Publications | seandavi(s12)

Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Jaclyn N. Taroni, Vincent Carey, Casey Greene, Levi Waldron, Sean Davis (2021). GenomicSuperSignature: interpretation of RNA-seq experiments through robust, efficient comparison to public databases. bioRxiv.

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Sehyun Oh, Jasmine Abdelnabi, Ragheed Al-Dulaimi, Ayush Aggarwal, Marcel Ramos, Sean Davis, Markus Riester, Levi Waldron (2020). HGNChelper: identification and correction of invalid gene symbols for human and mouse. F1000Research.

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Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity Law, Sean Davis, Vincent Carey, Martin Morgan, Ralf Zimmer, Levi Waldron (2020). Toward a gold standard for benchmarking gene set enrichment analysis. Briefings in Bioinformatics.

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Shian Su, Vincent J Carey, Lori Shepherd, Matthew Ritchie, Martin T Morgan, Sean Davis (2019). BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem. F1000Research.

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Shweta Gopaulakrishnan, Samuela Pollack, B J Stubbs, Hervé Pagès, John Readey, Sean Davis, Levi Waldron, Martin Morgan, Vincent Carey (2019). restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor. F1000Research.

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Sean Davis, Marcel Ramos, Lori Shepherd, Nitesh Turaga, Ludwig Geistlinger, Martin T Morgan, Benjamin Haibe-Kains, Levi Waldron (2018). Orchestrating a community-developed computational workshop and accompanying training materials. F1000Research.

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Hsinyi Tsang, KanakaDurga Addepalli, Sean R. Davis (2017). Resources for Interpreting Variants in Precision Genomic Oncology Applications. Frontiers in Oncology.

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Y. Liu-Chittenden, M. Jain, K. Gaskins, S. Wang, M. J. Merino, S. Kotian, S. Kumar Gara, S. Davis, L. Zhang, E. Kebebew (2017). RARRES2 functions as a tumor suppressor by promoting $β$-catenin phosphorylation/degradation and inhibiting p38 phosphorylation in adrenocortical carcinoma. Oncogene.

Martin T. Morgan, Sean R. Davis (2017). GenomicDataCommons: a Bioconductor Interface to the NCI Genomic Data Commons. bioRxiv.

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Xiaotu Ma, Yu Liu, Yanling Liu, Michael Edmonson, Charles Gawad, Xin Zhou, Yongjin Li, Michael Rusch, John Easton, Mark Wilkinson, others (2017). Comparison of somatic alterations in the genome and transcriptome of 1,705 pediatric leukemia and solid tumors: a report from the Children’s Oncology Group (COG)-NCI TARGET Project. AACR.

Feng Zhu, Jami Willette-Brown, Na-Young Song, Dakshayani Lomada, Yongmei Song, Liyan Xue, Zane Gray, Zitong Zhao, Sean R. Davis, Zhonghe Sun, Peilin Zhang, Xiaolin Wu, Qimin Zhan, Ellen R. Richie, Yinling Hu (2017). Autoreactive T Cells and Chronic Fungal Infection Drive Esophageal Carcinogenesis . *Cell Host & Microbe *.

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Vivek Shukla, Mahadev Rao, Hongen Zhang, Jeanette Beers, Darawalee Wangsa, Danny Wangsa, Floryne O Buishand, Yonghong Wang, Zhiya Yu, Holly S Stevenson, others (2017). ASXL3 is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer. Cancer Research.

L. Kannan, M. Ramos, A. Re, N. El-Hachem, Z. Safikhani, D. M. Gendoo, S. Davis, D. Gomez-Cabrero, R. Castelo, K. D. Hansen, V. J. Carey, M. Morgan, A. C. Culhane, B. Haibe-Kains, L. Waldron (2016). Public data and open source tools for multi-assay genomic investigation of disease. Brief. Bioinformatics.

