev Lett 97:
258103.
Pfeiffer T, MA Nowak (2006). Climate change: All in the game. K HYPERLINK
"http://www.nature.com/nature/journal/v441/n7093/index.html" nNatureD 441:
583-584.
Pfeiffer T, MA Nowak (2006). Digital cows grazing on digital grounds. Curr
Biol 16: R946-R949.
PROT9
Rulicke T, N Guncz, C Wedekind (2006). Early maternal investment in mice:
No evidence for `compatible-genes' sexual selection despite hybrid vigor.
J Evol Biol 19: 922-928.
Santos FC, JM Pacheco, T Lenaerts (2006). Cooperation prevails when individuals adjust their social ties. PLoS Comput Biol 2: e140.
Santos FC, JM Pacheco, T Lenaerts (2006). Evolutionary dynamics of social
dilemmas in structured heterogeneous populations. P Natl Acad Sci USA 103:
3490-3494.
Taylor C, Y Iwasa, MA Nowak (2006). A symmetry of fixation times in evolutionary dynamics. J theor Biol 243: 245-251.
Taylor C, MA Nowak (2006). Evolutionary game dynamics with non-uniform
interaction rates. Theor Popul Biol 69: 243-252.
Traulsen A, JC Claussen, C Hauert (2006). Coevolutionary dynamics in large
but finite populations. Phys Rev E 74: 011901.
Traulsen A, MA Nowak (2006). Evolution of cooperation by multilevel selection. P Natl Acad Sci USA 103: 10952-10955.
Traulsen A, MA Nowak, J Pacheco (2006). Stochastic dynamics of invasion
and fixation. Phys Rev E 74: 011909.
Traulsen A, JM Pacheco, L Imhof (2006). Stochasticity and evolutionary
stability. Phys Rev E 74: 021905.
Trivers R, JT Manning, A Jacobson (2006). A longitudinal study of digit
ratio (2D:4D) and other finger ratios in Jamaican children. Horm Behav 49:
150-156.
Warnow T, SN Evans, D Ringe, L Nakhleh (2006). A stochastic model of language evolution that incorporates homoplasy and borrowing. In
Phylogenetic Methods and the Prehistory of Languages, eds. P Forster, C
Renfrew. Series eds. C Scarre, DA Kemp. McDonald Institute for
Archaeological Research/University of Cambridge, 75-87.
2007
Antal T, I Bena, M Droz, K Martens, Z Racz (2007). Guiding-fields for phase-separation: Controlling liesegang patterns. Phys Rev E 76: 046203.
Antal T, KB Blagoev, SA Trugman, S Redner (2007). Aging and immortality in
a cell proliferation model. J theor Biol 248: 411-417.
Antal T, PL Krapivsky (2007). Molecular spiders with memory. Phys Rev E
76: 021121.
Antal T, PL Krapivsky, K Mallick (2007). Molecular spiders in one dimension. J Stat Mech-Theory E: P08027.
Antal T, PL Krapivsky, S Redner, M Mailman, B Chakraborty (2007). Dynamics
of an idealized model of microtubule growth and catastrophe. Phys Rev E
76: 041907.
Beerenwinkel N, T Antal, D Dingli, A Traulsen, KW Kinzler, VE Velculescu,
B Vogelstein, MA Nowak (2007). Genetic progression and the waiting time to
cancer. PLoS Comput Biol 3: e225.
Brandt H, H Ohtsuki, Y Iwasa, K Sigmund (2007). A survey of indirect reciprocity. In Mathematics for Ecology and Evolution, eds. Y Takeuchi, Y
Iwasa, K Sato. Berlin: Springer, 21-50.
Burnham TC (2007). High-testosterone men reject low ultimatum game offers.
Proc R Soc B 274: 2327-2330.
Burnham TC, B Hare (2007). Engineering human cooperation. Hum Nat 18: 88-
108.
Dingli D, F Michor, T Antal, JM Pacheco (2007). The emergence of tumor
metastases. Cancer Biol Ther 6: el-e8.
Dingli D, JM Pacheco (2007). Ontogenic growth of the haematopoietic stem
cell pool in humans. Proc R Soc B 274: 2497-2501.
PROT10
Dingli D, JM Pacheco, A Dispenzieri, S Hayman, S Kumar, M Lacy, D
Gastineau, M Gertz (2007). In vivo and in silica studies on single versus
multiple transplants for multiple myeloma. Cancer Sci 98: 734-739.
Dingli D, A Traulsen, F Michor (2007). (A)Symmetric stem cell replication
and cancer. PLoS Comput Biol 3: e53.
