Publications

203. Cheng Y-C, Zhang Y, Tripathi S, BV H, Jolly MH, Schiebinger G, Levine H, McDonald TO, Michor F+ (2024) Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition. Proceedings of the National Academy of Sciences 121(32), e2406842121. + Corresponding author. (PDF)

202. Parra ER*, Zhang J*, Duose DY*, Gonzalez-Kozlova E*, Redman MW, Chen H, Manyam GC, Kumar G, Zhang J, Song X, Lazcano R, Piubelli M, Fernandez CL, Rojas F, Zhang B, Taing L, Jhaveri A, Geisberg J, Altreuter J, Michor F, Provencher J, Yu J, Cerami E, Moravec R, Kannan K, Luthra R, Al-Atrash G, Huang H-H, Xie H, Pate M, Nie K, Harris J, Argueta K, Lindsay J, Biswas R, Van Nostrand S, Kim-Schulze S, Gray JE, Herbst R, Wistuba II, Gettinger S, Kelly K, Bazhenova L, Gnjatic S, Lee JJ, Zhang J+, Haymaker C+ (2024) Multi-omics analysis reveals immune features associated with immunotherapy benefit in patients with squamous cell lung cancer from phase III Lung-MAP S1400I Trial. Clinical Cancer Research 30(8), 1655-1668. * Equal contribution. + Co-corresponding authors. (PDF)

201. Jovanović B*, Temko D*, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai A, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F+, Polyak K+ (2023) Heterogeneity and transcriptional drivers of triple-negative breast cancer. Cell Reports 42, 113564. * Equal contribution. + Co-corresponding authors. (PDF)

200. Kaczanowska S*, Murty T*, Alimadadi A*, Contreras CF, Duault C, Subrahmanyan PB, Reynolds W, Gutierrez N, Baskar R, Wu CJ, Michor F, Altreuter J, Liu Y, Jhaveri A, Duong V, Anbunathan H, Zhang H, Moravec R, Yu J, Biswas R, Van Nostrand S, Lindsay J, Pichavant M, Sotillo E, Sahaf B, Bendall S, Maecker H, Highfill SL, Stroncek D, Bernstein D, Carbonell A, Glod J, Merchant M, Hedrick CC, Mackall C, Ramakrishna S+, Kaplan R+ (2023) Immune determinants of CAR-T cell expansion in solid tumor patients receiving GD2 CAR-T cell therapy. Cancer Cell 42, 1-17. * Equal contribution. + Co-corresponding authors. (PDF)

199. Sozen B, Flavell RA, Lamming DW, Silver DL, Parrinello S, Abate-Shen C, Michor F, Sankaran VG (2023) What approaches are needed to understand human development and disease? Developmental Cell 58(24), 2822-2825. (PDF)

198. Liu Y, Altreuter J, Bodapati S, Cristea S, Wong CJ, Wu CJ, Michor F (2023) Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities. Cell Genomics 4, 100444. (PDF)

197. Nishida J*, Cristea S*+, Bodapati S*, Puleo J, Bai G, Patel A, Hughes M, Snow C, Borges V, Ruddy KJ, Collins LC, Feeney A-M, Slowik K, Bossuyt V, Dillon D, Lin NU, Partridge A, Michor F+, Polyak K+ (2023) Peripheral blood TCR clonotype diversity as an age-associated marker of breast cancer progression. Proceedings of the National Academy of Sciences 120(49), e2316763120. * Equal contribution. + Co-corresponding authors. (PDF)

196. Cheng Y-C, Stein S, Nardone A, Liu W, Ma W, Cohen G, Guarducci C, McDonald T, Jeselsohn R+, Michor F+ (2023) Mathematical modeling identifies optimum palbociclib-fulvestrant dose administration schedules for the treatment of patients with estrogen receptor–positive breast cancer. Cancer Research Communications 3(11), 2331–2344. + Co-corresponding authors. (PDF)

195. Chen Z*, Giotti B*, Kaluzova M, Rawat K, Price G, Herting CJ, Pinero G, Vallcorba MP, Cristea S, Ross JL, Ackley J, Maximov V, Szulzewsky F, Thomason W, Marquez-Ropero M, Angione A, Nichols N, Tsankova N, Michor F, Shayakhmetov DM, Gutmann DH, Tsankov AM+, Hambardzumyan D+ (2023) A paracrine circuit of IL-1β/IL-1R1 between myeloid and tumor cells drives genotype-dependent glioblastoma progression. Journal of Clinical Investigation 133(22), e163802. * Equal contribution. + Co-corresponding authors. (PDF)

