| fc38a875 |
@article{Yuan2012,
title = {An {{Overview}} of {{Population Genetic Data Simulation}}},
volume = {19},
issn = {1066-5277},
doi = {10.1089/cmb.2010.0188},
number = {1},
journal = {Journal of Computational Biology},
author = {Yuan, Xiguo and Miller, David J. and Zhang, Junying and Herrington, David and Wang, Yue},
year = {2012},
pages = {42--54},
mendid = {18055},
pmid = {22149682}
}
@book{nowak_evolutionary_2006,
address = {Cambridge, Mass.},
title = {Evolutionary Dynamics: Exploring the Equations of Life},
isbn = {978-0-674-02338-3},
shorttitle = {Evolutionary Dynamics},
publisher = {{Belknap Press of Harvard University Press}},
author = {Nowak, M. A},
year = {2006}
}
|
| c95df82d |
@article{Hothorn_2006,
title = {A Lego System for Conditional Inference},
author = {Torsten Hothorn and Kurt Hornik and Mark A. van de Wiel
and Achim Zeileis},
journal = {The American Statistician},
year = {2006},
volume = {60},
number = {3},
pages = {257--263},
}
|
| 2f97de14 |
|
| c95df82d |
@article{Hothorn_2008,
title = {Implementing a Class of Permutation Tests: The {coin}
Package},
author = {Torsten Hothorn and Kurt Hornik and Mark A. van de Wiel
and Achim Zeileis},
journal = {Journal of Statistical Software},
year = {2008},
volume = {28},
number = {8},
pages = {1--23},
url = {http://www.jstatsoft.org/v28/i08/},
}
|
| 2f97de14 |
@article{Desper1999JCB,
author = {Desper, R and Jiang, F and Kallioniemi, O P and
Moch, H and Papadimitriou, C H and Sch\"{a}ffer, A A},
journal = {J Comput Biol},
number = {1},
pages = {37--51},
title = {{Inferring tree models for oncogenesis from
comparative genome hybridization data.}},
volume = {6},
year = {1999},
|
| 50a94207 |
issn = {1066-5277},
|
| 2f97de14 |
url = {http://view.ncbi.nlm.nih.gov/pubmed/10223663},
}
@incollection{Szabo2008,
author = {Szabo, A and Boucher, Kenneth M},
booktitle = {Handbook of cancer models with applications},
chapter = {1},
editor = {Tan, W-Y and Hanin, L},
pages = {1--24},
publisher = {World Scientific},
title = {{Oncogenetic trees}},
year = {2008},
url = {http://www.worldscibooks.com/lifesci/6677.html},
}
@article{Beerenwinkel2007,
author = {Beerenwinkel, Niko and Eriksson, Nicholas and
Sturmfels, Bernd},
journal = {Bernoulli},
month = nov,
number = {4},
pages = {893--909},
title = {{Conjunctive Bayesian networks}},
volume = {13},
year = {2007},
doi = {10.3150/07-BEJ6133},
issn = {1350-7265},
url = {http://projecteuclid.org/euclid.bj/1194625594},
}
|
| 6610ac26 |
@article{Farahani2013,
author = {Farahani, H and Lagergren, J},
journal = {PloS one},
month = jan,
number = {6},
pages = {e65773},
title = {{Learning oncogenetic networks by reducing to mixed
integer linear programming.}},
volume = {8},
year = {2013},
doi = {10.1371/journal.pone.0065773},
issn = {1932-6203},
url = {http://www.pubmedcentral.nih.gov/},
}
|
| 2f97de14 |
@article{Gerstung2009,
author = {Gerstung, Moritz and Baudis, Michael and Moch, Holger and
Beerenwinkel, Niko},
journal = {Bioinformatics (Oxford, England)},
month = nov,
number = {21},
pages = {2809--2815},
title = {{Quantifying cancer progression with conjunctive
Bayesian networks.}},
volume = {25},
year = {2009},
doi = {10.1093/bioinformatics/btp505},
issn = {1367-4811},
|
| e693f153 |
url = {http://dx.doi.org/10.1093/bioinformatics/btp505 http://
www.bsse.ethz.ch/cbg/software/ct-cbn},
|
| 2f97de14 |
}
@article{Gerstung2011,
author = {Gerstung, Moritz and Eriksson, Nicholas and
