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154. Shank K, Dunbar A, Koppikar P, Kleppe M, Teruya-Feldstein J, Csete IS, Bhagwat N, Keller M, Kilpivaara O, Michor F, Levine R, De Vargas Roditi L (2019) Mathematical modeling reveals alternative JAK inhibitor treatment in myeloproliferative neoplasms. Haematologica, in press.

153. Janiszewska M*, Tabassum DP*, Castano Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Gil Del Alcazar C, Aleckovic M, Ekram MB, Cohen O, Kwak M, Qin Y, Laszewski T, Luoma A, Marusyk A, Wucherpfennig KW, Wagle N, Fan R, Michor F, McAllister S, Polyak K (2019) Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Nat Cell Biol 21, 879-888. * Equal contribution. (PDF)

152. Yamamoto KN, Liu LL, Nakamura A, Haeno H, Michor F (2019) Stochastic evolution of pancreatic cancer metastases during logistic clonal expansion. JCO Clinical Cancer Informatics 3, 1-11. (PDF)

151. Yamamoto KN, Nakamura A, Liu LL, Stein S, Tramontano AC, Kartoun U, Shimizu T, Inoue Y, Asakuma M, Haeno H, Kong CY, Uchiyama K, Gonen M, Hur C, Michor F (2019) Computational modeling of pancreatic cancer patients receiving FOLFIRINOX and gemcitabine-based therapies identifies optimum intervention strategies. PLoS ONE 14, e0215409. (PDF)

150. Ferlic J, Shi J, McDonald TO, Michor F (2019) DIFFpop: A stochastic computational approach to simulate differentiation hierarchies with single cell barcoding. Bioinformatics, btz074. (PDF)

149. Altrock PM, Ferlic J, Galla T, Tomasson M, Michor F (2018) A computational model of MGUS progression to multiple myeloma identifies optimum screening strategies and their effects on mortality. JCO Clinical Cancer Informatics 2, 1-12.  (PDF)

148. Chakrabarti S*, Paek AL*, Reyes J, Lasick KA, Lahav G+, Michor F+ (2018) Hidden heterogeneity and circadian-controlled cell fate inferred from single cell lineages. Nat Comm 9, 5372. * Equal contribution. + Co-corresponding authors. (PDF)

147. Hinohara K*, Wu H-J*, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrandt AA, Michor F+, Polyak K+ (2018) KDM5 histone demethylase activity links cellular transcriptomic heterogeneity to therapeutic resistance. Cancer Cell 34, 939-953. * Equal contribution. + Co-corresponding authors. (PDF)

146. McDonald TO*, Chakrabarti S*, Michor F (2018) Currently available bulk sequencing data does not necessarily support a model of neutral tumor evolution. Nat Gen 50, 1620-1623. * Equal contribution. (PDF)

145. Van Egeren D, Madsen T, Michor F (2018) Fitness variation in isogenic populations leads to a novel evolutionary mechanism for crossing fitness valleys. Communications Biology 1, 151. (PDF)

144. Karaayvaz M*, Cristea S*, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F+, Ellisen LW+ (2018) Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nature Communications 9, 3588. * Equal contribution. + Co-corresponding authors. (PDF)

143. Jun HJ, Appleman VA, Wu H-J, Rose CM, Pineda JJ, Yeo AT, Delcuze B, Lee C, Gyuris A, Zhu H, Woolfenden S, Bronisz A, Nakano I, Chiocca EA, Bronson RT, Ligon KL, Sarkaria JN, Gygi SP, Michor F, Mitchison TJ, Charest A (2018) A PDGFRalpha-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine. Nature Communications 9, 3116. (PDF)

142. Stover D, Del Alcazar CG, Brock J, Guo H, Overmoyer B, Balko J, Xu Q, Bardia A, Tolaney S, Gelman R, Lloyd M, Wang Y, Xu Y, Michor F, Wang V, Winer E, Polyak K, Lin N (2018) Phase II study of ruxolitinib, a selective JAK1/2 inhibitor, in patients with metastatic triple-negative breast cancer. NPJ Breast Cancer 4, 10. (PDF)

141. Cimino PJ, Kim Y, Wu HJ, Alexander J, Wirsching H-G, Szulzewsky F, Pitter K, Ozawa T, Wang J, Vazquez J, Arora S, Rabadan R, Levine RL, Michor F, Holland EC (2018) Increased HOXA5 expression provides a selective advantage for gain of whole chromosome 7 in IDH-wildtype glioblastoma. Genes & Development 32, 512-523. (PDF)

140. Stein S, Zhao R, Haeno H, Vivanco I, Michor F (2018) Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients. PLoS Computational Biology 14, e1005924. (PDF)

139. Riester M*, Xu Q*, Moreira A, Zheng J, Michor F+, Downey RD+ (2017) The Warburg effect: persistence of stem cell metabolism in cancers as a failure of differentiation. Annals of Oncology 29, 264-270. * Equal contribution. + Co-corresponding authors. (PDF)

