Breast Cancer Program
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Selected Publications
2008
Antoniou AC, Spurdle AB, Sinilnikova OM, Healey S, Pooley KA, Schmutzler RK, Versmold B, Engel C, Meindl A, Arnold N, Hofmann W, Sutter C, Niederacher D, Deissler H, Caldes T, Kampjarvi K, Nevanlinna H, Simard J, Beesley J, Chen X, Neuhausen SL, Rebbeck TR, Wagner T, Lynch HT, Isaacs C, Weitzel J, Ganz PA, Daly MB, Tomlinson G, Olopade OI, Blum JL, Couch FJ, Peterlongo P, Manoukian S, Barile M, Radice P, Szabo CI, Pereira LH, Greene MH, Rennert G, Lejbkowicz F, Barnett-Griness O, Andrulis IL, Ozcelik H, Gerdes AM, Caligo MA, Laitman Y, Kaufman B, Milgrom R, Friedman E, Domchek SM, Nathanson KL, Osorio A, Llort G, Milne RL, Benitez J, Hamann U, Hogervorst FB, Manders P, Ligtenberg MJ, van den Ouweland AM, Peock S, Cook M, Platte R, Evans DG, Eeles R, Pichert G, Chu C, Eccles D, Davidson R, Douglas F, Godwin AK, Barjhoux L, Mazoyer S, Sobol H, Bourdon V, Eisinger F, Chompret A, Capoulade C, Bressac-de Paillerets B, Lenoir GM, Gauthier-Villars M, Houdayer C, Stoppa-Lyonnet D, Chenevix-Trench G, Easton DF. Common breast cancer-predisposition alleles are associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers. Am J Hum Genet 2008;82(4):937-948.
Bird BR, Swain SM. Cardiac toxicity in breast cancer survivors: review of potential cardiac problems. Clin Cancer Res 2008;14(1):14-24.
Calvo A, Catena R, Noble MS, Carbott D, Gil-Bazo I, Gonzalez-Moreno O, Huh JI, Sharp R, Qiu TH, Anver MR, Merlino G, Dickson RB, Johnson MD, and Green JE. Identification of VEGF-regulated genes associated with increased lung metastatic potential: functional involvement of tenascin-C in tumor growth and lung metastasis Oncogene 2008;27:5373-84.
Chen J, Higby R, Tian D, Tan D, Johnson MD, Xiao Y, Kellar KJ, Feng S, Shields PG. Toxicological analysis of low-nicotine and nicotine-free cigarettes. Toxicology 2008;249(2-3):194-203.
Chen l, Eang C, Shih M, Wang T, Zhang Z, Clarke R, Hoffman E, Wang Y, Xuan J. Biomarker identification by knowledge driven multilevel ICA and motif analysis. Int J Data Mining Bioinformatics 2008.
Chen L, Xuan J, Riggins RB, Wang Y, Hoffman EP, Clarke R. Identification of condition-specific regulatory modules by multi-level motif and mRNA expression analysis. 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08) 2008.
Chen L, Xuan J, Wang C, Shih IeM, Wang Y, Zhang Z, Hoffman E, Clarke R. Knowledge-guided multi-scale independent component analysis for biomarker identification. BMC Bioinformatics 2008;9:416.
Chia S, Swain SM, Byrd DR, Mankoff DA. Locally advanced and inflammatory breast cancer. J Clin Oncol 2008;26(5):786-790.
Chizea JP, Dailey VK, Williams E, Johnson MD, Pestell RG, and Ojeifo JO. Endothelial progenitor cells significantly contribute to vasculatures in human and mouse breast tumors. Open Hematology Journal 2008;1:30-62.
Clarke R, Ressom HW, Wang A, Xuan J, Liu MC, Gehan EA, Wang Y. The properties of high-dimensional data spaces: implications for exploring gene and protein expression data. Nat Rev Cancer 2008;8(1):37-49.
Clarke R, Shajahan AN, Riggins RB, Crawford A, Xuan J, Wang Y, Zwart A, Nehra R, Liu MC. Gene network signaling in hormone responsiveness modifies apoptosis and autophagy in breast cancer cells. J Steroid Biochem Mol Biol 2008.