Dingli D, A Traulsen, JM Pacheco (2007). Stochastic dynamics of hematopoietic tumor stem cells. Cell Cycle 6: el-e6.
Dingli D, A Traulsen, JM Pacheco (2007). Compartmental architecture and
dynamics of hematopoiesis. PLoS One 2: e345.
D'Orsogna MR, T Chou, T Antal (2007). Exact steady-state velocity of ratchets driven by random sequential absorption. J Phys A: Math Theor 40:
5575-5584.
Hauert C, A Traulsen, H Brandt, MA Nowak, K Sigmund (2007). Via freedom to
coercion: The emergence of costly punishment. Science 316: 1905-1907.
Imhof LA, D Fudenberg, MA Nowak (2007). Tit-for-tat or win-stay, lose-
shift? J theor Biol 247: 574-580.
Iwasa Y, F Michor, MA Nowak (2007). Directional evolution of virus within
a host under immune selection. In Mathematics for Life Science and
Medicine, eds. Y Takeuchi, Y Iwasa, K Sato. Springer: New York.
Lieberman E, JB Michel, J Jackson, T Tang, MA Nowak (2007). Quantifying
the evolutionary dynamics of language. Nature 449: 713-716.
Lopes JV, JM Pacheco, D Dingli (2007). Acquired hematopoietic stem-cell
disorders and mammalian size. Blood 110: 4120-4122.
Masuda N, H Ohtsuki (2007). Tag-based indirect reciprocity by incomplete
social information. Proc R Soc B 274: 689-695.
Nowak MA, S Roch (2007). Upstream reciprocity and the evolution of gratitude. O HYPERLINK
"http://www.journals.royalsoc.ac.uk/openurl.asp?genreearticle&id•doi:10.10
98/rspb.2006.0125" OProc R Soc BO 274: 605-609.
Nowak MA, K Sigmund (2007). How populations cohere: Five rules for cooperation. In Theoretical Ecology: Principles and Applications, eds. RM
May, A McLean. Oxford: Oxford University Press, 7-16.
Ohtsuki H, P Bordalo, MA Nowak (2007). The one third law of evolutionary
dynamics. J theor Biol 249: 289-295.
Ohtsuki H, Y Iwasa (2007). Global analyses of evolutionary dynamics and
exhaustive search for social norms that maintain cooperation by reputation. J theor Biol 244: 518-531.
Ohtsuki H, MA Nowak (2007). Direct reciprocity on graphs. J theor Biol
247: 462-470.
Ohtsuki H, J Pacheco, MA Nowak (2007). Evolutionary graph theory: Breaking
the symmetry between interaction and replacement. J theor Biol 246: 681-
694.
Ohtsuki H, J Pacheco, MA Nowak (2007). Breaking the symmetry between interaction and replacement in evolutionary dynamics on graphs. Phys Rev
Lett 98: 108106.
Pfeiffer T, R Hoffman (2007). Temporal patterns of genes in scientific
publications. P Natl Acad Sci USA 104: 12052-12056.
Pinker S (2007). Games people play. In The Stuff of Thought: Language as a
Window Into Human Nature. New York: Viking Press.
Roehl T, C Roehl, HG Schuster, A Traulsen (2007). The impact of fraud on
the mean-field dynamics of cooperative social systems. Phys Rev E 76:
026114.
PROT11
Steiner UK, T Pfeiffer (2007). Optimizing time and resource allocation
trade-offs for investment in morphological and behavioral defense. Am Nat
169: 118-129.
Taylor C, J Chen, Y Iwasa (2007). Cooperation maintained by fitness adjustment. Evol Ecol Res 9: 1023-1041.
Taylor C, MA Nowak (2007). Transforming the dilemma. Evolution 61: 2281-
2292.
Traulsen A, Y Iwasa, MA Nowak (2007). The fastest evolutionary trajectory.
J theor Biol 249: 617-623.
Traulsen A, MA Nowak (2007). Chromodynamics of cooperation in finite populations. PLoS ONE 2: e270.
Traulsen A, MA Nowak, J Pacheco (2007). Stochastic payoff evaluation increases the temperature of selection. J theor Biol 244: 349-356.
Traulsen A, JM Pacheco, D Dingli (2007). On the origin of multiple mutant
clones in paroxysmal nocturnal hemoglobinuria. Stem Cells 25: 3081-3084.
Traulsen A, JM Pacheco, MA Nowak (2007). Pairwise comparison and selection
temperature in evolutionary game dynamics. J theor Biol 246: 522-529.
Uehara T, Y Iwasa, H Ohtsuki (2007). ESS distribution of display duration
in animal contests to assess an opponent before fighting or fleeing. Evol
Ecol Res 9: 395-408.
