Manuscripts in preparation or under review
Primary publications
Collaborative publications
Book chapters

Manuscripts in preparation or under review

1. Bi, Y. and Davuluri, R.V. (2012) Empirical Bayesian based Method for Normalization and Differential Expression Analysis of RNA-seq Data. (Submitted).

2. Ota, H., Sakurai, M., Gupta, R., Valente, L., Wulff, B.-E., Ariyoshi, K., Iizasa, H., Davuluri, R.V. and Nishikura, K. (2012) ADAR1 complexes with Dicer and plays a role in microRNA processing and RNA-induced gene silencing mechanisms. (Submitted).

Publications (primary publications)

1. Pal, S., Gupta, R. and Davuluri, R.V. (2012) Alternative transcription and alternative splicing in cancer (Invited review, Pharmacology & Therapeutics, In press)

2. Pal, S., Gupta, R., Kim, H., Wickramasinghe, P., Baubet, V., Showe, L.C., Dahmane, N. and Davuluri, R.V. (2011) Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development, Genome Research, 21(8): 1260-1272.

3. Bi, Y., Kim, H., Gupta, R. and Davuluri, R.V. (2011) Tree-based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles, PLOS One 6(9): e24210. doi:10.1371/journal.pone.0024210.

4. Kim, H., Bi, Y., Pal, S., Gupta, R., and Davuluri, R.V. (2011) IsoformEx: Isoform level expression estimation using weighted non-negetive least squares from mRNA-seq data, BMC Bioinformatics, 12(1):305.

5. Sun, H., Wu, J., Wickramasinghe, P., Pal, S., Gupta, R., Bhattacharyya, A., Agosto-Perez, F.J., Showe, L.C., Huang, T.H. and Davuluri, R.V. (2011) Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq, Nucleic Acids Res, 39, 190-201.

6. Gupta, R., Bhattacharyya, A., Agosto-Perez, F.J., Wickramasinghe, P. and Davuluri, R.V. (2011) MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data, Nucleic Acids Res, 39, D92-97.

7. Kim, H. and Davuluri, R.V. (2010) Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targets. Proceedings of the 1st ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB). Niagara Falls, New York, USA, 499-501.

8. Kim, H., Bi, Y. and Davuluri, R.V. (2010) Estimating the Expression of Transcript Isoforms from mRNA-Seq via Nonnegative Least Squares. Proceedings of the the 10th IEEE International Conference on Bioinformatics and Bioengineering (BIBE-2010). Philadelphia, PA, USA, 296-297.

9. Nicoloso, M.S., Sun, H., Spizzo, R., Kim, H., Wickramasinghe, P., Shimizu, M., Wojcik, S.E., Ferdin, J., Kunej, T., Xiao, L., Manoukian, S., Secreto, G., Ravagnani, F., Wang, X., Radice, P., Croce, C.M., Davuluri, R.V.* and Calin, G.A.* (2010) Single-Nucleotide Polymorphisms Inside MicroRNA Target Sites Influence Tumor Susceptibility, Cancer Res. (*Joint corresponding authors)

10. Gupta, R., Wikramasinghe, P., Bhattacharyya, A., Perez, F.A., Pal, S. and Davuluri, R.V. (2010) Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data, BMC Bioinformatics, 11 Suppl 1, S65.

11. Qin, H., Chan, M.W., Liyanarachchi, S., Balch, C., Potter, D., Souriraj, I.J., Cheng, A.S., Agosto-Perez, F.J., Nikonova, E.V., Yan, P.S., Lin, H.J., Nephew, K.P., Saltz, J.H., Showe, L.C., Huang, T.H. and Davuluri, R.V. (2009) An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules, BMC Syst Biol, 3, 73.

12. 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.

13. 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.

14. 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, 6:1426-31. (*Joint corresponding authors)

15. Palaniswamy, S.K., James, S., Sun, H., Lamb, R.S., Davuluri, R.V.*, Grotewold, E. (2006) AGRIS and AtRegNet: A platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiology 140:818-829. (*Joint corresponding authors)

16. Jin, V., Singer, G.A.C., Agosto-Pérez, F.J., Liyanarachchi, S., Davuluri, R.V. (2006) Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC Bioinformatics 7(1):114.

