Publications
Key Publications |
Other Publications |
Papers in preparation/submitted
Key Publications
- Qin, H., Chan, M.W.Y., Liyanarachchi, S., Balch, C., Potter, D., Souriraj, I.J., Cheng, A.S.L., Agosto-Pérez, F.J., Nikonova, E.N., Yan, P. et al. (2009) An Integrative ChIP-chip and Gene Expression Profiling to Model SMAD Regulatory Modules. BMC Systems Biology, (Accepted).
- Davuluri, R.V., Suzuki, Y., Sugano, S., Plass, C. and Huang, T.H. (2008) The functional consequences of alternative promoter use in mammalian genomes. Trends Genet, 24, 167-177.
- Singer, G.A., Wu, J., Yan, P., Plass, C., Huang, T.H. and Davuluri, R.V. (2008) Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array. BMC Genomics, 9, 349.
- Kulshreshtha, R., Ferracin, M., Negrini, M., Calin, G.A., Davuluri, R.V. and Ivan, M. (2007) Regulation of microRNA expression: the hypoxic component. Cell Cycle, 6, 1426-1431.
- Davuluri, R.V. (2007) Bioinformatics tools for modeling transcription factor target genes and epigenetic changes. Methods Mol Biol, 408, 129-151.
- Sun, H., Palaniswamy, S.K., Pohar, T.T., Jin, V.X., Huang, T.H. and Davuluri, R.V. (2006) MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. Nucleic Acids Res, 34, D98-103.
- Jin, V.X., Singer, G.A., Agosto-Perez, F.J., Liyanarachchi, S. and Davuluri, R.V. (2006) Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC Bioinformatics, 7, 114.
- Cheng, A.S., Jin, V.X., Fan, M., Smith, L.T., Liyanarachchi, S., Yan, P.S., Leu, Y.W., Chan, M.W., Plass, C., Nephew, K.P. et al. (2006) Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. Mol Cell, 21, 393-404.
- Palaniswamy, S.K., Jin, V.X., Sun, H. and Davuluri, R.V. (2005) OMGProm: a database of orthologous mammalian gene promoters. Bioinformatics, 21, 835-836.
- Jin, V.X., Sun, H., Pohar, T.T., Liyanarachchi, S., Palaniswamy, S.K., Huang, T.H. and Davuluri, R.V. (2005) ERTargetDB: an integral information resource of transcription regulation of estrogen receptor target genes. J Mol Endocrinol, 35, 225-230.
- Sun, H. and Davuluri, R.V. (2004) Java-based application framework for visualization of gene regulatory region annotations. Bioinformatics, 20, 727-734.
- Pohar, T.T., Sun, H. and Davuluri, R.V. (2004) HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. Nucleic Acids Res, 32, D86-90.
- Jin, V.X., Leu, Y.W., Liyanarachchi, S., Sun, H., Fan, M., Nephew, K.P., Huang, T.H. and Davuluri, R.V. (2004) Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucleic Acids Res, 32, 6627-6635.
- Davuluri, R.V. (2003) Application of FirstEF to find promoters and first exons in the human genome. Curr Protoc Bioinformatics, Chapter 4, Unit4 7.
- Davuluri, R.V., Grosse, I. and Zhang, M.Q. (2001) Computational identification of promoters and first exons in the human genome. Nat Genet, 29, 412-417.
- Davuluri, R.V., Suzuki, Y., Sugano, S. and Zhang, M.Q. (2000) CART classification of human 5' UTR sequences. Genome Res, 10, 1807-1816.
Other Publications:
- Whitman, S.P., Hackanson, B., Liyanarachchi, S., Liu, S., Rush, L.J., Maharry, K., Margeson, D., Davuluri, R., Wen, J., Witte, T. et al. (2008) DNA hypermethylation and epigenetic silencing of the tumor suppressor gene, SLC5A8, in acute myeloid leukemia with the MLL partial tandem duplication. Blood, 112, 2013-2016.
- Han, J., Potter, D., Kurc, T., Singer, G., Yan, P.S., Hao, S., Hastings, S., Langella, S., Oster, S., Davuluri, R.V. et al. (2008) An Application of a Service-oriented System to Support ArrayAnnotation in Custom Chip Design for Epigenomic Analysis. Cancer Inform, 6, 111-125.
- Kulshreshtha, R., Davuluri, R.V., Calin, G.A. and Ivan, M. (2008) A microRNA component of the hypoxic response. Cell Death Differ, 15, 667-671.
- Chan, M.W., Huang, Y.W., Hartman-Frey, C., Kuo, C.T., Deatherage, D., Qin, H., Cheng, A.S., Yan, P.S., Davuluri, R.V., Huang, T.H. et al. (2008) Aberrant transforming growth factor beta1 signaling and SMAD4 nuclear translocation confer epigenetic repression of ADAM19 in ovarian cancer. Neoplasia, 10, 908-919.
