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Computational Model of Progression to Multiple Myeloma Identifies Optimum Screening Strategies.

Altrock PM, Ferlic J, Galla T, Tomasson MH, Michor F.

JCO Clin Cancer Inform. 2018 Dec;(2):1-12. doi: 10.1200/CCI.17.00131.


Hidden heterogeneity and circadian-controlled cell fate inferred from single cell lineages.

Chakrabarti S, Paek AL, Reyes J, Lasick KA, Lahav G, Michor F.

Nat Commun. 2018 Dec 18;9(1):5372. doi: 10.1038/s41467-018-07788-5.


KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.

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.

Cancer Cell. 2018 Dec 10;34(6):939-953.e9. doi: 10.1016/j.ccell.2018.10.014. Epub 2018 Nov 21.


Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution.

McDonald TO, Chakrabarti S, Michor F.

Nat Genet. 2018 Dec;50(12):1620-1623. doi: 10.1038/s41588-018-0217-6. No abstract available.


Fitness variation in isogenic populations leads to a novel evolutionary mechanism for crossing fitness valleys.

Van Egeren D, Madsen T, Michor F.

Commun Biol. 2018 Sep 26;1:151. doi: 10.1038/s42003-018-0160-1. eCollection 2018.


Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq.

Karaayvaz M, Cristea S, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F, Ellisen LW.

Nat Commun. 2018 Sep 4;9(1):3588. doi: 10.1038/s41467-018-06052-0.


A PDGFRα-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine.

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.

Nat Commun. 2018 Aug 6;9(1):3116. doi: 10.1038/s41467-018-05036-4.


Phase II study of ruxolitinib, a selective JAK1/2 inhibitor, in patients with metastatic triple-negative breast cancer.

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.

NPJ Breast Cancer. 2018 May 4;4:10. doi: 10.1038/s41523-018-0060-z. eCollection 2018.


Increased HOXA5 expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma.

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.

Genes Dev. 2018 Apr 1;32(7-8):512-523. doi: 10.1101/gad.312157.118. Epub 2018 Apr 9.


Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients.

Stein S, Zhao R, Haeno H, Vivanco I, Michor F.

PLoS Comput Biol. 2018 Jan 2;14(1):e1005924. doi: 10.1371/journal.pcbi.1005924. eCollection 2018 Jan.


The Warburg effect: persistence of stem-cell metabolism in cancers as a failure of differentiation.

Riester M, Xu Q, Moreira A, Zheng J, Michor F, Downey RJ.

Ann Oncol. 2018 Jan 1;29(1):264-270. doi: 10.1093/annonc/mdx645.


Nuclear topology modulates the mutational landscapes of cancer genomes.

Smith KS, Liu LL, Ganesan S, Michor F, De S.

Nat Struct Mol Biol. 2017 Nov;24(11):1000-1006. doi: 10.1038/nsmb.3474. Epub 2017 Oct 2.


mTOR and HDAC Inhibitors Converge on the TXNIP/Thioredoxin Pathway to Cause Catastrophic Oxidative Stress and Regression of RAS-Driven Tumors.

Malone CF, Emerson C, Ingraham R, Barbosa W, Guerra S, Yoon H, Liu LL, Michor F, Haigis M, Macleod KF, Maertens O, Cichowski K.

Cancer Discov. 2017 Dec;7(12):1450-1463. doi: 10.1158/2159-8290.CD-17-0177. Epub 2017 Sep 29.


Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer.

Smith ZD, Shi J, Gu H, Donaghey J, Clement K, Cacchiarelli D, Gnirke A, Michor F, Meissner A.

Nature. 2017 Sep 28;549(7673):543-547. doi: 10.1038/nature23891. Epub 2017 Sep 20.


Analysis of somatic microsatellite indels identifies driver events in human tumors.

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.

Nat Biotechnol. 2017 Oct;35(10):951-959. doi: 10.1038/nbt.3966. Epub 2017 Sep 11.


Estimating mono- and bi-phasic regression parameters using a mixture piecewise linear Bayesian hierarchical model.

Zhao R, Catalano P, DeGruttola VG, Michor F.

PLoS One. 2017 Jul 19;12(7):e0180756. doi: 10.1371/journal.pone.0180756. eCollection 2017.


Immune Escape in Breast Cancer During In Situ to Invasive Carcinoma Transition.

