Publications

Books (authored / co-authored)

B5. Wodarz, D., Komarova, N. Dynamics of Cancer (2014): Mathematical Foundations of Oncology. 510 pp. World Scientific Publishing.

B4. Komarova, N., Wodarz, D. (2013) Targeted cancer treatment in silico: small molecule inhibitors and oncolytic viruses. 250 pp. Birkhauser.

B3. Wodarz D. (2006) Killer cell dynamics: Mathematical and Computational Approaches to Immunology. 220pp, Springer.

B2. Wodarz D and Komarova NL (2005): Computational Biology of Cancer: Lecture notes and mathematical modeling. 264pp, World Scientific Publishing.

Edited Volumes

B1. Guest Editor for Seminars in Cancer Biology, December 2005 issue: Somatic evolution of cancer cells. This volume contains a number of contributions on the topic of somatic evolution of cancer cells by leading scientists in the field.

Papers

192. Chung W & Wodarz D (2024): Compartmental structure of the secondary lymphoid tissue can slow down in vivo HIV-1 evolution in the presence of strong CTL responses. In revision (bioRxiv
doi:https://doi.org/10.1101/2024.06.24.600465)

191. Kim E, Chen SS, Sivina M, Hwang H, Huang X, Ferrajoli A, Jain N, Wierda WG, Wodarz D, Chiorazzi N, Burger JA (2024). Deuterated water labeling in ibrutinib-treated patients with CLL: leukemia cell kinetics correlate with IGHV, ZAP-70, and MRD. Blood Oct 23: blood-2024025683.

190. Weiss S, Lin H, Acosta E, Komarova NL, Chen P, Wodarz D, Baine I, Duerr R, Wajnberg A, Gervais A, Bastard P, Casanova JL, Arinsburg S, Swartz TH, Aberg JA, Bouvier N, Liu ST, Alvarez RA & Chen BK (2024) Identification of correlates of hazard in a COVID-19 convalescent plasma donor-recipient network. Journal of Clinical Investigation, to appear.

189. Komarova NL, Rignot C, Fleischman AG & Wodarz D (2024) Dynamically adjusted cell fate decisions and resilience to mutant invasion during steady state hematopoiesis revealed by an experimentally parameterized mathematical model. Proc. Natl. Acad. Sci. USA 121(38), e2321525121

188. Leighow SM, Reynolds JA, Sokirniy I, Yao S, Yang Z, Inam H, Wodarz D, Archetti M, Pritchard JR (2024). Programming tumor evolution with selection gene drives to proactively combat drug resistance. Nature Biotechnology, doi: 10.1038/s41587-024-02271-7

187. Chung W, Connick E & Wodarz D (2024). Human immunodeficiency virus (HIV) dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte (CTL) escape mutants. Virus Evolution vead084.

186. Huang Z, Hwang J, Zhang J, Baik J, Zhang W, Wodarz D, Sun Y, Gu Q, Wang W (2023). Causal Graph ODE: Continuous Treatment Effect Modeling in Multi-agent Dynamical Systems. In The Symbiosis of Deep Learning and Differential Equations III 2023 Oct 31.

185. Wodarz D and Komarova NK (2023) Mutant fixation in the presence of a natural enemy. Nature Communications 14, 6642

184. Kreger J, Brown D, Komarova NL, Wodarz D. & Pritchard J (2023) The role of migration in mutant dynamics in fragmented populations. Journal of Evolutionary Biology, 26(2) 444-460.

183. Patel AG, Chen X, Huang X, Clay MR, Komarova N, Krasin MJ, Pappo A, Tillman H, Orr BA, McEvoy J, Gordon B, Blankenship K, Reilly C, Zhou X, Norrie JL, Karlstrom A, Yu J, Wodarz D, Stewart E, Dyer MA (2022). The myogenesis program drives clonal selection and drug resistance in
rhabdomyosarcoma. Developmental Cell 57(10):1226-40.

182. Komarova NL, Rodriguez-Brenes IA, & Wodarz D (2022). Laws of Spatially Structured Population Dynamics on a Lattice. Physics 4(3), 812-832.

181. Uhl P, Lowengrub J, Komarova NL & Wodarz D (2022) Spatial dynamics of feedback and feedforward regulation in cell lineages. PLOS Computational Biology, 18(5):e1010039.

180. Wang Y, Boland CR, Goel A, Wodarz D, & Komarova NL (2022) Aspirin’s effect on kinetic parameters of cells contributes to its role in reducing incidence of advanced colorectal adenomas, shown by a multiscale computational study. eLife, 11:e71953.

179. Azizi A, Komarova NL, & Wodarz D (2022) Effect of human behavior on the evolution of viral strains during an epidemic. Bulletin of Mathematical Biology 84(12), 144.

178. Wodarz D, Komarova NL, & Schang LM (2021) Effect of hot zone infection outbreaks on the dynamics of SARS-CoV-2 spread in the community at large.” medRxiv https://www.medrxiv.org/content/10.1101/20 0.11.23.20237172v1

177. Kim JT, Zhang TH, Carmona C, Lee B, Seet CS, Kostelny M, Shah N, Chen H, Farrell K, Soliman MSA, Dimapasoc M, Sinani M, Blanco KYR, Bojorquez D, Jiang H, Shi Y, Du Y, Komarova NL, Wodarz D, Wender PA, Marsden MD, Sun R, Zack JA (2022) Latency reversal plus natural killer
cells diminish HIV reservoir in vivo. Nature Communications. 2022 Jan 10;13(1):1-4.