194. Hoetker MS, Yagi M, Di Stefano B, Langerman J, Cristea S, Wong LP, Huebner AJ, Charlton J, Deng W, Haggerty C, Sadreyev RI, Meissner A, Michor F, Plath K, Hochedlinger K (2023) H3K36 methylation maintains cell identity by regulating opposing lineage programmes. Nature Cell Biology 25(8), 1121-1134. (PDF)

193. McDonald TO, Cheng Y-C, Graser C, Nicol PB, Temko D, Michor F (2023) Computational approaches to modelling and optimizing cancer treatment. Nature Reviews Bioengineering 1, 695-711. (PDF)

192. Yang L*, Wang J*, Altreuter J*, Jhaveri A*, Wong CJ, Song L, Fu J, Taing L, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M, Qui X, Long H, Michor F, Liu Y+, Liu XS+ (2023) Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nature Protocols 18(8), 2404-2414. * Equal contribution. + Co-corresponding authors. (PDF)

191. Elkrief A, Makhnin A, Moses KA, Ahn LS, Preeshagul IR, Iqbal AN, Hayes SA, Plodkowski AJ, Paik PK, Ladanyi M, Kris MG, Riely GJ, Michor F, Yu HA (2023) Brief Report: Combination of osimertinib and dacomitinib to mitigate primary and acquired resistance in EGFR-Mutant lung adenocarcinomas. Clinical Cancer Research 29(8), 1423-1428. (PDF)

190. Penter L, Liu Y, Yang L, Taing L, Jhaveri A, Southard J, Patel M, Wolff JO, Cullen N, Pfaff K, Cieri N, Oliveira G, Kim-Schulze S, Ranasinghe S, Leonard R, Robertson T, Chen H, Thurin M, Li S, Rodig SJ, Cibulskis C, Gabriel S, Bachireddy P, Ritz J, Streicher H, Neuberg DS, Hodi FS, Gnjatic S, Livak KJ, Altreuter J, Michor F, Soiffer RJ, Garcia JS, Wu CJ (2023) Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease. Blood 141(15), 1817-1830. (PDF)

189. Walentynowicz KA*, Engelhardt D*, Cristea S*, Yadav S, Onubogu U, Salatino R, Maerken M, Vincentelli C, Jhaverit A, Geisberg J, McDonald TO, Michor F+, Janiszewska M+ (2023) Single-cell heterogeneity of EGFR and CDK4 coamplification is linked to immune infiltration in glioblastoma. Cell Reports 42(3), 112235. * Equal contribution. + Co-corresponding authors. (PDF)

188. Landshammer A*, Bolondi A*, Kretzmer H, Much C, Buschow R, Rose A, Wu H-J, Mackowiak SD, Braendl B, Giesselmann P, Tornisiello R, Parsi KM, Huey J, Mielke T, Meierhofer D, Maehr R, Hnisz D, Michor F, Rinn JL, Meissner A (2023) T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. eLife 12, e83077. * Equal contribution. (PDF)

187. Dean JA*, Tanguturi SK*, Cagney D, Shin K-Y, Youssef G, Aizer A, Rahman R, Hammoudeh L, Reardon D, Lee E, Dietrich J, Tamura K, Aoyagi M, Wickersham L, Wen PY, Catalano P, Haas-Kogan D+, Alexander BM+, Michor F+ (2023) Phase I study of a novel glioblastoma radiation therapy schedule exploiting cell-state plasticity. Neuro-Oncology 25(6), 1100-1112. * Equal contribution. + Co-corresponding authors. (PDF)

186. Stevens LE*, Peluffo G*, Qiu X*, Temko D*, Trinh A, Fassl A, Zheqi L, Seehawer M, Jovanović B, Alečković M, Wilde CM, Geck RC, Shu S, Kingston NL, Harper NW, Almendro V, Pyke AL, Egri SB, Papanastasiou M, Clement K, Zhou N, Walker S, Salas J, Park SY, Frank DA, Meissner A, Jaffe JD, Sicinski P, Toker A, Michor F, Long HW, Overmoyer BA, Polyak K (2022) JAK-STAT signaling in inflammatory breast cancer enables chemotherapy-resistant cell states. Cancer Research 83, 264-284. * Equal contribution. (PDF)

