Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Del Alcazar CG, 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 SS, Polyak K. Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Nat Cell Biol. 2019 Jul; 21(7):879-888.
View in:
PubMed
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. Computational modeling of pancreatic cancer patients receiving FOLFIRINOX and gemcitabine-based therapies identifies optimum intervention strategies. PLoS One. 2019; 14(4):e0215409.
View in:
PubMed
Yamamoto KN, Liu LL, Nakamura A, Haeno H, Michor F. Stochastic Evolution of Pancreatic Cancer Metastases During Logistic Clonal Expansion. JCO Clin Cancer Inform. 2019 Mar; 3:1-11.
View in:
PubMed
Ferlic J, Shi J, McDonald TO, Michor F. DIFFpop: A stochastic computational approach to simulate differentiation hierarchies with single cell barcoding. Bioinformatics. 2019 Feb 28.
View in:
PubMed
Hinohara K, Wu HJ, 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, Gimelbrant AA, Michor F, Polyak K. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell. 2019 Feb 11; 35(2):330-332.
View in:
PubMed
Chakrabarti S, Paek AL, Reyes J, Lasick KA, Lahav G, Michor F. Hidden heterogeneity and circadian-controlled cell fate inferred from single cell lineages. Nat Commun. 2018 12 18; 9(1):5372.
View in:
PubMed
Altrock PM, Ferlic J, Galla T, Tomasson MH, Michor F. Computational Model of Progression to Multiple Myeloma Identifies Optimum Screening Strategies. JCO Clin Cancer Inform. 2018 12; 2:1-12.
View in:
PubMed
McDonald TO, Chakrabarti S, Michor F. Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution. Nat Genet. 2018 12; 50(12):1620-1623.
View in:
PubMed
Hinohara K, Wu HJ, 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, Gimelbrant AA, Michor F, Polyak K. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell. 2018 12 10; 34(6):939-953.e9.
View in:
PubMed
Van Egeren D, Madsen T, Michor F. Fitness variation in isogenic populations leads to a novel evolutionary mechanism for crossing fitness valleys. Commun Biol. 2018; 1:151.
View in:
PubMed
Karaayvaz M, Cristea S, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F, Ellisen LW. Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nat Commun. 2018 09 04; 9(1):3588.
View in:
PubMed
Jun HJ, Appleman VA, Wu HJ, 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. A PDGFRa-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine. Nat Commun. 2018 08 06; 9(1):3116.
View in:
PubMed
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. Phase II study of ruxolitinib, a selective JAK1/2 inhibitor, in patients with metastatic triple-negative breast cancer. NPJ Breast Cancer. 2018; 4:10.
View in:
PubMed
Cimino PJ, Kim Y, Wu HJ, Alexander J, Wirsching HG, Szulzewsky F, Pitter K, Ozawa T, Wang J, Vazquez J, Arora S, Rabadan R, Levine R, Michor F, Holland EC. Increased HOXA5 expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma. Genes Dev. 2018 04 01; 32(7-8):512-523.
View in:
PubMed
Stein S, Zhao R, Haeno H, Vivanco I, Michor F. Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients. PLoS Comput Biol. 2018 01; 14(1):e1005924.
View in:
PubMed
Riester M, Xu Q, Moreira A, Zheng J, Michor F, Downey RJ. The Warburg effect: persistence of stem-cell metabolism in cancers as a failure of differentiation. Ann Oncol. 2018 01 01; 29(1):264-270.
View in:
PubMed
Smith KS, Liu LL, Ganesan S, Michor F, De S. Nuclear topology modulates the mutational landscapes of cancer genomes. Nat Struct Mol Biol. 2017 Nov; 24(11):1000-1006.
View in:
PubMed
Malone CF, Emerson C, Ingraham R, Barbosa W, Guerra S, Yoon H, Liu LL, Michor F, Haigis M, Macleod KF, Maertens O, Cichowski K. mTOR and HDAC Inhibitors Converge on the TXNIP/Thioredoxin Pathway to Cause Catastrophic Oxidative Stress and Regression of RAS-Driven Tumors. Cancer Discov. 2017 12; 7(12):1450-1463.
