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Clinical and Therapeutic Implications of Cancer Stem Cells.

Clarke MF.

N Engl J Med. 2019 Jun 6;380(23):2237-2245. doi: 10.1056/NEJMra1804280. Review. No abstract available.


Stimulation of natural killer cells with a CD137-specific antibody enhances trastuzumab efficacy in xenotransplant models of breast cancer.

Kohrt HE, Houot R, Weiskopf K, Goldstein MJ, Scheeren F, Czerwinski D, Colevas AD, Weng WK, Clarke MF, Carlson RW, Stockdale FE, Mollick JA, Chen L, Levy R.

J Clin Invest. 2019 Jun 3;129(6):2595. doi: 10.1172/JCI129688. Epub 2019 Jun 3. No abstract available.


Animal movements in fire-prone landscapes.

Nimmo DG, Avitabile S, Banks SC, Bliege Bird R, Callister K, Clarke MF, Dickman CR, Doherty TS, Driscoll DA, Greenville AC, Haslem A, Kelly LT, Kenny SA, Lahoz-Monfort JJ, Lee C, Leonard S, Moore H, Newsome TM, Parr CL, Ritchie EG, Schneider K, Turner JM, Watson S, Westbrooke M, Wouters M, White M, Bennett AF.

Biol Rev Camb Philos Soc. 2019 Jun;94(3):981-998. doi: 10.1111/brv.12486. Epub 2018 Dec 18.


Usp16 modulates Wnt signaling in primary tissues through Cdkn2a regulation.

Adorno M, di Robilant BN, Sikandar SS, Acosta VH, Antony J, Heller CH, Clarke MF.

Sci Rep. 2018 Nov 30;8(1):17506. doi: 10.1038/s41598-018-34562-w.


Serially transplantable mammary epithelial cells express the Thy-1 antigen.

Lobo NA, Zabala M, Qian D, Clarke MF.

Breast Cancer Res. 2018 Oct 10;20(1):121. doi: 10.1186/s13058-018-1006-y.


Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis.

Sikandar SS, Kuo AH, Kalisky T, Cai S, Zabala M, Hsieh RW, Lobo NA, Scheeren FA, Sim S, Qian D, Dirbas FM, Somlo G, Quake SR, Clarke MF.

Nat Commun. 2017 Nov 21;8(1):1669. doi: 10.1038/s41467-017-01666-2.


Targeted chromatin ligation, a robust epigenetic profiling technique for small cell numbers.

Zarnegar MA, Reinitz F, Newman AM, Clarke MF.

Nucleic Acids Res. 2017 Sep 29;45(17):e153. doi: 10.1093/nar/gkx648.


A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer.

Betancur PA, Abraham BJ, Yiu YY, Willingham SB, Khameneh F, Zarnegar M, Kuo AH, McKenna K, Kojima Y, Leeper NJ, Ho P, Gip P, Swigut T, Sherwood RI, Clarke MF, Somlo G, Young RA, Weissman IL.

Nat Commun. 2017 Apr 5;8:14802. doi: 10.1038/ncomms14802.


Stromal Gli2 activity coordinates a niche signaling program for mammary epithelial stem cells.

Zhao C, Cai S, Shin K, Lim A, Kalisky T, Lu WJ, Clarke MF, Beachy PA.

Science. 2017 Apr 21;356(6335). pii: eaal3485. doi: 10.1126/science.aal3485. Epub 2017 Mar 9.


Colorectal Cancer Liver Metastasis: Evolving Paradigms and Future Directions.

Zarour LR, Anand S, Billingsley KG, Bisson WH, Cercek A, Clarke MF, Coussens LM, Gast CE, Geltzeiler CB, Hansen L, Kelley KA, Lopez CD, Rana SR, Ruhl R, Tsikitis VL, Vaccaro GM, Wong MH, Mayo SC.

Cell Mol Gastroenterol Hepatol. 2017 Jan 20;3(2):163-173. doi: 10.1016/j.jcmgh.2017.01.006. eCollection 2017 Mar. Review.