J. Li, S. L. Woods, S. Healey, J. Beesley, X. Chen, J. S. Lee, H. Sivakumaran, N. Wayte, K. Nones, J. J. Waterfall, J. Pearson, A. M. Patch, J. Senz, M. A. Ferreira, P. Kaurah, R. Mackenzie, A. Heravi-Moussavi, S. Hansford, T. R. Lannagan, A. B. Spurdle, P. T. Simpson, L. da Silva, S. R. Lakhani, A. D. Clouston, M. Bettington, F. Grimpen, R. A. Busuttil, N. Di Costanzo, A. Boussioutas, M. Jeanjean, G. Chong, A. Fabre, S. Olschwang, G. J. Faulkner, E. Bellos, L. Coin, K. Rioux, O. F. Bathe, X. Wen, H. C. Martin, D. W. Neklason, S. R. Davis, R. L. Walker, K. A. Calzone, I. Avital, T. Heller, C. Koh, M. Pineda, U. Rudloff, M. Quezado, P. N. Pichurin, P. J. Hulick, S. M. Weissman, A. Newlin, W. S. Rubinstein, J. E. Sampson, K. Hamman, D. Goldgar, N. Poplawski, K. Phillips, L. Schofield, J. Armstrong, C. Kiraly-Borri, G. K. Suthers, D. G. Huntsman, W. D. Foulkes, F. Carneiro, N. M. Lindor, S. L. Edwards, J. D. French, N. Waddell, P. S. Meltzer, D. L. Worthley, K. A. Schrader, G. Chenevix-Trench (2016). Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. Am. J. Hum. Genet..

R. Sorber, Y. Teper, A. Abisoye-Ogunniyan, J. J. Waterfall, S. Davis, J. K. Killian, M. Pineda, S. Ray, M. R. McCord, H. Pflicke, S. S. Burkett, P. S. Meltzer, U. Rudloff (2016). Whole Genome Sequencing of Newly Established Pancreatic Cancer Lines Identifies Novel Somatic Mutation (c.2587G>A) in Axon Guidance Receptor Plexin A1 as Enhancer of Proliferation and Invasion. PLoS ONE.

Sean Davis, Ewy Mathe (2016). Statistical Genomics. Springer.

DOI

M. Comas-Garcia, S. R. Davis, A. Rein (2016). On the Selective Packaging of Genomic RNA by HIV-1. Viruses.

H. Zhang, P. S. Meltzer, S. R. Davis (2016). caOmicsV: an R package for visualizing multidimensional cancer genomic data. BMC Bioinformatics.

A. Mehta, L. Zhang, M. Boufraqech, Y. Liu-Chittenden, Y. Zhang, D. Patel, S. Davis, A. Rosenberg, K. Ylaya, R. Aufforth, Z. Li, M. Shen, E. Kebebew (2015). Inhibition of Survivin with YM155 Induces Durable Tumor Response in Anaplastic Thyroid Cancer. Clin. Cancer Res..

L. Mirabello, R. Koster, B. S. Moriarity, L. G. Spector, P. S. Meltzer, J. Gary, M. J. Machiela, N. Pankratz, O. A. Panagiotou, D. Largaespada, Z. Wang, J. M. Gastier-Foster, R. Gorlick, C. Khanna, S. R. de Toledo, A. S. Petrilli, A. Patino-Garcia, L. Sierrasesumaga, F. Lecanda, I. L. Andrulis, J. S. Wunder, N. Gokgoz, M. Serra, C. Hattinger, P. Picci, K. Scotlandi, A. M. Flanagan, R. Tirabosco, M. F. Amary, D. Halai, M. L. Ballinger, D. M. Thomas, S. Davis, D. A. Barkauskas, N. Marina, L. Helman, G. M. Otto, K. L. Becklin, N. K. Wolf, M. T. Weg, M. Tucker, S. Wacholder, J. F. Fraumeni, N. E. Caporaso, J. F. Boland, B. D. Hicks, A. Vogt, L. Burdett, M. Yeager, R. N. Hoover, S. J. Chanock, S. A. Savage (2015). A Genome-Wide Scan Identifies Variants in NFIB Associated with Metastasis in Patients with Osteosarcoma. Cancer Discov.

G. Vahedi, Y. Kanno, Y. Furumoto, K. Jiang, S. C. Parker, M. R. Erdos, S. R. Davis, R. Roychoudhuri, N. P. Restifo, M. Gadina, Z. Tang, Y. Ruan, F. S. Collins, V. Sartorelli, J. J. O'Shea (2015). Super-enhancers delineate disease-associated regulatory nodes in T cells. Nature.

J. D. Figueroa, H. Yang, M. Garcia-Closas, S. Davis, P. Meltzer, J. Lissowska, H. N. Horne, M. E. Sherman, M. Lee (2015). Integrated analysis of DNA methylation, immunohistochemistry and mRNA expression, data identifies a methylation expression index (MEI) robustly associated with survival of ER-positive breast cancer patients. Breast Cancer Res. Treat..