Wild G, A Traulsen (2007). The different limits of weak selection and the
evolutionary dynamics of finite populations. J theor Biol 247: 382-390.
Willensdorfer M, R Burger, MA Nowak (2007). Phenotypic mutation rates and
the abundance of abnormal proteins in yeast. PLoS Comput Biol 3: e203.
Worden L, SA Levin (2007). Evolutionary escape from the prisoner's dilemma. J theor Biol 245: 411-422.
2008
Apicella CL, A Dreber, B Campbell, PB Gray, M Hoffman, AC Little (2008).
Testosterone and financial risk preferences. Evol Hum Behav 29: 384-390.
Bomze I, C Pawlowitsch (2008). One-third rules with equality: Second-order
evolutionary stability conditions in finite populations. J theor Biol 254:
616-620.
Dingli D, MA Nowak (2008). Evolutionary dynamics of cancer. Book review of
Dynamics of Cancer: Incidence, Inheritance, and Evolution, SA Frank.
Trends Ecol Evol 23: 254-255.
Dreber A, M Johannesson (2008). Gender differences in deception. Econ Lett
99: 197-199.
Dreber A, MA Nowak (2008). Gambling for global goods. P Natl Acad Sci USA
105: 2261-2262.
Dreber A, DG Rand, D Fudenberg, MA Nowak (2008). Winners don't punish.
Nature 452: 348-351.
Fu F, C Hauert, MA Nowak, L Wang (2008). Reputation-based partner choice
promotes cooperation in social networks. Phys Rev E 78: 026117. appears
in Vir J Bio Phys Res 16(5).
Goldstein R, J Almenberg, A Dreber, JW Emerson, A Herschkowitsch, J Katz
(2008). Do more expensive wines taste better? Evidence from a large sample
of blind tastings. J Wine Econ 3: 1-9.
Hauert C, A Traulsen, H Brandt, MA Nowak, K Sigmund (2008). Public goods
with punishment and abstaining in finite and infinite populations.
Biological Theory 3(2): 114-122.
Hauert C, JY Wakano, M Doebeli (2008). Ecological public goods games:
Cooperation and bifurcation. Theor Popul Biol 73: 257-263.
Jones 5, W Chen, G Parmigiani, F Diehl, N Beerenwinkel, T Antal, A
Traulsen, MA Nowak, C Siegel, VE Velculescu, KW Kinzler, B Vogelstein, J
PROT12
Willis, SD Markowitz (2008). Comparative lesion sequencing provides insights into tumor evolution. P Natl Acad Sci USA 105: 4283-4288.
Langer P, MA Nowak, C Hauert (2008). Spatial invasion of cooperation. J
theor Biol 250: 634-641.
Michel JB, PJ Yeh, R Chait, RC Moellering, R Kishony (2008). Drug interactions modulate the potential for evolution of resistance. P Natl
Acad Sci USA 105: 14918-14923.
Nowak MA (2008). Generosity: A winner's advice. Nature. 456: 579.
Nowak MA, H Ohtsuki (2008). Prevolutionary dynamics and the origin of evolution. P Natl Acad Sci USA 105: 14924-14927.
Ohtsuki H, MA Nowak (2008). Evolutionary stability on graphs. J theor Biol
251: 698-707.
Pacheco JM, A Traulsen, H Ohtsuki, MA Nowak (2008). Repeated games and
direct reciprocity under active linking. J theor Biol 250: 723-731.
Peischl 5, R BUrger (2008). Evolution of dominance under frequencydependent intraspecific competition. J theor Biol 251: 210-226.
Pinker 5, MA Nowak, JJ Lee (2008). The logic of indirect speech. P Natl
Acad Sci USA 105: 833-838.
Schuster S, JU Kreft, A Schroeter, T Pfeiffer (2008). Use of gametheoretical methods in biochemistry and biophysics. J Biol Phys. 34: 1-17.
Schuster S, T Pfeiffer, DA Fell (2008). Is maximization of molar yield in
metabolic networks a universal principle? J Theor Biol. 252: 497-504.
Traulsen A, N Shoresh, MA Nowak (2008). Analytical results for individual
and group selection of any intensity. B Math Biol 70: 1410-1424.
Willensdorfer M (2008). Organism size promotes the evolution of specialized cells in multicellular digital organisms. J Evol Biol 21: 104-
110.
2009
Almenberg J, K Kittlitz, T Pfeiffer(2009). An experiment on prediction
markets in science. PLoS ONE 4: e8500.
Antal T, H Ohtsuki, J Wakeley, PD Taylor, MA Nowak (2009). Evolution of
cooperation by phenotypic similarity. P Natl Acad Sci USA 106: 8597-8600.
