Publications

1. Palmieri, D, Lockman, PR, Thomas, FC, Hua, E, Herring, J, Hargrave, E, Johnson, M, Flores, N, Qian, Y, Vega-Valle, E, Taskar, KS, Rudraraju, V, Mittapalli, RK, Gaasch, JA, Bohn, KA, Thorsheim, HR, Liewehr, DJ, Davis, S, Reilly, JF, Walker, R, Bronder, JL, Feigenbaum, L, Steinberg, SM, Camphausen, K, Meltzer, PS, Richon, VM, Smith, QR, Steeg, PS. Vorinostat inhibits brain metastatic colonization in a model of triple-negative breast cancer and induces DNA double-strand breaks. Clin. Cancer Res. 2009; 15:6148-57 PubMed
2. Palmieri, D, Fitzgerald, D, Shreeve, SM, Hua, E, Bronder, JL, Weil, RJ, Davis, S, Stark, AM, Merino, MJ, Kurek, R, Mehdorn, HM, Davis, G, Steinberg, SM, Meltzer, PS, Aldape, K, Steeg, PS. Analyses of resected human brain metastases of breast cancer reveal the association between up-regulation of hexokinase 2 and poor prognosis. Mol. Cancer Res. 2009; 7:1438-45 PubMed
3. Kauer, M, Ban, J, Kofler, R, Walker, B, Davis, S, Meltzer, P, Kovar, H. A molecular function map of Ewing's sarcoma. PLoS ONE 2009; 4:e5415 PubMed
4. Palavalli, LH, Prickett, TD, Wunderlich, JR, Wei, X, Burrell, AS, Porter-Gill, P, Davis, S, Wang, C, Cronin, JC, Agrawal, NS, Lin, JC, Westbroek, W, Hoogstraten-Miller, S, Molinolo, AA, Fetsch, P, Filie, AC, O'Connell, MP, Banister, CE, Howard, JD, Buckhaults, P, Weeraratna, AT, Brody, LC, Rosenberg, SA, Samuels, Y. Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma. Nat. Genet. 2009; 41:518-20 PubMed
5. John, S, Johnson, TA, Sung, MH, Biddie, SC, Trump, S, Koch-Paiz, CA, Davis, SR, Walker, R, Meltzer, PS, Hager, GL. Kinetic complexity of the global response to glucocorticoid receptor action. Endocrinology 2009; 150:1766-74 PubMed
6. Killian, JK, Bilke, S, Davis, S, Walker, RL, Killian, MS, Jaeger, EB, Chen, Y, Hipp, J, Pittaluga, S, Raffeld, M, Cornelison, R, Smith, WI, Bibikova, M, Fan, JB, Emmert-Buck, MR, Jaffe, ES, Meltzer, PS. Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome. Cancer Res. 2009; 69:758-64 PubMed
7. Zhu, Y, Davis, S, Stephens, R, Meltzer, PS, Chen, Y. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics 2008; 24:2798-800 PubMed
8. Walsh, T, McClellan, JM, McCarthy, SE, Addington, AM, Pierce, SB, Cooper, GM, Nord, AS, Kusenda, M, Malhotra, D, Bhandari, A, Stray, SM, Rippey, CF, Roccanova, P, Makarov, V, Lakshmi, B, Findling, RL, Sikich, L, Stromberg, T, Merriman, B, Gogtay, N, Butler, P, Eckstrand, K, Noory, L, Gochman, P, Long, R, Chen, Z, Davis, S, Baker, C, Eichler, EE, Meltzer, PS, Nelson, SF, Singleton, AB, Lee, MK, Rapoport, JL, King, MC, Sebat, J. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science 2008; 320:539-43 PubMed
9. Rahman, M, Davis, SR, Pumphrey, JG, Bao, J, Nau, MM, Meltzer, PS, Lipkowitz, S. TRAIL induces apoptosis in triple-negative breast cancer cells with a mesenchymal phenotype. Breast Cancer Res. Treat. 2009; 113:217-30 PubMed
