Adaptation and selection shape clonal evolution of tumors during residual disease and recurrence

[1]  Kristian Cibulskis,et al.  Calling Somatic SNVs and Indels with Mutect2 , 2019, bioRxiv.

[2]  K. Hunter,et al.  Integrated analyses of murine breast cancer models reveal critical parallels with human disease , 2019, Nature Communications.

[3]  K. Owzar,et al.  Mutational landscape in genetically engineered, carcinogen-induced, and radiation-induced mouse sarcoma. , 2019, JCI insight.

[4]  Daniel L. Cameron,et al.  Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer , 2019, Nature Communications.

[5]  Jeffrey T. Chang,et al.  Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state , 2019, Science Translational Medicine.

[6]  Shan Jiang,et al.  Pre-existing Functional Heterogeneity of Tumorigenic Compartment as the Origin of Chemoresistance in Pancreatic Tumors. , 2019, Cell reports.

[7]  Lai Guan Ng,et al.  Dimensionality reduction for visualizing single-cell data using UMAP , 2018, Nature Biotechnology.

[8]  Jeffrey T. Chang,et al.  High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer , 2018, Nature Communications.

[9]  J. Thompson,et al.  Epigenetic silencing of tumor suppressor Par-4 promotes chemoresistance in recurrent breast cancer , 2018, The Journal of clinical investigation.

[10]  L. Trusolino,et al.  Known and novel roles of the MET oncogene in cancer: a coherent approach to targeted therapy , 2018, Nature Reviews Cancer.

[11]  Paul Hoffman,et al.  Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.

[12]  Jeffrey S. Damrauer,et al.  Foxo-dependent Par-4 Upregulation Prevents Long-term Survival of Residual Cells Following PI3K–Akt Inhibition , 2018, Molecular Cancer Research.

[13]  Nancy R. Zhang,et al.  CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing , 2017, Genome Biology.

[14]  K. Vandyke,et al.  DNA Barcoding Reveals Habitual Clonal Dominance of Myeloma Plasma Cells in the Bone Marrow Microenvironment , 2017, Neoplasia.

[15]  Richard A. Moore,et al.  Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy , 2017, Nature.

[16]  P. Lønning,et al.  Genomic Evolution of Breast Cancer Metastasis and Relapse , 2017, Cancer cell.

[17]  R. Weinberg,et al.  EMT, CSCs, and drug resistance: the mechanistic link and clinical implications , 2017, Nature Reviews Clinical Oncology.

[18]  Hans Bitter,et al.  The allosteric inhibitor ABL001 enables dual targeting of BCR–ABL1 , 2017, Nature.

[19]  R. Doebele,et al.  A framework for understanding and targeting residual disease in oncogene-driven solid cancers , 2016, Nature Medicine.

[20]  G. Getz,et al.  Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition , 2016, Nature Medicine.

[21]  M. Hirst,et al.  Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells , 2015, Nature.

[22]  Tien-chi Pan,et al.  Notch promotes recurrence of dormant tumor cells following HER2/neu-targeted therapy. , 2015, The Journal of clinical investigation.

[23]  Joshua M. Korn,et al.  Studying clonal dynamics in response to cancer therapy using high-complexity barcoding , 2015, Nature Medicine.

[24]  Steffen Dickopf,et al.  A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis , 2015, Nature.

[25]  Cyrus M. Ghajar Metastasis prevention by targeting the dormant niche , 2015, Nature Reviews Cancer.

[26]  Martin Hirst,et al.  DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts , 2014, Nature Communications.

[27]  Hua Yu,et al.  Revisiting STAT3 signalling in cancer: new and unexpected biological functions , 2014, Nature Reviews Cancer.

[28]  Paul Theodor Pyl,et al.  HTSeq – A Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[29]  P. Bragado,et al.  Mechanisms of disseminated cancer cell dormancy: an awakening field , 2014, Nature Reviews Cancer.

[30]  Tien-chi Pan,et al.  SPSB1 promotes breast cancer recurrence by potentiating c-MET signaling. , 2014, Cancer discovery.

[31]  P. Mieczkowski,et al.  Practical innovations for high-throughput amplicon sequencing , 2013, Nature Methods.

[32]  Tien-chi Pan,et al.  Par-4 downregulation promotes breast cancer recurrence by preventing multinucleation following targeted therapy. , 2013, Cancer cell.