17. Sun, H., Palaniswamy, S.K., Pohar, T.T., Jin, V.X., Huang, T.H., 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.

18. Jin, V., Sun, H., Pohar, T.T., Liyanarachchi, S., Palaniswamy, S.K., Huang, T.H., Davuluri R.V. (2005). ERTargetDB: An integral information resource of transcription regulation of ER target genes. J of Molecular Endocrinology 35: 225-230.

19. Palaniswamy, S.K., Jin, V., Sun H., Davuluri, R.V. (2005). OMGProm: A Database of Orthologous Mammalian Gene Promoters. Bioinformatics. 21:835-836.

20. Jin, V., Leu, Y.W., Liyanarachchi, S., Sun, H., Fan, M., Nephew, K.P., Huang, T.H. and Davuluri, R.V. (2004). Identifying Estrogen Receptor a Target Genes Using Integrated Computational Genomics and Chromatin Immunoprecipitation Microarray. Nucleic Acids Res. 32: 6627-6635.
Sun, H. and Davuluri, R.V. (2004) Java-based Application Framework for Visualization of Gene Regulatory Region Annotations. Bioinformatics. 20:727-734.

21. 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. (Note: This database was featured in Science, 303: 291 (in NetWatch, Database: Bad Blood), January 16, 2004).

22. 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.

23. Davuluri R.V., Grosse, I. and Zhang, M.Q. (2001). Computational identification of first exons and promoters in the human genome. Nature Genetics, 29: 412-417. (Note: This work was featured in Nature Reviews Genetics, 3: 3-9; in Bioinformatics section of Highlights as “Filling the gap in gene prediction” January, 2002).

24. Davuluri, R.V., Suzuki, Y., Sugano, S. and Zhang, M.Q. (2000). CART classification of human 5'UTR sequences, Genome Research 10: 1817-1827.

Publications (collaborative publications)

1.      Deng, Z., Wang, Z., Stong, N., Plasschaert, R., Moczan, A., Chen, H.-S., Hu, S., Wickramasinghe, P., Davuluri, R.V., Bartolomei, M. et al. (2012) A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection EMBO J., 31(21):4165-78.

2.      Gupta, R., Ratan, A., Rajesh, C., Chen, R., Kim, H. L., Burhans, R., Miller, W., Santosh, S., Davuluri, R. V., Bhutte, A., Schuster, S. C., Seshagiri, S., & Thomas, G. (2012). Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics, Aug 31;13(1):440.

3.      Jendrzejewski, J., He, H., Radomska, H.S., Li, W., Tomsic, J., Liyanarachchi, S., Davuluri, R.V., Nagy, R. and de la Chapelle, A. (2012) The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type. Proc Natl Acad Sci U S A, 109, 8646-8651.

4.      Lu, F., Tsai, K., Chen, H.S., Wikramasinghe, P., Davuluri, R.V., Showe, L., Domsic, J., Marmorstein, R. and Lieberman, P.M. (2012) Identification of Host-Chromosome Binding Sites and Candidate Gene Targets for Kaposi's Sarcoma-Associated Herpesvirus LANA. J Virol, 86, 5752-5762.

5.      Xiang, C., Baubet, V., Pal, S., Holderbaum, L., Tatard, V., Jiang, P., Davuluri, R.V. and Dahmane, N. (2012) RP58/ZNF238 directly modulates proneurogenic gene levels and is required for neuronal differentiation and brain expansion. Cell Death Differ, 19, 692-702.