- Yoon, H., He, H., Nagy, R., Davuluri, R., Suster, S., Schoenberg, D., Pellegata, N. and Chapelle Ade, L. (2007) Identification of a novel noncoding RNA gene, NAMA, that is downregulated in papillary thyroid carcinoma with BRAF mutation and associated with growth arrest. Int J Cancer, 121, 767-775.
- Wang, H., Hertlein, E., Bakkar, N., Sun, H., Acharyya, S., Wang, J., Carathers, M., Davuluri, R. and Guttridge, D.C. (2007) NF-kappaB regulation of YY1 inhibits skeletal myogenesis through transcriptional silencing of myofibrillar genes. Mol Cell Biol, 27, 4374-4387.
- Sevignani, C., Calin, G.A., Nnadi, S.C., Shimizu, M., Davuluri, R.V., Hyslop, T., Demant, P., Croce, C.M. and Siracusa, L.D. (2007) MicroRNA genes are frequently located near mouse cancer susceptibility loci. Proc Natl Acad Sci U S A, 104, 8017-8022.
- Opavsky, R., Wang, S.H., Trikha, P., Raval, A., Huang, Y., Wu, Y.Z., Rodriguez, B., Keller, B., Liyanarachchi, S., Wei, G. et al. (2007) CpG island methylation in a mouse model of lymphoma is driven by the genetic configuration of tumor cells. PLoS Genet, 3, 1757-1769.
- Kulshreshtha, R., Ferracin, M., Wojcik, S.E., Garzon, R., Alder, H., Agosto-Perez, F.J., Davuluri, R., Liu, C.G., Croce, C.M., Negrini, M. et al. (2007) A microRNA signature of hypoxia. Mol Cell Biol, 27, 1859-1867.
- Brena, R.M., Morrison, C., Liyanarachchi, S., Jarjoura, D., Davuluri, R.V., Otterson, G.A., Reisman, D., Glaros, S., Rush, L.J. and Plass, C. (2007) Aberrant DNA methylation of OLIG1, a novel prognostic factor in non-small cell lung cancer. PLoS Med, 4, e108.
- Yu, J., Wei, M., Becknell, B., Trotta, R., Liu, S., Boyd, Z., Jaung, M.S., Blaser, B.W., Sun, J., Benson, D.M., Jr. et al. (2006) Pro- and antiinflammatory cytokine signaling: reciprocal antagonism regulates interferon-gamma production by human natural killer cells. Immunity, 24, 575-590.
- Wei, S.H., Balch, C., Paik, H.H., Kim, Y.S., Baldwin, R.L., Liyanarachchi, S., Li, L., Wang, Z., Wan, J.C., Davuluri, R.V. et al. (2006) Prognostic DNA methylation biomarkers in ovarian cancer. Clin Cancer Res, 12, 2788-2794.
- Li, L., Cheng, A.S., Jin, V.X., Paik, H.H., Fan, M., Li, X., Zhang, W., Robarge, J., Balch, C., Davuluri, R.V. et al. (2006) A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. Bioinformatics, 22, 2210-2216.
- Palaniswamy, S.K., James, S., Sun, H., Lamb, R.S., Davuluri, R.V. and Grotewold, E. (2006) AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiol, 140, 818-829.
- Cunningham, D., Swartzlander, D., Liyanarachchi, S., Davuluri, R.V. and Herman, G.E. (2005) Changes in gene expression associated with loss of function of the NSDHL sterol dehydrogenase in mouse embryonic fibroblasts. J Lipid Res, 46, 1150-1162.
- Yu, L., Liu, C., Bennett, K., Wu, Y.Z., Dai, Z., Vandeusen, J., Opavsky, R., Raval, A., Trikha, P., Rodriguez, B. et al. (2004) A NotI-EcoRV promoter library for studies of genetic and epigenetic alterations in mouse models of human malignancies. Genomics, 84, 647-660.
- Rush, L.J., Raval, A., Funchain, P., Johnson, A.J., Smith, L., Lucas, D.M., Bembea, M., Liu, T.H., Heerema, N.A., Rassenti, L. et al. (2004) Epigenetic profiling in chronic lymphocytic leukemia reveals novel methylation targets. Cancer Res, 64, 2424-2433.
- Nakagawa, H., Liyanarachchi, S., Davuluri, R.V., Auer, H., Martin, E.W., Jr., de la Chapelle, A. and Frankel, W.L. (2004) Role of cancer-associated stromal fibroblasts in metastatic colon cancer to the liver and their expression profiles. Oncogene, 23, 7366-7377.
- Leu, Y.W., Yan, P.S., Fan, M., Jin, V.X., Liu, J.C., Curran, E.M., Welshons, W.V., Wei, S.H., Davuluri, R.V., Plass, C. et al. (2004) Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer. Cancer Res, 64, 8184-8192.