176. Kreger J, Komarova NL & Wodarz D (2021) A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV. PLOS Computational Biology, 17(12), p.e1009713.

175. Wodarz D (2021) Adaptive therapy and the cost of drug-resistant mutants. Cancer Research 81, 811-812.

174. Kreger J, Garcia J, Zhang H, Komarova NL, Wodarz D, Levy DN (2021) Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection. Virus Evolution 7(1) veab026

173. Wodarz D, Komarova NL, Schang LM. (2021) Role of high-dose exposure in transmission hot zones as a driver of SARS-CoV2 dynamics. Journal of the Royal Society Interface 18(176):20200916

172. Komarova NL, Azizi A, and Wodarz D (2021) Network models and the interpretation of prolonged infection plateaus in the COVID19 pandemic. Epidemics 24, 100463.

171. Weiss LD, ven den Driessche P, Lowengrub JS, Wodarz D, and Komarova NL (2021) Effect of feedback regulation on stem cell fractions in tissues and tumors: Understanding chemoresistance in
cancer. J. Theor. Biol. 509:110499.

170. Komarova NL, Schang LM and Wodarz D (2020) Patterns of the COVID19 pandemic spread around the world: exponential vs power laws. The Journal of the Royal Society Interface, 17, no. 170 (2020): 20200518.

169. Wodarz D. and Komarova NL (2020) Mutant evolution in spatially structured and fragmented expanding populations. Genetics Jul 13:genetics.303422.2020

168. Eastman B., Wodarz D. and Kohandel M (2020). The effects of phenotypic plasticity on the fixation probability of mutant cancer stem cells. Journal of Theoretical Biology 503:110384.

167. Wodarz, D., Stipp, S., Hirshleifer, D., & Komarova, N. L. (2020). Evolutionary dynamics of culturally transmitted, fertility-reducing traits. Proceedings of the Royal Society B, 287(1925), 20192468.

166. Rodriguez-Brenes, I. A., Wodarz, D., & Komarova, N. L. (2020). Beyond the pair approximation: Modeling colonization population dynamics. Physical Review E, 101(3), 032404.

165. Kreger, J., Komarova, N. L., & Wodarz, D. (2020). Effect of synaptic cell-to-cell transmission and recombination on the evolution of double mutants in HIV. Journal of the Royal Society Interface, 17(164), 20190832.

164. Komarova, N. L., Boland, C. R., Goel, A., & Wodarz, D. (2020). Aspirin and the chemoprevention of cancers: A mathematical and evolutionary dynamics perspective. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, e1487.

163. Shimura, T., Toden, S., Komarova, N.L., Boland, C., Wodarz, D. and Goel, A. (2020). A comprehensive in vivo and mathematic modeling-based kinetic characterization for aspirin-induced chemoprevention in colorectal cancer. Carcinogenesis. bgz195. doi: 10.1093/carcin/bgz195

162. Rockne RC, Hawkins-Daarud A, Swanson KR, Sluka JP, Glazier JA, Macklin P, Hormuth D, Jarrett AM, Lima EABDF, Oden J, Biros G, Yankeelov TE, Curtius K, Bakir IA, Wodarz D, Komarova N, Aparicio L, Bordyuh M, Rabadan R, Finley S, Enderling H, Caudell JJ, Moros EG, Anderson ARA,
Gatenby R, Kaznatcheev A, Jeavons P, Krishnan N, Pelesko J, Wadhwa RR, Yoon N, Nichol D, Marusyk A, Hinczewski M, Scott JG. (2019) The 2019 mathematical oncology roadmap. Phys Biol. doi: 10.1088/1478-3975/ab1a09.

161. Wodarz D., Levy D.N. & Komarova N.L. (2019) Multiple infection of cells changes the dynamics of basic viral evolutionary processes. Evolution Letters, 3-1: 104–115

160. Rodriguez-Brenes I.A., Komarova N.L. & Wodarz D. (2019): The role of telomere shortening in carcinogenesis: A hybrid stochastic-deterministic approach. J. Theor. Biol. 460: 144-152

159. Rodriguez-Brenes I.A. & Wodarz D. (2018): Population Dynamics and Evolution of Cancer Cells. Integrated Population Biology and Modeling 39 (2018): 1-35.

158. Kaushansky A., Hedstrom L., Goldman A., Singh J., Yang P.L., Rathod P.K., Cynamon M., Wodarz D., Mahadevan D., Tomaras D., Navia M.A. & Schiffer C.A. (2018) A call to arms: Unifying the fight against resistance. Science Signaling 11(553). pii: eaav0442.

157. Wodarz D., Skinner P.J., Levy D.N. & Connick E. (2018) Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques. PLoS Comput. Biol. 14(10):e1006461.

156. Wodarz D., Newell A.C., & Komarova N.L. (2018) Passenger mutations can accelerate tumour suppressor gene inactivation in cancer evolution. J. Roy. Soc. Interface. 15(143). pii: 20170967.