138. Malone CF, Emerson C, Ingraham R, Barbosa W, Guerra S, Yoon H, Liu LL, Michor F, Haigis M, Macleod KF, Maertens O, Cichowski K (2017) mTOR and HDAC inhibitors converge on the TXNIP/thioredoxin pathway to cause catastrophic oxidative stress and regression of RAS-driven tumors. Cancer Discovery 7, 1450-1463. (PDF)

137. Smith K*, Lin LL*, Ganesan S, Michor F+, De S+ (2017) Nuclear topology modulates the mutational landscapes of cancer genomes. Nat Struct Mol Biol 24, 1000-1006. * Equal contribution. + Co-corresponding authors. (PDF)

136. Maruvka YE, Mouw KW, Karlic R, Parasuraman P, Kamburov A, Polak P, Haradhvala NJ, Hess JM, Rheinbay E, Brody Y, Koren A, Braunstein LZ, D'Andrea A, Lawrence MS, Bass A, Bernards A, Michor F, Getz G (2017) Analysis of somatic microsatellite indels identifies driver events in human tumors. Nature Biotechnology 35, 951–959. (PDF)

135. Del Alcazar CRG, Huh SJ, Ekram MB, Trinh A, Liu LL, Beca F, Zi X, Kwak M, Bergholtz H, Su Y, Ding L, Russnes HG, Richardson AL, Babski K, Kim EMH, McDonnell III CH, Wagner J, Rowberry R, Freeman GJ, Dillon D, Sorlie T, Coussens LM, Garber JE, Fan R, Bobolis K, Allred DC, Jeong J, Park SY, Michor F, Polyak K (2017) Immune escape in breast cancer during in situ to invasive carcinoma transition. Cancer Discovery 7, 1098-1115. (PDF)

134. Smith ZD*, Shi J*, Gu H, Dongahey J, Clement K, Cacciarelli D, Gnirke A, Michor F+, Meissner A+ (2017) Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature 549, 543–547. * and + Equal contribution. (PDF)

133. Chakrabarti S, Michor F (2017) Pharmacokinetics and drug-interactions determine optimum combination strategies in computational models of cancer evolution. Can Res 77, 3908-3921. (PDF)

132. Zhao R, Catalano PJ, DeGruttola VG, Michor F (2017) Estimating mono- and bi-phasic regression parameters using a mixture piecewise linear Bayesian hierarchical model. PLoS One 12, e0180756. (PDF)

131. Mishima Y, Paiva B, Shi J, Massoud M, Manier S, Flores L, Perilla-Glen A, Aljawai Y, Takagi S, Huynh D, Roccaro AM, Sacco A, Alginani D, Mateos M-V, Blade J, Lahuerta J-J, Richardson P, Laubach J, Schlossman R, Anderson K, Munshi N, Prosper F, San Miguel JF, Michor F, Ghobrial IM (2017) The mutational landscape of circulating tumor cells in multiple myeloma. Cell Reports 19, 218–224. (PDF)

130. Temko D, Cheng Y-K, Polyak K, Michor F (2017) Mathematical modeling links pregnancy-associated changes and breast cancer risk. Can Res 77, 2800-2809. (PDF)

129. McDonald TO, Michor F (2017) SIApopr: A computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution. Bioinformatics 33, 2221–2223. (PDF)

128. Gibson CJ, Lindsley RC, Tchekmedyian V, Mar B, Shi J, Jaiswal S, Bosworth A, Francisco LF, He J, Bansal A, Morgan EA, Lacasce A, Freedman A, Fisher DC, Jacobsen E, Armand P, ALyea EP, Koreth J, Ho V, Soiffer R, Antin JH, Ritz J, Nikiforow S, Forman SJ, Michor F, Neuberg D, Bhatia R, Bhatia S, Ebert BL (2017) Clonal hematopoiesis associated with adverse outcomes following autologous stem cell transplantation for lymphoma. Jour Clin Oncol 35, 1598-1605. (PDF)

127. Riester M, Wu H-J, Zehir A, Gonen M, Moreira AL, Downey RJ, Michor F (2017) Distance in cancer gene expression from stem cells predicts patient survival. PLoS One 12, e0173589. (PDF)

126. Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip N S, Michor F, Nevo D, Peters U, Phipps AI, Poole EM, Qian ZR, Quackenbush J, Robins H, Rogan PK, Slattery ML, Smith‐Warner SA, Song M, VanderWeele TJ, Xia Daniel, Zabor EC, Zhang X, Wang M, Ogino S (2017) Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control 28, 167-176. (PDF)

125. Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, Fan R, Pan X (2017) Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucl Acids Res 45, e77. (PDF)