Lin, Jimmy and Vogelstein, Bert and
Beerenwinkel, Niko},
journal = {PLoS ONE},
month = nov,
number = {11},
pages = {e27136},
title = {{The Temporal Order of Genetic and Pathway
Alterations in Tumorigenesis}},
volume = {6},
year = {2011},
doi = {10.1371/journal.pone.0027136},
issn = {1932-6203},
|
| 6610ac26 |
url = {http://dx.plos.org/10.1371/journal.pone.0027136},
|
| e693f153 |
}
|
| fc38a875 |
@article{Carvajal-Rodriguez2010,
title = {Simulation of Genes and Genomes Forward in Time.},
volume = {11},
issn = {1875-5488},
doi = {10.2174/138920210790218007},
number = {1},
journal = {Current genomics},
author = {Carvajal-Rodriguez, Antonio},
month = mar,
year = {2010},
pages = {58--61},
mendid = {16487},
pmid = {20808525}
}
@article{Hoban2011,
title = {Computer Simulations: Tools for Population and Evolutionary Genetics.},
volume = {13},
issn = {1471-0064},
doi = {10.1038/nrg3130},
number = {2},
journal = {Nature reviews. Genetics},
author = {Hoban, Sean and Bertorelle, Giorgio and Gaggiotti, Oscar E},
month = feb,
year = {2011},
pages = {110--22},
mendid = {16510},
pmid = {22230817}
}
@article{ramazzotti_capri_2015,
title = {{{CAPRI}}: Efficient Inference of Cancer Progression Models from Cross-Sectional Data},
volume = {31},
issn = {1367-4811},
shorttitle = {{{CAPRI}}},
doi = {10.1093/bioinformatics/btv296},
number = {18},
journal = {Bioinformatics (Oxford, England)},
author = {Ramazzotti, Daniele and Caravagna, Giulio and Olde Loohuis, Loes and Graudenzi, Alex and Korsunsky, Ilya and Mauri, Giancarlo and Antoniotti, Marco and Mishra, Bud},
month = sep,
year = {2015},
pages = {3016--3026},
pmid = {25971740}
}
|
| e693f153 |
@article{Korsunsky2014,
author = {Korsunsky, Ilya and Ramazzotti, Daniele and
Caravagna, Giulio and Mishra, Bud},
month = aug,
pages = {1--29},
title = {{Inference of Cancer Progression Models with
Biological Noise}},
year = {2014},
url = {http://arxiv.org/abs/1408.6032v1 http://biorxiv.org/content/
early/2014/08/25/00832},
}
@article{Ortmann2015,
author = {Ortmann, Christina a. and Kent, David G. and
Nangalia, Jyoti and Silber, Yvonne and
Wedge, David C. and Grinfeld, Jacob and
Baxter, E. Joanna and Massie, Charles E. and
Papaemmanuil, Elli and Menon, Suraj and
Godfrey, Anna L. and Dimitropoulou, Danai and
Guglielmelli, Paola and Bellosillo, Beatriz and
Besses, Carles and D\"{o}hner, Konstanze and
Harrison, Claire N. and Vassiliou, George S. and
Vannucchi, Alessandro and Campbell, Peter J. and
Green, Anthony R.},
journal = {New England Journal of Medicine},
pages = {601--612},
title = {{Effect of Mutation Order on Myeloproliferative
Neoplasms}},
volume = {372},
year = {2015},
doi = {10.1056/NEJMoa1412098},
issn = {0028-4793},
}
@article{Raphael2014a,
author = {Raphael, Benjamin J and Vandin, Fabio},
journal = {Journal of Computational Biology},
number = {00},
pages = {250--264},
title = {{Simultaneous Inference of Cancer Pathways and Tumor
Progression from Cross-Sectional Mutation Data}},
volume = {22},
year = {2015},
doi = {10.1089/cmb.2014.0161},
isbn = {1557-8666 (Electronic) 1066-5277 (Linking)},
issn = {1066-5277},
|
| 2f97de14 |
}
@article{Mather2012,
author = {Mather, William H and Hasty, Jeff and
Tsimring, Lev S},
journal = {Bioinformatics (Oxford, England)},
month = mar,
number = {9},
pages = {1230--1238},
title = {{Fast stochastic algorithm for simulating
evolutionary population dynamics.}},