185. Aleckovic M*, Cristea S*, Gil Del Alcazar CR*, Yan P, Ding L, Krop E, Harper N, Jimenez ER, Lu D, Gulvady A, Foidart P, Seehawer M, Diciaccio B, Murphy K, Pyrdol J, Anand J, Garza K, Wucherpfennig K, Tamimi R, Michor F+, Polyak K+ (2022) Breast cancer prevention by short-term inhibition of TGFβ signaling. Nature Communications 13, 7558. * Equal contribution. + Co-corresponding authors. (PDF)

184. Van Egeren D*, Kohli K*, Warner JL, Bedard PL, Riely G, Lepisto E, Schrag D, LeNoue-Newton M, Catalano P, Kehl KL, Michor F, for the AACR Project GENIE Consortium (2022) Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis. Scientific Reports 12, 19055. * Equal contribution. (PDF)

183. Mercier FE*+, Shi J*, Sykes DB, Oki T, Jankovic M, Man CH, Kfoury YS, Miller E, He S, Zhu A, Vasic R, Doench J, Orthwein A, Michor F+, Scadden DT+ (2022) In vivo genome-wide CRISPR screening in murine acute myeloid leukemia uncovers microenvironmental dependencies. Blood Advances 6, 5072-5084. * Equal contribution. + Co-corresponding authors. (PDF)

182. Wu H-J*, Temko D*, Maliga Z*, Moreira AL, Sei E, Minussi DC, Dean J, Lee C, Xu Q, Hochart G, Jacobson CA, Yapp C, Schapiro D, Sorger PK, Seeley EH, Navin N, Downey RJ+, Michor F+ (2022) Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients. Cell Genomics 2, e100165, 1-22. * Equal contribution. + Co-corresponding authors. (PDF)

181. Dean J, Goldberg E, Michor F (2022) Designing optimal allocations for cancer screening using queuing network models. PLoS Computational Biology 14, e1010179, 1-30. (PDF)

180. Nguyen Ba AN, Lawrence KR, Rego-Costa A, Gopalakrishnan S, Temko D, Michor F, Desai MM (2022) Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast. eLife 11, e73983, 1-83. (PDF)

179. Van Egeren D, Kamaz B, Liu S, Nguyen M, Reilly CR, Kalyva M, DeAngelo DJ, Galinsky I, Wadleigh M, Winer ES, Luskin MR, Stone RM, Garcia JS, Hobbs GS, Michor F, Cortes-Ciriano I, Mullally A, Hormoz S (2022) Transcriptional differences between JAK2-V617F and wild-type bone marrow cells in patients with myeloproliferative neoplasms. Experimental Hematology 107, 14-19. (PDF)

178. Nicholson MD, Endler L, Popa A, Genger J-W, Bock C, Michor F, Bergthaler A (2021) A Response to comment on “Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2.” Science Translational Medicine 13, eabj3222, 1-3. (PDF)

177. Koh S-B, Dontchos BN, Bossuyt V, Edmonds C, Cristea S, Melkonjan N, Mortensen L, Ma A, Beyerlin K, Denault E, Niehoff E, Hirz T, Sykes DB, Michor F, Specht M, Lehman C, Ellisen LW, Spring LM (2021) Systematic tissue collection during clinical breast biopsy is feasible, safe and enables high-content translational analyses. npj|Precision Oncology 5(1), 1-7. (PDF)

176. Yagi M, Ji F, Charlton J*, Cristea S*, Messemer K, Horwitz N, Di Stefano B, Tsopoulidis N, Hoetker MS, Huebner AJ, Bar-Nur O, Almada AE, Yamamoto M, Patelunas A, Goldhamer DJ, Wagers AJ, Michor F, Meissner A, Sadreyev RI & Hochedlinger K (2021) Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells. Genes & Development 35, 1209–1228. * Equal contribution. (PDF)