View in:
PubMed
Smith ZD, Shi J, Gu H, Donaghey J, Clement K, Cacchiarelli D, Gnirke A, Michor F, Meissner A. Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature. 2017 09 28; 549(7673):543-547.
View in:
PubMed
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. Analysis of somatic microsatellite indels identifies driver events in human tumors. Nat Biotechnol. 2017 Oct; 35(10):951-959.
View in:
PubMed
Zhao R, Catalano P, DeGruttola VG, Michor F. Estimating mono- and bi-phasic regression parameters using a mixture piecewise linear Bayesian hierarchical model. PLoS One. 2017; 12(7):e0180756.
View in:
PubMed
McDonald TO, Michor F. SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution. Bioinformatics. 2017 Jul 15; 33(14):2221-2223.
View in:
PubMed
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, Min Hui Kim E, McDonnell 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. Immune Escape in Breast Cancer During In Situ to Invasive Carcinoma Transition. Cancer Discov. 2017 10; 7(10):1098-1115.
View in:
PubMed
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. Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic Acids Res. 2017 Jun 02; 45(10):e77.
View in:
PubMed
Chakrabarti S, Michor F. Pharmacokinetics and Drug Interactions Determine Optimum Combination Strategies in Computational Models of Cancer Evolution. Cancer Res. 2017 07 15; 77(14):3908-3921.
View in:
PubMed
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. The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma. Cell Rep. 2017 04 04; 19(1):218-224.
View in:
PubMed
Temko D, Cheng YK, Polyak K, Michor F. Mathematical Modeling Links Pregnancy-Associated Changes and Breast Cancer Risk. Cancer Res. 2017 06 01; 77(11):2800-2809.
View in:
PubMed
Riester M, Wu HJ, Zehir A, Gönen M, Moreira AL, Downey RJ, Michor F. Distance in cancer gene expression from stem cells predicts patient survival. PLoS One. 2017; 12(3):e0173589.
View in:
PubMed
Yu HA, Sima C, Feldman D, Liu LL, Vaitheesvaran B, Cross J, Rudin CM, Kris MG, Pao W, Michor F, Riely GJ. Phase 1 study of twice weekly pulse dose and daily low-dose erlotinib as initial treatment for patients with EGFR-mutant lung cancers. Ann Oncol. 2017 02 01; 28(2):278-284.
View in:
PubMed
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. Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2017 02; 28(2):167-176.
View in:
PubMed
Gibson CJ, Lindsley RC, Tchekmedyian V, Mar BG, Shi J, Jaiswal S, Bosworth A, Francisco L, 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. Clonal Hematopoiesis Associated With Adverse Outcomes After Autologous Stem-Cell Transplantation for Lymphoma. J Clin Oncol. 2017 May 10; 35(14):1598-1605.
View in:
PubMed
Liu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell Rep. 2016 12 20; 17(12):3395-3406.
View in:
PubMed
Wu HJ, Michor F. A computational strategy to adjust for copy number in tumor Hi-C data. Bioinformatics. 2016 12 15; 32(24):3695-3701.
View in:
PubMed
Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, Tsai PC, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F, Navin NE. Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nat Genet. 2016 10; 48(10):1119-30.
View in:
PubMed
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. ABCG2 regulates self-renewal and stem cell marker expression but not tumorigenicity or radiation resistance of glioma cells. Sci Rep. 2016 07 26; 6:25956.
View in:
PubMed
Altrock PM, Brendel C, Renella R, Orkin SH, Williams DA, Michor F. Mathematical modeling of erythrocyte chimerism informs genetic intervention strategies for sickle cell disease. Am J Hematol. 2016 09; 91(9):931-7.
View in:
PubMed
Tang M, Zhao R, van de Velde H, Tross JG, Mitsiades C, Viselli S, Neuwirth R, Esseltine DL, Anderson K, Ghobrial IM, San Miguel JF, Richardson PG, Tomasson MH, Michor F. Myeloma Cell Dynamics in Response to Treatment Supports a Model of Hierarchical Differentiation and Clonal Evolution. Clin Cancer Res. 2016 Aug 15; 22(16):4206-4214.
