Now showing items 1-20 of 108

    • Abstract 2374: Reconstructing the evolutionary history of metastatic cancers 

      Reiter, Johannes; Makohon-Moore, Alvin P.; Gerold, Jeffrey; Bozic, Ivana; Chatterjee, Krishnendu; Iacobuzio-Donahue, Christine A.; Vogelstein, Bert; Nowak, Martin A. (American Association for Cancer Research (AACR), 2016)
      Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic ...
    • Accumulation of Driver and Passenger Mutations During Tumor Progression 

      Bozic, Ivana; Antal, Tibor; Ohtsuki, Hisashi; Carter, Hannah; Kim, Dewey; Chen, Sining; Karchin, Rachel; Kinzler, Kenneth; Vogelstein, Bert; Nowak, Martin A. (National Academy of Sciences, 2010)
      Major efforts to sequence cancer genomes are now occurring throughout the world. Though the emerging data from these studies are illuminating, their reconciliation with epidemiologic and clinical observations poses a major ...
    • Adaptive Dynamics of Extortion and Compliance 

      Hilbe, Christian; Nowak, Martin A.; Traulsen, Arne (Public Library of Science, 2013)
      Direct reciprocity is a mechanism for the evolution of cooperation. For the iterated prisoner’s dilemma, a new class of strategies has recently been described, the so-called zero-determinant strategies. Using such a strategy, ...
    • Amplification on Undirected Population Structures: Comets Beat Stars 

      Pavlogiannis, Andreas; Tkadlec, Josef; Chatterjee, Krishnendu; Nowak, Martin A. (Springer Nature, 2017)
      The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and ...
    • Analytical Results for Individual and Group Selection of Any Intensity 

      Traulsen, Arne; Shoresh, Noam; Nowak, Martin A. (Springer Verlag, 2008)
      The idea of evolutionary game theory is to relate the payoff of a game to reproductive success (= fitness). An underlying assumption in most models is that fitness is a linear function of the payoff. For stochastic ...
    • Antiretroviral dynamics determines HIV evolution and predicts therapy outcome 

      Rosenbloom, Daniel Scholes; Hill, Alison Lynn; Rabi, S. Alireza; Siliciano, Robert F.; Nowak, Martin A. (Nature Publishing Group, 2012)
      Despite the high inhibition of viral replication achieved by current anti-HIV drugs, many patients fail treatment, often with emergence of drug-resistant virus. Clinical observations show that the relationship between ...
    • The Basic Reproductive Ratio of Life 

      Manapat, Michael L.; Chen, Irene Ann; Nowak, Martin A. (Elsevier, 2010)
      Template-directed polymerization of nucleotides is believed to be a pathway for the replication of genetic material in the earliest cells. We assume that activated monomers are produced by prebiotic chemistry. These monomers ...
    • Breaking the Symmetry Between Interaction and Replacement in Evolutionary Dynamics on Graphs 

      Ohtsuki, Hisashi; Nowak, Martin A.; Pacheco, Jorge M. (American Physical Society, 2007)
      We study the evolution of cooperation modeled as symmetric 2×2 games in a population whose structure is split into an interaction graph defining who plays with whom and a replacement graph specifying evolutionary competition. ...
    • Calculating Evolutionary Dynamics in Structured Populations 

      Nathanson, Charles Gordon; Tarnita, Corina Elena; Nowak, Martin A. (Public Library of Science, 2009)
      Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a ...
    • Cancer Biology: Infectious Tumour Cells 

      Dingli, David; Nowak, Martin A. (Nature Publishing Group, 2006)
      Cancer cells are generally viewed as a problem innate to their host, but evidence is mounting that they can evolve to become infectious agents and be transmitted between individuals. The current view of cancer development ...
    • Cellular cooperation with shift updating and repulsion 

      Pavlogiannis, Andreas; Chatterjee, Krishnendu; Adlam, Ben; Nowak, Martin A. (Nature Publishing Group, 2015)
      Population structure can facilitate evolution of cooperation. In a structured population, cooperators can form clusters which resist exploitation by defectors. Recently, it was observed that a shift update rule is an ...
    • Challenging Cooperation: Inequality, Global Commons, Future Generations 