155. Wodarz D. (2018) Effect of cellular de-differentiation on the dynamics and evolution of tissue and tumor cells in mathematical models with feedback regulation. J. Theor. Biol. 448: 86-93

154. Harris D., Wodarz D. & Komarova N.L. (2018) Spatial evolution of regularization in learned behavior of animals. Math. Biosci. 299: 103-116.

153. Wodarz D. and Rodriguez-Brenes I.A. (2017) Early stochastic dynamics in human cytomegalovirus infection. J. Virol. 91(18), e00949-17.

152. Wodarz, D., Goel, A., Boland, C.R., Komarova, N.L. (2017) Effect of aspirin on tumor cell colony formation and evolution. The Journal of the Royal Society Interface, 14(134). pii: 20170374 doi: 10.1098/rsif.2017.0374.

151. Wodarz, D., Goel, A., Komarova, N.L. (2017) Effect of cell cycle duration on somatic evolutionary dynamics. Evolutionary Applications, 10(10), 1121-1129.

150. Wodarz D. and Levy DN (2017) Pyroptosis, superinfection, and the maintenance of the latent reservoir in HIV-1 infection. Scientific Reports Jun 19;7(1):3834. doi: 10.1038/s41598-017-04130-9.

149. Zhang J, Fleischman AG, Wodarz D & Komarova NL (2017) Determining the role of inflammation in the selection of JAK2 mutant cells in myeloproliferative neoplasms. J. Theor. Biol 425: 43-52

148. Rodriguez-Brenes IA, Kurtova AV, Lin C, Lee YC, Xiao J, Mims MP, Chan KS, & Wodarz D. (2017) Cellular hierarchy as a determinant of tumor sensitivity to chemotherapy. Cancer Research, 77(9), pp.2231-2241.

147. Rodriguez-Brenes IA, Hofacre A, Fan H & Wodarz D (2017) Complex dynamics of virus spread from low infection multiplicities: implications for the spread of oncolytic viruses. PLoS Computational Biology 13(1):e1005241.

146. Zumwalt TJ, Wodarz D, Komarova NL, Toden S, Turner J, Cardenas J, Burn J, Chan AT, Boland CR & Goel A. (2017) Aspirin-induced chemoprevention and response kinetics are enhanced by PIK3CA mutations in colorectal cancer cells. Cancer Prev. Res. Feb 2. pii: canprevres.0175.2016

145. Burger JA, Li KW, Keating MJ, Sivina M, Amer AM, Garg N, Ferrajoli A, Huang X, Kantarjian H, Wierda WG, O’Brien S, Hellerstein MK, Turner SM, Emson CL, Chen SS, Yan XJ, Wodarz D & Chiorazzi N. (2017) Leukemia cell proliferation and death in chronic lymphocytic leukemia patients on therapy with the BTK inhibitor ibrutinib. JCI insight 26, 2(2):e89904

144. Law KM, Komarova NL, Yewdall AW, Lee RK, Herrera OL, Wodarz D & Chen BK (2016) In Vivo HIV-1 Cell-to-Cell Transmission Promotes Multicopy Micro-compartmentalized Infection. Cell Reports 15(12): 2771-83

143. Rodriguez-Brenes I, Wodarz D & Komarova NL (2016) Cellular replication limits in the Luria–Delbrück mutation model. Physica D: Nonlinear Phenomena 328: 44-51

142. Wodarz D (2016) Computational modeling approaches to the dynamics of oncolytic viruses. Wiley Interdiscip Rev Syst Biol Med. 8(3):242-52.

141. Stipp SR, Iniguez A, Wan F & Wodarz D (2016): Timing of CD8 T cell effector responses in viral infections. Royal Society Open Science 3.2: 150661:

140. Rodriguez-Brenes IA & Wodarz D (2016). Telomeres open a window on stem cell division. eLife 5. pii: e12481.

139. Chan CN, Trinite B, Lee CS, Mahajan S, Anand A, Wodarz D, Sabbaj S, Bansal A, Goepfert PA & Levy DN (2016): HIV-1 latency and virus production from unintegrated genomes following direct infection of resting CD4 T cells. Retrovirology 13(1): 1.

138. Rodriguez-Brenes IA, Wodarz D & Komarova NL (2015) Quantifying replicative senescence as a tumor suppressor pathway and a target for cancer therapy. Scientific Reports 5:17660.

137. Rodriguez-Brenes IA, Wodarz D, & Komaorva NL (2015) Characterizing inhibited tumor growth in stem cell-driven non-spatial cancers. Math. Biosci. 270: 135-141.

136. Rodriguez-Brenes IA & Wodarz D (2015) Preventing clonal evolutionary processes in cancer: insights from mathematical models. Proc. Natl. Acad. Sci. USA. 112, 8843-50.

135. Asatryan A, Wodarz D, and Komarova NL (2015): New virus dynamics in the presence of multiple infection. J. Theor. Biol. 377, 98-109.