View in:
PubMed
Altrock PM, Liu LL, Michor F. The mathematics of cancer: integrating quantitative models. Nat Rev Cancer. 2015 Dec; 15(12):730-45.
View in:
PubMed
Michor F, Beal K. Improving Cancer Treatment via Mathematical Modeling: Surmounting the Challenges Is Worth the Effort. Cell. 2015 Nov 19; 163(5):1059-1063.
View in:
PubMed
Liu LL, Li F, Pao W, Michor F. Dose-Dependent Mutation Rates Determine Optimum Erlotinib Dosing Strategies for EGFR Mutant Non-Small Cell Lung Cancer Patients. PLoS One. 2015; 10(11):e0141665.
View in:
PubMed
Foo J, Liu LL, Leder K, Riester M, Iwasa Y, Lengauer C, Michor F. An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer. PLoS Comput Biol. 2015 Sep; 11(9):e1004350.
View in:
PubMed
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. In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer. Nat Genet. 2015 Oct; 47(10):1212-9.
View in:
PubMed
Roccaro AM, Mishima Y, Sacco A, Moschetta M, Tai YT, 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. CXCR4 Regulates Extra-Medullary Myeloma through Epithelial-Mesenchymal-Transition-like Transcriptional Activation. Cell Rep. 2015 Jul 28; 12(4):622-35.
View in:
PubMed
Mumenthaler SM, Foo J, Choi NC, Heise N, Leder K, Agus DB, Pao W, Michor F, Mallick P. The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells. Cancer Inform. 2015; 14(Suppl 4):19-31.
View in:
PubMed
Badri H, Pitter K, Holland EC, Michor F, Leder K. Optimization of radiation dosing schedules for proneural glioblastoma. J Math Biol. 2016 Apr; 72(5):1301-36.
View in:
PubMed
Bhang HE, Ruddy DA, Krishnamurthy Radhakrishna V, 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, Stegmeier F. Studying clonal dynamics in response to cancer therapy using high-complexity barcoding. Nat Med. 2015 May; 21(5):440-8.
View in:
PubMed
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. DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors. BMC Cancer. 2015 Apr 09; 15:242.
View in:
PubMed
Selmecki AM, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson AL, De S, Kishony R, Michor F, Dowell R, Pellman D. Polyploidy can drive rapid adaptation in yeast. Nature. 2015 Mar 19; 519(7543):349-52.
View in:
PubMed
Ashcroft P, Michor F, Galla T. Stochastic tunneling and metastable states during the somatic evolution of cancer. Genetics. 2015 Apr; 199(4):1213-28.
View in:
PubMed
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. JAK-STAT pathway activation in malignant and nonmalignant cells contributes to MPN pathogenesis and therapeutic response. Cancer Discov. 2015 Mar; 5(3):316-31.
View in:
PubMed
Shaknovich R, De S, Michor F. Epigenetic diversity in hematopoietic neoplasms. Biochim Biophys Acta. 2014 Dec; 1846(2):477-84.
View in:
PubMed
Olshen A, Tang M, Cortes J, Gonen M, Hughes T, Branford S, Quintás-Cardama A, Michor F. Dynamics of chronic myeloid leukemia response to dasatinib, nilotinib, and high-dose imatinib. Haematologica. 2014 Nov; 99(11):1701-9.
View in:
PubMed
Ozawa T, Riester M, Cheng YK, Huse JT, Squatrito M, Helmy K, Charles N, Michor F, Holland EC. Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma. Cancer Cell. 2014 Aug 11; 26(2):288-300.
View in:
PubMed
Marusyk A, Tabassum DP, Altrock PM, Almendro V, Michor F, Polyak K. Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity. Nature. 2014 Oct 02; 514(7520):54-8.
View in:
PubMed
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. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 2014 Aug 14; 512(7513):155-60.
View in:
PubMed
Maruvka YE, Tang M, Michor F. On the validity of using increases in 5-year survival rates to measure success in the fight against cancer. PLoS One. 2014; 9(7):e83100.