L. Zhang, Y. Zhang, A. Mehta, M. Boufraqech, S. Davis, J. Wang, Z. Tian, Z. Yu, M. B. Boxer, J. A. Kiefer, J. A. Copland, R. C. Smallridge, Z. Li, M. Shen, E. Kebebew (2015). Dual inhibition of HDAC and EGFR signaling with CUDC-101 induces potent suppression of tumor growth and metastasis in anaplastic thyroid cancer. Oncotarget.

W. Huber, V. Carey, S. Davis, K. D. Hansen, M. Morgan (2015). The Bioconductor channel in F1000Research. F1000Res.

M. Boufraqech, N. Nilubol, L. Zhang, S. K. Gara, S. M. Sadowski, A. Mehta, M. He, S. Davis, J. Dreiling, J. A. Copland, R. C. Smallridge, M. M. Quezado, E. Kebebew (2015). miR30a inhibits LOX expression and anaplastic thyroid cancer progression. Cancer Res..

X. R. Yang, J. K. Killian, S. Hammond, L. S. Burke, H. Bennett, Y. Wang, S. R. Davis, L. C. Strong, J. Neglia, M. Stovall, R. E. Weathers, L. L. Robison, S. Bhatia, K. Mabuchi, P. D. Inskip, P. Meltzer (2015). Characterization of genomic alterations in radiation-associated breast cancer among childhood cancer survivors, using comparative genomic hybridization (CGH) arrays. PLoS ONE.

Z. Kang, Y. Yu, Y. J. Zhu, S. Davis, R. Walker, P. S. Meltzer, L. J. Helman, L. Cao (2014). Downregulation of IGFBP2 is associated with resistance to IGF1R therapy in rhabdomyosarcoma. Oncogene.

R. J. Ellis, Y. Wang, H. S. Stevenson, M. Boufraqech, D. Patel, N. Nilubol, S. Davis, D. C. Edelman, M. J. Merino, M. He, L. Zhang, P. S. Meltzer, E. Kebebew (2014). Genome-wide methylation patterns in papillary thyroid cancer are distinct based on histological subtype and tumor genotype. J. Clin. Endocrinol. Metab..

W. C. Reinhold, S. Varma, F. Sousa, M. Sunshine, O. D. Abaan, S. R. Davis, S. W. Reinhold, K. W. Kohn, J. Morris, P. S. Meltzer, J. H. Doroshow, Y. Pommier (2014). NCI-60 whole exome sequencing and pharmacological CellMiner analyses. PLoS ONE.

J. J. Waterfall, E. Arons, R. L. Walker, M. Pineda, L. Roth, J. K. Killian, O. D. Abaan, S. R. Davis, R. J. Kreitman, P. S. Meltzer (2014). High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias. Nat. Genet..

L. R. Webster, P. J. Provan, D. J. Graham, K. Byth, R. L. Walker, S. Davis, E. L. Salisbury, A. L. Morey, R. L. Ward, N. J. Hawkins, C. L. Clarke, P. S. Meltzer, R. L. Balleine (2013). Prohibitin expression is associated with high grade breast cancer but is not a driver of amplification at 17q21.33. Pathology.

S. Bilke, R. Schwentner, F. Yang, M. Kauer, G. Jug, R. L. Walker, S. Davis, Y. J. Zhu, M. Pineda, P. S. Meltzer, H. Kovar (2013). Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer. Genome Res..

J. J. Gartner, S. C. Parker, T. D. Prickett, K. Dutton-Regester, M. L. Stitzel, J. C. Lin, S. Davis, V. L. Simhadri, S. Jha, N. Katagiri, V. Gotea, J. K. Teer, X. Wei, M. A. Morken, U. K. Bhanot, G. Chen, L. L. Elnitski, M. A. Davies, J. E. Gershenwald, H. Carter, R. Karchin, W. Robinson, S. Robinson, S. A. Rosenberg, F. S. Collins, G. Parmigiani, A. A. Komar, C. Kimchi-Sarfaty, N. K. Hayward, E. H. Margulies, Y. Samuels, J. Becker, B. Benjamin, R. Blakesley, G. Bouffard, S. Brooks, H. Coleman, M. Dekhtyar, M. Gregory, X. Guan, J. Gupta, J. Han, A. Hargrove, S. L. Ho, T. Johnson, R. Legaspi, S. Lovett, Q. Maduro, C. Masiello, B. Maskeri, J. McDowell, C. Montemayor, J. Mullikin, M. Park, N. Riebow, K. Schandler, B. Schmidt, C. Sison, M. Stantripop, J. Thomas, P. Thomas, M. Vemulapalli, A. Young (2013). Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc. Natl. Acad. Sci. U.S.A..