124. Yu HA, Sima C, Feldman D, Liu LL, Vaitheesvaran B, Cross J, Rudin CM, Kris MG, Pao W, Michor F, Riely GJ (2017) Phase 1 study of twice weekly pulse dose and daily low dose erlotinib as initial treatment for patients with EGFR-mutant lung cancers. Annals of Oncology 28, 278-284. (PDF)

123. Liu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F (2016) Probabilistic modeling of reprogramming to induced pluripotent stem cells. Cell Reports 17, 3395-3401. (PDF)

122. Wu HJ, Michor F (2016) A computational strategy to adjust for copy number in tumor Hi-C data. Bioinformatics 32, 3695-3701. (PDF)

121. Gao R, Davis A, McDonald T, Sei E, Shi X, Wang Y, Tsai P-C, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F, Navin NE (2016) Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nature Genetics 48, 1119–1130. (PDF)

120. Altrock PM*, Brendel C*, Renella R, Orkin SH, Williams DA, Michor F (2016) Mathematical modeling of erythrocyte chimerism informs genetic intervention strategies for sickle cell disease. Am J Hematol 91, 931–937. * Equal contribution. (PDF)

119. Wee B, Pietras A, Ozawa T, Bazzoli E, Podlaha O, Antczak C, Westermark B, Nelander S, Uhrbom L, Forsberg-Nilsson K, Djaballah H, Michor F, Holland EC (2016) ABCG2 regulates self-renewal and stem cell marker expression but not tumorigenicity or radiation resistance of glioma cells. Scientific Reports 6, 25956. (PDF)

118. Tang M*, Zhao R*, van de Velde H, Ge Y, Mitsiades C, Viselli S, Neuwirth R, Esseltine D-L, Anderson K, Ghobrial IM, San Miguel JF, Richardson PG, Tomasson MH, Michor F (2016) Myeloma cell dynamics in response to treatment supports a model of hierarchical differentiation and clonal evolution. Clin Can Res 22, 4206-4214. * Equal contribution (PDF)

117. Badri H, Pitter K, Holland EC, Michor F, Leder K (2016) Optimization of radiation dosing schedules for proneural glioblastoma. Jour Math Biol. 72, 1301-36. (PDF)

116. Liu LL, Li F, Pao W, Michor F (2015) Dose-dependent mutation rates determine optimum erlotinib dosing strategies for EGFR mutant non-small cell lung cancer patients. PLoS ONE 10, e0141665. (PDF)

115. Foo J, Liu LL, Leder K, Riester M, Iwasa Y, Lengauer C, Michor F (2015) An evolutionary approach for identifying driver mutations in colorectal cancer. PLoS CB 11, e1004350. (PDF)

114. Altrock PM*, Liu LL*, Michor F (2015) The mathematics of cancer: integrating quantitative models. Nat Rev Can 15, 730-745. * Equal contribution (PDF).

113. Michor F, Beal K (2015) Improving cancer treatment via mathematical modeling of population dynamics. Cell 163, 1059-1063. (PDF)

112. Janiszewska M, Liu LL, Almendro V, Kuang Y, Paweletz, Sakr RA, Weigelt B, Hanker AB, Chandarlapaty S, King TA, Reis-Filho JS, Arteaga CL, Park SY, Michor F, Polyak K (2015) In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer. Nature Genetics 47, 1212-1219. (PDF)

111. Roccaro AM, Mishima Y, Sacco A, Moschetta M, Tai Y-T, Shi J, Zhang Y, Reagan MR, Huynh D, Kawano Y, Sahin I, Chiarini M, Manier S, Cea M, Aljawai Y, Glavey S, Morgan E, Pan C, Michor F, Cardarelli P, Kuhne M, Ghobrial IM (2015) CXCR4 regulates extra-medullary myeloma through epithelial-mesenchymal-transition-like transcriptional activation. Cell Reports 12, 622-635. (PDF)

110. Mumenthaler SM, Foo J, Choi NC, Heise N, Leder K, Agus DB, Pao W, Michor F, Mallick P (2015) The impact of microenvironmental heterogeneity on the evolution of drug resistance in cancer cells. Cancer Informatics 14, 19-31. (PDF)

109. Bambury RM, Bhatt AS, Riester M, Pedamallu CS, Duke F, Bellmunt J, Stack EC, Werner L, Park R, Iyer G, Loda M, Kantoff PM, Michor F, Meyerson M, Rosenberg JE (2015) DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors. BMC Cancer 15, 242. (PDF)

108. Bhang HC, Ruddy DA, Radhakrishna VK, Caushi JX, Zhao R, Hims MM, Singh AP, Kao I, Rakiec D, Shaw P, Balak M, Raza A, Ackley E, Keen N, Schlabach MR, Palmer M, Leary RJ, Chiang DY, Sellers WR, Michor F, Cooke VG, Korn JM, Stegmaier F (2015) High complexity barcoding to study clonal dynamics in response to cancer therapy. Nature Medicine 5, 440-448. (PDF)