175. Wu H-J*, Landshammer A*, Stamenova EK, Bolondi A, Kretzmer H, Meissner A+, Michor F+ (2021) Topological isolation of developmental regulators in mammalian genomes. Nature Communications 12, 4897, 1-19. * Equal contribution. + Co-corresponding authors. (PDF)

174. Filho OM*, Viale G*, Stein S*, Trippa L, Yardley DA, Mayer IA, Abramson VG, Arteaga CL, Spring LM, Waks AG, Wrabel E, DeMeo MK, Bardia A, Dell’Orto P, Russo L, King TA, Polyak K, Michor F+, Winer EP, Krop IE+ (2021) Impact of HER2 heterogeneity on treatment response of early-stage HER2-positive breast cancer: phase II neoadjuvant trial of T-DM1 combined with pertuzumab. Cancer Discovery 11, 1-14. * Equal contribution. + Co-corresponding authors. (PDF)

173. Zee BM, Poels KE, Yao C-H, Kawabata KC, Wu G, Duy C, Jacobus WD, Senior E, Endress JE, Jambhekar A, Lovitch SB, Ma J, Dhall A, Harris IS, Blanco MA, Sykes DB, Licht JD, Weinstock DM, Melnick A, Haigis MC, Michor F, Shi Y (2021) Combined epigenetic and metabolic treatments overcome differentiation blockade in acute myeloid leukemia. iScience 24, 102651, 1-23. (PDF)

172. Poels KE, Schoenfeld AJ, Makhnin A, Tobi Y, Wang Y, Frisco-Cabanos H, Chakrabarti S, Shi M, Napoli C, McDonald TO, Tan W, Hata A, Weinrich SL, Yu HA+, Michor F+ (2021) Identification of optimal dosing schedules of dacomitinib and osimertinib for a phase I/II trial in advanced EGFR-mutant non-small cell lung cancer. Nature Communications 12, 3697, 1-12. + Co-corresponding authors. (PDF)

171. Janiszewska M*, Stein S*, Metzger Filho OM, Eng J, Kingston NL, Harper NW, Rye IH, Aleckovic M, Trinh A, Murphy KC, Marangoni E, Cristea S, Oakes B, Winer EP, Krop IE, Russness HG, Spellman PT, Bucher E, Hu Z, Chin K, Gray JW, Michor F+, Polyak K+ (2021) The impact of tumor epithelial and microenvironmental heterogeneity on treatment responses in HER2-positive breast cancer. JCI Insights 6, e147617, 1-19. *Equal contribution. + Co-corresponding authors. (PDF)

170. Randles A, Wirsching H-G, Dean JA, Cheng Y-K, Emerson S, Pattwell SS, Holland EC*, Michor F* (2021) Computational modelling of perivascular-niche dynamics for the optimization of treatment schedules for glioblastoma. Nature Biomedical Engineering 5, 346-359. * Co-corresponding authors. (PDF)

169. Minussi DC*, Nicholson MD*, Ye H*, Davis A, Wang K, Baker T, Tarabichi M, Sei E, Du H, Rabbani M, Peng C, Hu M, Bai S, Lin Y-W, Schalck A, Multani A, Ma J, McDonald TO, Casasent A, Barrera A, Chen H, Lim B, Arun B, Meric-Bernstam F, Van Loo P, Michor F+, Navin NE+ (2021) Breast tumors maintain a reservoir of subclonal diversity during expansion. Nature 592, 302-308. * Equal contribution. + Co-corresponding authors. (PDF)

168. Engelhardt D, Michor F (2021) A quantitative paradigm for decision-making in precision oncology. Trends in Cancer 7, 293-300. (PDF)

167. Van Egeren D*, Escabi J*, Nguyen M*, Liu S, Reilly CR, Patel S, Kamaz B, Kalyva M, DeAngelo DJ, Galinsky I, Wadleigh M, Winer ES, Luskin MR, Stone RM, Garcia JS, Hobbs GS, Camargo FD, Michor F, Mullally A+, Cortes-Ciriano I+, Hormoz S+ (2021) Reconstructing the lineage histories and differentiation trajectories of individual cancer cells in myeloproliferative neoplasms. Cell Stem Cell 28, 514-523. * Equal contribution. + Co-corresponding authors. (PDF)

166. van Dorp L, Shey MS, Ghedin E, Michor F, Koonin EV, Hampson K (2021) How does large-scale genomic analysis shape our understanding of COVID variants in real time? Cell Systems 12, 109-111. (PDF)