View in:
PubMed
Podlaha O, De S, Gonen M, Michor F. Histone modifications are associated with transcript isoform diversity in normal and cancer cells. PLoS Comput Biol. 2014 Jun; 10(6):e1003611.
View in:
PubMed
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 PW, Rosenberg JE. FGFR3 expression in primary and metastatic urothelial carcinoma of the bladder. Cancer Med. 2014 Aug; 3(4):835-44.
View in:
PubMed
Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ. Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. J Natl Cancer Inst. 2014 Apr 03; 106(5).
View in:
PubMed
Michor F, Weaver VM. Understanding tissue context influences on intratumour heterogeneity. Nat Cell Biol. 2014 Apr; 16(4):301-2.
View in:
PubMed
Foo J, Michor F. Evolution of acquired resistance to anti-cancer therapy. J Theor Biol. 2014 Aug 21; 355:10-20.
View in:
PubMed
Riester M, Werner L, Bellmunt J, Selvarajah S, Guancial EA, Weir BA, Stack EC, Park RS, O'Brien R, Schutz FA, 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. Integrative analysis of 1q23.3 copy-number gain in metastatic urothelial carcinoma. Clin Cancer Res. 2014 Apr 01; 20(7):1873-83.
View in:
PubMed
Leder K, Pitter K, LaPlant Q, Hambardzumyan D, Ross BD, Chan TA, Holland EC, Michor F. Mathematical modeling of PDGF-driven glioblastoma reveals optimized radiation dosing schedules. Cell. 2014 Jan 30; 156(3):603-616.
View in:
PubMed
Almendro V, Cheng YK, Randles A, Itzkovitz S, Marusyk A, Ametller E, Gonzalez-Farre X, Muñoz M, Russnes HG, Helland A, Rye IH, Borresen-Dale AL, Maruyama R, van Oudenaarden A, Dowsett M, Jones RL, Reis-Filho J, Gascon P, Gönen M, Michor F, Polyak K. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell Rep. 2014 Feb 13; 6(3):514-27.
View in:
PubMed
Almendro V, Kim HJ, Cheng YK, Gönen M, Itzkovitz S, Argani P, van Oudenaarden A, Sukumar S, Michor F, Polyak K. Genetic and phenotypic diversity in breast tumor metastases. Cancer Res. 2014 Mar 01; 74(5):1338-48.
View in:
PubMed
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. Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood. 2014 Mar 13; 123(11):1699-708.
View in:
PubMed
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. 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. 2013 Dec; 163(5):674-6.
View in:
PubMed
Haeno H, Maruvka YE, Iwasa Y, Michor F. Stochastic Tunneling of Two Mutations in a Population of Cancer Cells. PLoS One. 2013; 8(6):e65724.
View in:
PubMed
Zhao R, Michor F. Patterns of proliferative activity in the colonic crypt determine crypt stability and rates of somatic evolution. PLoS Comput Biol. 2013; 9(6):e1003082.
View in:
PubMed
Choudhury S, Almendro V, Merino VF, Wu Z, Maruyama R, Su Y, Martins FC, Fackler MJ, Bessarabova M, Kowalczyk A, Conway T, Beresford-Smith B, Macintyre G, Cheng YK, Lopez-Bujanda 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 AL, Rosson GD, Pike M, Garber JE, Nikolsky Y, Blum JL, Au A, Hwang ES, Tamimi RM, Michor F, Haviv I, Liu XS, Sukumar S, Polyak K. Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics. Cell Stem Cell. 2013 Jul 03; 13(1):117-30.
View in:
PubMed
Jia P, Jin H, Meador CB, Xia J, Ohashi K, Liu L, Pirazzoli V, Dahlman KB, Politi K, Michor F, Zhao Z, Pao W. 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 Res. 2013 Sep; 23(9):1434-45.
View in:
PubMed
Riester M, Bellmunt J, Stack EC, Werner L, Park R, Iyer G, Loda M, Kantoff PW, Michor F, Rosenberg JE. Genomic characterization of metastatic urothelial carcinoma. J Clin Oncol. 2013 Feb 20; 31(6_suppl):247.