O. D. Abaan, E. C. Polley, S. R. Davis, Y. J. Zhu, S. Bilke, R. L. Walker, M. Pineda, Y. Gindin, Y. Jiang, W. C. Reinhold, S. L. Holbeck, R. M. Simon, J. H. Doroshow, Y. Pommier, P. S. Meltzer (2013). The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. Cancer Res..

D. Hirsch, R. Kemmerling, S. Davis, J. Camps, P. S. Meltzer, T. Ried, T. Gaiser (2013). Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma. Cancer Res..

I. Petrini, A. Rajan, T. Pham, D. Voeller, S. Davis, J. Gao, Y. Wang, G. Giaccone (2013). Whole genome and transcriptome sequencing of a B3 thymoma. PLoS ONE.

Y. Zhu, R. M. Stephens, P. S. Meltzer, S. R. Davis (2013). SRAdb: query and use public next-generation sequencing data from within R. BMC Bioinformatics.

H. Zhang, P. Meltzer, S. Davis (2013). RCircos: an R package for Circos 2D track plots. BMC Bioinformatics.

T. Barrett, S. E. Wilhite, P. Ledoux, C. Evangelista, I. F. Kim, M. Tomashevsky, K. A. Marshall, K. H. Phillippy, P. M. Sherman, M. Holko, A. Yefanov, H. Lee, N. Zhang, C. L. Robertson, N. Serova, S. Davis, A. Soboleva (2013). NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res..

N. Kouprina, N. C. Lee, A. Pavlicek, A. Samoshkin, J. H. Kim, H. S. Lee, S. Varma, W. C. Reinhold, J. Otstot, G. Solomon, S. Davis, P. S. Meltzer, J. Schleutker, V. Larionov (2012). Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked families. Genes Chromosomes Cancer.

J. Debbache, M. R. Zaidi, S. Davis, T. Guo, K. Bismuth, X. Wang, S. Skuntz, D. Maric, J. Pickel, P. Meltzer, G. Merlino, H. Arnheiter (2012). In vivo role of alternative splicing and serine phosphorylation of the microphthalmia-associated transcription factor. Genetics.

P. J. O'Shea, D. W. Kim, J. G. Logan, S. Davis, R. L. Walker, P. S. Meltzer, S. Y. Cheng, G. R. Williams (2012). Advanced bone formation in mice with a dominant-negative mutation in the thyroid hormone receptor Î² gene due to activation of Wnt/Î²-catenin protein signaling. J. Biol. Chem..

J. K. Killian, R. L. Walker, S. Bilke, Y. Chen, S. Davis, R. Cornelison, W. I. Smith, P. S. Meltzer (2012). Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples. Methods Mol. Biol..

J. J. Gartner, S. Davis, X. Wei, J. C. Lin, N. S. Trivedi, J. K. Teer, P. S. Meltzer, S. A. Rosenberg, Y. Samuels (2012). Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma. BMC Genomics.

G. Zoppoli, S. Solier, W. C. Reinhold, H. Liu, J. W. Connelly, A. Monks, R. H. Shoemaker, O. D. Abaan, S. R. Davis, P. S. Meltzer, J. H. Doroshow, Y. Pommier (2012). CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute. Oncogene.

M. M. Martin, M. Ryan, R. Kim, A. L. Zakas, H. Fu, C. M. Lin, W. C. Reinhold, S. R. Davis, S. Bilke, H. Liu, J. H. Doroshow, M. A. Reimers, M. S. Valenzuela, Y. Pommier, P. S. Meltzer, M. I. Aladjem (2011). Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res..

J. K. Killian, S. Bilke, S. Davis, R. L. Walker, E. Jaeger, M. S. Killian, J. J. Waterfall, M. Bibikova, J. B. Fan, W. I. Smith, P. S. Meltzer (2011). A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology. Am. J. Pathol..