Coticchia CM, Revankar CM, Deb TB, Dickson RB, Johnson MD. Calmodulin modulates Akt activity in human breast cancer cell lines. Breast Cancer Res Treat 2008 Jun 28 [Epub ahead of print].
Deb TB, Coticchia CM, Barndt R, Zuo H, Dickson RB, Johnson MD. Pregnancy-upregulated nonubiquitous calmodulin kinase induces ligand-independent EGFR degradation. Am J Physiol Cell Physiol 2008;295(2):C365-C377.
Denduluri N, Swain SM. Ixabepilone for the treatment of solid tumors: a review of clinical data. Expert Opin Investig Drugs 2008;17(3):423-435.
Denduluri N, Yang SX, Berman AW, Nguyen D, Liewehr DJ, Steinberg SM, Swain SM. Circulating biomarkers of bevacizumab activity in patients with breast cancer. Cancer Biol Ther 2008;7(1):15-20.
Eng-Wong J, Zujewski JA. Current NCI-sponsored Cooperative Group trials of endocrine therapies in breast cancer. Cancer 2008;112(3 Suppl):723-729.
Eng-Wong J, Orzano-Birgani J, Chow CK, Venzon D, Yao J, Galbo CE, Zujewski JA, Prindiville S. Effect of raloxifene on mammographic density and breast magnetic resonance imaging in premenopausal women at increased risk for breast cancer. Cancer Epidemiol Biomarkers Prev 2008;17(7):1696-1701.
Fereshteh MP, Tilli MT, Kim SE, Xu J, O'Malley BW, Wellstein A, Furth PA, Riegel AT. The nuclear receptor coactivator amplified in breast cancer-1 is required for Neu (ErbB2/HER2) activation, signaling, and mammary tumorigenesis in mice. Cancer Res 2008;68(10):3697-3706.
Fishbein T, Novitskiy G, Mishra L, Matsuomoto C, Kaufman S, Goyal S, Shetty K, Johnson L, Lu A, Wang A, Hu F, Kallakury B, Lough P, Zasloff M. NOD2-expressing bone marrow-derived cells appear to regulate epithelial innate immunity of the transplanted human small intestine. Gut 2008;57(3):323-30.
Ginsburg O, Ghadirian P, Lubinski J, Cybulski C, Lynch H, Neuhausen S, Kim-Sing C, Robson M, Domchek S, Isaacs C, Klijn J, Armel S, Foulkes WD, Tung N, Moller P, Sun P, Narod SA. Smoking and the risk of breast cancer in BRCA1 and BRCA2 carriers: an update. Breast Cancer Res Treat 2008;114(1):127-35.
Glazer RI, Wang XY, Yuan H, Yin Y. Musashi: a stem cell marker no longer in search of a function. Cell Cycle 2008;7(17):2635-2639.
Glazer RI, Yuan H, Xie Z, Yin Y. PPARgamma and PPARdelta as Modulators of Neoplasia and Cell Fate. PPAR Res 2008;2008:247379.
Gong T, Xuan J, Chen L, Riggins RB, Wang Y, Hoffman E, Clarke R. Sparse decomposition of gene expression data to infer transcriptional modules guided by motif information. Proc 4th Intl Symp Bioinformatics Res Applications 2008.
Gong T, Xuan J, Wang C, Li H, Hoffman E, Clarke R, Wang Y. Gene module identification from microarray data using nonnegative independent component analysis. Gene Reg Sys Biol 2008.
Jamshed S, Farhan MI, Marshall MB, Nahabedian MY, Liu MC. Fibromatosis of the breast after mammary prosthesis implantation. Clin Adv Hematol Oncol 2008;6(9):687-694.
Jiao X, Katiyar S, Liu M, Mueller SC, Lisanti MP, Li A, Pestell TG, Wu K, Ju X, Li Z, Wagner EF, Takeya T, Wang C, Pestell RG. Disruption of c-Jun Reduces Cellular Migration and Invasion through Inhibition of c-Src and Hyperactivation of ROCK II Kinase. Mol Biol Cell 2008;19(4):1378-1390.