6.      Fabbri, M., Bottoni, A., Shimizu, M., Spizzo, R., Nicoloso, M.S., Rossi, S., Barbarotto, E., Cimmino, A., Adair, B., Wojcik, S.E., Valeri, N., Calore, F., Sampath, D., Fanini, F., Vannini, I., Musuraca, G., Dell'Aquila, M., Alder, H., Davuluri, R.V., Rassenti, L.Z., Negrini, M., Nakamura, T., Amadori, D., Kay, N.E., Rai, K.R., Keating, M.J., Kipps, T.J., Calin, G.A. and Croce, C.M. (2011) Association of a microRNA/TP53 feedback circuitry with pathogenesis and outcome of B-cell chronic lymphocytic leukemia, JAMA, 305, 59-67.

7.      Spizzo, R., Nicoloso, M.S., Lupini, L., Lu, Y., Fogarty, J., Rossi, S., Zagatti, B., Fabbri, M., Veronese, A., Liu, X., Davuluri, R., Croce, C.M., Mills, G., Negrini, M. and Calin, G.A. (2010) miR-145 participates with TP53 in a death-promoting regulatory loop and targets estrogen receptor-alpha in human breast cancer cells, Cell Death Differ, 17, 246-254.

8.      Herz, H.M., Madden, L.D., Chen, Z., Bolduc, C., Buff, E., Gupta, R., Davuluri, R., Shilatifard, A., Hariharan, I.K. and Bergmann, A. (2010) The H3K27me3-demethylase dUTX is a suppressor of Notch- and Rb-dependent tumors in Drosophila, Mol Cell Biol, 30, 2485-2497.

9.      Lu, F., Wikramasinghe, P., Norseen, J., Tsai, K., Wang, P., Showe, L., Davuluri, R.V. and Lieberman, P.M. (2010) Genome-wide analysis of host-chromosome binding sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1), Virol J, 7, 262.

10.   Chou, J.L., Su, H.Y., Chen, L.Y., Liao, Y.P., Hartman-Frey, C., Lai, Y.H., Yang, H.W., Deatherage, D.E., Kuo, C.T., Huang, Y.W., Yan, P.S., Hsiao, S.H., Tai, C.K., Lin, H.J., Davuluri, R.V., Chao, T.K., Nephew, K.P., Huang, T.H., Lai, H.C. and Chan, M.W. (2010) Promoter hypermethylation of FBXO32, a novel TGF-beta/SMAD4 target gene and tumor suppressor, is associated with poor prognosis in human ovarian cancer, Lab Invest, 90, 414-425.

11.   Rossi, S., Kopetz, S., Davuluri, R., Hamilton, S.R. and Calin, G.A. (2009) MicroRNAs, ultraconserved genes and colorectal cancers, Int J Biochem Cell Biol, 42, 1291-1297.

12.   Chen, S.S., Raval, A., Johnson, A.J., Hertlein, E., Liu, T.H., Jin, V.X., Sherman, M.H., Liu, S.J., Dawson, D.W., Williams, K.E., Lanasa, M., Liyanarachchi, S., Lin, T.S., Marcucci, G., Pekarsky, Y., Davuluri, R., Croce, C.M., Guttridge, D.C., Teitell, M.A., Byrd, J.C. and Plass, C. (2009) Epigenetic changes during disease progression in a murine model of human chronic lymphocytic leukemia, Proc Natl Acad Sci U S A, 106, 13433-13438.

13.   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., Nephew, K.P. and Lin, H.J. (2008) Aberrant transforming growth factor beta1 signaling and SMAD4 nuclear translocation confer epigenetic repression of ADAM19 in ovarian cancer, Neoplasia, 10, 908-919.

14.   Han, J., Potter, D., Kurc, T., Singer, G., Yan, P.S., Hao, S., Hastings, S., Langella, S., Oster, S., Davuluri, R.V., Huang, T.H. and Saltz, J.H. (2008) An Application of a Service-oriented System to Support ArrayAnnotation in Custom Chip Design for Epigenomic Analysis, Cancer Inform, 6, 111-125.

15.   Whitman, S.P., Hackanson, B., Liyanarachchi, S., Liu, S., Rush, L.J., Maharry, K., Margeson, D., Davuluri, R., Wen, J., Witte, T., Yu, L., Liu, C., Bloomfield, C.D., Marcucci, G., Plass, C. and Caligiuri, M.A. (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.

