- Mitra, R., and Gupta M. (2010).
A continuous-index Bayesian hidden Markov model for prediction of nucleosome positioning in genomic DNA.
*Biostatistics,*in press. [PREPRINT] - Gupta, M., Cheung, C.L., Hsu, Y.H., Demissie, S., Cupples, L.A., Kiel,
D.P., and Karasik, D. (2010)
Identification of homogeneous genetic architecture of multiple
genetically correlated traits by block clustering of Genome-wide associations.
*Journal of Bone and Mineral Research,*in press. - Meltzer, M., Long, K., Nie, Y., Gupta, M., Yang, J., and Montano, M. (2010).
The RNA editor gene ADAR1 is induced in myoblasts by inflammatory
ligands and buffers stress response.
*Clin Transl Sci. 3(3):73-80.* - Cheng, F., Hartmann, S., Gupta, M., Ibrahim, J. G., and Vision,
T. J. (2009).
A hierarchical model for incomplete alignments in phylogenetic
inference.
*Bioinformatics,*25(5):592-8. - Gupta, M. and Ibrahim, J. G. (2009).
An information matrix prior for
Bayesian analysis in generalized linear models with high dimensional data.
*Statistica Sinica,*19, 1641-1663. [PREPRINT] - Gelfond, J. L., Gupta, M. and Ibrahim, J. G. (2009).
A Bayesian hidden Markov model for motif discovery through joint modeling of
genomic sequence and ChIP-chip data.
*Biometrics,*65(4):1087-95. - Jeong, Y. C., Walker, N. J., Burgin, D. E., Kissling, G., Gupta, M.,
Kupper, L., Birnbaum, L. S., Swenberg, J. A. (2008).
Accumulation of M(1)dG DNA adducts after chronic exposure to PCBs, but not from acute exposure to polychlorinated aromatic hydrocarbons.
*Free Radic Biol Med.*45(5):585-91. - Gupta, M. (2007). Generalized hierarchical Markov
models for discovery of length-constrained sequence features from
genome tiling arrays.
*Biometrics,*63 (3): 797-805. [PREPRINT] - Gupta, M. and Ibrahim, J. G. (2007). Variable
selection in regression mixture modeling for the discovery of gene
regulatory networks.
*Journal of the American Statistical Association,*102 (479): 867-880. [PREPRINT] - Gupta, M. (2007).
Model selection and sensitivity analysis for
sequence pattern models.
*Beyond Parametrics in Interdisciplinary Research: a festschrift in honour of Prof. P. K. Sen.*Lecture Notes series of the IMS, in press. - Zhou, Q. and Gupta, M. (2007).
Regulatory Motif Discovery- from Decoding to Meta-Analysis.
*Frontiers of Statistics*1, in press. - Gupta, M., Qu, P. and Ibrahim, J. G. (2007). A temporal hidden Markov regression model for the analysis of gene regulatory networks.
*Biostatistics,*8: 805-820. [PREPRINT] - Giresi, P. G., Gupta, M. and Lieb, J. D. (2006).
Regulation of nucleosome stability as a mediator of chromatin function.
*Curr. Opin. Genet. Dev.*16 (2): 171-176. - Gupta, M. and Liu, J. S. (2006).
Bayesian modeling and inference for motif discovery.
*Bayesian inference for gene expression and proteomics.*Do et al., (eds.). Cambridge University Press. - Gelfond, J. L. and Gupta, M. (2006).
Bayesian models
for motif discovery from ChIP-chip and
sequence data.
*International Society for Bayesian Analysis Bulletin*13 (4): 2-4. - Gupta, M. and Ibrahim, J. G. (2006). Bayesian methods for some missing
data problems in functional genomics.
*International Society for Bayesian Analysis Bulletin,*13 (1): 6-10. - Maki, A., Kono, H., Gupta, M. , Asakawa, M., Suzuki,
T., Matsuda, M., Fujii, H., Rusyn, I. (2006).
Predictive power of biomarkers of oxidative stress and inflammation in patients with
hepatitis C virus-associated hepatocellular carcinoma.
*Annals of Surgical Oncology*14:1182-1190. -
Gupta, M. and Ray, S. (2006). Sequence pattern discovery with
applications to understanding gene regulation and vaccine design.
*Handbook of Statistics, C. R. Rao and R. Chakraborty (eds.),*Elsevier Press. - Gupta, M. and Liu, J. S. (2005). De-novo cis-regulatory module elicitation for
eukaryotic genomes.
*Proceedings of the National Academy of Sciences, U. S. A.*102 (20): 7079-7084.**Software** -
Gupta, M. and Liu, J. S. (2004). Discussion on ``A Bayesian approach to DNA
sequence segmentation'' by R. J. Boys and D. A. Henderson,
*Biometrics,*60 (3): 573-844. - Gupta, M. and Liu, J. S. (2003).
Discovery of conserved sequence patterns using a
stochastic dictionary model.
*Journal of the American Statistical Association*98 (461), 55-66.**Software** - Liu, J. S., Gupta, M., Liu, X. L. and Lawrence,
C. L.(2002). Statistical models for
motif discovery. (with discussion)
*Case Studies in Bayesian Statistics,*Vol. 6, Springer-Verlag, New York.