107. Selmecki A, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson A, De S, Kishony R, Michor F, Dowell R, Pellman D (2015) Polyploidy can drive rapid adaptation in yeast. Nature 519, 349-352. (PDF)

106. Ashcroft P, Michor F, Galla T (2015) Stochastic tunneling and metastable states during the somatic evolution of cancer. Genetics 199, 1213-1228. (PDF)

105. Kleppe M, Kwak M, Koppikar P, Riester M, Keller M, Bastian L, Hricik T, Bhagwat N, Abdel-Wahab O, Rampal R, Marubayashi S, Chen JC, Romanet V, Fridman J, Bromberg J, Teruya-Feldstein J, Murakami M, Radimerski T, Michor F, Fan R, Levine R (2015) JAK-STAT pathway activation in malignant and non-malignant cells contributes to MPN pathogenesis and therapeutic response. Cancer Discovery 5, 316-331. (PDF)

104. Randles A, Driscoll M, Draeger EW, Michor F (2014) A Feasibility Study using Image-based Parallel Modeling for Treatment Planning. In Computing in Cardiology. Cambridge, MA (PDF)

103. Randles A, Draeger E, and Michor F (2014) Analysis of pressure gradient across aortic stenosis with massively parallel computational simulations. Computing in Cardiology 41, 217-220. (PDF)

102. Olshen A, Tang M, Cortes J, Gonen M, Hughes T, Branford S, Quintas-Cardama A, Michor F (2014) Dynamics of chronic myeloid leukemia response to dasatinib, nilotinib, and high-dose imatinib. Haematologica 99, 1701-1709. (PDF)

101. Shaknovich S, De S, Michor F (2014) Epigenetic diversity in hematopoietic neoplasms. BBA Reviews on Cancer 1846, 477-484. (PDF)

100. Marusyk A, Tabassum D, Altrock P, Almendro V, Michor F, Polyak K (2014) Non-cell-autonomous driving of tumor growth supports sub-clonal heterogeneity. Nature 514, 54-58. (PDF)

99. Wang Y, Leung M, Waters J, Unruh A, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE (2014) Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512, 155-160. (PDF)

98. Ozawa T*, Riester M*, Cheng Y-K, Huse JT, Squatrito M, Helmy K, Charles N, Michor F+, Holland EC+ (2014) Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma. Cancer Cell 26, 288-300. * Equal contribution. + Equal contribution. (PDF)

97. Maruvka YE, Tang M, Michor F (2014) On the validity of using increases in 5-year survival rates to measure success in the fight against cancer. PLoS One 9, e83100. (PDF)

96. Podlaha O, De S, Gonen M, Michor F (2014) Histone modifications are associated with transcript isoform diversity in normal and cancer cells. PLoS CB 10, e1003611. (PDF)

95. Guancial EA, Werner L, Bellmunt J, Bamias A, Choueiri TK, Ross R, Schutz FA, Park R, O'Brien RJ, Hirsch M, Barletta JA, Berman DM, Lis R, Loda M, Stack EC, Garraway L, Riester M, Michor F, Chehab NH, Kantoff P, Rosenberg J (2014) FGFR3 expression in primary and metastatic urothelial carcinoma of the bladder. Can Med 3, 835-844. (PDF)

94. Riester M, Wei W, Walden L, Culhane A, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer M (2014) Risk prediction for late-stage ovarian cancer by meta-analysis of 1,525 patient samples. JNCI 106, 1-12. (PDF)

93. Foo J, Michor F (2014) Evolution of acquired resistance to anti-cancer therapy. J Theor Biol 355, 10-20. (PDF)

92. Michor F, Weaver VM (2014) Understanding tissue context influences on intratumor heterogeneity. Nat Cell Biol 16, 301-302. (PDF)

91. Almendro V, Kim HJ, Cheng Y-K, Gonen M, Itzkovitz S, Argani P, van Oudenaarden A, Sukumar S, Michor F, Polyak K (2014) Genetic and phenotypic diversity in breast tumor metastases. Cancer Research 74, 1338-1348. (PDF)

90. Riester M, Werner L, Bellmunt J, Selvarajah S, Guancial EA, Weir BA, Stack EC, Park RS, O'Brien R, Schutz FAB, Choueiri TK, Signoretti S, Lloreta J, Marchionni L, Gallardo E, Rojo F, Garcia DI, Chekaluk Y, Kwiatkowski D, Bochner B, Hahn WC, Ligon AH, Barletta JA, Loda M, Berman DM, Kantoff P, Michor F, Rosenberg JE (2014) Integrative analysis of 1q23.3 copy number gain in metastatic urothelial carcinoma. Clinical Cancer Research 20, 1873-1883. (PDF)

89. Chambwe N, Kormaksson M, Geng H, De S, Michor F, Johnson N, Morin RD, Scott DW, Godley LA, Gascoyne RD, Melnick A, Campagne F, Shaknovich R (2014) Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood 123, 1699-1708. (PDF)