volume = {28},
year = {2012},
doi = {10.1093/bioinformatics/bts130},
issn = {1367-4811},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22437850},
}
@article{Bozic2010,
author = {Bozic, Ivana and Antal, Tibor and Ohtsuki, Hisashi and
Carter, Hannah and Kim, Dewey and Chen, Sining and
Karchin, Rachel and Kinzler, Kenneth W and
Vogelstein, Bert and Nowak, Martin A},
journal = {Proceedings of the National Academy of Sciences of
the United States of America},
month = sep,
pages = {18545--18550},
title = {{Accumulation of driver and passenger mutations
during tumor progression.}},
volume = {107},
year = {2010},
doi = {10.1073/pnas.1010978107},
issn = {1091-6490},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20876136},
}
|
| fc38a875 |
@article{McFarland2014,
title = {A Tug-of-War between Driver and Passenger Mutations in Cancer and Other Adaptive Processes},
volume = {111},
issn = {10916490},
doi = {10.1101/003053},
number = {42},
journal = {Proc Natl Acad Sci U S A},
author = {McFarland, Christopher and Mirny, Leonid and Korolev, Kirill S.},
year = {2014},
pages = {15138--15143},
}
|
| 2f97de14 |
@article{McFarland2013,
author = {McFarland, Christopher D and Korolev, Kirill S and
Kryukov, Gregory V and Sunyaev, Shamil R and
|
| e693f153 |
Mirny, Leonid A},
|
| 2f97de14 |
journal = {Proceedings of the National Academy of Sciences of
the United States of America},
month = feb,
number = {8},
pages = {2910--5},
title = {{Impact of deleterious passenger mutations on cancer
progression.}},
volume = {110},
year = {2013},
doi = {10.1073/pnas.1213968110},
issn = {1091-6490},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23388632},
}
|
| e693f153 |
@article{Diaz-Uriarte2015,
|
| 2f97de14 |
author = {Diaz-Uriarte, R},
|
| e693f153 |
journal = {BMC Bioinformatics},
number = {41},
|
| 2f97de14 |
pages = {0--36},
|
| e693f153 |
title = {{Identifying restrictions in the order of
accumulation of mutations during tumor progression:
effects of passengers, evolutionary models, and
|
| 2f97de14 |
sampling}},
|
| e693f153 |
volume = {16},
year = {2015},
doi = {doi:10.1186/s12859-015-0466-7},
url = {http://www.biomedcentral.com/1471-2105/16/41/abstract},
|
| 2f97de14 |
}
@incollection{Reiter2013a,
address = {Berlin, Heidelberg},
author = {Reiter, JG and Bozic, Ivana and
Chatterjee, Krishnendu and Nowak, MA},
booktitle = {Computer Aided Verification, Lecture Notes in
Computer Science},
editor = {Sharygina, Natasha and Veith, Helmut},
pages = {101--106},
publisher = {Springer-Verlag},
title = {{TTP: tool for tumor progression}},
year = {2013},
|
| e693f153 |
url = {http://link.springer.com/chapter/10.1007/
978-3-642-39799-8\_6 http://dx.doi.org/10.1007/
978-3-642-39799-8\_6 http://pub.ist.ac.at/ttp/},
}
@article{Zanini2012,
author = {Zanini, Fabio and Neher, Richard a.},
journal = {Bioinformatics},
number = {24},
pages = {3332--3333},
title = {{FFPopSim: An efficient forward simulation package
for the evolution of large populations}},
volume = {28},
year = {2012},
doi = {10.1093/bioinformatics/bts633},
isbn = {1010001000},
issn = {13674803},
url = {http://webdav.tuebingen.mpg.de/ffpopsim/ http://
bioinformatics.oxfordjournals.org/content/28/24/3332 http://
github.com/neherlab/ffpopsim/},
}
@article{Gillespie1993,
author = {Gillespie, J. H.},
journal = {Genetics},
number = {3},
pages = {971--981},
title = {{Substitution processes in molecular evolution. I.