View in:
PubMed
Iyer G, Riester M, Werner L, Schultz N, Stack EC, Park R, Loda M, Ostrovnaya I, Kantoff PW, Bajorin DF, Solit DB, Michor F, Bellmunt J, Rosenberg JE. Peroxisome proliferator-activated receptor gamma (PPARG) gene amplifications in urothelial carcinoma (UC). J Clin Oncol. 2013 Feb 20; 31(6_suppl):279.
View in:
PubMed
Ohashi K, Maruvka YE, Michor F, Pao W. Epidermal growth factor receptor tyrosine kinase inhibitor-resistant disease. J Clin Oncol. 2013 Mar 10; 31(8):1070-80.
View in:
PubMed
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. Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genet. 2013; 9(1):e1003137.
View in:
PubMed
Liu L, De S, Michor F. DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes. Nat Commun. 2013; 4:1502.
View in:
PubMed
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. Sci Rep. 2013; 3:1449.
View in:
PubMed
De S, Michor F. Analyzing the association of SCNA boundaries with replication timing. Nat Biotechnol. 2012 Nov; 30(11):1045-6.
View in:
PubMed
Foo J, Chmielecki J, Pao W, Michor F. Effects of pharmacokinetic processes and varied dosing schedules on the dynamics of acquired resistance to erlotinib in EGFR-mutant lung cancer. J Thorac Oncol. 2012 Oct; 7(10):1583-93.
View in:
PubMed
Martins FC, De S, Almendro V, Gönen M, Park SY, Blum JL, Herlihy W, Ethington G, Schnitt SJ, Tung N, Garber JE, Fetten K, Michor F, Polyak K. Evolutionary pathways in BRCA1-associated breast tumors. Cancer Discov. 2012 Jun; 2(6):503-11.
View in:
PubMed
Tang M, Foo J, Gönen M, Guilhot J, Mahon FX, Michor F. Selection pressure exerted by imatinib therapy leads to disparate outcomes of imatinib discontinuation trials. Haematologica. 2012 Oct; 97(10):1553-61.
View in:
PubMed
Podlaha O, Riester M, De S, Michor F. Evolution of the cancer genome. Trends Genet. 2012 Apr; 28(4):155-63.
View in:
PubMed
Iwami S, Haeno H, Michor F. A race between tumor immunoescape and genome maintenance selects for optimum levels of (epi)genetic instability. PLoS Comput Biol. 2012; 8(2):e1002370.
View in:
PubMed
Haeno H, Gonen M, Davis MB, Herman JM, Iacobuzio-Donahue CA, Michor F. Computational modeling of pancreatic cancer reveals kinetics of metastasis suggesting optimum treatment strategies. Cell. 2012 Jan 20; 148(1-2):362-75.
View in:
PubMed
Riester M, Taylor JM, Feifer A, Koppie T, Rosenberg JE, Downey RJ, Bochner BH, Michor F. Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer. Clin Cancer Res. 2012 Mar 01; 18(5):1323-33.
View in:
PubMed
Cheng YK, Beroukhim R, Levine RL, Mellinghoff IK, Holland EC, Michor F. A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS Comput Biol. 2012 Jan; 8(1):e1002337.
View in:
PubMed
Leder K, Foo J, Skaggs B, Gorre M, Sawyers CL, Michor F. Fitness conferred by BCR-ABL kinase domain mutations determines the risk of pre-existing resistance in chronic myeloid leukemia. PLoS One. 2011; 6(11):e27682.
View in:
PubMed
De S, Michor F. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat Biotechnol. 2011 Nov 20; 29(12):1103-8.
View in:
PubMed
Mumenthaler SM, Foo J, Leder K, Choi NC, Agus DB, Pao W, Mallick P, Michor F. Evolutionary modeling of combination treatment strategies to overcome resistance to tyrosine kinase inhibitors in non-small cell lung cancer. Mol Pharm. 2011 Dec 05; 8(6):2069-79.