- de Stanchina, E., Querido, E., Narita, M., Davuluri, R.V., Pandolfi, P.P., Ferbeyre, G. and Lowe, S.W. (2004) PML is a direct p53 target that modulates p53 effector functions. Mol Cell, 13, 523-535.
- Besco, J., Popesco, M.C., Davuluri, R.V., Frostholm, A. and Rotter, A. (2004) Genomic structure and alternative splicing of murine R2B receptor protein tyrosine phosphatases (PTPkappa, mu, rho and PCP-2). BMC Genomics, 5, 14.
- Baldus, C.D., Liyanarachchi, S., Mrozek, K., Auer, H., Tanner, S.M., Guimond, M., Ruppert, A.S., Mohamed, N., Davuluri, R.V., Caligiuri, M.A. et al. (2004) Acute myeloid leukemia with complex karyotypes and abnormal chromosome 21: Amplification discloses overexpression of APP, ETS2, and ERG genes. Proc Natl Acad Sci U S A, 101, 3915-3920.
- Aldred, M.A., Huang, Y., Liyanarachchi, S., Pellegata, N.S., Gimm, O., Jhiang, S., Davuluri, R.V., de la Chapelle, A. and Eng, C. (2004) Papillary and follicular thyroid carcinomas show distinctly different microarray expression profiles and can be distinguished by a minimum of five genes. J Clin Oncol, 22, 3531-3539.
- Savage, H., Rothstein, M., Davuluri, G., El Ghormli, L. and Zaetta, D.M. (2003) Myopic astigmatism and presbyopia trial. Am J Ophthalmol, 135, 628-632.
- Davuluri, R.V. and Zhang, M.Q. (2003) Computer software to find genes in plant genomic DNA. Methods Mol Biol, 236, 87-108.
- Davuluri, R.V., Sun, H., Palaniswamy, S.K., Matthews, N., Molina, C., Kurtz, M. and Grotewold, E. (2003) AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics, 4, 25.
- Borrego, S., Wright, F.A., Fernandez, R.M., Williams, N., Lopez-Alonso, M., Davuluri, R., Antinolo, G. and Eng, C. (2003) A founding locus within the RET proto-oncogene may account for a large proportion of apparently sporadic Hirschsprung disease and a subset of cases of sporadic medullary thyroid carcinoma. Am J Hum Genet, 72, 88-100.
- Yoon, H., Liyanarachchi, S., Wright, F.A., Davuluri, R., Lockman, J.C., de la Chapelle, A. and Pellegata, N.S. (2002) Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53. Proc Natl Acad Sci U S A, 99, 15632-15637.
- Nahle, Z., Polakoff, J., Davuluri, R.V., McCurrach, M.E., Jacobson, M.D., Narita, M., Zhang, M.Q., Lazebnik, Y., Bar-Sagi, D. and Lowe, S.W. (2002) Direct coupling of the cell cycle and cell death machinery by E2F. Nat Cell Biol, 4, 859-864.
- Gupta, V.K., Ramana, D.V.V. and Parsad, R. (2002) Weighted A-optimal block designs for comparing test treatments with controls with unequal precision. J of Statistical Planning and Inference, 17, 602-607.
- Dai, Z., Weichenhan, D., Wu, Y.Z., Hall, J.L., Rush, L.J., Smith, L.T., Raval, A., Yu, L., Kroll, D., Muehlisch, J. et al. (2002) An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands. Genome Res, 12, 1591-1598.
- Tabaska, J.E., Davuluri, R.V. and Zhang, M.Q. (2001) Identifying the 3'-terminal exon in human DNA. Bioinformatics, 17, 602-607.
- Pavy, N., Rombauts, S., Dehais, P., Mathe, C., Ramana, D.V., Leroy, P. and Rouze, P. (1999) Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics, 15, 887-899.
- Gupta, V.K., Ramana, D.V.V. and and Parsad, R. (1999) Weighted A-efficiency of block designs for making treatment-control and treatment-treatment comparisons. J of Statistical Planning and Inference, 77, 301-319.
- Gupta, V.K., Ramana, D.V.V. and Agarwal, S.K. (1998) Weighted A-optimal row-column designs for making treatment-control and treatment-treatment comparisons. J. Combinatorics, Information and System Sciences, 23, 333-344.
Papers in preparation/submitted:
- Nicoloso, M.S., Sun, H., Spizzo, R., Shimizu, M., Wojcik, S.E., Manoukian, S., Secreto, G., Ravagnani, F., Radice, P., Croce, C.M. et al. (2008) Single nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility. Submitted.
- Sun, H., Wu, J., Wikramasinghe, P., Bhattacharyya, A., Agosto-Perez F., Huang, T.H., Davuluri, R.V. (2009) Genomewide mapping of alternative promoter usage in five mouse tissues by massive parallel sequencing. (In preparation).
- Bhattacharyya, A., Pal, S., Davuluri, R.V. (2009) Usage of Alternative First Exons affect Splicing. (In preparation).
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