Jordan V, Ariazi E, Lewis-Wambi J, Swaby R, Cunliffe H, Riegel A, Wellstein A. Oestrogen is bad for patients with breast cancer? Breast Cancer 2008.
Kauff ND, Domchek SM, Friebel TM, Robson ME, Lee J, Garber JE, Isaacs C, Evans DG, Lynch H, Eeles RA, Neuhausen SL, Daly MB, Matloff E, Blum JL, Sabbatini P, Barakat RR, Hudis C, Norton L, Offit K, Rebbeck TR. Risk-reducing salpingo-oophorectomy for the prevention of B. J Clin Oncol 2008;26(8):1331-1337.
Lee JJ, Swain SM. The epothilones: translating from the laboratory to the clinic. Clin Cancer Res 2008;14(6):1618-1624.
Li H, Armando I, Yu P, Escano C, Mueller SC, Asico L, Pascua A, Lu Q, Wang X, Villar VA, Jones JE, Wang Z, Periasamy A, Lau YS, Soares-da-Silva P, Creswell K, Guillemette G, Sibley DR, Eisner G, Felder RA, Jose PA. Dopamine 5 receptor mediates Ang II type 1 receptor degradation via a ubiquitin-proteasome pathway in mice and human cells. J Clin Invest 2008;118(6):2180-2189.
Jones LP, Tilli MT, Assefnia S, Torre K, Halama ED, Parrish A, Rosen EM, Furth PA. Activation of estrogen signaling pathways collaborates with loss of Brca1 to promote development of ERalpha-negative and ERalpha-positive mammary preneoplasia and cancer. Oncogene 2008;27(6):794-802.
Li H, Armando I, Yu P, Escano C, Mueller SC, Asico L, Pascua A, Lu Q, Wang X, Villar VA, Jones JE, Wang Z, Periasamy A, Lau YS, Soares-da-Silva P, Creswell K, Guillemette G, Sibley DR, Eisner G, Gildea JJ, Felder RA, Jose PA. Erratum. J Clin Invest 2008;118(8):2986.
Lin CY, Tseng IC, Chou FP, Su SF, Chen YW, Johnson MD, and Dickson RB. Zymogen activation, inhibition, and ectodomain shedding of matriptase. Front Biosci 2008;13:621-35.
Lin NU, Carey LA, Liu MC, Younger J, Come SE, Ewend M, Harris GJ, Bullitt E, Van den Abbeele AD, Henson JW, Li X, Gelman R, Burstein HJ, Kasparian E, Kirsch DG, Crawford A, Hochberg F, Winer EP. Phase II trial of lapatinib for brain metastases in patients with human epidermal growth factor receptor 2-positive breast cancer. J Clin Oncol 2008;26(12):1993-1999.
Liu MC, Demetri GD, Berry DA, Norton L, Broadwater G, Robert NJ, Duggan D, Hayes DF, Henderson IC, Lyss A, Hopkins J, Kaufman PA, Marcom PK, Younger J, Lin N, Tkaczuk K, Winer EP, Hudis CA. Dose-escalation of filgrastim does not improve efficacy: clinical tolerability and long-term follow-up on CALGB study 9141 adjuvant chemotherapy for node-positive breast cancer patients using dose-intensified doxorubicin plus cyclophosphamide followed by paclitaxel. Cancer Treat Rev 2008;34(3):223-230.
Lof M, Hilakivi-Clarke L, Sandin S, Weiderpass E. Effects of pre-pregnancy physical activity and maternal BMI on gestational weight gain and birth weight. Acta Obstet Gynecol Scand 2008;87(5):524-530.
Lynce F, Swain SM. First, do no harm. Onkologie 2008;31(10):511-512.
Metcalfe KA, Lubinski J, Ghadirian P, Lynch H, Kim-Sing C, Friedman E, Foulkes WD, Domchek S, Ainsworth P, Isaacs C, Tung N, Gronwald J, Cummings S, Wagner T, Manoukian S, Moller P, Weitzel J, Sun P, Narod SA. Predictors of contralateral prophylactic mastectomy in women with a BRCA1 or BRCA2 mutation: the Hereditary Breast Cancer Clinical Study Group. J Clin Oncol 2008;26(7):1093-1097.