View in:
PubMed
Hambardzumyan D, Cheng YK, Haeno H, Holland EC, Michor F. The probable cell of origin of NF1- and PDGF-driven glioblastomas. PLoS One. 2011; 6(9):e24454.
View in:
PubMed
Michor F, Liphardt J, Ferrari M, Widom J. What does physics have to do with cancer? Nat Rev Cancer. 2011 Aug 18; 11(9):657-70.
View in:
PubMed
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 A. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood. 2011 Sep 29; 118(13):3559-69.
View in:
PubMed
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. Optimization of dosing for EGFR-mutant non-small cell lung cancer with evolutionary cancer modeling. Sci Transl Med. 2011 Jul 06; 3(90):90ra59.
View in:
PubMed
De S, Michor F. DNA secondary structures and epigenetic determinants of cancer genome evolution. Nat Struct Mol Biol. 2011 Jul 03; 18(8):950-5.
View in:
PubMed
Tang M, Gonen M, Quintas-Cardama A, Cortes J, Kantarjian H, Field C, Hughes TP, Branford S, Michor F. Dynamics of chronic myeloid leukemia response to long-term targeted therapy reveal treatment effects on leukemic stem cells. Blood. 2011 Aug 11; 118(6):1622-31.
View in:
PubMed
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 I. A novel tumour-suppressor function for the Notch pathway in myeloid leukaemia. Nature. 2011 May 12; 473(7346):230-3.
View in:
PubMed
Iwasa Y, Michor F. Evolutionary dynamics of intratumor heterogeneity. PLoS One. 2011 Mar 30; 6(3):e17866.
View in:
PubMed
Durrett R, Foo J, Leder K, Mayberry J, Michor F. Intratumor heterogeneity in evolutionary models of tumor progression. Genetics. 2011 Jun; 188(2):461-77.
View in:
PubMed
Foo J, Leder K, Michor F. Stochastic dynamics of cancer initiation. Phys Biol. 2011 Feb; 8(1):015002.
View in:
PubMed
De Vargas Roditi L, Michor F. Evolutionary dynamics of BRCA1 alterations in breast tumorigenesis. J Theor Biol. 2011 Mar 21; 273(1):207-15.
View in:
PubMed
Leder K, Holland EC, Michor F. The therapeutic implications of plasticity of the cancer stem cell phenotype. PLoS One. 2010 Dec 17; 5(12):e14366.
View in:
PubMed
Michor F, Polyak K. The origins and implications of intratumor heterogeneity. Cancer Prev Res (Phila). 2010 Nov; 3(11):1361-4.
View in:
PubMed
Attolini CS, Cheng YK, Beroukhim R, Getz G, Abdel-Wahab O, Levine RL, Mellinghoff IK, Michor F. A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc Natl Acad Sci U S A. 2010 Oct 12; 107(41):17604-9.
View in:
PubMed
Danielson LS, Menendez S, Attolini CS, Guijarro MV, Bisogna M, Wei J, Socci ND, Levine DA, Michor F, Hernando E. A differentiation-based microRNA signature identifies leiomyosarcoma as a mesenchymal stem cell-related malignancy. Am J Pathol. 2010 Aug; 177(2):908-17.
View in:
PubMed
Durrett R, Foo J, Leder K, Mayberry J, Michor F. Evolutionary dynamics of tumor progression with random fitness values. Theor Popul Biol. 2010 Aug; 78(1):54-66.
View in:
PubMed
Riester M, Stephan-Otto Attolini C, Downey RJ, Singer S, Michor F. A differentiation-based phylogeny of cancer subtypes. PLoS Comput Biol. 2010 May 06; 6(5):e1000777.
View in:
PubMed
Park SY, Gönen M, Kim HJ, Michor F, Polyak K. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. J Clin Invest. 2010 Feb; 120(2):636-44.
View in:
PubMed
Foo J, Michor F. Evolution of resistance to anti-cancer therapy during general dosing schedules. J Theor Biol. 2010 Mar 21; 263(2):179-88.
View in:
PubMed
Haeno H, Michor F. The evolution of tumor metastases during clonal expansion. J Theor Biol. 2010 Mar 07; 263(1):30-44.