P. J. Grohar, G. M. Woldemichael, L. B. Griffin, A. Mendoza, Q. R. Chen, C. Yeung, D. G. Currier, S. Davis, C. Khanna, J. Khan, J. B. McMahon, L. J. Helman (2011). Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screening. J. Natl. Cancer Inst..

X. Wei, V. Walia, J. C. Lin, J. K. Teer, T. D. Prickett, J. Gartner, S. Davis, K. Stemke-Hale, M. A. Davies, J. E. Gershenwald, W. Robinson, S. Robinson, S. A. Rosenberg, Y. Samuels (2011). Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat. Genet..

M. S. Valenzuela, Y. Chen, S. Davis, F. Yang, R. L. Walker, S. Bilke, J. Lueders, M. M. Martin, M. I. Aladjem, P. P. Massion, P. S. Meltzer (2011). Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences. PLoS ONE.

M. R. Zaidi, S. Davis, F. P. Noonan, C. Graff-Cherry, T. S. Hawley, R. L. Walker, L. Feigenbaum, E. Fuchs, L. Lyakh, H. A. Young, T. J. Hornyak, H. Arnheiter, G. Trinchieri, P. S. Meltzer, E. C. De Fabo, G. Merlino (2011). Interferon-$γ$ links ultraviolet radiation to melanomagenesis in mice. Nature.

S. Morisot, A. S. Wayne, O. Bohana-Kashtan, I. M. Kaplan, C. D. Gocke, R. Hildreth, M. Stetler-Stevenson, R. L. Walker, S. Davis, P. S. Meltzer, S. J. Wheelan, P. Brown, R. J. Jones, L. D. Shultz, C. I. Civin (2010). High frequencies of leukemia stem cells in poor-outcome childhood precursor-B acute lymphoblastic leukemias. Leukemia.

J. K. Killian, R. L. Walker, M. Suuriniemi, L. Jones, S. Scurci, P. Singh, R. Cornelison, S. Harmon, N. Boisvert, J. Zhu, Y. Wang, S. Bilke, S. Davis, G. Giaccone, W. I. Smith, P. S. Meltzer (2010). Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling. J Mol Diagn.

F. Liu, J. K. Killian, M. Yang, R. L. Walker, J. A. Hong, M. Zhang, S. Davis, Y. Zhang, M. Hussain, S. Xi, M. Rao, P. A. Meltzer, D. S. Schrump (2010). Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate. Oncogene.

A. Camilleri, M. R. Johnston, M. Brennan, S. Davis, D. G. Caldicott (2010). Chemical analysis of four capsules containing the controlled substance analogues 4-methylmethcathinone, 2-fluoromethamphetamine, alpha-phthalimidopropiophenone and N-ethylcathinone. Forensic Sci. Int..

K. L. Bolton, M. Garcia-Closas, R. M. Pfeiffer, M. A. Duggan, W. J. Howat, S. M. Hewitt, X. R. Yang, R. Cornelison, S. L. Anzick, P. Meltzer, S. Davis, P. Lenz, J. D. Figueroa, P. D. Pharoah, M. E. Sherman (2010). Assessment of automated image analysis of breast cancer tissue microarrays for epidemiologic studies. Cancer Epidemiol. Biomarkers Prev..

D. Palmieri, D. Fitzgerald, S. M. Shreeve, E. Hua, J. L. Bronder, R. J. Weil, S. Davis, A. M. Stark, M. J. Merino, R. Kurek, H. M. Mehdorn, G. Davis, S. M. Steinberg, P. S. Meltzer, K. Aldape, P. S. Steeg (2009). Analyses of resected human brain metastases of breast cancer reveal the association between up-regulation of hexokinase 2 and poor prognosis. Mol. Cancer Res..

S. John, T. A. Johnson, M. H. Sung, S. C. Biddie, S. Trump, C. A. Koch-Paiz, S. R. Davis, R. Walker, P. S. Meltzer, G. L. Hager (2009). Kinetic complexity of the global response to glucocorticoid receptor action. Endocrinology.

J. K. Killian, S. Bilke, S. Davis, R. L. Walker, M. S. Killian, E. B. Jaeger, Y. Chen, J. Hipp, S. Pittaluga, M. Raffeld, R. Cornelison, W. I. Smith, M. Bibikova, J. B. Fan, M. R. Emmert-Buck, E. S. Jaffe, P. S. Meltzer (2009). Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome. Cancer Res..