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 3rd, 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.

Cancer Discov. 2017 Oct;7(10):1098-1115. doi: 10.1158/2159-8290.CD-17-0222. Epub 2017 Jun 26.


Pharmacokinetics and Drug Interactions Determine Optimum Combination Strategies in Computational Models of Cancer Evolution.

Chakrabarti S, Michor F.

Cancer Res. 2017 Jul 15;77(14):3908-3921. doi: 10.1158/0008-5472.CAN-16-2871. Epub 2017 May 31.


The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma.

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.

Cell Rep. 2017 Apr 4;19(1):218-224. doi: 10.1016/j.celrep.2017.03.025.


Mathematical Modeling Links Pregnancy-Associated Changes and Breast Cancer Risk.

Temko D, Cheng YK, Polyak K, Michor F.

Cancer Res. 2017 Jun 1;77(11):2800-2809. doi: 10.1158/0008-5472.CAN-16-2504. Epub 2017 Mar 30.


SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution.

McDonald TO, Michor F.

Bioinformatics. 2017 Jul 15;33(14):2221-2223. doi: 10.1093/bioinformatics/btx146.


Distance in cancer gene expression from stem cells predicts patient survival.

Riester M, Wu HJ, Zehir A, Gönen M, Moreira AL, Downey RJ, Michor F.

PLoS One. 2017 Mar 23;12(3):e0173589. doi: 10.1371/journal.pone.0173589. eCollection 2017.


Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells.

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.

Nucleic Acids Res. 2017 Jun 2;45(10):e77. doi: 10.1093/nar/gkx026.


Proceedings of the third international molecular pathological epidemiology (MPE) meeting.

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.

Cancer Causes Control. 2017 Feb;28(2):167-176. doi: 10.1007/s10552-016-0845-z. Epub 2017 Jan 17. Review.


Phase 1 study of twice weekly pulse dose and daily low-dose erlotinib as initial treatment for patients with EGFR-mutant lung cancers.

Yu HA, Sima C, Feldman D, Liu LL, Vaitheesvaran B, Cross J, Rudin CM, Kris MG, Pao W, Michor F, Riely GJ.

Ann Oncol. 2017 Feb 1;28(2):278-284. doi: 10.1093/annonc/mdw556.


Clonal Hematopoiesis Associated With Adverse Outcomes After Autologous Stem-Cell Transplantation for Lymphoma.

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.

J Clin Oncol. 2017 May 10;35(14):1598-1605. doi: 10.1200/JCO.2016.71.6712. Epub 2017 Jan 9.


Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells.

Liu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F.

Cell Rep. 2016 Dec 20;17(12):3395-3406. doi: 10.1016/j.celrep.2016.11.080.


A computational strategy to adjust for copy number in tumor Hi-C data.

Wu HJ, Michor F.

Bioinformatics. 2016 Dec 15;32(24):3695-3701. Epub 2016 Aug 16.


Punctuated copy number evolution and clonal stasis in triple-negative breast cancer.

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.

Nat Genet. 2016 Oct;48(10):1119-30. doi: 10.1038/ng.3641. Epub 2016 Aug 15.


ABCG2 regulates self-renewal and stem cell marker expression but not tumorigenicity or radiation resistance of glioma cells.

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.

Sci Rep. 2016 Jul 26;6:25956. doi: 10.1038/srep25956.


Mathematical modeling of erythrocyte chimerism informs genetic intervention strategies for sickle cell disease.

Altrock PM, Brendel C, Renella R, Orkin SH, Williams DA, Michor F.

Am J Hematol. 2016 Sep;91(9):931-7. doi: 10.1002/ajh.24449. Epub 2016 Jul 14.


Myeloma Cell Dynamics in Response to Treatment Supports a Model of Hierarchical Differentiation and Clonal Evolution.

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.

Clin Cancer Res. 2016 Aug 15;22(16):4206-4214. doi: 10.1158/1078-0432.CCR-15-2793. Epub 2016 Mar 22.


The mathematics of cancer: integrating quantitative models.

Altrock PM, Liu LL, Michor F.

Nat Rev Cancer. 2015 Dec;15(12):730-45. doi: 10.1038/nrc4029. Review.


Improving Cancer Treatment via Mathematical Modeling: Surmounting the Challenges Is Worth the Effort.

Michor F, Beal K.