Uniform and clustered substitutions in a haploid
model}},
volume = {134},
year = {1993},
issn = {00166731},
}
@article{Datta2013,
author = {Datta, Ruchira S and Gutteridge, Alice and
Swanton, Charles and Maley, Carlo C and
Graham, Trevor A},
journal = {Evolutionary applications},
month = jan,
number = {1},
pages = {20--33},
title = {{Modelling the evolution of genetic instability
during tumour progression.}},
volume = {6},
year = {2013},
doi = {10.1111/eva.12024},
issn = {1752-4571},
url = {http://www.pubmedcentral.nih.gov/
articlerender.fcgi?artid=3567468\&tool=pmcentrez\&rendertype=abstract},
}
@phdthesis{McFarland2014-phd,
author = {McFarland, CD},
school = {Harvard University},
title = {{The role of deleterious passengers in cancer}},
year = {2014},
url = {http://nrs.harvard.edu/urn-3:HUL.InstRepos:13070047},
}
@article{Hjelm2006,
address = {SBC and Dept. of Numerical Analysis and Computer
Science, KTH, Stockholm, Sweden.},
author = {Hjelm, M and H\"{o}glund, M and Lagergren, J},
journal = {J Comput Biol},
month = may,
number = {4},
pages = {853--865},
title = {{New probabilistic network models and algorithms for
oncogenesis.}},
volume = {13},
year = {2006},
doi = {10.1089/cmb.2006.13.853},
issn = {1066-5277},
url = {http://dx.doi.org/10.1089/cmb.2006.13.853},
}
@article{Ashworth2011,
author = {Ashworth, Alan and Lord, Christopher J and
Reis-Filho, Jorge S},
journal = {Cell},
number = {1},
pages = {30--38},
publisher = {Elsevier Inc.},
title = {{Genetic interactions in cancer progression and
treatment.}},
volume = {145},
year = {2011},
doi = {10.1016/j.cell.2011.03.020},
isbn = {1097-4172 (Electronic)$\backslash$r0092-8674
(Linking)},
issn = {00928674},
url = {http://dx.doi.org/10.1016/j.cell.2011.03.020},
}
@article{Hartman2001,
author = {Hartman, J L and Garvik, B and Hartwell, L},
journal = {Science (New York, N.Y.)},
number = {5506},
pages = {1001--1004},
title = {{Principles for the buffering of genetic variation.}},
volume = {291},
year = {2001},
doi = {10.1126/science.291.5506.1001},
isbn = {0036-8075},
issn = {00368075},
}
@article{Misra2014,
author = {Misra, Navodit and Szczurek, Ewa and Vingron, Martin},
journal = {Bioinformatics (Oxford, England)},
month = may,
number = {17},
pages = {2456--2463},
title = {{Inferring the paths of somatic evolution in
cancer.}},
volume = {30},
year = {2014},
doi = {10.1093/bioinformatics/btu319},
issn = {1367-4811},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24812340},
}
@article{Bauer2014,
author = {Bauer, Benedikt and Siebert, Reiner and
Traulsen, Arne},
journal = {Journal of Theoretical Biology},
pages = {52--60},
publisher = {Elsevier},
title = {{Cancer initiation with epistatic interactions
between driver and passenger mutations}},
volume = {358},
year = {2014},
doi = {10.1016/j.jtbi.2014.05.018},
issn = {10958541},
url = {http://dx.doi.org/10.1016/j.jtbi.2014.05.018},
}
@article{Ochs2015,
author = {Ochs, Ian E and Desai, Michael M},
journal = {BMC Evolutionary Biology},
number = {1},
pages = {1--9},
title = {{The competition between simple and complex
evolutionary trajectories in asexual populations}},
volume = {15},
year = {2015},
doi = {10.1186/s12862-015-0334-0},
issn = {1471-2148},
url = {http://www.biomedcentral.com/1471-2148/15/55},
}
@article{Weissman2009,
author = {Weissman, Daniel B. and Desai, Michael M. and
Fisher, Daniel S. and Feldman, Marcus W.},
journal = {Theoretical Population Biology},
number = {4},
pages = {286--300},