View in:
PubMed
Foo J, Michor F. Evolution of resistance to targeted anti-cancer therapies during continuous and pulsed administration strategies. PLoS Comput Biol. 2009 Nov; 5(11):e1000557.
View in:
PubMed
Haeno H, Levine RL, Gilliland DG, Michor F. A progenitor cell origin of myeloid malignancies. Proc Natl Acad Sci U S A. 2009 Sep 29; 106(39):16616-21.
View in:
PubMed
Foo J, Drummond MW, Clarkson B, Holyoake T, Michor F. Eradication of chronic myeloid leukemia stem cells: a novel mathematical model predicts no therapeutic benefit of adding G-CSF to imatinib. PLoS Comput Biol. 2009 Sep; 5(9):e1000503.
View in:
PubMed
Attolini CS, Michor F. Evolutionary theory of cancer. Ann N Y Acad Sci. 2009 Jun; 1168:23-51.
View in:
PubMed
Liso A, Castiglione F, Cappuccio A, Stracci F, Schlenk RF, Amadori S, Thiede C, Schnittger S, Valk PJ, 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. A one-mutation mathematical model can explain the age incidence of acute myeloid leukemia with mutated nucleophosmin (NPM1). Haematologica. 2008 Aug; 93(8):1219-26.
View in:
PubMed
Michor F. Mathematical models of cancer stem cells. J Clin Oncol. 2008 Jun 10; 26(17):2854-61.
View in:
PubMed
Haeno H, Iwasa Y, Michor F. The evolution of two mutations during clonal expansion. Genetics. 2007 Dec; 177(4):2209-21.
View in:
PubMed
Michor F. Quantitative approaches to analyzing imatinib-treated chronic myeloid leukemia. Trends Pharmacol Sci. 2007 May; 28(5):197-9.
View in:
PubMed
Dingli D, Michor F, Antal T, Pacheco JM. The emergence of tumor metastases. Cancer Biol Ther. 2007 Mar; 6(3):383-90.
View in:
PubMed
Dingli D, Traulsen A, Michor F, Michor F. (A)symmetric stem cell replication and cancer. PLoS Comput Biol. 2007 Mar 16; 3(3):e53.
View in:
PubMed
Michor F. Chronic myeloid leukemia blast crisis arises from progenitors. Stem Cells. 2007 May; 25(5):1114-8.
View in:
PubMed
Abbott LH, Michor F. Mathematical models of targeted cancer therapy. Br J Cancer. 2006 Nov 06; 95(9):1136-41.
View in:
PubMed
Michor F, Iwasa Y, Nowak MA. The age incidence of chronic myeloid leukemia can be explained by a one-mutation model. Proc Natl Acad Sci U S A. 2006 Oct 03; 103(40):14931-4.
View in:
PubMed
Dingli D, Michor F. Successful therapy must eradicate cancer stem cells. Stem Cells. 2006 Dec; 24(12):2603-10.
View in:
PubMed
Iwasa Y, Nowak MA, Michor F. Evolution of resistance during clonal expansion. Genetics. 2006 Apr; 172(4):2557-66.
View in:
PubMed
Michor F, Iwasa Y. Dynamics of metastasis suppressor gene inactivation. J Theor Biol. 2006 Aug 07; 241(3):676-89.
View in:
PubMed
Nowak MA, Michor F, Iwasa Y. Genetic instability and clonal expansion. J Theor Biol. 2006 Jul 07; 241(1):26-32.
View in:
PubMed
Brumer Y, Michor F, Shakhnovich EI. Genetic instability and the quasispecies model. J Theor Biol. 2006 Jul 21; 241(2):216-22.
View in:
PubMed
Michor F, Nowak MA, Iwasa Y. Evolution of resistance to cancer therapy. Curr Pharm Des. 2006; 12(3):261-71.
View in:
PubMed
Michor F, Nowak MA, Iwasa Y. Stochastic dynamics of metastasis formation. J Theor Biol. 2006 Jun 21; 240(4):521-30.