M. Rahman, S. R. Davis, J. G. Pumphrey, J. Bao, M. M. Nau, P. S. Meltzer, S. Lipkowitz (2009). TRAIL induces apoptosis in triple-negative breast cancer cells with a mesenchymal phenotype. Breast Cancer Res. Treat..

M. Paoloni, S. Davis, S. Lana, S. Withrow, L. Sangiorgi, P. Picci, S. Hewitt, T. Triche, P. Meltzer, C. Khanna (2009). Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression. BMC Genomics.

M. Kauer, J. Ban, R. Kofler, B. Walker, S. Davis, P. Meltzer, H. Kovar (2009). A molecular function map of Ewing's sarcoma. PLoS ONE.

R. L. Balleine, L. R. Webster, S. Davis, E. L. Salisbury, J. P. Palazzo, G. F. Schwartz, D. B. Cornfield, R. L. Walker, K. Byth, C. L. Clarke, P. S. Meltzer (2008). Molecular grading of ductal carcinoma in situ of the breast. Clin. Cancer Res..

Y. Zhu, S. Davis, R. Stephens, P. S. Meltzer, Y. Chen (2008). GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics.

S. John, P. J. Sabo, T. A. Johnson, M. H. Sung, S. C. Biddie, S. L. Lightman, T. C. Voss, S. R. Davis, P. S. Meltzer, J. A. Stamatoyannopoulos, G. L. Hager (2008). Interaction of the glucocorticoid receptor with the chromatin landscape. Mol. Cell.

A. Bhoumik, B. Fichtman, C. Derossi, W. Breitwieser, H. M. Kluger, S. Davis, A. Subtil, P. Meltzer, S. Krajewski, N. Jones, Z. Ronai (2008). Suppressor role of activating transcription factor 2 (ATF2) in skin cancer. Proc. Natl. Acad. Sci. U.S.A..

A. P. Boyle, S. Davis, H. P. Shulha, P. Meltzer, E. H. Margulies, Z. Weng, T. S. Furey, G. E. Crawford (2008). High-resolution mapping and characterization of open chromatin across the genome. Cell.

K. T. Kim, K. Baird, S. Davis, O. Piloto, M. Levis, L. Li, P. Chen, P. Meltzer, D. Small (2007). Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells. Br. J. Haematol..