publisher = {Elsevier Inc.},
title = {{The rate at which asexual populations cross fitness
valleys}},
volume = {75},
year = {2009},
doi = {10.1016/j.tpb.2009.02.006},
isbn = {1096-0325 (Electronic)$\backslash$r0040-5809
(Linking)},
issn = {00405809},
url = {http://dx.doi.org/10.1016/j.tpb.2009.02.006},
|
| 2f97de14 |
}
@misc{Oncotree,
author = {Szabo, Aniko and Pappas, Lisa},
title = {{Oncotree: Estimating oncogenetic trees}},
year = {2013},
|
| e693f153 |
url = {http://cran.r-project.org/package=Oncotree},
|
| 2f97de14 |
}
|
| 2db2644d |
@article{Beerenwinkel2007b,
author = {Beerenwinkel, Niko and Antal, Tibor and Dingli, David and Traulsen, Arne and Kinzler, Kenneth W and Velculescu, Victor E and Vogelstein, Bert and Nowak, Martin A},
doi = {10.1371/journal.pcbi.0030225},
issn = {1553-7358},
journal = {PLoS computational biology},
month = nov,
number = {11},
pages = {e225},
pmid = {17997597},
title = {{Genetic progression and the waiting time to cancer.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2065895\&tool=pmcentrez\&rendertype=abstract},
volume = {3},
year = {2007}
}
|
| 50a94207 |
|
| fc38a875 |
@article{szendro_predictability_2013,
title = {Predictability of Evolution Depends Nonmonotonically on Population Size},
volume = {110},
issn = {0027-8424, 1091-6490},
doi = {10.1073/pnas.1213613110},
number = {2},
journal = {Proceedings of the National Academy of Sciences},
author = {Szendro, Ivan G. and Franke, Jasper and de Visser, J. Arjan G. M. and Krug, Joachim},
month = aug,
year = {2013},
pages = {571--576},
pmid = {23267075}
}
|
| 50a94207 |
@article{szendro_quantitative_2013,
title = {Quantitative analyses of empirical fitness landscapes},
volume = {2013},
issn = {1742-5468},
url = {http://stacks.iop.org/1742-5468/2013/i=01/a=P01005},
doi = {10.1088/1742-5468/2013/01/P01005},
language = {en},
number = {01},
journal = {Journal of Statistical Mechanics: Theory and Experiment},
author = {Szendro, Ivan G. and Schenk, Martijn F. and Franke, Jasper and Krug, Joachim and Visser, J. Arjan G. M. de},
year = {2013},
pages = {P01005},
}
@article{franke_evolutionary_2011,
title = {Evolutionary {Accessibility} of {Mutational} {Pathways}},
volume = {7},
url = {http://dx.doi.org/10.1371/journal.pcbi.1002134},
doi = {10.1371/journal.pcbi.1002134},
number = {8},
journal = {PLoS Comput Biol},
author = {Franke, Jasper and Klözer, Alexander and de Visser, J. Arjan G. M. and Krug, Joachim},
month = aug,
year = {2011},
keywords = {anki\_processed},
pages = {e1002134},
}
@article{greene_changing_2014,
title = {The changing geometry of a fitness landscape along an adaptive walk.},
volume = {10},
issn = {1553-7358},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4031059&tool=pmcentrez&rendertype=abstract},
doi = {10.1371/journal.pcbi.1003520},
number = {5},
journal = {PLoS computational biology},
author = {Greene, Devin and Crona, Kristina},
month = may,
year = {2014},
pmid = {24853069},
pages = {e1003520},
}
@article{brouillet_magellan:_2015,
title = {{MAGELLAN}: a tool to explore small fitness landscapes},
copyright = {© 2015, Published by Cold Spring Harbor Laboratory Press. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
shorttitle = {{MAGELLAN}},
url = {http://biorxiv.org/content/early/2015/11/13/031583},
doi = {10.1101/031583},
journal = {bioRxiv},
author = {Brouillet, Sophie and Annoni, Harry and Ferretti, Luca and Achaz, Guillaume},
month = nov,
year = {2015},
note = {bibtex: brouillet\_magellan:\_2015},