16.   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.

17.   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.

18.   Opavsky, R., Wang, S.H., Trikha, P., Raval, A., Huang, Y., Wu, Y.Z., Rodriguez, B., Keller, B., Liyanarachchi, S., Wei, G., Davuluri, R.V., Weinstein, M., Felsher, D., Ostrowski, M., Leone, G. and Plass, C. (2007) CpG island methylation in a mouse model of lymphoma is driven by the genetic configuration of tumor cells, PLoS Genet, 3, 1757-1769.

19.   Yoon, H., He, H., Nagy, R., Davuluri, R., Suster, S., Schoenberg, D., Pellegata, N. and Chapelle, A.D. (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, 121:767-75.

20.   Wang, H., Hertlein, E., Bakkar, N., Sun, H., Acharyya, S., Wang, J., Carathers, M., Davuluri, R. and Guttridge, D.C. (2007) NF-{kappa}B Regulation of YY1 Inhibits Skeletal Myogenesis through Transcriptional Silencing of Myofibrillar Genes. Mol Cell Biol. 27:4374-87.

21.   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.104:8017-22.

22.   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.

23.   Li, L., Cheng, A.S., Jin, V.X., Paik, H.H., Fan, M., Li, X., Zhang, W., Robarge, J., Balch, C., Davuluri, R.V. Kim, S., Huang, T.H., and Nephew, K.P. (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.

24.   Yu, J., Wei, M., Becknell, B., Trotta, R., Liu, S., Boyd, Z., Jaung., M.S., Sun, J., Benson, JrD.M., Mao, H., Yokohama, A., Bhatt, D., Shen, L., Davuluri, R.V., Weinstein, M., Marcucci, G., Caligiuri M.A. (2006) Pro- and Anti-inflammatory Cytokine Signaling: Reciprocal Antagonism Regulates Interferon-gamma Production by Human Natural Killer Cells. Immunity 24:575-590.

25.   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., Karlan, B.Y., Gifford, G., Brown, R., Kim, S., Huang, T.H., Nephew, K.P. (2006) Prognostic DNA methylation biomarkers in ovarian cancer. Clinical Cancer Research 12:2788-2294.

26.   Cheng, A.S.L., Jin, V.X., Fan, M., Smith, L.T., Liyanarachchi, S., Yan, P.S., Leu, Y.W., Chan, M.W.Y., Plass, C., Nephew, K.P., Davuluri, R.V., Huang, T.H. (2006) Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor a- responsive promoters. Molecular Cell 23:393-404.

27.   Cunningham, D., Swartzlander, D., Liyanarachchi, S., Davuluri R.V., 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. 46:1150-62.

28.   Leu, Y.W., Yan P.S., Fan, M., Jin, V.X., Liu, J.C., Edward, M.C., Welshons, W.V., Wei, S.H., Davuluri, R.V. Plass, C., Nephew, K.P., and Huang, T.H. (2004). Loss of estrogen signaling triggers epigenetic silencing of its downstream targets in breast cancer. Cancer Res. 64:8184-8192.

29.   Nakagawa, H.,  Liyanarachchi, S., Davuluri, R.V., Auer, H., Martin Jr., ED., and de la Chapelle, A., Frankel, W.L. (2004). The Role of Cancer-associated Stromal Fibroblasts in Metastatic Colon Cancer to the Liver and Their Expression Profiles. Oncogene. 23:7366-7377.

30.   Yu, L., Liu, C., Bennett, K., Wu, YZ, Dai, Z, Vandeusen, J., Opavsky, R. Raval, A., Trikha, P., Rodriguez, B., Brian Becknell, B., Mao, C., Lee, S., Davuluri, R.V., Leone, G., den Veyver, IBV, Caligiuri, MA. and Plass, C. (2004). A NotI-EcoRV promoter library for studies of genetic and epigenetic alterations in mouse models of human malignancies. Genomics. 84:647-660.

31.   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. Clinical Oncology, 22:3540–3548.