165. Oki T, Mercier F, Kato H, Jung Y, McDonald TO, Spencer JA, Mazzola MC, van Gastel N, Lin CP, Michor F, Kitamura T, Scadden DT (2021) Imaging dynamic mTORC1 pathway activity in vivo reveals marked shifts that support time-specific inhibitor therapy in AML. Nature Communications 12, 245, 1-13. (PDF)

164. Shen YJ*, Mishima Y*, Shi J*, Sklavenitis-Pistofidis R*, Redd RA, Moschetta M, Manier S, Roccaro AM, Sacco A, Tai Y-T, Mercier F, Kawano Y, Su NK, Berrios B, Doench JG, Root DE, Michor F, Scadden DT, Ghobrial IM (2020) Progression signature underlies clonal evolution and dissemination of multiple myeloma. Blood 137, 2360-2372. * Equal contribution. (PDF)

163. Popa A*, Genger J-W*, Nicholson MD*, Penz T*, Schmid D*, Aberle SW*, Agerer B*, Lercher A*, Endler L, Colaço H, Smyth M, Schuster M, Grau ML, Martinez-Jimenez F, Pich O, Borena W, Pawelka E, Keszei Z, Senekowitsch M, Laine J, Aberle JH, Redlberger-Fritz M, Karolyi M, Zoufaly A, Maritschnik S, Borkovec M, Hufnagl P, Nairz M, Weiss G, Wolfinger MT, von Laer D, Superti-Furga G, Lopez-Bigas N, Puchhammer-Stoeckl E, Allergerger F, Michor F, Bock C, Bergthaler A+ (2020) Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2. Science Translational Medicine 12, eabe2555, 1-13. * Equal contribution. + Co-corresponding authors. (PDF)

162. Irurzun-Arana I, McDonald TO, Troconiz IF, Michor F (2020) Pharmacokinetic profiles determine optimal combination treatment schedules in computational models of drug resistance. Cancer Research 80, 3372-3382. (PDF)

161. Chakrabarti C, Michor F (2020) Circadian clock effects on cellular proliferation: insights from theory and experiments. Current Opinion in Cell Biology 67, 17-26. (PDF)

160. Feiger B, Gounley J, Adler D, Leopold JA, Draeger EW, Chaudhury R, Ryan J, Pathangey G, Winarta K, Frakes D, Michor F, Randles A (2020) Accelerating massively parallel hemodynamic models of coarctation of the aorta using neural networks. Nature Scientific Reports 10, 9508, 1-13. (PDF)

159. Roney JP*, Ferlic J*, Michor F+, McDonald TO+ (2020) ESTIpop: A computational tool to simulate and estimate parameters for continuous-time Markov branching processes. Bioinformatics 36, 4372-4373. * Equal contribution. + Co-corresponding authors. (PDF)

158. Shu S*, Wu H-J*, Ge JY, Zeid R, Harris IS, Jovanovic B, Murphy K, Wang B, Qiu X, Endress JE, Reyes J, Lim K, Font-Tello A, Syamala S, Xiao T, Chilamakuri CSR, Papachristou EK, D’Santos C, Anand J, Hinohara K, Li W, McDonald TO, Luoma A, Modiste RJ, Nguyen Q-D, Michel B, Cejas P, Kadoch C, Jaffe JD, Wucherpfennig KW, Qi J, Liu XS, Long H, Brown M, Carroll JS, Brugge JS, Bradner J, Michor F+, Polyak K+ (2020) Synthetic lethal and resistance interactions with BET bromodomain inhibitors in tripe-negative breast cancer. Molecular Cell 78, 1096-1113. * Equal contribution. + Co-corresponding authors. (PDF)

157. Ge JY, Shu S, Kwon M, Jovanovic B, Murphy K, Gulvady A, Fassl A, Trinh A, Kuang Y, Heavey GA, Luoma A, Paweletz C, Thorner AR, Wucherpfennig KW, Qi J, Brown M, Sicinski P, McDonald TO, Pellman D, Michor F*, Polyak K* (2020) Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer. Nature Communications 11, 2350, 1-17. * Co-corresponding authors. (PDF)