pages = {031583},
}
@article{gerrish_complete_2007,
title = {Complete genetic linkage can subvert natural selection},
volume = {104},
issn = {0027-8424},
doi = {10.1073/pnas.0607280104},
language = {eng},
number = {15},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
author = {Gerrish, Philip J. and Colato, Alexandre and Perelson, Alan S. and Sniegowski, Paul D.},
month = apr,
year = {2007},
pages = {6266--6271},
pmid = {17405865},
pmcid = {PMC1851075}
}
@article{tomlinson_mutation_1996,
title = {The mutation rate and cancer},
volume = {93},
issn = {0027-8424},
language = {eng},
number = {25},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
author = {Tomlinson, I. P. and Novelli, M. R. and Bodmer, W. F.},
month = dec,
year = {1996},
pages = {14800--14803},
pmid = {8962135},
pmcid = {PMC26216}
}
|
| fd073de1 |
@article{ferretti_measuring_2016,
title = {Measuring Epistasis in Fitness Landscapes: {{The}} Correlation of Fitness Effects of Mutations},
volume = {396},
issn = {0022-5193},
shorttitle = {Measuring Epistasis in Fitness Landscapes},
journal = {Journal of Theoretical Biology},
doi = {10.1016/j.jtbi.2016.01.037},
url = {http://www.sciencedirect.com/science/article/pii/S0022519316000771},
author = {Ferretti, Luca and Schmiegelt, Benjamin and Weinreich, Daniel and Yamauchi, Atsushi and Kobayashi, Yutaka and Tajima, Fumio and Achaz, Guillaume},
month = may,
year = {2016},
pages = {132-143}
}
|
| 4068375e |
@article {Axelrod2006,
author = {Axelrod, Robert and Axelrod, David E. and Pienta, Kenneth J.},
title = {Evolution of cooperation among tumor cells},
volume = {103},
number = {36},
pages = {13474--13479},
year = {2006},
doi = {10.1073/pnas.0606053103},
issn = {0027-8424},
URL = {http://www.pnas.org/content/103/36/13474},
journal = {Proceedings of the National Academy of Sciences}
}
@article{hurlbut2018,
title = {Game {{Theoretical Model}} of {{Cancer Dynamics}} with {{Four Cell Phenotypes}}},
volume = {9},
issn = {2073-4336},
number = {3},
journal = {Games},
doi = {10.3390/g9030061},
url = {http://www.mdpi.com/2073-4336/9/3/61},
author = {Hurlbut, Elena and Ortega, Ethan and Erovenko, Igor and Rowell, Jonathan},
month = sep,
year = {2018},
pages = {61}
}
@article{wuA2016,
title = {Evolutionary Game between Commensal and Pathogenic Microbes in Intestinal Microbiota},
volume = {7},
issn = {2073-4336},
number = {3},
journal = {Games},
doi = {10.3390/g7030026},
url = {https://www.mdpi.com/2073-4336/7/3/26},
author = {Amy Wu and David Ross},
month = sep,
year = {2016},
}
@article{Barton2018,
title = {Modeling of breast cancer through evolutionary game theory},
volume = {11},
issn = {1944-4176},
number = {4},
journal = {Mathematical Sciences Publishers},
doi = {10.2140/involve.2018.11.541},
url = {https://msp.org/involve/2018/11-4/p01.xhtml},
author = {Barton, K. Y., Smith, C., Rychtář, J. and Sendova, T.},
month = jan,
year = {2018},
}
@book{Otto2007,
address = {Princeton},
title = {A Biologist's Guide to Mathematical Modeling in Ecology and Evolution},
isbn = {978-1-4008-4091-5},
publisher = {{Princeton University Press}},
author = {Otto, Sarah P and Day, T.},
year = {2007},
mendid = {17476}
}
@article{gerstung2011,
title = {Evolutionary {{Games}} with {{Affine Fitness Functions}}: {{Applications}} to {{Cancer}}},
volume = {1},
issn = {2153-0785, 2153-0793},
shorttitle = {Evolutionary {{Games}} with {{Affine Fitness Functions}}},
number = {3},