134. Phan D & Wodarz D (2015): Modeling multiple infection of cells by viruses: challenges and insights. Mathematical Biosciences, 264: 21-28

133. Toden S, Okugawa Y, Jascur T, Wodarz D, Komarova NL, Buhrmann C, Shakibaei M, Boland CR & Goel A (2015) Curcumin mediates chemosensitization of 5-fluorouracil through miRNA-induced suppression of epithelial-to-mesenchymal transition in chemoresistant colorectal cancer.
Carcinogenesis 36: 355-367

132. Wodarz D & Zauber AG (2015): Cancer: risk factors and random chances. Nature (News and Views) 517: 563-564.

131. Lau, JW, Levy DN & Wodarz D (2015): Contribution of HIV-1 genomes that do not integrate to the basic reproductive ratio of the virus. Journal of Theoretical Biology 367: 222-229.

130. Komarova NL, Burger JA & Wodarz D (2014) Evolution of ibrutinib resistance in chronic lymphocytic leukemia (CLL). Proc. Natl. Acad. Sci. USA 111(38):13906-11.

129. Wodarz D (2014) Modeling T cell responses to antigenic challenge. J Pharmacokinet Pharmacodyn. 41(5), 415-429

128. Wodarz D (2014) Systems biology models and conceptualizations applied to eco-immunology. In Eco-immunology: evolutive aspects and future perspectives (Ed. Malagoli D & Ottaviani E.), pp 21-47, Springer, Netherlands.

127. Wodarz D, Chan CN, Trinite B, Komarova NL & Levy DN (2014) On the laws of virus spread through cell populations. Journal of Virology. 88(22) 13240-13248.

126. Wodarz D. (2014) Mathematical models of HIV replication and pathogenesis. Methods Mol. Biol. 1184:563-581

125. Wodarz D., Garg, N., Komarova, N.L., Benjamini, O., Keating, M.J., Wierda, W.G., Kantarjian, H., James, D., O’Brien, S. & Burger, J.A. (2014) Kinetics of CLL cells in tissues and blood during therapy with the BTK inhibitor ibrutinib. Blood 123(26):4132-4135

124. Wodarz D., Sorace, R. & Komarova, N.L. (2014) Dynamics of cellular responses to radiation. PLoS Comput. Biol. 10(4): e1003513.

123. Komarova, N.L, Shahriyari, L. & Wodarz D (2014) Complex role of space in the crossing of fitness valleys by asexual populations. J. R. Interface 11(95): 20140014

122. Rodriguez-Brenes, I. A., Komarova, N. L., & Wodarz, D. (2014). Cancer-associated mutations in healthy individuals: assessing the risk of carcinogenesis. Cancer Research, 74:1661-9

121. Roy, S. M., Wodarz, D (2014). Tissue architecture, feedback regulation, and resilience to viral infection. Journal of Theoretical Biology,340, 131-138

120. Trinite, B., Ohlson, E. C., Voznesensky, I., Rana, S. P., Chan, C. N., Mahajan, S., Alster, J., Burke, S. A., Wodarz, D., Levy, D. N. (2013) An HIV 1 replication pathway utilizing reverse transcript products that fail to integrate. Journal of Virology, 87, 12701-20.

119. Wodarz, D., Komarova, N. (2013). Dependence of the firearm-related homicide rate on gun availability: a mathematical analysis. PLoS ONE. 8(7):e71606.

118. Wodarz, D. (2013). Evolutionary dynamics of giant viruses and their virophages. Ecology and Evolution, 3, 2103-15.

117. Wodarz, D., Boland, R., Goel, A., Komarova, N. (2013). Methylation kinetics and CpG-island methylator phenotype status in colorectal cancer cell lines.. Biology Direct 8:14.

116. Rodriguez-Brenes, I., Wodarz, D., Komarova, N. (2013). Minimizing the risk of cancer: tissue architecture and cellular replication limits. Journal of the Royal Society Interface. 10(86):20130410.

115. Wodarz, D., Sun, Z., Lau, J. W., Komarova, N. (2013). Nearest neighbor interactions, habitat fragmentation, and the persistence of host-pathogen systems. American Naturalist, 182(3), E94-E111.

114. Rodriguez-Brenes, I., Komarova, N., Wodarz, D. (2013). Tumor growth dynamics: insights into somatic evolutionary processes. Trends in Ecology and Evolution pii: S0169-5347(13)00142-0. doi: 10.1016/j.tree.2013.05.020.

113. Komarova, N., Levy, D. N., Wodarz, D. (2013). Synaptic transmission and the susceptibility of HIV infection to anti-viral drugs.. Scientific Reports 3:2103. doi: 10.1038/srep02103.

112. Wodarz D. 2013 Computational modeling approaches to studying the dynamics of oncolytic viruses. Mathematical Biosciences and Engineering 10(3): 939-957.

111. Rodriguez-Brenes I.A., Wodarz D., and Komarova N.L. 2013 Stem cell control, oscillations, and tissue regeneration in spatial and non-spatial models. Front. Oncol. 3:82.

110. Komarova N.L. and Wodarz D. 2013 Virus dynamics in the presence of synaptic transmission. Mathematical Biosciences 242(2):161-71

109. Komarova N.L., Anghelina D., Voznesensky I., Trinité B., Levy D.N., Wodarz D. 2012 Relative contribution of free-virus and synaptic transmission to the spread of HIV-1 through target cell populations. Biol Lett. 9(1):20121049.