156. Starrett JH, Guernet AA, Cuomo ME, Poels KE, van Alderwerelt van Rosenburgh IK, Nagelberg A, Farnsworth D, Price KS, Khan H, Ashtekar KD, Gaefele M, Ayeni D, Stewart TF, Kuhlman A, Kaech SM, Unni AM, Homer R, Lockwood WW, Michor F, Goldberg SB, Lemmon MA, Smith PD, Cross DAE, Politi K (2020) Drug sensitivity and allele-specificity of first-line osimertinib resistance EGFR mutations. Cancer Research 80, 2017-2030. (PDF)

155. Murata K, Jadhav U, Madha S, van ES JH, Dean J, Cavazza A, Wucherpfennig K, Michor F, Clevers H, Shivdasani RA (2020) Ascl2-Dependent cell dedifferentiation drives regeneration of ablated intestinal stem cells. Cell Stem Cell 26, 377-390. (PDF)

154. Shank K, Dunbar A, Koppikar P, Kleppe M, Teruya-Feldstein J, Csete I, Bhagwat N, Keller M, Kilpivaara O, Michor F, Levine RL, De Vargas Roditi L (2019) Mathematical modeling reveals alternative JAK inhibitor treatment in myeloproliferative neoplasms. Haematologica 105, 91-94. (PDF)

153. Janiszewska M*, Tabassum DP*, Castano Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Gil Del Alcazar C, Alečković M, Ekram MB, Cohen O, Kwak M, Qin Y, Laszewski T, Luoma A, Marusyk A, Wucherpfennig KW, Wagle N, Fan R, Michor F, McAllister SS, Polyak K (2019) Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Nature Cell Biology 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, 1-19. (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 35, 3849-3851. (PDF)

149. Altrock PM, Ferlic J, Galla T, Tomasson MH, Michor F (2018) Computational model of progression to multiple myeloma identifies optimum screening strategies. 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. Nature Communications 9, 5372, 1-13. * 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 do not necessarily support a model of neutral tumor evolution. Nature Genetics 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, 1-9. (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(1), 3588, 1-10. * 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(1), 3116, 1-13. (PDF)

142. Stover DG, Gil Del Alcazar CR, Brock J, Guo H, Overmoyer B, Balko J, Xu Q, Bardia A, Tolaney SM, Gelman R, Lloyd M, Wang Y, Xu Y, Michor F, Wang V, Winer EP, Polyak K, Lin NU (2018) Phase II study of ruxolitinib, a selective JAK1/2 inhibitor, in patients with metastatic triple-negative breast cancer. NPJ Breast Cancer 4, 1-9. (PDF)

141. Cimino PJ, Kim Y, Wu H-J, 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, 1-24. (PDF)

139. Riester M*, Xu Q*, Moreira A, Zheng J, Michor F+, Downey RJ+ (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 KS*, Lin LL*, Ganesan S, Michor F+, De S+ (2017) Nuclear topology modulates the mutational landscapes of cancer genomes. Nature Structural & Molecular Biology 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. Gil Del Alcazar CR, 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. * Equal contribution. + Co-corresponding authors. (PDF)

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

132. Zhao R, Catalano P, DeGruttola VG, Michor F (2017) Estimating mono- and bi-phasic regression parameters using a mixture piecewise linear Bayesian hierarchical model. PLoS One 12, e0180756, 1-19. (PDF)

131. Mishima Y, Paiva B, Shi J, Park J, Manier S, Takagi S, Massoud M, Perilla-Glen A, Aljawai Y, Huynh D, Roccaro AM, Sacco A, Capelletti M, Detappe A, Alignani D, Anderson KC, Munshi NC, Prosper F, Lohr JG, Ha G, Freeman SS, Van Allen EM, Adalsteinsson VA, Michor F, San Miguel JF, 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. Cancer Research 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 AS, Freedman AS, Fisher DC, Jacobsen E, Armand P, Alyea EP, Koreth J, Ho V, Soiffer RJ, 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 after autologous stem-cell transplantation for lymphoma. Journal of Clinical Oncology 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, 1-17. (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 NS, 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 D, 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 H-J, Zhu H, Kim K-Y, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park I-H, 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. Nucleic Acids Research 45, e77, 1-13. (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 H-J, 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 TO, 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. American Journal of Hematology 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, 1-9. (PDF)