A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland.

Cai S, Kalisky T, Sahoo D, Dalerba P, Feng W, Lin Y, Qian D, Kong A, Yu J, Wang F, Chen EY, Scheeren FA, Kuo AH, Sikandar SS, Hisamori S, van Weele LJ, Heiser D, Sim S, Lam J, Quake S, Clarke MF.

Cell Stem Cell. 2017 Feb 2;20(2):247-260.e5. doi: 10.1016/j.stem.2016.11.007. Epub 2016 Dec 29.


Prescribed burning consumes key forest structural components: implications for landscape heterogeneity.

Holland GJ, Clarke MF, Bennett AF.

Ecol Appl. 2017 Apr;27(3):845-858. doi: 10.1002/eap.1488. Epub 2017 Mar 13.


Do multiple fires interact to affect vegetation structure in temperate eucalypt forests?

Haslem A, Leonard SW, Bruce MJ, Christie F, Holland GJ, Kelly LT, MacHunter J, Bennett AF, Clarke MF, York A.

Ecol Appl. 2016 Dec;26(8):2412-2421. doi: 10.1002/eap.1399. Epub 2016 Oct 14.


Control of inflammation by stromal Hedgehog pathway activation restrains colitis.

Lee JJ, Rothenberg ME, Seeley ES, Zimdahl B, Kawano S, Lu WJ, Shin K, Sakata-Kato T, Chen JK, Diehn M, Clarke MF, Beachy PA.

Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):E7545-E7553. Epub 2016 Nov 4.


CDX2 as a Prognostic Biomarker in Colon Cancer.

Dalerba P, Sahoo D, Clarke MF.

N Engl J Med. 2016 Jun 2;374(22):2184. doi: 10.1056/NEJMc1602584. No abstract available.


Historical Maps from Modern Images: Using Remote Sensing to Model and Map Century-Long Vegetation Change in a Fire-Prone Region.

Callister KE, Griffioen PA, Avitabile SC, Haslem A, Kelly LT, Kenny SA, Nimmo DG, Farnsworth LM, Taylor RS, Watson SJ, Bennett AF, Clarke MF.

PLoS One. 2016 Mar 30;11(3):e0150808. doi: 10.1371/journal.pone.0150808. eCollection 2016.


CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer.

Dalerba P, Sahoo D, Paik S, Guo X, Yothers G, Song N, Wilcox-Fogel N, Forgó E, Rajendran PS, Miranda SP, Hisamori S, Hutchison J, Kalisky T, Qian D, Wolmark N, Fisher GA, van de Rijn M, Clarke MF.

N Engl J Med. 2016 Jan 21;374(3):211-22. doi: 10.1056/NEJMoa1506597.


Termites Are Resistant to the Effects of Fire at Multiple Spatial Scales.

Avitabile SC, Nimmo DG, Bennett AF, Clarke MF.

PLoS One. 2015 Nov 16;10(11):e0140114. doi: 10.1371/journal.pone.0140114. eCollection 2015.


KIT Signaling Promotes Growth of Colon Xenograft Tumors in Mice and Is Up-Regulated in a Subset of Human Colon Cancers.

Chen EC, Karl TA, Kalisky T, Gupta SK, O'Brien CA, Longacre TA, van de Rijn M, Quake SR, Clarke MF, Rothenberg ME.

Gastroenterology. 2015 Sep;149(3):705-17.e2. doi: 10.1053/j.gastro.2015.05.042. Epub 2015 May 28.


miR-142 regulates the tumorigenicity of human breast cancer stem cells through the canonical WNT signaling pathway.

Isobe T, Hisamori S, Hogan DJ, Zabala M, Hendrickson DG, Dalerba P, Cai S, Scheeren F, Kuo AH, Sikandar SS, Lam JS, Qian D, Dirbas FM, Somlo G, Lao K, Brown PO, Clarke MF, Shimono Y.

Elife. 2014 Nov 18;3. doi: 10.7554/eLife.01977.


A cell-intrinsic role for TLR2-MYD88 in intestinal and breast epithelia and oncogenesis.