108. Komarova N.L., Urwin E. and Wodarz D. 2012 Accelerated crossing of fitness valleys through division of labor and cheating in asexual populations. Scientific Reports 2:917.

107. Komarova N.L., Levy D.N., & Wodarz D. 2012 Effect of synaptic transmission on viral fitness in HIV infection. PLoS ONE 7(11):e48361.

106. Wodarz D., Hofacre A., Lau J.W., Sun Z., Fan H., & Komarova N.L. 2012 Complex spatial dynamics of oncolytic viruses in vitro: mathematical and experimental approaches. PLoS Computational Biology 8(6):e1002547.

105. Cummings, K.W., Levy D.N. & Wodarz D. 2012 Increased burst size in multiply infected cells can alter basic virus dynamics. Biology Direct, 7(1):16.

104. Roy S.M. and Wodarz D. 2012 Infection of HIV-specific CD4 T helper cells and the clonal composition of the response. J. Theor. Biol. 304, 143-151.

103. Hofacre A., Wodarz D., Komarova, N.L. & Fan H. 2012 Early infection and spread of a conditionally replicating adenovirus under conditions of plaque formation. Virology 423: 89-96

102. Rodriguez-Brenes, I.A., Komarova, N.L. & Wodarz D. 2011 Evolutionary Dynamics of feedback escape and the development of stem-cell driven cancers. Proc. Natl. Acad. Sci USA 108, 18983-8

101. Wodarz D. and Levy D.N. 2011 Effect of multiple infection of cells on the evolutionary dynamics of HIV in vivo: implications for host adaptation mechanisms. Exp. Biol. Med. 236, 926-37.

100. Del Portillo A., Tripodi J., Najfeld V., Wodarz D., Levy D.N. & Chen B.K. 2011 Multiploid inheritance of HIV-1 during cell-to-cell infection. J. Virol. 85, 7169-76.

99. Wodarz D. and Levy D.N. 2011 Effect of different modes of viral spread on the dynamics of multiply infected cells in human immunodeficiency virus infection. J. R. Soc. Interface, 6, 289-300.

98. Wodarz D 2010 Heterogeneity in chronic myeloid leukemia dynamics during imatinib treatment: role of immune responses. Proc. Biol. Sci. 277, 1875-80

97. Komarova N.L. and Wodarz D. 2010 ODE models for oncolytic virus dynamics. J. Theor. Biol. 263, 530-43.

96. Wodarz D. and Levy D.N. 2009 Multiple HIV-1 infection of cells and the evolutionary dynamics of cytotoxic T lymphocyte escape mutants. Evolution 63, 2326-39.

95. Komarova N.L. and Wodarz D. 2009 Combination therapies against chronic myeloid leukemia: short-term vs. long-term strategies. Cancer Research 69, 4904-10

94. Komarova N.L., Katouli A.A., & Wodarz D. 2009 Combination of two but not three current targeted drugs can improve therapy of chronic myeloid leukemia. PLoS One 4(2), e4423.

93. Wodarz D and Komarova N.L. 2009 Towards predictive computational models of oncolytic virus therapy: basis for experimental validation and model selection. PLoS One 4(1):e4271.

92. Wodarz D. 2009 Use of oncolytic viruses for the eradication of drug resistant cancer cells. J. R. Soc. Interface 6, 179-186.

91. Wodarz D. 2008 Immunity and protection by live attenuated HIV/SIV vaccines. Virology 378, 299-305.

90. Wodarz D. and Levy DN 2007 Human immunodeficiency virus evolution towards reduced replicative fitness in vivo and the development of AIDS. Proc. Biol. Sci. 274, 2481-90

89. Komarova NL and Wodarz D 2007 Effect of cellular quiescence on the success of targeted CML therapy. PLoS ONE 2(10): e990

88. Komarova NL and Wodarz D 2007 Stochastic modeling of cellular colonies with quiescence: an application to drug resistance in cancer. Theor. Popul. Biol. 72, 523-38

87. Wodarz D 2007 On the relative fitness of early and late stage simian immunodeficiency virus isolates. Theor. Pop. Biol. 72, 426-35.

86. Wodarz D 2007 Stem cell regulation and the development of blast crisis in chronic myeloid leukemia: implications for the outcome of imatinib treatment and discontinuation. Medical Hypotheses, 70, 128-36

85. Wodarz D and Komarova NL 2007 Can loss of apoptosis protect against cancer? Trends in Genetics. 23, 232-7

84. Wodarz D and Hamer DH 2007 Infection dynamics in HIV-specific CD4 T cells: does a CD4 T cell boost benefit the host or the virus? Mathematical Biosciences, 209, 14-29

83. Komarova NL and Wodarz D 2007 Cancer as a microevolutionary process. In Stephen C. Stearns, and Jacob C. Koella (eds), Evolution in Health and Disease, 2nd edn (Oxford, 2007;online edn, Oxford Academic, 1 Apr. 2010)

82. Komarova, N.L., Wodarz, D., Boland, C.R. & Goel, A. (2007) Genetic and epigenetic pathways to colon cancer: relating experimental evidence with modeling. In Selected Topics in Cancer Modeling: Genesis, Evolution, Immune Competition, and Therapy (pp. 1-30). Boston: Birkhäuser Boston.