Antal T, MA Nowak, A Traulsen (2009). Strategy abundance in 2x2 games for
arbitrary mutation rates. J theor Biol 257: 340-344.
Antal T, A Traulsen, H Ohtsuki, CE Tarnita, MA Nowak (2009). Mutation-
selection equilibrium in games with multiple strategies. J theor Biol 258:
614-622.
BUrger R (2009). Multilocus selection in subdivided populations I:
Convergence properties for weak or strong migration. J Math Biol 58: 939-
978.
BUrger R (2009). Multilocus selection in subdivided populations II:
Maintenance of polymorphism under weak or strong migration. J Math Biol
58: 979-997.
BUrger R (2009). Polymorphism in the two-locus Levene model with nonepistatic directional selection. Theor Popul Biol 76: 214-228.
Dingli D, T Antal, A Traulsen, JM Pacheco (2009). Progenitor cell self-
renewal and cyclic neutropenia. Cell proliferation 42: 330-338.
Dreber A, CL Apicella, DTA Eisenberg, JR Garcia, RS Zamore, JK Lum, B
Campbell (2009). The 7R polymorphism in the dopamine receptor D4 gene
(DRD4) is associated with financial risk taking in men. Evol Hum Behav 30:
85-92
Fu F, L Wang, MA Nowak, C Hauert (2009). Evolutionary dynamics on graphs:
Efficient method for weak selection. Phys Rev E 79: 046707.
PROT13
Gokhale CS, Y Iwasa, MA Nowak, A Traulsen (2009). The pace of evolution
across fitness valleys. J theor Biol 259: 613-620.
Lieberman E, NL Berkum, L Williams, M Imakaev, T Ragoczy, A Telling, I
Amit, BR Lajoie, PJ Sabo, MO Dorschner, R Sandstrom, B Bernstein, MA
Bender, M Groudine, A Gnirke, J Stamatoyannopoulos, LA Mirny, ES Lander, J
Dekker (2009). Comprehensive Mapping of Long-Range Interactions Reveals
Folding Principles of the Human Genome. Science 326: 289-293.
Manapat M, H Ohtsuki, R Burger, MA Nowak (2009). Originator dynamics. J
theor Biol 256: 586-595.
Nathanson CG, CE Tarnita, MA Nowak (2009). Calculating evolutionary dynamics in structured populations. PLoS Comput Biol 5: e1000615.
Novak M, T Pfeiffer, M Ackermann, S Bonhoeffer (2009). Bacterial growth
properties at low optical densities. Antonie van Leeuwenhoek 96: 267-274.
Ohtsuki H, Y Iwasa, MA Nowak (2009). Indirect reciprocity provides only a
narrow margin of efficiency for costly punishment. Nature 457: 79-82.
Ohtsuki H, MA Nowak (2009). Prelife catalysts and replicators. Proc R Soc
B 276: 3783-3790.
Pfeiffer T, R Hoffmann (2009). Large-scale assessment of the effect of
popularity on the reliability of research. PLoS ONE 4: e5996.
Pfeiffer T, D Rand, A Dreber (2009). Decision-making in research tasks
with sequential testing. PLoS ONE 4: e4607.
Rand DG, A Dreber, T Ellingsen, D Fudenberg, MA Nowak (2009). Positive
interactions promote public cooperation. Science 325: 1272-1275.
Rand DG, A Dreber, T Ellingsen, D Fudenberg, MA Nowak (2009). Weighing
Reward and Punishment - Response. Science 326: 1632-1633.
Rand DG, MA Nowak (2009). Name and shame: How reputation could save the
Earth. New Scientist 2734: 28-29.
Rand DG, H Ohtsuki, MA Nowak (2009). Direct reciprocity with costly punishment: Generous tit-for-tat prevails. J theor Biol 256: 45-57.
Rand DG, T Pfeiffer (2009). Systematic differences in impact across publication tracks at PNAS. PLoS ONE 4: e8092.
Rand DG, T Pfeiffer, A Dreher, RW Sheketoff, NC Wernerfelt, Y Benkler
(2009). Dynamic remodeling of in-group bias during the 2008 presidential
election. P Natl Acad Sci USA 106: 6187-6191.
Rutte C, T Pfeiffer (2009). Evolution of reciprocal altruism by copying of
observed behavior. Current Science 97: 1573-1578.
Tarnita CE, T Antal, MA Nowak (2009). Mutation-selection equilibrium in
games with mixed strategies. J theor Biol 261: 50-57.