118. Tang M*, Zhao R*, van de Velde H, Tross JG, 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. Clinical Cancer Research 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. Journal of Mathematical Biology 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, 1-17. (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 Computational Biology 11, e1004350, 1-19. (PDF)

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

113. Michor F, Beal K (2015) Improving cancer treatment via mathematical modeling: surmounting the challenges is worth the effort. Cell 163, 1059-1063. (PDF)

112. Janiszewska M, Liu L, Almendro V, Kuang Y, Paweletz C, 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 PW, Michor F, Meyerson M, Rosenberg JE (2015) DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors. BioMed Central Cancer 15, 242, 1-11. (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) Studying clonal dynamics in response to cancer therapy using high-complexity barcoding. Nature Medicine 5, 440-448. (PDF)

107. Selmecki AM, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson AL, 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, McKenney AS, Papalexi E, Abdel-Wahab O, Rampal R, Marubayashi S, Chen JJ, Romanet V, Fridman JS, Bromberg J, Teruya-Feldstein J, Murakami M, Radimerski T, Michor F, Fan R, Levine RL (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 E, Michor F (2014) A feasibility study using image-based parallel modeling for treatment planning. In Computing in Cardiology. Cambridge, MA, 1-4. (PDF)

103. Randles A, Draeger E, 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 DP, Altrock PM, 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, Waters J, Leung ML, Unruh A, Roh W, Shi X, 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, 1-7. (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 Computational Biology 10, e1003611, 1-13. (PDF)

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

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

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

92. Michor F, Weaver VM (2014) Understanding tissue context influences on intratumor heterogeneity. Nature Cell Biology 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 DJ, Bochner BH, Hahn WC, Ligon AH, Barletta JA, Loda M, Berman DM, Kantoff PW, 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 NA, 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 R, 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. British Journal of Haematology 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, 1-13. * 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, 1-15. (PDF)

81. Cite Physical Sciences – Oncology Centers Network; Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, Damania D, Davies PC, Decuzzi P, Dickinson L, Estevez-Salmeron L, Estrella V, Ferrari M, Fischbach C, Foo J, Fraley SI, Frantz C, Fuhrmann A, Gascard P, Gatenby RA, Geng Y, Gerecht S, Gillies RJ, Godin B, Grady WM, Greenfield A, Hemphill C, Hempstead BL, Hielscher A, Hillis WD, Holland EC, Ibrahim-Hashim A, Jacks T, Johnson RH, Joo A, Katz JE, Kelbauskas L, Kesselman C, King MR, Konstantopoulos K, Kraning-Rush CM, Kuhn P, Kung K, Kwee B, Lakins JN, Lambert G, Liao D, Licht JD, Liphardt JT, Liu L, Lloyd MC, Lyubimova A, Mallick P, Marko J, McCarty OJ, Meldrum DR, Michor F, Mumenthaler SM, Nandakumar V, O’Halloran TV, Oh S, Pasqualini R, Paszek MJ, Philips KG, Poultney CS, Rana K, Reinhart-King CA, Ros R, Semenza GL, Senechal P, Shuler ML, Srinivasan S, Staunton JR, Stypula Y, Subramanian H, Tlsty TD, Tormoen GW, Tseng Y, van Oudenaarden A, Verbridge SS, Wan JC, Weaver VM, Widom J, Will C, Wirtz D, Wojtkowiak J, Wu PH. A physical sciences network characterization of non-tumorigenic and metastatic cells. Scientific Reports 3, 1449. (PDF)

80. Liu LL, 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 YE, Michor F, Pao W (2013) Epidermal growth factor receptor tyrosine kinase inhibitor-resistant disease. Journal of Clinical Oncology 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(1), 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*, Gönen 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, Gönen M, So Yeon Park SY, Blum JL, Herlihy W, Ethington G, 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(2), e1002370. *Equal contribution. (PDF)

69. Haeno H*, Gönen 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(12), 1103-1108. (PDF)

66. Leder K*, Foo J*, Skaggs B, Gorre M, Sawyers CL, 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(11), 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(9), 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 TJ, 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, Gönen 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(90), 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(3), 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. Proceedings of the National Academy of Science USA 108, E16, 1. (PDF)