Cell. 2015 Nov 19;163(5):1059-1063. doi: 10.1016/j.cell.2015.11.002. Review.


Dose-Dependent Mutation Rates Determine Optimum Erlotinib Dosing Strategies for EGFR Mutant Non-Small Cell Lung Cancer Patients.

Liu LL, Li F, Pao W, Michor F.

PLoS One. 2015 Nov 4;10(11):e0141665. doi: 10.1371/journal.pone.0141665. eCollection 2015.


An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer.

Foo J, Liu LL, Leder K, Riester M, Iwasa Y, Lengauer C, Michor F.

PLoS Comput Biol. 2015 Sep 17;11(9):e1004350. doi: 10.1371/journal.pcbi.1004350. eCollection 2015 Sep.


In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer.

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.

Nat Genet. 2015 Oct;47(10):1212-9. doi: 10.1038/ng.3391. Epub 2015 Aug 24.


The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells.

Mumenthaler SM, Foo J, Choi NC, Heise N, Leder K, Agus DB, Pao W, Michor F, Mallick P.

Cancer Inform. 2015 Jul 15;14(Suppl 4):19-31. doi: 10.4137/CIN.S19338. eCollection 2015.


CXCR4 Regulates Extra-Medullary Myeloma through Epithelial-Mesenchymal-Transition-like Transcriptional Activation.

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.

Cell Rep. 2015 Jul 28;12(4):622-35. doi: 10.1016/j.celrep.2015.06.059. Epub 2015 Jul 16.


Optimization of radiation dosing schedules for proneural glioblastoma.

Badri H, Pitter K, Holland EC, Michor F, Leder K.

J Math Biol. 2016 Apr;72(5):1301-36. doi: 10.1007/s00285-015-0908-x. Epub 2015 Jun 21.


DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors.

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.

BMC Cancer. 2015 Apr 9;15:242. doi: 10.1186/s12885-015-1192-2.


Studying clonal dynamics in response to cancer therapy using high-complexity barcoding.

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.

Nat Med. 2015 May;21(5):440-8. doi: 10.1038/nm.3841. Epub 2015 Apr 13.


Polyploidy can drive rapid adaptation in yeast.

Selmecki AM, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson AL, De S, Kishony R, Michor F, Dowell R, Pellman D.

Nature. 2015 Mar 19;519(7543):349-52. doi: 10.1038/nature14187. Epub 2015 Mar 2.


Stochastic tunneling and metastable states during the somatic evolution of cancer.

Ashcroft P, Michor F, Galla T.

Genetics. 2015 Apr;199(4):1213-28. doi: 10.1534/genetics.114.171553. Epub 2015 Jan 26.


JAK-STAT pathway activation in malignant and nonmalignant cells contributes to MPN pathogenesis and therapeutic response.

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.

Cancer Discov. 2015 Mar;5(3):316-31. doi: 10.1158/2159-8290.CD-14-0736. Epub 2015 Jan 8.


Epigenetic diversity in hematopoietic neoplasms.

Shaknovich R, De S, Michor F.

Biochim Biophys Acta. 2014 Dec;1846(2):477-84. doi: 10.1016/j.bbcan.2014.09.003. Epub 2014 Sep 18. Review.


Dynamics of chronic myeloid leukemia response to dasatinib, nilotinib, and high-dose imatinib.

Olshen A, Tang M, Cortes J, Gonen M, Hughes T, Branford S, Quintás-Cardama A, Michor F.

Haematologica. 2014 Nov;99(11):1701-9. doi: 10.3324/haematol.2013.085977. Epub 2014 Sep 12.


Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma.

Ozawa T, Riester M, Cheng YK, Huse JT, Squatrito M, Helmy K, Charles N, Michor F, Holland EC.

Cancer Cell. 2014 Aug 11;26(2):288-300. doi: 10.1016/j.ccr.2014.06.005.


Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity.

Marusyk A, Tabassum DP, Altrock PM, Almendro V, Michor F, Polyak K.

Nature. 2014 Oct 2;514(7520):54-8. doi: 10.1038/nature13556. Epub 2014 Jul 30.


Clonal evolution in breast cancer revealed by single nucleus genome sequencing.

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.

Nature. 2014 Aug 14;512(7513):155-60. doi: 10.1038/nature13600. Epub 2014 Jul 30.

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