81. Zurakowski R and Wodarz D 2007 Model-driven approaches for in vitro combination therapy using ONYX-015 replicating oncolytic adenovirus. J. Theor. Biol., 245, 1-8.

80. Wodarz D, Sierro S, and Klenerman, P 2007 Dynamics of killer T cell inflation in viral infections. J R Soc Interface 4, 533-543.

79. Wodarz D. 2007 Effect of stem cell turnover rates on protection against cancer and aging. J. Theor. Biol. 245, 449-58.

78. Wodarz D. 2006 Somatic evolution of cells and the development of cancer. Biological Theory, 1, 119-122.

77. Wodarz D 2006 Targeted cancer treatment: resisting arrest. Nature Medicine, 12, 1125-1126

76. Wodarz D 2006 Ecological and evolutionary principles in immunology. Ecology Letters, 9, 694-705.

75. Wodarz D 2006 Pathogens as biological tools in host competition. Research Journal Parasitology, 1, 19-30.

74. Lloyd AL and Wodarz D 2006 Drug resistance in acute viral infections: rhinovirus as a case study. In Disease Evolution: models, concepts, and data analysis, DIMACS series in discrete mathematics and theoretical computer science, volume 71 (Z. Feng, U. Dieckmann, S. Levin ed).

73. Wodarz D and Komarova NL 2005 Evolutionary dynamics of drug resistance in cancer. Gene Therapy and Molecular Biology, 9, 247-256.

72. Wodarz D 2005 Somatic evolution of cancer cells. Seminars in Cancer Biology, 15, 421-422.

71. Wodarz D and Komarova NL 2005 Emergence and prevention of resistance against small molecule inhibitors. Seminars in Cancer Biology, 15, 506-14.

70. Komarova NL and Wodarz D 2005 Drug resistance in cancer: principles of emergence and resistance. Proc. Natl. Acad. Sci USA, 102, 9714-9

69. Wodarz D and Anton-Culver H 2005 Dynamical interactions between multiple cancers. Cell Cycle, 4, 764-71

68. Wodarz D and Thomsen AR 2005 Effect of the CTL proliferation program on virus dynamics. International immunology, 17, 1269-76

67. Wodarz D & Thomsen AR 2005 Does programmed CTL proliferation optimize virus control? Trends in immunology, 26, 305-310

66. Wodarz D 2004 Checkpoint genes, ageing, and the development of cancer. Oncogene 23, 7799-809.

65. Jansen VA, Korthals Altes H, Funk GA & Wodarz D 2005. Contrasting B and T cell based vaccines. Journal of Theoretical Biology, 234, 39-48

64. Wodarz D and Iwasa Y & Komarova NL 2004 On the emergence of multifocal cancers. Journal of Carcinogenesis 3, 13.

63. Wodarz D. 2005 Mathematical models of immune effector responses to viral infections: virus control versus the development of pathology. Journal of computational and applied mathematics 184, 301-313.

62. Zurakowsky R, Teel AR & Wodarz D. 2004. Utilizing alternate target cells in treating HIV infection through scheduled treatment interruptions. 2004. Procceedings of the American Control Conference

61. Wodarz D 2004. Computational approaches to study oncolytic virus therapy: insights and challenges. Gene Therapy and Molecular Biology 8, 137-146

60. Komarova NL & Wodarz D. 2004. The optimal rate of chromosome loss for the inactivation of tumor suppressor genes in cancer. Proc. Natl. Acad. Sci. USA. 101, 7017-21

59. Wodarz D & Lloyd AL 2004 Immune responses and the emergence of drug resistant virus strains in vivo. Proc. Roy. Soc. Lond. B. 271, 1101-1109.

58. Wodarz D & Sasaki A 2004 Apparent competition and recovery from infection. J. Theor. Biol. 227, 403-12

57. Christensen JE, Wodarz D, Christensen JP & Thomsen AR 2004. Perforin and IFN-gamma do not significantly regulate the virus-specific CD8+ T cell response in the absence of antiviral effector activity. Eur. J. Immunol. 34, 1389-94

56. Wodarz D. 2003 Mathematical models of HIV and the immune system. Novartis Found Symp. 254,193-207; discussion 207-22, 250-2.

55. Wodarz D 2003 Correspondence re: L. M. Wein et al., validation and analysis of a mathematical model of a replication-competent oncolytic virus for cancer treatment: implications for virus design and delivery. Cancer Res., 63, 1317-1324.

54. Komarova NL & Wodarz D 2003 Evolutionary dynamics of mutator phenotypes in cancer: implications for chemotherapy. Cancer Research, 63, 6635-6642.

53. Wodarz D. 2003 Mutants escape killer T cells, invade population! Nature Medicine 9,1254-1255.

52. Wodarz D 2003 Evolution of immunological memory and the regulation of competition between pathogens. Current Biology, 13, 1648-1652. Also, see article in Science News, September 27 2003: Faulty Memory: long-term immunity isn’t always beneficial.