54. Foo J*, Leder K*, Michor F (2010) Stochastic dynamics of cancer initiation. Physical Biology 8(1), 015002. * Equal contribution. (PDF)

53. De Vargas Roditi L, Michor F (2010) Evolutionary dynamics of BRCA1 alterations in breast tumorigenesis. Journal of Theoretical Biology 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(12), 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. Proceedings of the National Academy of Science USA 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 MicroRNA Signature Identifies Leiomyosarcoma as a Mesenchymal Stem Cell-Related Malignancy. American Journal of Pathology 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. Theoretical Population Biology 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(5), e1000777. *Equal contribution. (PDF)

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

45. Haeno H, Michor F (2010) The evolution of tumor metastases during clonal expansion. Journal of Theoretical Biology 263, 30-44. (PDF)

44. Park SY, Gönen 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. Journal of Clinical Investigation 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(11), e1000557. (PDF)

42. Haeno H, Levine RL, Gilliland DG, Michor F (2009) A progenitor cell origin of myeloid malignancies. Proceedings of the National Academy of Science USA 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, 1-11. (PDF)

40. Stephan-Otto Attolini C, Michor F (2009) Evolutionary theory of cancer. The Year in Evolutionary Biology 2009. Annals NY Academy of Science 1168, 23-51. (PDF)

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

38. Michor F (2008) Mathematical models of cancer stem cells. Journal of Clinical Oncology 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 Biology & Theory 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, 1-6. (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. Proceedings of the National Academy of Science USA 103, 14931-14934. (PDF)

28. Michor F, Iwasa Y (2006) Dynamics of metastasis suppressor gene inactivation. Journal of Theoretical Biology 241, 676-689. (PDF)

27. Brumer Y, Michor F, Shakhnovich EI (2006) Genetic instability and the quasispecies model. Journal of Theoretical Biology 241, 216-222. (PDF)

26. Iwasa Y, Michor F, Nowak MA (2006) Directional evolution of virus within a host under immune selection. Springer, 155-178. (PDF)

25. Nowak MA, Michor F, Iwasa Y (2006) Genetic instability and clonal expansion. Journal of Theoretical Biology 241, 26-32. (PDF)

24. Michor F, Nowak MA, Iwasa Y (2006) Stochastic dynamics of metastasis formation. Journal of Theoretical Biology 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. Journal of Theoretical Biology 239, 195-202. (PDF)

21. Michor F, Nowak MA, Iwasa Y (2006) Evolution of resistance to cancer therapy. Current Pharmaceutical 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. Proceedings of the Royal Society London B 360, 631-635. (PDF)

17. Iwasa Y, Michor F, Komarova NL, Nowak MA (2005) Population genetics of tumor suppressor genes. Journal of Theoretical Biology 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. Journal of Theoretical Biology 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. Journal of Experimental Medicine 200, 1243-1256. (PDF)

13. Nowak MA, Michor F, Komarova NL, Iwasa Y (2004) Evolutionary dynamics of tumor suppressor gene inactivation. Proceedings of the National Academy of Science USA 101, 10635-10638. (PDF)

12. Iwasa Y, Michor F, Nowak MA (2004) Some basic properties of immune selection. Journal of Theoretical Biology 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. Nature Reviews Cancer 4, 197-205. (PDF)

8. Iwasa Y, Michor F, Nowak MA (2004) Evolutionary dynamics of invasion and escape. Journal of Theoretical Biology 226, 205-214. (PDF)

7. Iwasa Y, Michor F, Nowak MA (2003) Evolutionary dynamics of escape from biomedical intervention. Proceedings of the Royal Society London B 270, 2573-2578. (PDF)

6. Nowak MA, Michor F, Iwasa Y (2003) The linear process of somatic evolution. Proceedings of the National Academy of Science USA 100, 14966-14969. (PDF)

5. Michor F, Frank SA, May RM, Iwasa Y, Nowak MA (2003) Somatic selection for and against cancer. Journal of Theoretical Biology 225, 377-382. (PDF)

4. Michor F, Nowak MA, Frank SA, Iwasa Y (2003) Stochastic elimination of cancer cells. Proceedings of the Royal Society London B 270, 2017-2024. (PDF)

3. Michor F, Iwasa Y, Komarova NL, Nowak MA (2003) Local regulation of homeostasis favors chromosomal instability. Current Biology 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)