journal = {Dynamic Games and Applications},
doi = {10.1007/s13235-011-0029-0},
url = {http://link.springer.com/10.1007/s13235-011-0029-0},
author = {Gerstung, Moritz and Nakhoul, Hani and Beerenwinkel, Niko},
month = sep,
year = {2011},
pages = {370-385}
}
@article{archetti2019,
title = {Cooperation among Cancer Cells: Applying Game Theory to Cancer},
volume = {19},
issn = {1474-175X, 1474-1768},
shorttitle = {Cooperation among Cancer Cells},
number = {2},
journal = {Nature Reviews Cancer},
doi = {10.1038/s41568-018-0083-7},
url = {http://www.nature.com/articles/s41568-018-0083-7},
author = {Archetti, Marco and Pienta, Kenneth J.},
month = feb,
year = {2019},
pages = {110-117}
}
@article{tomlinson1997a,
title = {Game-Theory Models of Interactions between Tumour Cells},
volume = {33},
issn = {09598049},
number = {9},
journal = {European Journal of Cancer},
doi = {10.1016/S0959-8049(97)00170-6},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0959804997001706},
author = {Tomlinson, I.P.M.},
month = aug,
year = {1997},
pages = {1495-1500}
}
@incollection{basanta2008,
address = {Boston},
series = {Modeling and {{Simulation}} in {{Science}}, {{Engineering}} and {{Technology}}},
title = {A {{Game Theoretical Perspective}} on the {{Somatic Evolution}} of Cancer},
isbn = {978-0-8176-4713-1},
booktitle = {Selected {{Topics}} in {{Cancer Modeling}}: {{Genesis}}, {{Evolution}}, {{Immune Competition}}, and {{Therapy}}},
publisher = {{Birkh\"auser Boston}},
url = {https://doi.org/10.1007/978-0-8176-4713-1_5},
author = {Basanta, David and Deutsch, Andreas},
year = {2008},
pages = {1-16},
doi = {10.1007/978-0-8176-4713-1_5}
}
@book{maynardsmith1982,
address = {Cambridge},
title = {Evolution and the Theory of Games},
isbn = {978-0-521-24673-6 978-0-521-28884-2},
publisher = {{Cambridge Univ. Press}},
author = {Maynard Smith, John Maynard},
year = {1982}
}
@article{doebeli2017,
title = {Towards a Mechanistic Foundation of Evolutionary Theory},
volume = {6},
issn = {2050-084X},
journal = {eLife},
doi = {10.7554/eLife.23804},
url = {https://doi.org/10.7554/eLife.23804},
author = {Doebeli, Michael and Ispolatov, Yaroslav and Simon, Burt},
editor = {Shou, Wenying},
month = feb,
year = {2017},
pages = {e23804}
}
@article{tsigelny2007,
title = {Dynamics of a-synuclein aggregation and inhibition of pore-like oligomer development by b-synuclein},
volume = {274},
issn = {1862-1877},
number = {7},
journal = {FEBS},
doi = {10.1111/j.1742-4658.2007.05733.x},
url = {https://febs.onlinelibrary.wiley.com/doi/full/10.1111/j.1742-4658.2007.05733.x},
author = {Igor F. Tsigelny Pazit Bar‐On Yuriy Sharikov Leslie Crews Makoto Hashimoto Mark A. Miller Steve H. Keller Oleksandr Platoshyn Jason X.‐J. Yuan Eliezer Masliah},
month = mar,
year = {2007},
pages = {16}
}
@book{maynardsmith1982,
address = {{Cambridge}},
title = {Evolution and the Theory of Games},
isbn = {978-0-521-24673-6 978-0-521-28884-2},
publisher = {{Cambridge Univ. Press}},
author = {Maynard Smith, John Maynard},
year = {1982}
}
@article{kaznatcheev2017,
title = {Cancer Treatment Scheduling and Dynamic Heterogeneity in Social Dilemmas of Tumour Acidity and Vasculature},
volume = {116},
issn = {0007-0920, 1532-1827},
number = {6},
journal = {Br J Cancer},
url = {http://www.nature.com/articles/bjc20175},
doi = {10.1038/bjc.2017.5},
author = {Kaznatcheev, Artem and Vander Velde, Robert and Scott, Jacob G and Basanta, David},
month = mar,
year = {2017},
pages = {785-792}
}