51. Liu H, Wodarz D, Andreansky S, Diaz G, Turner SG & Doherty PC 2003 Quantitative analysis of long-term virus-specific CD8+-T-cell memory in mice challenged with unrelated pathogens. J. Virol. 77, 7756-7763.

50. Wodarz D 2003 Dynamics of Hepatitis C virus disease progression: role of CTL and antibody responses. J. Gen. Virol. 84, 1743-1750

49. Wodarz D 2003 Gene therapy for killing p53 negative cancer cells: the use of replicating versus non-replicating agents. Human Gene Therapy 14, 153-159.

48. Wodarz D & Jansen VAA 2003 A dynamical perspective of CTL cross-priming and regulation: implications for tumor immunology. Immunology Letters, 86, 213-307.

47. Komarova NL, Barnes E, Klenerman P & Wodarz D 2003 Boosting immunity by anti-viral therapy: a simple relationship between timing, efficacy and success. Proc. Natl. Acad. Sci. USA 100, 1855-1860.

46. Wodarz D 2003 Mathematical models of HIV and the immune system. In: Immunoinformatics: Bioinformatic strategies for better understanding immune function. Novartis Foundation symposium, Wiley.

45. Wodarz D 2002 Acquired immunodeficiency syndrome: Dynamics of HIV transmission and infection. Encyclopedia of Evolution. Ed. Mark Pagel. Oxford University Press.

44. Wodarz D 2002 The persistence of CTL memory. The Netherland Journal of Medicine 60, 4-13.

43. Wodarz D, Christensen JP & Thomsen AR 2002 The importance of lytic and non-lytic immune responses in viral infections. Trends in Immunology 23, 194-200.

42. Wodarz D & Nowak MA 2002 Mathematical Models of HIV Pathogenesis and Treatment. Bioessays, 24, 1178-1187.

41. Altes H, Wodarz D & Jansen VAA 2002 The dual role of CD4 T helper cells in the infection dynamics of HIV and their importance for vaccination. J. Theor. Biol. 21, 633-46.

40. Belz GT, Wodarz D, Turner SJ, Diaz G, Nowak MA & Doherty PC 2002 Compromised influenza-specific CD8+ T cell memory in CD4+ T cell deficient mice. J. Virol. 76, 12388-12393.

39. Wodarz D 2001 Viruses as anti-tumor weapons: defining conditions for tumor remission. Cancer Research, 61, 3501-3507.

38. Wodarz D 2001 Mechanisms underlying antigen-specific CD8 T cell homeostasis. Science, 292, 595.

37. Wodarz D 2001 Cytotoxic T lymphocyte memory, virus clearance and antigenic heterogeneity. Proc. Roy. Soc. Lond. B. 268, 429-436.

36. Wodarz D 2001 Helper dependent versus helper independent CTL responses in HIV infection: Implications for drug therapy and resistance. J. Theor. Biol 213, 447-459.

35. Wodarz D 2001 The persistence of CTL memory. Proceedings of the 13th Smithklein Beecham Workshop on infectious diseases.

34. Wodarz D, Hall SE, Usuku K, Ogg GS, McMichael AJ, Nowak MA & Bangham CRM 2001 Cytotoxic T lymphocyte abundance and virus load in HIV-1 and HTLV-1. Proc. Roy. Soc. Lond. B, 268, 1215-1221.

33. Wodarz D & Jansen VAA 2001 The role of T cell help for anti-viral CTL responses. J. Theor. Biol., 211, 419-432.

32. Wodarz D and Krakauer DC 2001 Genetic instability and the evolution of angiogenic tumor cell lines. Oncology Reports 8: 1195-1201.

31. Christensen JP, Bartholdy C, Wodarz D & Thomsen AR 2001 Depletion of CD4+ T cells precipitates immunopathology in immunodeficient mice infected with a noncytocidal virus. J. Immunol. 166, 3384-91

30. Lifson JD, Rossio JL, Piatak M, Parks T, Li L, Kiser R, Coalter V, Fisher B, Flynn BM, Hirsch VM, Means RE, Czajak S, Reimann KA, Schmitz JE, Ghrayeb J, Bischofberger N, Nowak MA, Desrosiers RC & Wodarz D 2001 Role of CD8+ Lymphocytes in control of simian immunodeficiency virus infection and resistance to rechallenge after transient early antiretroviral treatment. J. Virol. 75, 10187-99.

29. Wodarz D 2000 CTL dynamics and immune impairment: implications for HIV therapy. Mod. Asp. Immunobiol. 1, 24-27.

28. Wodarz D, Arnaout RA, Nowak MA & Lifson JD 2000 Transient antiretroviral treatment during acute simian immunodeficiency virus infection facilitates long-term control of the virus. Phil. Trans. Roy. Soc. Lond. B. 355, 1021-1029.

27. Wodarz D & Bangham CR 2000 Evolutionary dynamics of HTLV-I. J Mol Evol 50, 448-55.

26. Wodarz D & Krakauer DC 2000 Defining CTL-induced pathology: implications for HIV Virology 274, 94-104.

25. Wodarz D, May RM & Nowak MA 2000 The role of antigen-independent persistence of memory cytotoxic T lymphocytes. Int Immunol 12, 467-77.