      Hauser, Oliver Paul (2016-04-25)
      Cooperation is abundant in the world around us, spanning all levels of biological and social organisation. Yet the existence and maintenance of cooperation is puzzling from an evolutionary perspective because the costs ...
    • Chromodynamics of Cooperation in Finite Populations 

      Traulsen, Arne; Nowak, Martin (Public Library of Science, 2007)
      Background: The basic idea of tag-based models for cooperation is that individuals recognize each other via arbitrary signals, so-called tags. If there are tags of different colors, then cooperators can always establish ...
    • Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition 

      Burger, Jan A.; Landau, Dan A.; Taylor-Weiner, Amaro; Bozic, Ivana; Zhang, Huidan; Sarosiek, Kristopher; Wang, Lili; Stewart, Chip; Fan, Jean; Hoellenriegel, Julia; Sivina, Mariela; Dubuc, Adrian M.; Fraser, Cameron; Han, Yulong; Li, Shuqiang; Livak, Kenneth J.; Zou, Lihua; Wan, Youzhong; Konoplev, Sergej; Sougnez, Carrie; Brown, Jennifer R.; Abruzzo, Lynne V.; Carter, Scott L.; Keating, Michael J.; Davids, Matthew S.; Wierda, William G.; Cibulskis, Kristian; Zenz, Thorsten; Werner, Lillian; Cin, Paola Dal; Kharchencko, Peter; Neuberg, Donna; Kantarjian, Hagop; Lander, Eric; Gabriel, Stacey; O'Brien, Susan; Letai, Anthony; Weitz, David A.; Nowak, Martin A.; Getz, Gad; Wu, Catherine J. (Nature Publishing Group, 2016)
      Resistance to the Bruton's tyrosine kinase (BTK) inhibitor ibrutinib has been attributed solely to mutations in BTK and related pathway molecules. Using whole-exome and deep-targeted sequencing, we dissect evolution of ...
    • Comparative Lesion Sequencing Provides Insights into Tumor Evolution 

      Jones, Siân; Chen, Wei-dong; Parmigiani, Giovanni; Diehl, Frank; Beerenwinkel, Niko; Antal, Tibor; Traulsen, Arne; Nowak, Martin A.; Siegel, Christopher; Velculescu, Victor E.; Kinzler, Kenneth W.; Vogelstein, Bert; Willis, Joseph; Markowitz, Sanford D. (Proceedings of the National Academy of Sciences, 2008)
      We show that the times separating the birth of benign, invasive, and metastatic tumor cells can be determined by analysis of the mutations they have in common. When combined with prior clinical observations, these analyses ...
    • Comparing reactive and memory-one strategies of direct reciprocity 

      Baek, Seung Ki; Jeong, Hyeong-Chai; Hilbe, Christian; Nowak, Martin A. (Nature Publishing Group, 2016)
      Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be ...
    • Competition-Colonization Dynamics in an RNA Virus 

      Ojosnegros, Samuel; Beerenwinkel, Niko; Antal, Tibor; Nowak, Martin A.; Escarmis, Christina; Domingo, Esteban (National Academy of Sciences, 2010)
      During replication, RNA viruses rapidly generate diverse mutant progeny which differ in their ability to kill host cells. We report that the progeny of a single RNA viral genome diversified during hundreds of passages in ...
    • Cooperate without looking: Why we care what people think and not just what they do 

      Hoffman, Moshe H.; Yoeli, Erez; Nowak, Martin A. (Proceedings of the National Academy of Sciences, 2015)
      Evolutionary game theory typically focuses on actions but ignores motives. Here, we introduce a model that takes into account the motive behind the action. A crucial question is why do we trust people more who cooperate ...
    • Cooperation and the Fate of Microbial Societies 

      Allen, Benjamin Isaac; Nowak, Martin A. (Public Library of Science, 2013)
      Microorganisms have been cooperating with each other for billions of years: by sharing resources, communicating with each other, and joining together to form biofilms and other large structures. These cooperative behaviors ...
    • Direct Reciprocity on Graphs 

      Ohtsuki, Hisashi; Nowak, Martin A. (Elsevier, 2007)
      Direct reciprocity is a mechanism for the evolution of cooperation based on the idea of repeated encounters between the same two individuals. Here we examine direct reciprocity in structured populations, where individuals ...