@article{basanta_investigating_2012,
title = {Investigating Prostate Cancer Tumour\textendash{}Stroma Interactions: Clinical and Biological Insights from an Evolutionary Game},
volume = {106},
copyright = {\textcopyright{} 2011 Nature Publishing Group},
issn = {0007-0920},
shorttitle = {Investigating Prostate Cancer Tumour\textendash{}Stroma Interactions},
number = {1},
journal = {Br J Cancer},
url = {http://www.nature.com/bjc/journal/v106/n1/full/bjc2011517a.html},
doi = {10.1038/bjc.2011.517},
author = {Basanta, D. and Scott, J. G. and Fishman, M. N. and Ayala, G. and Hayward, S. W. and Anderson, A. R. A.},
month = jan,
year = {2012},
pages = {174-181}
}
@article{sartakhti2016,
title = {Evolutionary {{Dynamics}} of {{Tumor}}-{{Stroma Interactions}} in {{Multiple Myeloma}}},
volume = {11},
issn = {1932-6203},
number = {12},
journal = {PLOS ONE},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168856},
doi = {10.1371/journal.pone.0168856},
author = {Sartakhti, Javad Salimi and Manshaei, Mohammad Hossein and Bateni, Soroosh and Archetti, Marco},
month = dec,
year = {2016},
pages = {e0168856}
}
@article{kerr2002a,
title = {Local Dispersal Promotes Biodiversity in a Real-Life Game of Rock-Paper-Scissors},
author = {Kerr, Benjamin and Riley, Margaret A. and Feldman, Marcus W. and Bohannan, Brendan J. M.},
year = {2002},
month = jul,
volume = {418},
pages = {171--174},
issn = {0028-0836},
doi = {10.1038/nature00823},
journal = {Nature},
number = {6894},
pmid = {12110887}
}
@article{PhysRevE,
title = {Nonlinear adaptive control of competitive release and chemotherapeutic resistance},
author = {Newton, P. K. and Ma, Y.},
journal = {Phys. Rev. E},
volume = {99},
issue = {2},
pages = {022404},
numpages = {10},
year = {2019},
month = {Feb},
publisher = {American Physical Society},
doi = {10.1103/PhysRevE.99.022404},
url = {https://link.aps.org/doi/10.1103/PhysRevE.99.022404}
}
@article{Archetti2013,
title = {Evolutionary game theory of growth factor production: implications for tumour heterogeneity and resistance to therapies},
volume = {109},
issn = {0007-0920},
number = {4},
journal = {British Journal of Cancer},
doi = {10.1038/bjc.2013.336},
url = {https://doi.org/10.1038/bjc.2013.336},
author = {Archetti, Marco},
month = aug,
year = {2013},
pages = {1056–1062}
}
|
| 43ee9bac |
@article{krug2019,
title = {Accessibility Percolation in Random Fitness Landscapes},
author = {Krug, Joachim},
year = {2019},
month = mar,
url = {http://arxiv.org/abs/1903.11913},
urldate = {2021-04-23},
archiveprefix = {arXiv},
eprint = {1903.11913},
eprinttype = {arxiv},
journal = {arXiv:1903.11913 [math, q-bio]},
}
@article{orr_population_2002,
title = {The Population Genetics of Adaptation: The Adaptation of Dna Sequences},
shorttitle = {The Population Genetics of Adaptation},
author = {Orr, H. Allen},
year = {2002},
month = jul,
volume = {56},
pages = {1317--1330},
issn = {0014-3820},
doi = {10.1554/0014-3820(2002)056[1317:TPGOAT]2.0.CO;2},
url = {http://www.bioone.org/doi/abs/10.1554/0014-3820%282002%29056%5B1317%3ATPGOAT%5D2.0.CO%3B2},
journal = {Evolution},
number = {7}
}
@article{gillespie1984,
title = {Molecular {{Evolution Over}} the {{Mutational Landscape}}},
author = {Gillespie, John H.},
year = {1984},
volume = {38},
pages = {1116--1129},
publisher = {{[Society for the Study of Evolution, Wiley]}},
issn = {0014-3820},
doi = {10.2307/2408444},
url = {https://www.jstor.org/stable/2408444},
journal = {Evolution},
number = {5}
}
|