S. Davis, P. S. Meltzer (2007). GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics.

E. Birney, J. A. Stamatoyannopoulos, A. Dutta, R. Guigo, T. R. Gingeras, E. H. Margulies, Z. Weng, M. Snyder, E. T. Dermitzakis, R. E. Thurman, M. S. Kuehn, C. M. Taylor, S. Neph, C. M. Koch, S. Asthana, A. Malhotra, I. Adzhubei, J. A. Greenbaum, R. M. Andrews, P. Flicek, P. J. Boyle, H. Cao, N. P. Carter, G. K. Clelland, S. Davis, N. Day, P. Dhami, S. C. Dillon, M. O. Dorschner, H. Fiegler, P. G. Giresi, J. Goldy, M. Hawrylycz, A. Haydock, R. Humbert, K. D. James, B. E. Johnson, E. M. Johnson, T. T. Frum, E. R. Rosenzweig, N. Karnani, K. Lee, G. C. Lefebvre, P. A. Navas, F. Neri, S. C. Parker, P. J. Sabo, R. Sandstrom, A. Shafer, D. Vetrie, M. Weaver, S. Wilcox, M. Yu, F. S. Collins, J. Dekker, J. D. Lieb, T. D. Tullius, G. E. Crawford, S. Sunyaev, W. S. Noble, I. Dunham, F. Denoeud, A. Reymond, P. Kapranov, J. Rozowsky, D. Zheng, R. Castelo, A. Frankish, J. Harrow, S. Ghosh, A. Sandelin, I. L. Hofacker, R. Baertsch, D. Keefe, S. Dike, J. Cheng, H. A. Hirsch, E. A. Sekinger, J. Lagarde, J. F. Abril, C. Flamm, C. Fried, J. Hackermuller, J. Hertel, M. Lindemeyer, K. Missal, A. Tanzer, S. Washietl, J. Korbel, O. Emanuelsson, J. S. Pedersen, N. Holroyd, R. Taylor, D. Swarbreck, N. Matthews, M. C. Dickson, D. J. Thomas, M. T. Weirauch, J. Gilbert, J. Drenkow, I. Bell, X. Zhao, K. G. Srinivasan, W. K. Sung, H. S. Ooi, K. P. Chiu, S. Foissac, T. Alioto, M. Brent, L. Pachter, M. L. Tress, A. Valencia, S. W. Choo, C. Y. Choo, C. Ucla, C. Manzano, C. Wyss, E. Cheung, T. G. Clark, J. B. Brown, M. Ganesh, S. Patel, H. Tammana, J. Chrast, C. N. Henrichsen, C. Kai, J. Kawai, U. Nagalakshmi, J. Wu, Z. Lian, J. Lian, P. Newburger, P. Bickel, J. S. Mattick, P. Carninci, Y. Hayashizaki, S. Weissman, T. Hubbard, R. M. Myers, J. Rogers, P. F. Stadler, T. M. Lowe, C. L. Wei, K. Struhl, M. Gerstein, S. E. Antonarakis, Y. Fu, E. D. Green, U. Karaoz, A. Siepel, J. Taylor, L. A. Liefer, K. A. Wetterstrand, P. J. Good, E. A. Feingold, M. S. Guyer, G. M. Cooper, G. Asimenos, C. N. Dewey, M. Hou, S. Nikolaev, J. I. Montoya-Burgos, A. Loytynoja, S. Whelan, F. Pardi, T. Massingham, H. Huang, N. R. Zhang, I. Holmes, J. C. Mullikin, A. Ureta-Vidal, B. Paten, M. Seringhaus, D. Church, K. Rosenbloom, W. J. Kent, E. A. Stone, S. Batzoglou, N. Goldman, R. C. Hardison, D. Haussler, W. Miller, A. Sidow, N. D. Trinklein, Z. D. Zhang, L. Barrera, R. Stuart, D. C. King, A. Ameur, S. Enroth, M. C. Bieda, J. Kim, A. A. Bhinge, N. Jiang, J. Liu, F. Yao, V. B. Vega, C. W. Lee, P. Ng, A. Shahab, A. Yang, Z. Moqtaderi, Z. Zhu, X. Xu, S. Squazzo, M. J. Oberley, D. Inman, M. A. Singer, T. A. Richmond, K. J. Munn, A. Rada-Iglesias, O. Wallerman, J. Komorowski, J. C. Fowler, P. Couttet, A. W. Bruce, O. M. Dovey, P. D. Ellis, C. F. Langford, D. A. Nix, G. Euskirchen, S. Hartman, A. E. Urban, P. Kraus, S. Van Calcar, N. Heintzman, T. H. Kim, K. Wang, C. Qu, G. Hon, R. Luna, C. K. Glass, M. G. Rosenfeld, S. F. Aldred, S. J. Cooper, A. Halees, J. M. Lin, H. P. Shulha, X. Zhang, M. Xu, J. N. Haidar, Y. Yu, Y. Ruan, V. R. Iyer, R. D. Green, C. Wadelius, P. J. Farnham, B. Ren, R. A. Harte, A. S. Hinrichs, H. Trumbower, H. Clawson, J. Hillman-Jackson, A. S. Zweig, K. Smith, A. Thakkapallayil, G. Barber, R. M. Kuhn, D. Karolchik, L. Armengol, C. P. Bird, P. I. de Bakker, A. D. Kern, N. Lopez-Bigas, J. D. Martin, B. E. Stranger, A. Woodroffe, E. Davydov, A. Dimas, E. Eyras, I. B. Hallgrimsdottir, J. Huppert, M. C. Zody, G. R. Abecasis, X. Estivill, G. G. Bouffard, X. Guan, N. F. Hansen, J. R. Idol, V. V. Maduro, B. Maskeri, J. C. McDowell, M. Park, P. J. Thomas, A. C. Young, R. W. Blakesley, D. M. Muzny, E. Sodergren, D. A. Wheeler, K. C. Worley, H. Jiang, G. M. Weinstock, R. A. Gibbs, T. Graves, R. Fulton, E. R. Mardis, R. K. Wilson, M. Clamp, J. Cuff, S. Gnerre, D. B. Jaffe, J. L. Chang, K. Lindblad-Toh, E. S. Lander, M. Koriabine, M. Nefedov, K. Osoegawa, Y. Yoshinaga, B. Zhu, P. J. de Jong (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature.