Scheeren FA, Kuo AH, van Weele LJ, Cai S, Glykofridis I, Sikandar SS, Zabala M, Qian D, Lam JS, Johnston D, Volkmer JP, Sahoo D, van de Rijn M, Dirbas FM, Somlo G, Kalisky T, Rothenberg ME, Quake SR, Clarke MF.

Nat Cell Biol. 2014 Dec;16(12):1238-48. doi: 10.1038/ncb3058. Epub 2014 Nov 2.


Optimal fire histories for biodiversity conservation.

Kelly LT, Bennett AF, Clarke MF, McCarthy MA.

Conserv Biol. 2015 Apr;29(2):473-81. doi: 10.1111/cobi.12384. Epub 2014 Aug 28.


Quantitative assessment of single-cell RNA-sequencing methods.

Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, Rothenberg ME, Mburu FM, Mantalas GL, Sim S, Clarke MF, Quake SR.

Nat Methods. 2014 Jan;11(1):41-6. doi: 10.1038/nmeth.2694. Epub 2013 Oct 20.


Usp16 contributes to somatic stem-cell defects in Down's syndrome.

Adorno M, Sikandar S, Mitra SS, Kuo A, Nicolis Di Robilant B, Haro-Acosta V, Ouadah Y, Quarta M, Rodriguez J, Qian D, Reddy VM, Cheshier S, Garner CC, Clarke MF.

Nature. 2013 Sep 19;501(7467):380-4. doi: 10.1038/nature12530. Epub 2013 Sep 11.


Oncogenic miRNAs and the perils of losing control of a stem cell's epigenetic identity.

Dalerba P, Clarke MF.

Cell Stem Cell. 2013 Jul 3;13(1):5-6. doi: 10.1016/j.stem.2013.06.012.


Identifying the metastatic seeds of breast cancer.

Kuo AH, Clarke MF.

Nat Biotechnol. 2013 Jun;31(6):504-5. doi: 10.1038/nbt.2599. No abstract available.


Randomized trial using ultrasound to assess intramuscular vaccination at a 60° or 90° needle angle.

Marshall HS, Clarke MF, Evans S, Piotto L, Gent RJ.

Vaccine. 2013 May 28;31(23):2647-52. doi: 10.1016/j.vaccine.2013.03.037. Epub 2013 Apr 6.


MicroRNA-30c inhibits human breast tumour chemotherapy resistance by regulating TWF1 and IL-11.

Bockhorn J, Dalton R, Nwachukwu C, Huang S, Prat A, Yee K, Chang YF, Huo D, Wen Y, Swanson KE, Qiu T, Lu J, Park SY, Dolan ME, Perou CM, Olopade OI, Clarke MF, Greene GL, Liu H.

Nat Commun. 2013;4:1393. doi: 10.1038/ncomms2393.


MicroRNA-30c targets cytoskeleton genes involved in breast cancer cell invasion.

Bockhorn J, Yee K, Chang YF, Prat A, Huo D, Nwachukwu C, Dalton R, Huang S, Swanson KE, Perou CM, Olopade OI, Clarke MF, Greene GL, Liu H.

Breast Cancer Res Treat. 2013 Jan;137(2):373-82. doi: 10.1007/s10549-012-2346-4. Epub 2012 Dec 7.


Innate immune response to homologous rotavirus infection in the small intestinal villous epithelium at single-cell resolution.

Sen A, Rothenberg ME, Mukherjee G, Feng N, Kalisky T, Nair N, Johnstone IM, Clarke MF, Greenberg HB.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20667-72. doi: 10.1073/pnas.1212188109. Epub 2012 Nov 27.


Fire mosaics and reptile conservation in a fire-prone region.

Nimmo DG, Kelly LT, Spence-Bailey LM, Watson SJ, Taylor RS, Clarke MF, Bennett AF.

Conserv Biol. 2013 Apr;27(2):345-53. doi: 10.1111/j.1523-1739.2012.01958.x. Epub 2012 Nov 19.