10. Bhoumik, A, Fichtman, B, Derossi, C, Breitwieser, W, Kluger, HM, Davis, S, Subtil, A, Meltzer, P, Krajewski, S, Jones, N, Ronai, Z. Suppressor role of activating transcription factor 2 (ATF2) in skin cancer. Proc. Natl. Acad. Sci. U.S.A. 2008; 105:1674-9 PubMed
11. Kamradt, J, Jung, V, Wahrheit, K, Tolosi, L, Rahnenfuehrer, J, Schilling, M, Walker, R, Davis, S, Stoeckle, M, Meltzer, P, Wullich, B. Detection of novel amplicons in prostate cancer by comprehensive genomic profiling of prostate cancer cell lines using oligonucleotide-based arrayCGH. PLoS ONE 2007; 2:e769 PubMed
12. Sean, D, Meltzer, PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 2007; 23:1846-7 PubMed
13. Johnston, JJ, Walker, RL, Davis, S, Facio, F, Turner, JT, Bick, DP, Daentl, DL, Ellison, JW, Meltzer, PS, Biesecker, LG. Zoom-in comparative genomic hybridisation arrays for the characterisation of variable breakpoint contiguous gene syndromes. J. Med. Genet. 2007; 44:e59 PubMed
14. Scacheri, PC, Davis, S, Odom, DT, Crawford, GE, Perkins, S, Halawi, MJ, Agarwal, SK, Marx, SJ, Spiegel, AM, Meltzer, PS, Collins, FS. Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. PLoS Genet. 2006; 2:e51 PubMed
15. Crawford, GE, Holt, IE, Whittle, J, Webb, BD, Tai, D, Davis, S, Margulies, EH, Chen, Y, Bernat, JA, Ginsburg, D, Zhou, D, Luo, S, Vasicek, TJ, Daly, MJ, Wolfsberg, TG, Collins, FS. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006; 16:123-31 PubMed
16. Balleine, RL, Webster, LR, Davis, S, Salisbury, EL, Palazzo, JP, Schwartz, GF, Cornfield, DB, Walker, RL, Byth, K, Clarke, CL, Meltzer, PS. Molecular grading of ductal carcinoma in situ of the breast. Clin. Cancer Res. 2008; 14:8244-52 PubMed
17. John, S, Sabo, PJ, Johnson, TA, Sung, MH, Biddie, SC, Lightman, SL, Voss, TC, Davis, SR, Meltzer, PS, Stamatoyannopoulos, JA, Hager, GL. Interaction of the glucocorticoid receptor with the chromatin landscape. Mol. Cell 2008; 29:611-24 PubMed
18. Boyle, AP, Davis, S, Shulha, HP, Meltzer, P, Margulies, EH, Weng, Z, Furey, TS, Crawford, GE. High-resolution mapping and characterization of open chromatin across the genome. Cell 2008; 132:311-22 PubMed
19. Kim, KT, Baird, K, Davis, S, Piloto, O, Levis, M, Li, L, Chen, P, Meltzer, P, Small, D. Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells. Br. J. Haematol. 2007; 138:603-15 PubMed
20. Birney, E, Stamatoyannopoulos, JA, Dutta, A, Guigó, R, Gingeras, TR, Margulies, EH, Weng, Z, Snyder, M, Dermitzakis, ET, Thurman, RE, Kuehn, MS, Taylor, CM, Neph, S, Koch, CM, Asthana, S, Malhotra, A, Adzhubei, I, Greenbaum, JA, Andrews, RM, Flicek, P, Boyle, PJ, Cao, H, Carter, NP, Clelland, GK, Davis, S, Day, N, Dhami, P, Dillon, SC, Dorschner, MO, Fiegler, H, Giresi, PG, Goldy, J, Hawrylycz, M, Haydock, A, Humbert, R, James, KD, Johnson, BE, Johnson, EM, Frum, TT, Rosenzweig, ER, Karnani, N, Lee, K, Lefebvre, GC, Navas, PA, Neri, F, Parker, SC, Sabo, PJ, Sandstrom, R, Shafer, A, Vetrie, D, Weaver, M, Wilcox, S, Yu, M, Collins, FS, Dekker, J, Lieb, JD, Tullius, TD, Crawford, GE, Sunyaev, S, Noble, WS, Dunham, I, Denoeud, F, Reymond, A, Kapranov, P, Rozowsky, J, Zheng, D, Castelo, R, Frankish, A, Harrow, J, Ghosh, S, Sandelin, A, Hofacker, IL, Baertsch, R, Keefe, D, Dike, S, Cheng, J, Hirsch, HA, Sekinger, EA, Lagarde, J, Abril, JF, Shahab, A, Flamm, C, Fried, C, Hackermüller, J, Hertel, J, Lindemeyer, M, Missal, K, Tanzer, A, Washietl, S, Korbel, J, Emanuelsson, O, Pedersen, JS, Holroyd, N, Taylor, R, Swarbreck, D, Matthews, N, Dickson, MC, Thomas, DJ, Weirauch, MT, Gilbert, J, Drenkow, J, Bell, I, Zhao, X, Srinivasan, KG, Sung, WK, Ooi, HS, Chiu, KP, Foissac, S, Alioto, T, Brent, M, Pachter, L, Tress, ML, Valencia, A, Choo, SW, Choo, CY, Ucla, C, Manzano, C, Wyss, C, Cheung, E, Clark, TG, Brown, JB, Ganesh, M, Patel, S, Tammana, H, Chrast, J, Henrichsen, CN, Kai, C, Kawai, J, Nagalakshmi, U, Wu, J, Lian, Z, Lian, J, Newburger, P, Zhang, X, Bickel, P, Mattick, JS, Carninci, P, Hayashizaki, Y, Weissman, S, Hubbard, T, Myers, RM, Rogers, J, Stadler, PF, Lowe, TM, Wei, CL, Ruan, Y, Struhl, K, Gerstein, M, Antonarakis, SE, Fu, Y, Green, ED, Karaöz, U, Siepel, A, Taylor, J, Liefer, LA, Wetterstrand, KA, Good, PJ, Feingold, EA, Guyer, MS, Cooper, GM, Asimenos, G, Dewey, CN, Hou, M, Nikolaev, S, Montoya-Burgos, JI, Löytynoja, A, Whelan, S, Pardi, F, Massingham, T, Huang, H, Zhang, NR, Holmes, I, Mullikin, JC, Ureta-Vidal, A, Paten, B, Seringhaus, M, Church, D, Rosenbloom, K, Kent, WJ, Stone, EA, Batzoglou, S, Goldman, N, Hardison, RC, Haussler, D, Miller, W, Sidow, A, Trinklein, ND, Zhang, ZD, Barrera, L, Stuart, R, King, DC, Ameur, A, Enroth, S, Bieda, MC, Kim, J, Bhinge, AA, Jiang, N, Liu, J, Yao, F, Vega, VB, Lee, CW, Ng, P, Shahab, A, Yang, A, Moqtaderi, Z, Zhu, Z, Xu, X, Squazzo, S, Oberley, MJ, Inman, D, Singer, MA, Richmond, TA, Munn, KJ, Rada-Iglesias, A, Wallerman, O, Komorowski, J, Fowler, JC, Couttet, P, Bruce, AW, Dovey, OM, Ellis, PD, Langford, CF, Nix, DA, Euskirchen, G, Hartman, S, Urban, AE, Kraus, P, Van Calcar, S, Heintzman, N, Kim, TH, Wang, K, Qu, C, Hon, G, Luna, R, Glass, CK, Rosenfeld, MG, Aldred, SF, Cooper, SJ, Halees, A, Lin, JM, Shulha, HP, Zhang, X, Xu, M, Haidar, JN, Yu, Y, Ruan, Y, Iyer, VR, Green, RD, Wadelius, C, Farnham, PJ, Ren, B, Harte, RA, Hinrichs, AS, Trumbower, H, Clawson, H, Hillman-Jackson, J, Zweig, AS, Smith, K, Thakkapallayil, A, Barber, G, Kuhn, RM, Karolchik, D, Armengol, L, Bird, CP, de Bakker, PI, Kern, AD, Lopez-Bigas, N, Martin, JD, Stranger, BE, Woodroffe, A, Davydov, E, Dimas, A, Eyras, E, Hallgrímsdóttir, IB, Huppert, J, Zody, MC, Abecasis, GR, Estivill, X, Bouffard, GG, Guan, X, Hansen, NF, Idol, JR, Maduro, VV, Maskeri, B, McDowell, JC, Park, M, Thomas, PJ, Young, AC, Blakesley, RW, Muzny, DM, Sodergren, E, Wheeler, DA, Worley, KC, Jiang, H, Weinstock, GM, Gibbs, RA, Graves, T, Fulton, R, Mardis, ER, Wilson, RK, Clamp, M, Cuff, J, Gnerre, S, Jaffe, DB, Chang, JL, Lindblad-Toh, K, Lander, ES, Koriabine, M, Nefedov, M, Osoegawa, K, Yoshinaga, Y, Zhu, B, de Jong, PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799-816 PubMed