Moussa CE, Rusnak M, Hailu A, Sidhu A, Fricke ST. Alterations of striatal glutamate transmission in rotenone-treated mice: MRI/MRS in vivo studies. Exp Neurol 2008;209(1):224-233.
Mueller SC, Artym VA, Kelly T. Invadopodia: interface for invasion. In: Dylan E, Hoyer-Hansen G, Blasi F, Sloan B, editors. The cancer degradome: proteases in cancer biology. New York: Springer, 2008
Narod SA, Neuhausen S, Vichodez G, Armel S, Lynch HT, Ghadirian P, Cummings S, Olopade O, Stoppa-Lyonnet D, Couch F, Wagner T, Warner E, Foulkes WD, Saal H, Weitzel J, Tulman A, Poll A, Nam R, Sun P, Danquah J, Domchek S, Tung N, Ainsworth P, Horsman D, Kim-Sing C, Maugard C, Eisen A, Daly M, McKinnon W, Wood M, Isaacs C, Gilchrist D, Karlan B, Nedelcu R, Meschino W, Garber J, Pasini B, Manoukian S, Bellati C. Rapid progression of prostate cancer in men with a BRCA2 mutation. Br J Cancer 2008;99(2):371-374.
Oh AS, Lahusen JT, Chien CD, Fereshteh MP, Zhang X, Dakshanamurthy S, Xu J, Kagan BL, Wellstein A, Riegel AT. Tyrosine phosphorylation of the nuclear receptor coactivator AIB1/SRC-3 is enhanced by Abl kinase and is required for its activity in cancer cells. Mol Cell Biol 2008;28(21):6580-93.
Olivo S, Zhu Y, Lee RY, Khan G, Zwart A, Wang Y, Clarke R, Hilakivi-Clarke L. Identification of gene signaling pathways mediating the breast cancer risk reducing effects of prepubertal dietary exposure to low fat n-3 polyunsaturated fatty acids. Cancer Prevention Research 2008.
Portera CC, Walshe JM, Rosing DR, Denduluri N, Berman AW, Vatas U, Velarde M, Chow CK, Steinberg SM, Nguyen D, Yang SX, Swain SM. Cardiac toxicity and efficacy of trastuzumab combined with pertuzumab in patients with [corrected] human epidermal growth factor receptor 2-positive metastatic breast cancer. Clin Cancer Res 2008;14(9):2710-2716.
Ressom HW, Varghese RS, Zhang Z, Xuan J, Clarke R. Classification algorithms for phenotype prediction in genomics and proteomics. Front Biosci 2008;13:691-708.
Riggins RB, Lan JP, Klimach U, Zwart A, Cavalli LR, Haddad BR, Chen L, Gong T, Xuan J, Ethier SP, Clarke R. ERRgamma mediates tamoxifen resistance in novel models of invasive lobular breast cancer. Cancer Res 2008;68(21):8908-8917.
Scheppke L, Aguilar E, Gariano RF, Jacobson R, Hood J, Doukas J, Cao J, Noronha G, Yee S, Weis S, Martin MB, Soll R, Cheresh DA, Friedlander M. Retinal vascular permeability suppression by topical application of a novel VEGFR2/Src kinase inhibitor in mice and rabbits. J Clin Invest 2008;118(6):2337-2346.
Schwartz GF, Hughes KS, Lynch HT, Fabian CJ, Fentiman IS, Robson ME, Domchek SM, Hartmann LC, Holland R, Winchester DJ; The International Consensus Conference Committee. Proceedings of the international consensus conference on breast cancer risk, genetics, & risk management, April, 2007. Cancer 2008;113(10):2627-37.
Shajahan AN, Riggins RB, Clarke R. Apoptosis, cell death, and breast cancer. In: Pasqualini JR, editor. Breast Cancer: Prognosis, Treatment, and Prevention. New York: Informa Healthcare, 2008:137-156.