Remodeling of endogenous mammary epithelium by breast cancer stem cells.

Parashurama N, Lobo NA, Ito K, Mosley AR, Habte FG, Zabala M, Smith BR, Lam J, Weissman IL, Clarke MF, Gambhir SS.

Stem Cells. 2012 Oct;30(10):2114-27. doi: 10.1002/stem.1205.


Effects of time since fire on birds: how informative are generalized fire response curves for conservation management?

Watson SJ, Taylor RS, Nimmo DG, Kelly LT, Haslem A, Clarke MF, Bennett AF.

Ecol Appl. 2012 Mar;22(2):685-96.


The pertussis epidemic: informing strategies for prevention of severe disease.

Clarke MF, Rasiah K, Copland J, Watson M, Koehler AP, Dowling K, Marshall HS.

Epidemiol Infect. 2013 Mar;141(3):463-71. doi: 10.1017/S095026881200091X. Epub 2012 May 17.


The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors.

Willingham SB, Volkmer JP, Gentles AJ, Sahoo D, Dalerba P, Mitra SS, Wang J, Contreras-Trujillo H, Martin R, Cohen JD, Lovelace P, Scheeren FA, Chao MP, Weiskopf K, Tang C, Volkmer AK, Naik TJ, Storm TA, Mosley AR, Edris B, Schmid SM, Sun CK, Chua MS, Murillo O, Rajendran P, Cha AC, Chin RK, Kim D, Adorno M, Raveh T, Tseng D, Jaiswal S, Enger PØ, Steinberg GK, Li G, So SK, Majeti R, Harsh GR, van de Rijn M, Teng NN, Sunwoo JB, Alizadeh AA, Clarke MF, Weissman IL.

Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6662-7. doi: 10.1073/pnas.1121623109. Epub 2012 Mar 26.


Identification of a cKit(+) colonic crypt base secretory cell that supports Lgr5(+) stem cells in mice.

Rothenberg ME, Nusse Y, Kalisky T, Lee JJ, Dalerba P, Scheeren F, Lobo N, Kulkarni S, Sim S, Qian D, Beachy PA, Pasricha PJ, Quake SR, Clarke MF.

Gastroenterology. 2012 May;142(5):1195-1205.e6. doi: 10.1053/j.gastro.2012.02.006. Epub 2012 Feb 11.


Stimulation of natural killer cells with a CD137-specific antibody enhances trastuzumab efficacy in xenotransplant models of breast cancer.

Kohrt HE, Houot R, Weiskopf K, Goldstein MJ, Scheeren F, Czerwinski D, Colevas AD, Weng WK, Clarke MF, Carlson RW, Stockdale FE, Mollick JA, Chen L, Levy R.

J Clin Invest. 2012 Mar;122(3):1066-75. doi: 10.1172/JCI61226. Epub 2012 Feb 13. Retraction in: J Clin Invest. 2019 Jun 3;129(6):2595.


Single-cell dissection of transcriptional heterogeneity in human colon tumors.

Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, Sim S, Okamoto J, Johnston DM, Qian D, Zabala M, Bueno J, Neff NF, Wang J, Shelton AA, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke MF, Quake SR.

Nat Biotechnol. 2011 Nov 13;29(12):1120-7. doi: 10.1038/nbt.2038.


Direct and indirect impact on rotavirus positive and all-cause gastroenteritis hospitalisations in South Australian children following the introduction of rotavirus vaccination.

Clarke MF, Davidson GP, Gold MS, Marshall HS.

Vaccine. 2011 Jun 24;29(29-30):4663-7. doi: 10.1016/j.vaccine.2011.04.109. Epub 2011 May 14.


Removal of lactate dehydrogenase-elevating virus from human-in-mouse breast tumor xenografts by cell-sorting.

Liu H, Bockhorn J, Dalton R, Chang YF, Qian D, Zitzow LA, Clarke MF, Greene GL.

J Virol Methods. 2011 May;173(2):266-70. doi: 10.1016/j.jviromet.2011.02.015. Epub 2011 Feb 24.