88. Leder K*, Pitter K*, LaPlante Q, Hambardzumyan D, Ross BD, Chan TA, Holland EC+, Michor F+ (2014) Mathematical modeling of PDGF-driven
glioblastoma reveals optimized radiation dosing schedules. Cell 156, 603-616. * Equal contribution. + Co-corresponding authors. (PDF)

87. Almendro V, Cheng Y-K, Randles A, Itzkovitz S, Marusyk A, Ametller E, Gonzalez-Farre X, Munoz M, Russness HG, Helland A, Rye IH, Borresen-Dale A-L, Maruyama R, van Oudenaarden A, Dowsett M, Jones RL, Reis-Filho J, Gascon P, Gonen M, Michor F, Polyak K (2014) Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell Reports 6, 514-527. (PDF)

86. Gallipoli P, Stobo J, Heaney N, Nicolini FE, Clark RE, Wilson G, Tighe J, McLintock L, Hughes T, Michor F, Paul J, Drummond M, Holyoake TL (2013) Safety and efficacy of pulsed imatinib with or without G-CSF versus continuous imatinib in chronic phase chronic myeloid leukaemia patients at 5 years follow-up. Br J Haematol 163, 674-676. (PDF)

85. Jia P, Jin H, Meador CB, Xia J, Ohashi K, Liu L, Pirazzoli V, Dahlman KB, Politi K, Michor F, Zhao Z, Pao W (2013) Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance. Genome Research 23, 1434-1445. (PDF)

84. Choudhury S, ALmendro V, Maruyama R, Wu Z, Merino VF, Su Y, Martins FC, Fackler MJ, Bessarabova M, Kowalczyk A, Conway T, Beresford-Smith B, Macinture G, Cheng Y-K, Lopez-Bujada Z, Kaspi A, Hu R, Robens J, Nikolskaya T, Haakensen VD, Schnitt SJ, Argani P, Ethington G, Panos L, Grant M, Clark J, Herlihy W, Lin SJ, Chew G, Thompson EW, Greene-Colozzi A, Richardson A, Rosson GD, Pike M, Nikolsky Y, Blum J, Tamimi RM, Michor F, Haviv I, Liu XS, Sukumar S, Polyak K (2013) Molecular profiling of human mammary gland links breast cancer risk to a p27+ cell population with progenitor characteristics. Cell Stem Cell 13, 117-130. (PDF)

83. Haeno H, Maruvka YE, Iwasa Y*, Michor F* (2013) Stochastic tunneling of two mutations in a population of cancer cells. PLoS One 8, e65724. * Equal contribution. (PDF)

82. Zhao R, Michor F (2013) Patterns of proliferative activity in the colonic crypt determine crypt stability and rates of somatic evolution. PLoS Computational Biology 9, e1003082. (PDF)

81. The Physical Sciences-Oncology Center Network (2013) A physical sciences network characterization of nonmalignant and metastatic cells. Scientific Reports 3, 1-12. (PDF)

80. Liu L, De S, Michor F (2013) DNA replication timing and higher-order nuclear organization determine single nucleotide substitution patterns in cancer genomes. Nature Communications 4, 1502. (PDF)

79. Ohashi K, Maruvka Y, Michor F, Pao W (2013) Epidermal growth factor receptor tyrosine kinase inhibitor-resistant disease. J Clin Oncol 31, 1070-1080. (PDF)

78. De S*, Shaknovich R*, Riester M*, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, Cerchietti L, Gascoyne RD, Melnick A+, Michor F+ (2013) Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genetics 9, e1003137. * Equal contribution. + Equal contribution. (PDF)

77. Agus DB, Michor F (2012) The sciences converge to fight cancer. Nature Physics 8, 773-774. (PDF)

76. De S, Michor F (2012) Analyzing the association of SCNA boundaries with replication timing. Nature Biotechnology 30, 1045-1046. (PDF)

75. Foo J, Chmielecki J, Pao W, Michor F (2012) Effects of pharmacokinetic processes and varied dosing schedules on the dynamics of acquired resistance to erlotinib in EGFR-mutant lung cancer. Journal of Thoracic Oncology 7, 1583-1593. (PDF)

74. Tang M*, Foo J*, Gonen M, Guilhot J, Mahon F-X, Michor F (2012) Selection pressure exerted by imatinib therapy leads to disparate outcomes of imatinib discontinuation trials. Haematologica 97, 1553-1561.* Equal contribution. (PDF)

73. Martins FC, De S, Almendro V, Gonen M, Park S-Y, Schnitt SJ, Tung N, Garber JE, Fetten K, Michor F, Polyak K (2012) Evolutionary pathways in BRCA1-associated breast tumors. Cancer Discovery 2, 503-511. (PDF)