24. Wodarz D & Nowak MA 2000 Immune responses and viral phenotype: do replication rate and cytopathogenicity influence virus load? Journal of Theoretical Medicine 2, 113-127.

23. Wodarz D & Nowak MA 2000 CD8 memory, immunodominance, and antigenic escape. Eur. J. Immunol. 30, 2704-2712.

22. Wodarz D & Nowak MA 2000 Correlates of cytotoxic T lymphocyte mediated virus control: implications for immunosuppressive infections and their treatment. Phil. Trans. Roy. Soc. Lond. B. 355, 1059-1070.

21. Wodarz D & Nowak MA 2000 HIV therapy: managing resistance. Proc Natl Acad Sci USA 97, 8193-5.

20. Wodarz D, Page KM, Arnaout RA, Thomsen AR, Lifson JD & Nowak MA 2000 A new theory of cytotoxic T-lymphocyte memory: implications for HIV treatment. Philos Trans R Soc Lond B Biol Sci 355, 329-43.

19. Arnaout RA, Nowak MA & Wodarz D 2000 HIV-1 dynamics revisited: biphasic decay by cytotoxic T lymphocyte killing? Proc. Roy. Soc. Lond. B. 267, 1347-1354.

18. Barchet W, Oehen S, Klenerman P, Wodarz D, Bocharov G, Lloyd AL, Nowak MA, Hengartner H, Zinkernagel RM & Ehl S. 2000 Direct quantitation of rapid elimination of viral antigen-positive lymphocytes by antiviral CD8(+) T cells in vivo. Eur J Immunol 30, 1356-63.

17. Bartholdy C, Christensen JP, Wodarz D & Thomsen AR 2000 Persistent virus infection despite chronic cytotoxic T lymphocyte activation in gamma interferon deficient mice infected with lymphocytic choriomeningitis virus. J. Virol. 74, 10304-11.

16. Lifson JD, Rossio JL, Arnaout R, Li L, Parks TL, Schneider DK, Kiser RF, Coalter VJ, Walsh G, Imming RJ, Fisher B, Flynn BM, Bischofberger N, Piatak M Jr., Hirsch VM, Nowak MA & Wodarz D 2000 Containment of simian immunodeficiency virus infection: cellular immune responses and protection from rechallenge following transient postinoculation antiretroviral treatment. J Virol 74, 2584-93.

15. Thomsen RA, Nansen A, Andreasen SO, Wodarz D & Christensen JP 2000 Host factors influencing viral persistence. Phil. Trans. Roy. Soc. Lond. B. 355, 1031-1041.

14. Smith MS, Foresman L, Lopez G, Tsay J, Page A, Wang C, Li Z, Adany I, Wodarz D, Lifson JD, Bischofsberger N & Narayan O 2000 Lasting effects of transient post-inoculation tenofovir treatment on SHIV(KU2) infection of rhesus macaques. Virology 277, 306-15.

13. Wodarz D, Lloyd AL, Jansen VA & Nowak MA 1999 Dynamics of macrophage and T cell infection by HIV. J Theor Biol 196, 101-13.

12. Wodarz D & Nowak MA 1999 Specific therapy regimes could lead to long-term immunological control of HIV. Proc Natl Acad Sci U S A 96, 14464-9.

11. Wodarz D & Nowak MA 1999 Dynamics of drug therapy and resistance in HIV-1 infection. Novartis Foundation Meeting Review

10. Wodarz D & Nowak MA 1999 Dynamics of HIV pathogenesis and treatment. In Origin and Evolution of Viruses, eds. E Domingo, R Webster, J Holland. London: Academic Press, 197- 223.

9. Wodarz D & Nowak MA 1999 Dynamics of immune escape in HIV infection. Wien Klin Wochenschr 111, 419-27.

8. Wodarz D & Nowak MA 1999 Evolutionary dynamics of HIV-induced subversion of the immune response. Immunol Rev 168, 75-89.

7. Wodarz D, Nowak MA & Bangham CR 1999 The dynamics of HTLV-I and the CTL response. Immunol Today 20, 220-7.

6. Bangham CR, Hall SE, Jeffery KJ, Vine AM, Witkover A, Nowak MA, Wodarz D, Usuku K & Osame M 1999 Genetic control and dynamics of the cellular immune response to the human T-cell leukaemia virus, HTLV-I. Philos Trans R Soc Lond B Biol Sci 354, 691-700.

5. Wodarz D, Klenerman P & Nowak MA 1998 Dynamics of cytotoxic T-lymphocyte exhaustion. Proc R Soc Lond B Biol Sci 265, 191-203.

4. Wodarz D & Nowak MA 1998 The effect of different immune responses on the evolution of virulent CXCR4-tropic HIV. Proc R Soc Lond B Biol Sci 265, 2149-58.

3. Wodarz D & Nowak MA 1998 Mathematical models of virus dynamics and resistance. Journal of HIV therapy 3, 36-41

2. Regoes RR, Wodarz D & Nowak MA 1998 Virus dynamics: the effect of target cell limitation and immune responses on virus evolution. J Theor Biol 191, 451-62

1. Wodarz D, Aescht E & Foissner W 1992 A weighted Coenotic Index (WCI): Description and application to soil animal assemblages. Biol. Fertil. Soils 14, 5-13.

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