HCG Bioinformatics and Computational Biology || Publications

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).