72. Podlaha O, Riester M, De S, Michor F (2012) Evolution of the cancer genome. Trends in Genetics 28, 155-163. (PDF)

71. Riester M*, Taylor JM*, Feifer A, Koppie T, Rosenberg JE, Downey RJ, Bochner BH, Michor F (2012) Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer. Clinical Cancer Research 18, 1323-1333. * Equal contribution. (PDF)

70. Iwami S*, Haeno H*, Michor F (2012) A race between tumor immunoescape and genome maintenance selects for optimum levels of (epi)genetic instability. PLoS Computational Biology 8, e1002370. *Equal contribution. (PDF)

69. Haeno H*, Gonen M*, Davis MB, Herman JM, Iacobuzio-Donahue CA, Michor F (2012) Computational modeling of pancreatic cancer reveals kinetics of metastasis suggesting optimum treatment strategies. Cell 148, 362-375. * Equal contribution. (PDF)

68. Cheng Y-K, Beroukhim R, Levine RL, Mellinghoff IK, Holland EC, Michor F (2012) A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS Computational Biology 8, e1002337. (PDF)

67. De S, Michor F (2011) DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nature Biotechnology 29, 1103-1108. (PDF)

66. Leder K*, Foo J*, Skaggs B, Gorre M, Sawyers C, Michor F (2011) Fitness conferred by BCR-ABL kinase domain mutations determines the risk of pre-existing resistance in chronic myeloid leukemia. PLoS ONE 6, e27682. * Equal contribution. (PDF)

65. Mumenthaler SM, Foo J, Leder K, Choi NC, Agus DB, Pao W, Mallick P, Michor F (2011) Evolutionary modeling of combination treatment strategies to overcome resistance to tyrosine kinase inhibitors in non-small cell lung cancer. Molecular Pharmaceutics 8, 2069-2079. (PDF)

64. Hambardzumyan D*, Cheng Y-K*, Haeno H*, Holland EC+, Michor F+ (2011) The probable cell of origin of NF1- and PDGF-driven glioblastomas. PLoS ONE 6, e24454. * Equal contribution. + Equal contribution. (PDF)

63. Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME, Ballon G, Yang SN, Weinhold N, Reimers M, Clozel T, Luttrop K, Ekstrom T, Frank J, Vasanthakumar A, Godley LA, Michor F, Elemento O, Melnick AM (2011) DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood 118, 3559-3569. (PDF)

62. Michor F, Liphardt J, Ferrari M, Widom J (2011) What does physics have to do with cancer? Nature Reviews Cancer 11, 657-670. (PDF)

61. Tang M, Gonen M, Quintas-Cardama A, Cortes J, Kantarjian H, Field C, Hughes TP, Branford S, Michor F (2011) Dynamics of chronic myeloid leukemia response to long-term targeted therapy reveal treatment effects on leukemic stem cells. Blood 118, 1622-1631. (PDF)

60. Chmielecki J, Foo J, Oxnard GR, Hutchinson K, Ohashi K, Somwar R, Wang L, Amato KR, Arcila M, Sos ML, Socci ND, Viale A, de Stanchina E, Ginsberg MS, Thomas RK, Kris MG, Inoue A, Ladanyi M, Miller VA, Michor F, Pao W (2011) Optimization of dosing for EGFR-mutant non-small cell lung cancer with evolutionary cancer modeling. Science Translational Medicine 3, 90ra59. (PDF)

59. De S, Michor F (2011) DNA secondary structures and epigenetic determinants of cancer genome evolution. Nature Structural and Molecular Biology 18, 950-955. (PDF)

58. Durrett R, Foo J, Leder K, Mayberry J, Michor F (2011) Intratumor heterogeneity in evolutionary models of tumor progression. Genetics 188, 461-477. (PDF)

57. Klinakis A, Lobry C, Abdel-Wahab O, Oh P, Haeno H, Buonamici S, van de Walle I, Cathelin S, Trimarchi T, Araldi E, Liu C, Ibrahim S, Beran M, Zavadil J, Efstratiadis A, Taghon T, Michor F, Levine RL, Aifantis A (2011) A novel tumor suppressor function for the Notch pathway in myeloid leukemia. Nature 473, 230-233. (PDF)

56. Iwasa Y, Michor F (2011) Evolutionary dynamics of intratumor heterogeneity. PLoS ONE 6, e17866. (PDF)

55. Cheng Y-K, Beroukhim R, Levine RL, Mellinghoff IK, Michor F (2011) Reply to Parsons: Many tumor types follow the monoclonal model of tumor initiation. Proc Natl Acad Sci U S A 108, E16. (PDF)

54. Foo J*, Leder K*, Michor F (2010) Stochastic dynamics of cancer initiation. Physical Biology 8, 015002. * Equal contribution. (PDF)

53. De Vargas Roditi L, Michor F (2010) Evolutionary dynamics of BRCA1 alterations in breast tumorigenesis. J Theor Biol 273, 207-215. (PDF)