Tarnita CE, T Antal, H Ohtsuki, MA Nowak (2009). Evolutionary dynamics in
set structured populations. P Natl Acad Sci USA 106: 8601-8604.
Tarnita CE, H Ohtsuki,T Antal, F Fu, MA Nowak (2009). Strategy selection
in structured populations. J theor Biol 259: 570-581.
Taylor C, MA Nowak (2009). How to evolve cooperation. pages 41-56. In
Games, Groups, and the Global Good, ed. S Levin. New York: Springer.
Traulsen A, C Hauert, H Brandt De Silva, MA Nowak, K Sigmund (2009).
Exploration dynamics in evolutionary games. P Natl Acad Sci USA 106: 709-
712.
Tu K, DG Cooper, HT Siegelmann (2009). Memory reconsolidation for natural
language processing. Cogn Neurodyn 3: 365-372.
Wakano JY, MA Nowak, C Hauert (2009). Spatial dynamics of ecological public goods. P Natl Acad Sci USA 106: 7910-7914.
Woelfing B, A Traulsen, M Milinski, T Boehm (2009). Does intra-individual
major histocompatibility complex diversity keep a golden mean? Phil Trans
R Soc B 364: 117-128.
PROT14
2010
Imhof LA, MA Nowak (2010). Stochastic evolutionary dynamics of direct reciprocity. Proc R Soc B 277: 463-468.
Manapat ML, IA Chen, MA Nowak (2010). The basic reproductive ratio of life. J theor Biol 263: 317-327.
Nowak MA, CE Tarnita, T Antal (2010). Evolutionary dynamics in structured
populations. Phil Trans R Soc B 365: 19-30.
Ojosnegros 5, N Beerenwinkel, T Antal, MA Nowak, C Escarmis, E Domingo
(2010). Competition-colonization dynamics in an RNA virus. P Natl Acad Sci
USA 107: 2108-2112.
Rajamani 5, JK Ichida, T Antal, DA Treco, K Leu, MA Nowak, JW Szostak, IA
Chen (2010). Offset of the error catastrophe in non-enzymatic nucleic acid
replication. J Am Chem Soc (in press).
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PROT101
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PROT102
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PROT103
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PROT104
chic B*0CJO WIlaaJE ph !DhSt
PROT105
ohyo 03O B*DCJO aJO ph
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PROT106
DhSt
PROT107
00hSt
PROT108
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PROT109
C OC hC iC jC kC z.0
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5OOB*OCJO \OOaJO ph OhSt
PROT110
DhSt
PROT111
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PROT112
OhyO 030 B*DCJO aJO ph
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PROT113
0h2O B*OCJO aJD ph
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PROT114
0h90 B*DCJD UDIDaJE ph
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PROT115
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PROT116
ohyo B*DCJO UCCIaJD ph
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PROT117
0h20 B*OCJO MaaJE ph DhSt
PROT118
O0hSt
PROT119
0h20 B*EICJO aJD ph +2L YL OL
PROT120
M IM *M °N ±N P UP aP A03060Ao
OM 1M 5M >M ?M MM NM tM "M •M 111.1 /N ON EN IN -N
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PROT121
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PROT122
DhSt
PROT123
DhSt
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00hSt
PROT125
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B*DCJD aJD ph $DhSt
PROT126
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PROT127
00hSt
PROT128
OhSt
PROT129
DhSt
PROT130
ohyo- B*OCJO ]DiDaJD ph <-W °W 'W
DX DX DX OX qX }X ,X iX Ax cx yX Y OY DY OY 'Y aY OY 'Y °Y EY
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PROT131
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PROT132
ohyo B*OCJO UE0aJE ph oohyo ipocso aJO ph 0OhSt
PROT133
OhSt
PROT134
DhSt
PROT135
Oh20 B*DCJD MIDaJD ph 00h90- B*DCJD )0DaJD ph 8h1 A\ [] Ill
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PROT136
DhSt
PROT137
00hSt
PROT138
Dh2D B*DCJD aJ0 ph 5ih )i Ai 'j 0k 'k 1 Al Cm On ,n Do -'o Kp Ep Cq Oci
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PROT139
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PROT141
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PROT142
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PROT143
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PROT144
DhSt
PROT145
00hSt
PROT146
❑hy0 B*DC.30 aJO ph
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PROT148
Ohk0 500B*OCJO aJO ph [Cho
PROT149
Ohk0 500CJO aJO 00h0
PROT150
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[repeated 20 times]
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A ❑6 06 06 '6 e
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[repeated 9 times]
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PROT156
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PROT158
PROT159
PROT160
PROT161
PROT162
PROT163
PROT164
PROT165
O
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PROT192
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