S. R. Davis, P. S. Meltzer (2007). Modeling synovial sarcoma: timing is everything. Cancer Cell.

J. J. Johnston, R. L. Walker, S. Davis, F. Facio, J. T. Turner, D. P. Bick, D. L. Daentl, J. W. Ellison, P. S. Meltzer, L. G. Biesecker (2007). Zoom-in comparative genomic hybridisation arrays for the characterisation of variable breakpoint contiguous gene syndromes. J. Med. Genet..

J. Kamradt, V. Jung, K. Wahrheit, L. Tolosi, J. Rahnenfuehrer, M. Schilling, R. Walker, S. Davis, M. Stoeckle, P. Meltzer, B. Wullich (2007). Detection of novel amplicons in prostate cancer by comprehensive genomic profiling of prostate cancer cell lines using oligonucleotide-based arrayCGH. PLoS ONE.

G. E. Crawford, S. Davis, P. C. Scacheri, G. Renaud, M. J. Halawi, M. R. Erdos, R. Green, P. S. Meltzer, T. G. Wolfsberg, F. S. Collins (2006). DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat. Methods.

S. Davis, P. S. Meltzer (2006). Ewing's sarcoma: general insights from a rare model. Cancer Cell.

P. C. Scacheri, S. Davis, D. T. Odom, G. E. Crawford, S. Perkins, M. J. Halawi, S. K. Agarwal, S. J. Marx, A. M. Spiegel, P. S. Meltzer, F. S. Collins (2006). Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. PLoS Genet..

P. C. Scacheri, G. E. Crawford, S. Davis (2006). Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Meth. Enzymol..

G. E. Crawford, I. E. Holt, J. Whittle, B. D. Webb, D. Tai, S. Davis, E. H. Margulies, Y. Chen, J. A. Bernat, D. Ginsburg, D. Zhou, S. Luo, T. J. Vasicek, M. J. Daly, T. G. Wolfsberg, F. S. Collins (2006). Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res..

K. Baird, S. Davis, C. R. Antonescu, U. L. Harper, R. L. Walker, Y. Chen, A. A. Glatfelter, P. H. Duray, P. S. Meltzer (2005). Gene expression profiling of human sarcomas: insights into sarcoma biology. Cancer Res..

S. Durinck, Y. Moreau, A. Kasprzyk, S. Davis, B. De Moor, A. Brazma, W. Huber (2005). BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics.

C. G. Son, S. Bilke, S. Davis, B. T. Greer, J. S. Wei, C. C. Whiteford, Q. R. Chen, N. Cenacchi, J. Khan (2005). Database of mRNA gene expression profiles of multiple human organs. Genome Res..

S. Davis, V. L. Nimgaonkar (2001). Impact of overlapping recruitment on linkage analysis of complex disorders: simulation studies. Am. J. Med. Genet..

R. H. Duerr, M. M. Barmada, L. Zhang, S. Davis, R. A. Preston, L. J. Chensny, J. L. Brown, G. D. Ehrlich, D. E. Weeks, C. E. Aston (1998). Linkage and association between inflammatory bowel disease and a locus on chromosome 12. Am. J. Hum. Genet..

S. Davis, D. E. Weeks (1997). Comparison of nonparametric statistics for detection of linkage in nuclear families: single-marker evaluation. Am. J. Hum. Genet..

C. Julier, M. Delepine, B. Keavney, J. Terwilliger, S. Davis, D. E. Weeks, T. Bui, X. Jeunemaitre, G. Velho, P. Froguel, P. Ratcliffe, P. Corvol, F. Soubrier, G. M. Lathrop (1997). Genetic susceptibility for human familial essential hypertension in a region of homology with blood pressure linkage on rat chromosome 10. Hum. Mol. Genet..

D. E. Weeks, S. Davis, M. Schroeder, L. R. Goldin (1997). Nonparametric simulation based linkage statistics for general pedigrees. J. Rheumatol..

S. Davis, E. Sobel, M. Marinov, D. E. Weeks (1997). Analysis of bipolar disorder using affected relatives. Genet. Epidemiol..

J. R. O'Connell, S. Davis, D. E. Weeks (1997). Analysis of a complex oligogenic disease. Genet. Epidemiol..

S. Davis, M. Schroeder, L. R. Goldin, D. E. Weeks (1996). Nonparametric simulation-based statistics for detecting linkage in general pedigrees. Am. J. Hum. Genet..