52. Leder K, Holland EC, Michor F (2010) The therapeutic implications of plasticity of the cancer stem cell phenotype. PLoS ONE 5, e14366. (PDF)

51. Michor F, Polyak K (2010) The origins and implications of intratumor heterogeneity. Cancer Prevention Research 3, 1361-1364. (PDF)

50. Stephan-Otto Attolini C*, Cheng Y-K*, Beroukhim R, Getz G, Abdel-Wahab O, Levine RL, Mellinghoff IK, Michor F (2010) A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc Natl Acad Sci U S A 107, 17604-17609. * Equal contribution. (PDF)

49. Danielson LS, Menendez S, Stephan-Otto Attolini C, Guijarro MV, Bisogna M, Wei J, Socci ND, Levine DA, Michor F, Hernando E (2010) A differentiation-based miRNA signature identifies leiomyosarcoma as a mesenchymal stem cell-related malignancy. Am J Pathol 177, 908-917. (PDF)

48. Durrett R, Foo J, Leder K, Mayberry J, Michor F (2010) Evolutionary dynamics of tumor progression with random fitness values. Theor Popul Biol 78, 54-66. (PDF)

47. Riester M*, Stephan-Otto Attolini C*, Downey RJ, Singer S, Michor F (2010) A differentiation-based phylogeny of cancer subtypes. PLoS Computational Biology 6, e1000777. *Equal contribution. (PDF) (Software)

46. Foo J, Michor F (2010) Evolution of resistance to anti-cancer therapy during general dosing schedules. J Theor Biol 263, 179-188. (PDF)

45. Haeno H, Michor F (2010) The evolution of tumor metastases during clonal expansion. J Theor Biol 263, 30-44. (PDF)

44. Park SY, Gonen M, Kim HJ, Michor F*, Polyak K* (2010) Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. Jour Clin Invest 120, 636-644. * Equal contribution. (PDF)

43. Foo J, Michor F (2009) Evolution of resistance to targeted anti-cancer therapy during continuous and pulsed administration strategies. PLoS Computational Biology 5, e1000557. (PDF)

42. Haeno H, Levine RL, Gilliland DG, Michor F (2009) A progenitor cell origin of myeloid malignancies. Proc Natl Acad Sci U S A 106, 16616-16621. (PDF)

41. Foo J, Drummond MW, Clarkson B, Holyoke T, Michor F (2009) Eradication of chronic myeloid leukemia stem cells: a novel mathematical model predicts no therapeutic benefit of adding G-CSF to imatinib. PLoS Computational Biology 5, e10000503. (PDF)

40. Stephan-Otto Attolini C, Michor F (2009) Evolutionary theory of cancer. The Year in Evolutionary Biology 2009: Ann NY Acad Sci 1168, 23-51. (PDF)

39. Liso A, Castiglione F, Cappuccio A, Stracci F, Schlenk RF, Amadori S, Thiede C, Schnittger S, Valk PJM, Doehner K, Martelli MF, Schaich M, Krauter J, Ganser A, Martelli MP, Bolli N, Loewenberg B, Haferlach T, Ehninger G, Mandelli F, Doehner H, Michor F, Falini B (2008) A one-mutation mathematical model can explain the age incidence of AML with mutated nucleophosmin (NPM1). Haematologica 93, 1219-1226. (PDF)

38. Michor F (2008) Mathematical models of cancer stem cells. J Clin Oncol 26, 2854-2861. (PDF)

37. Haeno H, Iwasa Y, Michor F (2007) The evolution of two mutations during clonal expansion. Genetics 177, 2209-2221. (PDF)

36. Michor F (2007) Quantitative approaches to analyzing imatinib-treated chronic myeloid leukemia. Trends in Pharmacological Sciences 28, 197-199. (PDF)

35. Dingli D, Michor F, Antal T, Pacheco JM (2007) The emergence of tumor metastases. Cancer Biol Ther 6, 383-390. (PDF)

34. Michor F (2007) Chronic myeloid leukemia blast crisis arises from progenitors. Stem Cells 25, 1114-1118. (PDF)

33. Dingli D, Traulsen A, Michor F (2007) (A)Symmetric stem cell replication and cancer. PLOS Computational Biology 3, e53. (PDF)

32. Michor F (2007) The long-term response to imatinib treatment of CML. British Journal of Cancer 96, 679-680. (PDF)

31. Dingli D, Michor F (2006) Successful therapy must eradicate cancer stem cells. Stem Cells 24, 2603-2610. (PDF)

30. Abbott LH, Michor F (2006) Mathematical models of targeted cancer therapy. British Journal of Cancer 95, 1136-1141. (PDF)

29. Michor F, Iwasa Y, Nowak MA (2006) The age incidence of chronic myeloid leukemia can be explained by a one-mutation model. Proc Natl Acad Sci U S A 103, 14931-14934. (PDF)

28. Michor F, Iwasa Y (2006) Dynamics of metastasis suppressor gene inactivation. J Theor Biol 241, 676-689. (PDF)

27. Brumer Y, Michor F, Shakhnovich EI (2006) Genetic instability and the quasispecies model. J Theor Biol 241, 216-222. (PDF)

26. Iwasa Y, Michor F, Nowak MA (2006) Directional evolution of virus within a host under immune selection. In Vol.2: Mathematical studies of dynamics and evolution of infectious diseases, editors Y. Takeuchi, K. Sato and Y. Iwasa. Springer, 155-178.

