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, e2406842121.

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 AG, 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 Rep 42, 113564. + Co-corresponding authors.

Nishida J, Cristea S, Bodapati S, Puleo J, Bai G, Patel A, Hughes M, Snow C, Borges V, Ruddy KJ, Collins LC, Feeney AM, Slowik K, Bossuyt V, Dillon D, Lin NU, Partridge AH, 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 of the United States of America 120, e2316763120.

Cheng Y-C, Stein S, Nardone A, Liu W, Ma W, Cohen G, Guarducci C, McDonald TO, 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, 2331–2344. + Co-corresponding authors.

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.

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 (2023) JAK-STAT signaling in inflammatory breast cancer enables chemotherapy-resistant cell states. Cancer Research 83, 264-284. * Equal contribution.

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.

Wu H-J*, Temko D*, Maliga Z*, Moreira A, Sei E, Minussi DC, Dean J, Lee C, Xu Q, Hochart G, Jacobson C, Yapp C, Schapiro D, Sorger P, Seeley EH, Navin N, Downey RJ+, Michor F+ (2022) Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients. Cell Genomics 2, 100165. * Equal contribution. + Co-corresponding authors.

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.

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.

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. *Equal contribution. + Co-corresponding authors.

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 N+ (2021) Breast tumors maintain a reservoir of subclonal diversity during expansion. Nature 592, 302-308. * Equal contribution. + Co-corresponding authors.

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

Oki T, Mercier F, Kato H, Jung Y, McDonald TO, Spencer J, Mazzola M, van Gastel N, Lin C, Michor F, Kitamura T, Scadden D (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.

Irurzun-Arana I+, Rackauckas C, McDonald TO, Trocóniz IF+ (2020) Beyond Deterministic Models in Drug Discovery and Development. Trends in Pharmacological Sciences 41, 882-895. + Co-corresponding authors.

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.

Roney J*, 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.

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.

Ge JY, Shu S, Kwon M, Jovanovic B, Murchpy 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. Nature Communications 11, 2350, 1-17. * Co-corresponding authors.

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

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.

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

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.

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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.

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.

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.

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

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

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

Franziska Michor

David Pellman

Kornelia Polyak