[33]  A. Chenchik,et al.  Measurement of Cancer Cell Growth Heterogeneity through Lentiviral Barcoding Identifies Clonal Dominance as a Characteristic of In Vivo Tumor Engraftment , 2013, PloS one.

[34]  V. Seshan,et al.  A CXCL1 Paracrine Network Links Cancer Chemoresistance and Metastasis , 2012, Cell.

[35]  P. Fasching,et al.  Definition and impact of pathologic complete response on prognosis after neoadjuvant chemotherapy in various intrinsic breast cancer subtypes. , 2012, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[36]  K. Polyak,et al.  Intra-tumour heterogeneity: a looking glass for cancer? , 2012, Nature Reviews Cancer.

[37]  Carmen Birchmeier,et al.  Targeting MET in cancer: rationale and progress , 2012, Nature Reviews Cancer.

[38]  G. Mills,et al.  Oncogenic PIK3CA-driven mammary tumors frequently recur via PI3K pathway-dependent and -independent mechanisms , 2011, Nature Medicine.

[39]  S. Digumarthy,et al.  Genotypic and Histological Evolution of Lung Cancers Acquiring Resistance to EGFR Inhibitors , 2011, Science Translational Medicine.

[40]  C. Klein Framework models of tumor dormancy from patient-derived observations. , 2011, Current opinion in genetics & development.

[41]  P. Goss,et al.  Does tumour dormancy offer a therapeutic target? , 2010, Nature Reviews Cancer.

[42]  Luke A. Gilbert,et al.  DNA Damage-Mediated Induction of a Chemoresistant Niche , 2010, Cell.

[43]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[44]  Luca Toschi,et al.  Preexistence and clonal selection of MET amplification in EGFR mutant NSCLC. , 2010, Cancer cell.

[45]  Jeffrey M. Rosen,et al.  Residual breast cancers after conventional therapy display mesenchymal as well as tumor-initiating features , 2009, Proceedings of the National Academy of Sciences.

[46]  E. Neilson,et al.  Biomarkers for epithelial-mesenchymal transitions. , 2009, The Journal of clinical investigation.

[47]  L. Trusolino,et al.  Drug development of MET inhibitors: targeting oncogene addiction and expedience , 2008, Nature Reviews Drug Discovery.

[48]  Stephen E. Jones Metastatic breast cancer: the treatment challenge. , 2008, Clinical breast cancer.

[49]  P. Jänne,et al.  Mechanisms of Acquired Resistance to Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Non–Small Cell Lung Cancer , 2008, Clinical Cancer Research.

[50]  Joon-Oh Park,et al.  MET Amplification Leads to Gefitinib Resistance in Lung Cancer by Activating ERBB3 Signaling , 2007, Science.

[51]  Robert D Cardiff,et al.  The transcriptional repressor Snail promotes mammary tumor recurrence. , 2005, Cancer cell.

[52]  Anne E Magurran,et al.  Biological diversity , 2005, Current Biology.

[53]  R. Demicheli,et al.  Menopausal status dependence of the timing of breast cancer recurrence after surgical removal of the primary tumour , 2004, Breast Cancer Research.

[54]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[55]  Flemming Topsøe,et al.  Jensen-Shannon divergence and Hilbert space embedding , 2004, International Symposium onInformation Theory, 2004. ISIT 2004. Proceedings..

[56]  G. Dontu,et al.  In vitro propagation and transcriptional profiling of human mammary stem/progenitor cells. , 2003, Genes & development.

[57]  Mitchell D Schnall,et al.  Conditional activation of Neu in the mammary epithelium of transgenic mice results in reversible pulmonary metastasis. , 2002, Cancer cell.

[58]  N. Stoecklein,et al.  Genetic heterogeneity of single disseminated tumour cells in minimal residual cancer , 2002, The Lancet.

[59]  W. Sauerbrei,et al.  Role of isolated locoregional recurrence of breast cancer: results of four prospective studies. , 2000, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[60]  R. Gray,et al.  Annual hazard rates of recurrence for breast cancer after primary therapy. , 1996, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[61]  D. Cox,et al.  Analysis of Survival Data. , 1985 .

[62]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[63]  G. Hortobagyi,et al.  Overview of resistance to systemic therapy in patients with breast cancer. , 2007, Advances in experimental medicine and biology.

[64]  N. W. PIRIE,et al.  Biological Diversity , 1964 .