32.   Stanchina, E.D., Querido, E., Narita, M., Davuluri, R.V., Pandolfi, P.P., Ferbeyre, G. and Lowe, S.W. (2004) PML as a direct p53 target that modulates p53 effector functions. Molecular Cell. 13: 523-535.

33.   Besco, J.A., Popesco, M.C., Davuluri, R.V., Frostholm, A.M. and Rotter, A. (2004) Genomic structure and alternative splicing of murine R2B receptor protein tyrosine phosphatases (PTP kappa, mu, rho and PCP-2). BMC Genomics, 5: 14.

34.   Baldus, C.D., Liyanarchchi, S., Mrózek, K., Auer, H., Tanner, S.M., Guimond, M. Ruppert, A.S., Mohamed, N., Davuluri, R.V., Caligiuri, M.A., Bloomfield, C.D. and de la Chapelle, A. (2004) Acute myeloid leukemia with complex karyotype: amplification of two chromosome 21 regions discloses overexpression of app, ets2 and erg genes. Proc Natl Acad Sci USA 101:3915-3920.

35.   Rush, L.J., Raval A., Funchain P., Johnson, A.J., Smith, L., Lucas, D., Bembea, M., Liu, T., Heerema, N.A., Rassenti, L., Liyanarachchi, S., Davuluri, R.V., Byrd, J.C., and Plass, C. (2004) Epigenetic profiling in chronic lymphocytic leukemia reveals novel methylation targets. Cancer Res. 64:2424-33.

36.   Borrego, S., Wright, F.A., Fernández, R.M, Williams, N., López-Alonso, M., Davuluri, R.V., Antiñolo, 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 sporadic medullary thyroid carcinoma cases. Am J Hum Genet 72:88-100.

37.   Nahle, Z., Polyakoff, J., Davuluri, R.V., Jacobson, M.D., McCurrach, M.E., 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 Biology, 4:859-64.

38.   Yoon, H., Liyanarchchi, S., Wright, F.A., Davuluri, R.V., Lockman, J., de la Chapelle, A., and Pellegata, N.S. (2002) Gene expression profiling of isogenic cells with different TP53 gene dosage reveals that many genes are affected by TP53 dosage and identifies CSPG2 (Versican) as a novel direct target of p53. Proc Natl Acad Sci. USA, 99:15632-15637.

39.   Dai, Z., Weichenhan, D., Wu, Y.Z., Hall, J.L., Rush, L.J., Smith, L.T., Raval, A., Yu, L. Kroll, D., Muehlisch, J. Frühwald, F.C., de Jong, P.,  Catanese, J., Davuluri, R.V., Smiraglia, J.D. and Plass, C. (2002) An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands. Genome Res., 12:1591-1598.

40.   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, 106:159-175.

41.   Tabaska, E. Jack, Davuluri, R.V., and Michael Q. Zhang (2001). A novel 3'-Terminal exon recognition program for Human DNA Sequences. Bioinformatics 17: 602-607.

42.   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 dataset: Application to Arabidopsis Thaliana sequences. Bioinformatics 15: 887-899.

43.   Gupta, V.K., Ramana, D.V.V. 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.

44.   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(1-4), 333-344.

Book Chapters

1. Gupta, R., Davuluri, R.V.  Bioinformatics Approaches to the study of microRNAs: Springer; 2012. (In Preparation)

2. Ochs, M.F., Casagrande, J.T., Davuluri, R.V. (Editors) Biomedical Informatics for Cancer Research: Springer; 2010.

3. Davuluri, R.V. Bioinformatics tools for modeling transcription factor target genes and epigenetic changes. Methods Mol Biol.- Gene Function Analysis, Ed. Michael Ochs, Human Press 2007.

4. Davuluri, R.V. and Zhang, M.Q. Computer software to find genes in plant genomic DNA. Methods Mol Biol., 236:87-108, 2003.

5. Davuluri, R.V. Application of FirstEF to find promoters and first exons in the human genome. Unit 4.7 in Current Protocols in Bioinformatics, edited by Andy Baxevanis, John Wiley & Sons, Inc. New York, NY, 2003.