View in:
PubMed
Michor F, Iwasa Y, Lengauer C, Nowak MA. Dynamics of colorectal cancer. Semin Cancer Biol. 2005 Dec; 15(6):484-93.
View in:
PubMed
Hauert C, Michor F, Nowak MA, Doebeli M. Synergy and discounting of cooperation in social dilemmas. J Theor Biol. 2006 Mar 21; 239(2):195-202.
View in:
PubMed
Michor F, Hughes TP, Iwasa Y, Branford S, Shah NP, Sawyers CL, Nowak MA. Dynamics of chronic myeloid leukaemia. Nature. 2005 Jun 30; 435(7046):1267-70.
View in:
PubMed
Michor F. Chromosomal instability and human cancer. Philos Trans R Soc Lond B Biol Sci. 2005 Mar 29; 360(1455):631-5.
View in:
PubMed
Michor F, Iwasa Y, Vogelstein B, Lengauer C, Nowak MA. Can chromosomal instability initiate tumorigenesis? Semin Cancer Biol. 2005 Feb; 15(1):43-9.
View in:
PubMed
Iwasa Y, Michor F, Nowak MA. Virus evolution within patients increases pathogenicity. J Theor Biol. 2005 Jan 07; 232(1):17-26.
View in:
PubMed
Iwasa Y, Michor F, Komarova NL, Nowak MA. Population genetics of tumor suppressor genes. J Theor Biol. 2005 Mar 07; 233(1):15-23.
View in:
PubMed
Jones NA, Wei X, Flower DR, Wong M, Michor F, Saag MS, Hahn BH, Nowak MA, Shaw GM, Borrow P. Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response. J Exp Med. 2004 Nov 15; 200(10):1243-56.
View in:
PubMed
Iwasa Y, Michor F, Nowak M. Some basic properties of immune selection. J Theor Biol. 2004 Jul 21; 229(2):179-88.
View in:
PubMed
Nowak MA, Michor F, Komarova NL, Iwasa Y. Evolutionary dynamics of tumor suppressor gene inactivation. Proc Natl Acad Sci U S A. 2004 Jul 20; 101(29):10635-8.
View in:
PubMed
Michor F, Iwasa Y, Rajagopalan H, Lengauer C, Nowak MA. Linear model of colon cancer initiation. Cell Cycle. 2004 Mar; 3(3):358-62.
View in:
PubMed
Michor F, Iwasa Y, Nowak MA. Dynamics of cancer progression. Nat Rev Cancer. 2004 Mar; 4(3):197-205.
View in:
PubMed
Iwasa Y, Michor F, Nowak MA. Stochastic tunnels in evolutionary dynamics. Genetics. 2004 Mar; 166(3):1571-9.
View in:
PubMed
Iwasa Y, Michor F, Nowak MA. Evolutionary dynamics of invasion and escape. J Theor Biol. 2004 Jan 21; 226(2):205-14.
View in:
PubMed
Iwasa Y, Michor F, Nowak MA. Evolutionary dynamics of escape from biomedical intervention. Proc Biol Sci. 2003 Dec 22; 270(1533):2573-8.
View in:
PubMed
Michor F, Frank SA, May RM, Iwasa Y, Nowak MA. Somatic selection for and against cancer. J Theor Biol. 2003 Dec 07; 225(3):377-82.
View in:
PubMed
Nowak MA, Michor F, Iwasa Y. The linear process of somatic evolution. Proc Natl Acad Sci U S A. 2003 Dec 09; 100(25):14966-9.
View in:
PubMed
Michor F, Nowak MA, Frank SA, Iwasa Y. Stochastic elimination of cancer cells. Proc Biol Sci. 2003 Oct 07; 270(1528):2017-24.
View in:
PubMed
Michor F, Iwasa Y, Komarova NL, Nowak MA. Local regulation of homeostasis favors chromosomal instability. Curr Biol. 2003 Apr 01; 13(7):581-4.
View in:
PubMed
Michor F, Nowak MA. Evolution: the good, the bad and the lonely. Nature. 2002 Oct 17; 419(6908):677, 679.
View in:
PubMed