21. Sutter, NB, Bustamante, CD, Chase, K, Gray, MM, Zhao, K, Zhu, L, Padhukasahasram, B, Karlins, E, Davis, S, Jones, PG, Quignon, P, Johnson, GS, Parker, HG, Fretwell, N, Mosher, DS, Lawler, DF, Satyaraj, E, Nordborg, M, Lark, KG, Wayne, RK, Ostrander, EA. A single IGF1 allele is a major determinant of small size in dogs. Science 2007; 316:112-5 PubMed
22. Davis, SR, Meltzer, PS. Modeling synovial sarcoma: timing is everything. Cancer Cell 2007; 11:305-7 PubMed
23. Crawford, GE, Davis, S, Scacheri, PC, Renaud, G, Halawi, MJ, Erdos, MR, Green, R, Meltzer, PS, Wolfsberg, TG, Collins, FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat. Methods 2006; 3:503-9 PubMed
24. Davis, S, Meltzer, PS. Ewing's sarcoma: general insights from a rare model. Cancer Cell 2006; 9:331-2 PubMed
25. Scacheri, PC, Crawford, GE, Davis, S. Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Meth. Enzymol. 2006; 411:270-82 PubMed
26. Baird, K, Davis, S, Antonescu, CR, Harper, UL, Walker, RL, Chen, Y, Glatfelter, AA, Duray, PH, Meltzer, PS. Gene expression profiling of human sarcomas: insights into sarcoma biology. Cancer Res. 2005; 65:9226-35 PubMed
27. Durinck, S, Moreau, Y, Kasprzyk, A, Davis, S, De Moor, B, Brazma, A, Huber, W. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 2005; 21:3439-40 PubMed
28. Son, CG, Bilke, S, Davis, S, Greer, BT, Wei, JS, Whiteford, CC, Chen, QR, Cenacchi, N, Khan, J. Database of mRNA gene expression profiles of multiple human organs. Genome Res. 2005; 15:443-50 PubMed
29. Davis, S, Nimgaonkar, VL. Impact of overlapping recruitment on linkage analysis of complex disorders: simulation studies. Am. J. Med. Genet. 2001; 105:141-4 PubMed
30. Duerr, RH, Barmada, MM, Zhang, L, Davis, S, Preston, RA, Chensny, LJ, Brown, JL, Ehrlich, GD, Weeks, DE, Aston, CE. Linkage and association between inflammatory bowel disease and a locus on chromosome 12. Am. J. Hum. Genet. 1998; 63:95-100 PubMed
31. Davis, S, Weeks, DE. Comparison of nonparametric statistics for detection of linkage in nuclear families: single-marker evaluation. Am. J. Hum. Genet. 1997; 61:1431-44 PubMed
32. Julier, C, Delépine, M, Keavney, B, Terwilliger, J, Davis, S, Weeks, DE, Bui, T, Jeunemaître, X, Velho, G, Froguel, P, Ratcliffe, P, Corvol, P, Soubrier, F, Lathrop, GM. Genetic susceptibility for human familial essential hypertension in a region of homology with blood pressure linkage on rat chromosome 10. Hum. Mol. Genet. 1997; 6:2077-85 PubMed
33. O'Connell, JR, Davis, S, Weeks, DE. Analysis of a complex oligogenic disease. Genet. Epidemiol. 1997; 14:861-6 PubMed
34. Davis, S, Sobel, E, Marinov, M, Weeks, DE. Analysis of bipolar disorder using affected relatives. Genet. Epidemiol. 1997; 14:605-10 PubMed
35. Weeks, DE, Davis, S, Schroeder, M, Goldin, LR. Nonparametric simulation based linkage statistics for general pedigrees. J. Rheumatol. 1997; 24:206-7 PubMed
36. Davis, S, Schroeder, M, Goldin, LR, Weeks, DE. Nonparametric simulation-based statistics for detecting linkage in general pedigrees. Am. J. Hum. Genet. 1996; 58:867-80 PubMed