Sikora MJ, Cordero KE, Larios JM, Johnson MD, Lippman ME, Rae JM. The androgen metabolite 5alpha-androstane-3beta,17beta-diol (3betaAdiol) induces breast cancer growth via estrogen receptor: implications for aromatase inhibitor resistance. Breast Cancer Res Treat 2008 Jun 4 [Epub ahead of print].
Spear SL, Boehmler JH, Bogue DP, Mafi AA. Options in reconstructing the irradiated breast. Plast Reconstr Surg 2008;122(2):379-388.
Spear SL, Parikh PM, Reisin E, Menon NG. Acellular dermis-assisted breast reconstruction. Aesthetic Plast Surg 2008;32(3):418-425.
Spear SL, Newman MK, Bedford MS, Schwartz KA, Cohen M, Schwartz JS. A retrospective analysis of outcomes using three common methods for immediate breast reconstruction. Plast Reconstr Surg 2008;122(2):340-347.
Spear SL. Fat for breast: where are we?. Plast Reconstr Surg 2008;122(3):983-984.
Spear SL, Schwarz KA, Venturi ML, Barbosa T, Al Attar A. Prophylactic mastectomy and reconstruction: clinical outcomes and patient satisfaction. Plast Reconstr Surg 2008;122(1):1-9.
Swain SM. Cardiovascular complications of breast cancer therapy. Clin Adv Hematol Oncol 2008;6(4):247-8, 282.
Swain SM, Arezzo JC. Neuropathy associated with microtubule inhibitors: diagnosis, incidence, and management. Clin Adv Hematol Oncol 2008;6(6):455-467.
Tan AR, Swain SM. Therapeutic strategies for triple-negative breast cancer. Cancer J 2008;14(6):343-351.
Tang Y, Kitisin K, Jogunoori W, Li C, Deng CX, Mueller SC, Ressom HW, Rashid A, He AR, Mendelson JS, Jessup JM, Shetty K, Zasloff M, Mishra B, Reddy EP, Johnson L, Mishra L. Progenitor/stem cells give rise to liver cancer due to aberrant TGF-beta and IL-6 signaling. Proc Natl Acad Sci U S A 2008;105(7):2445-2450.
Tilli MT, Parrish AR, Cotarla I, Jones LP, Johnson MD, Furth PA. Comparison of mouse mammary gland imaging techniques and applications: reflectance confocal microscopy, GFP imaging, and ultrasound. BMC Cancer 2008;8:21.
Tseng IC, Chou FP, Su SF, Oberst M, Madayiputhiya N, Lee MS, Wang JK, Sloane DE, Johnson M, Lin CY. Purification from human milk of matriptase complexes with secreted serpins: mechanism for inhibition of matriptase other than HAI-1. Am J Physiol Cell Physiol 2008;295(2):C423-C431.
Tummala MK, Alagarsamy S, McGuire WP. Intraperitoneal chemotherapy: standard of care for patients with minimal residual stage III ovarian cancer? Expert Rev Anticancer Ther 2008;8(7):1135-1147.
 Veselik DJ, Divekar S, Dakshanamurthy S, Storchan GB, Turner JM, Graham KL, Huang L, Stoica A, Martin MB. Activation of estrogen receptor-alpha by the anion nitrite. Cancer Res 2008;68(10):3950-3958.
Wang A. The analysis of bivariate truncated data using the Clayton Copula model. The International Journal of Biostatistics 2008.
Wang A. A note on checking the Clayton model assumption based on left truncated bivariate data. Statistics and Probability Letters 2008. Â
Wang C, Xuan J, Chen L, Zhao P, Wang Y, Clarke R, Hoffman E. Integrative network component analysis for regulatory network reconstruction. Proc 4th Intl Symp Bioinformatics Res Applications (ISBRA) 2008.
Wang C, Xuan J, Chen L, Zhao P, Wang Y, Clarke R, Hoffman E. Motif-directed network component analysis for regulatory network inference. BMC Bioinformatics 2008;9 Suppl 1:S21.