25. Nowak MA, Michor F, Iwasa Y (2006) Genetic instability and clonal expansion. J Theor Biol 241, 26-32. (PDF)

24. Michor F, Nowak MA, Iwasa Y (2006) Stochastic dynamics of metastasis formation. J Theor Biol 240, 521-530. (PDF)

23. Iwasa Y, Nowak MA, Michor F (2006) Evolution of resistance during clonal expansion. Genetics 172, 2557-2566. (PDF)

22. Hauert C, Michor F, Nowak MA, Doebeli M (2006) Synergy and discounting of cooperation in social dilemmas. J Theor Biol 239, 195-202. (PDF)

21. Michor F, Nowak MA, Iwasa Y (2006) Evolution of resistance to cancer therapy. Curr Pharm Design 12, 261-271. (PDF)

20. Michor F, Iwasa Y, Lengauer C, Nowak MA (2005) Dynamics of colorectal cancer. Seminars in Cancer Biology 15, 484-493. (PDF)

19. Michor F, Hughes TP, Iwasa Y, Branford S, Shah NP, Sawyers CL, Nowak MA (2005) Dynamics of chronic myeloid leukemia. Nature 435, 1267-1270. (PDF) (Supplementary Online Material)

18. Michor F (2005) Chromosomal instability and human cancer. Proc Roy Soc Lond B 360, 631-635. (PDF)

17. Iwasa Y, Michor F, Komarova NL, Nowak MA (2005) Population genetics of tumor suppressor genes. J Theor Biol 233, 15-23. (PDF)

16. Michor F, Iwasa Y, Lengauer C, Vogelstein B, Nowak MA (2005) Can chromosomal instability initiate tumorigenesis? Seminars in Cancer Biology 15, 43-49. (PDF)

15. Iwasa Y, Michor F, Nowak MA (2005) Virus evolution within patients increases pathogenicity. J Theor Biol 232, 17-26. (PDF)

14. Jones, NA, Wei X, Flower DR, Wong M, Michor F, Saag MS, Hahn BH, Nowak MA, Shaw GM, Borrow P (2004) Determinants of Human Immunodeficiency Virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response. J Exp Med 200, 1243-1256. (PDF)

13. Nowak MA, Michor F, Komarova NL, Iwasa Y (2004) Evolutionary dynamics of tumor suppressor gene inactivation. Proc Natl Acad Sci U S A 101, 10635-10638. (PDF)

12. Iwasa Y, Michor F, Nowak MA (2004) Some basic properties of immune selection. J Theor Biol 229, 179-188. (PDF)

11. Iwasa Y, Michor F, Nowak MA (2004) Stochastic tunnels in evolutionary dynamics. Genetics 166, 1571-1579. (PDF)

10. Michor F, Iwasa Y, Rajagopalan H, Lengauer C, Nowak MA (2004) Linear model of colon cancer initiation. Cell Cycle 3, 358-362. (PDF)

9. Michor F, Iwasa, Y, Nowak MA (2004) Dynamics of cancer progression. Nat Rev Cancer 4, 197-206. (PDF)

8. Iwasa Y, Michor F, Nowak MA (2004) Evolutionary dynamics of invasion and escape. J Theor Biol 226, 205-214. (PDF)

7. Iwasa Y, Michor F, Nowak MA (2003) Evolutionary dynamics of escape from biomedical intervention. Proc Roy Soc Lond B 270, 2573-2578. (PDF)

6. Nowak MA, Michor F, Iwasa Y (2003) The linear process of somatic evolution. Proc Natl Acad Sci U S A 100, 14966-14969. (PDF)

5. Michor F, Frank SA, May RM, Iwasa Y, Nowak MA (2003) Somatic selection for and against cancer. J Theor Biol 225, 377-382. (PDF)

4. Michor F, Nowak MA, Frank SA, Iwasa Y (2003) Stochastic elimination of cancer cells. Proc Roy Soc Lond B 270, 2017-2024. (PDF)

3. Michor F, Iwasa Y, Komarova NL, Nowak MA (2003) Local regulation of homeostasis favors chromosomal instability. Curr Biol 13, 581-584. (PDF)

2. Michor F, Nowak MA (2002) Immunology tomorrow. Nature 420, 741-742. (PDF)

1. Michor F, Nowak MA (2002) The good, the bad and the lonely. Nature 419, 677-679. (PDF)