The Myc connection: ES cells and cancer.

Rothenberg ME, Clarke MF, Diehn M.

Cell. 2010 Oct 15;143(2):184-6. doi: 10.1016/j.cell.2010.09.046.


Cancer stem cells from human breast tumors are involved in spontaneous metastases in orthotopic mouse models.

Liu H, Patel MR, Prescher JA, Patsialou A, Qian D, Lin J, Wen S, Chang YF, Bachmann MH, Shimono Y, Dalerba P, Adorno M, Lobo N, Bueno J, Dirbas FM, Goswami S, Somlo G, Condeelis J, Contag CH, Gambhir SS, Clarke MF.

Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):18115-20. doi: 10.1073/pnas.1006732107. Epub 2010 Oct 4.


Downregulation of miRNA-200c links breast cancer stem cells with normal stem cells.

Shimono Y, Zabala M, Cho RW, Lobo N, Dalerba P, Qian D, Diehn M, Liu H, Panula SP, Chiao E, Dirbas FM, Somlo G, Pera RA, Lao K, Clarke MF.

Cell. 2009 Aug 7;138(3):592-603. doi: 10.1016/j.cell.2009.07.011.


DLL4 blockade inhibits tumor growth and reduces tumor-initiating cell frequency.

Hoey T, Yen WC, Axelrod F, Basi J, Donigian L, Dylla S, Fitch-Bruhns M, Lazetic S, Park IK, Sato A, Satyal S, Wang X, Clarke MF, Lewicki J, Gurney A.

Cell Stem Cell. 2009 Aug 7;5(2):168-77. doi: 10.1016/j.stem.2009.05.019.


Radiation Therapy Oncology Group translational research program stem cell symposium: incorporating stem cell hypotheses into clinical trials.

Woodward WA, Bristow RG, Clarke MF, Coppes RP, Cristofanilli M, Duda DG, Fike JR, Hambardzumyan D, Hill RP, Jordan CT, Milas L, Pajonk F, Curran WJ, Dicker AP, Chen Y.

Int J Radiat Oncol Biol Phys. 2009 Aug 1;74(5):1580-91. doi: 10.1016/j.ijrobp.2009.03.047. Epub 2009 Jun 17.


Automated microfluidic chromatin immunoprecipitation from 2,000 cells.

Wu AR, Hiatt JB, Lu R, Attema JL, Lobo NA, Weissman IL, Clarke MF, Quake SR.

Lab Chip. 2009 May 21;9(10):1365-70. doi: 10.1039/b819648f. Epub 2009 Feb 27.


Therapeutic implications of the cancer stem cell hypothesis.

Diehn M, Cho RW, Clarke MF.

Semin Radiat Oncol. 2009 Apr;19(2):78-86. doi: 10.1016/j.semradonc.2008.11.002. Review.


Dysregulated gene expression networks in human acute myelogenous leukemia stem cells.

Majeti R, Becker MW, Tian Q, Lee TL, Yan X, Liu R, Chiang JH, Hood L, Clarke MF, Weissman IL.

Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3396-401. doi: 10.1073/pnas.0900089106. Epub 2009 Feb 13.


Association of reactive oxygen species levels and radioresistance in cancer stem cells.

Diehn M, Cho RW, Lobo NA, Kalisky T, Dorie MJ, Kulp AN, Qian D, Lam JS, Ailles LE, Wong M, Joshua B, Kaplan MJ, Wapnir I, Dirbas FM, Somlo G, Garberoglio C, Paz B, Shen J, Lau SK, Quake SR, Brown JM, Weissman IL, Clarke MF.

Nature. 2009 Apr 9;458(7239):780-3. doi: 10.1038/nature07733.


Analysis of the measurement precision of an amorphous silicon EPID used for MLC leaf position quality control and the long-term calibration stability of an optically controlled MLC.

Budgell GJ, Clarke MF.

Phys Med Biol. 2008 Aug 7;53(15):N297-306. doi: 10.1088/0031-9155/53/15/N01. Epub 2008 Jul 17.


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