Wang M, Yu B, Westerlind K, Strange R, Khan G, Patil D, Boeneman K, Hilakivi-Clarke L. Prepubertal physical activity up-regulates estrogen receptor beta, BRCA1 and p53 mRNA expression in the rat mammary gland. Breast Cancer Res Treat 2008 May 31 [Epub ahead of print].
Wang XY, Yin Y, Yuan H, Sakamaki T, Okano H, Glazer RI. Musashi1 modulates mammary progenitor cell expansion through proliferin-mediated activation of the Wnt and Notch pathways. Mol Cell Biol 2008;28(11):3589-3599.
Wang Y, Miller DJ, Clarke R. Approaches to working in high-dimensional data spaces: gene expression microarrays. Br J Cancer 2008;98(6):1023-1028.
Warri A, Saarinen NM, Makela S, Hilakivi-Clarke L. The role of early life genistein exposures in modifying breast cancer risk. Br J Cancer 2008;98(9):1485-1493.
Winter WE, III, Maxwell GL, Tian C, Sundborg MJ, Rose GS, Rose PG, Rubin SC, Muggia F, McGuire WP. Tumor residual after surgical cytoreduction in prediction of clinical outcome in stage IV epithelial ovarian cancer: a Gynecologic Oncology Group Study. J Clin Oncol 2008;26(1):83-89.
Wulfkuhle JD, Speer R, Pierobon M, Laird J, Espina V, Deng J, Mammano E, Yang SX, Swain SM, Nitti D, Esserman LJ, Belluco C, Liotta LA, Petricoin EF, III. Multiplexed cell signaling analysis of human breast cancer applications for personalized therapy. J Proteome Res 2008;7(4):1508-1517.
Xuan J, Wang Y, Hoffman E, Clarke R. Cross phenotype normalization of microarray data. Front Biosci 2008.
Xue F, Hilakivi-Clarke L, Maxwell G, Hankinson S, Michels K. Longitudinal study on birthweight and the incidence of endometrial cancer. Br J Cancer 2008;98(7):1288-1291.
Xue F, Hilakivi-Clarke LA, Maxwell GL, Hankinson SE, Michels KB. Infant feeding and the incidence of endometrial cancer. Cancer Epidemiol Biomarkers Prev 2008;17(6):1316-1321.
Yang SX, Steinberg SM, Nguyen D, Wu TD, Modrusan Z, Swain SM. Gene expression profile and angiogenic marker correlates with response to neoadjuvant bevacizumab followed by bevacizumab plus chemotherapy in breast cancer. Clin Cancer Res 2008;14(18):5893-5899.
Yu H, Gong X, Luo X, Han W, Hong G, Singh B, Tang CK. Co-expression of EGFRvIII with ErbB-2 enhances tumorigenesis: EGFRvIII mediated constitutively activated and sustained signaling pathways, whereas EGF-induced a transient effect on EGFR-mediated signaling pathways. Cancer Biol Ther 2008;7(11).
Zhang B, Li H, Riggins RB, Zhan M, Xuan J, Zhang Z, Hoffman EP, Clarke R, Wang Y. Differential Dependency Network Analysis to Identify Condition-Specific Topological Changes in Biological Networks. Bioinformatics 2008 Dec 26 [Epub ahead of print].
Zhang W, Chen Y, Swift MR, Tassi E, Stylianou DC, Gibby KA, Riegel AT, Wellstein A. Effect of FGF binding protein-3 on vascular permeability. J Biol Chem 2008;283(42):28329-37.
Zhang Y, Xuan J, los Reyes BG, Clarke R, Ressom HW. Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. BMC Bioinformatics 2008;9:203.
Zhu Y, Li H, Miller D, Wang Z, Xuan J, Clarke R, Hoffman EP, and Wang Y. caBIG VISDA: modeling, visualization and discovery for cluster analysis of genomic data. BMC Bioinformatics 2008;9:383 (18 pages as published online).
Zhu Y, Wang Z, Miller DJ, Clarke R, Xuan J, Hoffman EP, Wang Y. A ground truth based comparative study on clustering of gene expression data. Front Biosci 2008;13:3839-3849.
