Berhow, M. T., N. Hiroi, L. A. Kobierski, S. E. Hyman and E. J. Nestler (1996): “Influence of cocaine on the JAK-STAT pathway in the mesolimbic dopamine system,” J. Neurosci., 16(24), 8019–8026.
Berton, O., C. A. McClung, R. J. Dileone, V. Krishnan, W. Renthal, S. J. Russo, D. Graham, N. M. Tsankova, C. A. Bolanos, M. Rios, L. M. Monteggia, D. W. Self and E. J. Nestler (2006): “Essential role of BDNF in the mesolimbic dopamine pathway in social defeat stress,” Science, 311, 864–868. [Crossref] [PubMed]
Bird, A. (2007): “Perceptions of epigenetics,” Nature, 447(7143), 396–398. [Web of Science]
Buck, M. J., A. B. Nobel and J. D. Lieb (2005): “ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data,” Genome Biol., 6(11), R97. [Crossref]
Coryell, M. W., A. M. Wunsch, J. M. Haenfler, J. E. Allen, M. Schnizler, A. E. Ziemann, M. N. Cook, J. P. Dunning, M. P. Price, J. D. Rainier, Z. Liu, A. R. Light, D. R. Langbehn and J. A. Wemmie (2009): “Acid-sensing ion channel-1a in the amygdala, a novel therapeutic target in depression-related behavior,” J. Neurosci., 29(17), 5381–5388. doi:10.1523/JNEUROSCI.0360-09.2009.
Flight, M. H. (2009): “Mood disorders: channel inhibitor shows antidepressant potential,” Nat. Rev. Drug. Discov., 8(7), 540–540. [Crossref]
Gelfand, A. E., H. J. Kim, C. F. Sirmans and S. Banerjee (2003): “Spatial modeling with spatially varying coefficient processes,” J. Am. Stat. Assoc., 98, 387–396. [Crossref]
Gelfond, J.A., M. Gupta and J.G. Ibrahim (2009): “A Bayesian hidden Markov model for motif discovery through joint modeling of genomic sequence and ChIP-chip data,” Biometrics, 65, 1087–1095. [Crossref] [PubMed] [Web of Science]
Gottardo, R., W. Li, W. E. Johnson and X. S. Liu (2008): “A flexible and powerful bayesian hierarchical model for chip-chip experiments,” Biometrics, 64(2), 468–78. [Crossref] [Web of Science] [PubMed]
Hemby, S.E., B. Horman and W. Tang (2005): “Differential regulation of ionotropic glutamate receptor subunits following cocaine self-administration,” Brain Res., 1064(1–2), 75–82.
Humburg, P., D. Bulger and G. Stone (2008): “Parameter estimation for robust HMM analysis of ChIP-chip data,” Bioinformatics, 9, 343.
Iyer, V.R., C. E. Horak, C. S. Scafe, D. Botstein, M. Snyder and P. O. Brown (2001): “Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF,” Nature, 409(6819), 533–538.
Ji, H. and W. Wong (2005): “Tilemap: create chromosomal map of tiling array hybridizations,” Bioinformatics, 18, 3629–3636. [Crossref]
Johnson, W. E., W. Li, C. A. Meyer, R. Gottardo, J. S. Carroll, M. Brown and X. S. Liu (2006): “Model-based analysis of tiling-arrays for ChIP-chip,” PNAS, 103, 12457–12462. [Crossref]
Jones, R. S. (2007): “Epigenetics: reversing the ’irreversible’”, NatWure, 450(7168), 357–359.
Kim, T. H., L. O. Barrera, M. Zheng, C. Qu, M. A. Singer, T. A. Richmand, Y. Wu, R. D. Green and B. Ren (2005): “A high-resolution map of active promoters in the human genome,” Nature, 436, 876–880. [PubMed] [Crossref]
LaPlant, Q., V. Vialou, 3rd H. E. Covington, D. Dumitriu, J. Feng, B. L. Warren, I. Maze, D. M. Dietz, E. L. Watts, S. D. Iniguez, J. W. Koo, E. Mouzon, W. Renthal, F. Hollis, H. Wang, M. A. Noonan, Y. Ren, A. J. Eisch, C. A. Bolanos, M. Kabbaj, G. Xiao, R. L. Neve, Y. L. Hurd, R. S. Oosting, G. Fan, J. H. Morrison and E. J. Nestler (2010): “Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens,” Nat. Neurosci., 13(9), 1137–1143.
Liu, X. S., D. L. Brutlag and J. S. Liu (2002): “An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments,” Nat. Biotechnol., 20, 835–839.
Li, W., C. Meyer and X. Liu (2005): “A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences,” Bioinformatics, 21(suppl I), 274–282. [Crossref]
Mash, D. C., J. ffrench Mullen, N. Adi, Y. Qin, A. Buck and J. Pablo (2007): “Gene expression in human hippocampus from cocaine abusers identifies genes which regulate extracellular matrix remodeling,” PLoS One, 2(11), e1187.
Mo, Q. and F. Liang (2010): “Bayesian modeling of chip-chip data through a high-orderising model,” Biometrics, 66(4), 1284–1294. doi:10.1111/j.1541-0420.2009.01379.x. [PubMed] [Crossref] [Web of Science]
Nestler, E.J. and G. K. Aghajanian (1997): “Molecular and cellular basis of addiction,” Science 278(5335), 58–63.
Pan, W. and P. A. K. Wei (2008): “A parametric joint model of DNA-protein binding, gene expression and DNA sequence data to detect target genes of a transcription factor,” Pacific Symposium on Biocomputing, NIL:465–476.
Wei, P. and W. Pan (2008): “Incorporating gene functions into regression analysis of dna-protein binding data and gene expression data to construct transcriptional networks,” IEEE/ACM Transact. Comput. Biol. Bioinformatics, 5, 401–415. [Web of Science]
Qi, Y., A. Rolfe, K. D. MacIsaac, G. K. Gerber, D. Pokholok, J. Zeitlinger, T. Dan-ford, R. D. Dowell, E. Fraenkel, T. S. Jaakkola, R. A. Young and D. K. Gifford (2006): “High-resolution computational models of genome binding events,” Nat. Biotechnol., 21, 963–970.
Qiu, J. (2006): “Epigenetics: unfinished symphony,” Nature, 441(7090), 143–145.
Ren, B., F. Robert, J. J. Wyrick, O. Aparicio, E. G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, T. L. Volkert, C. J. Wilson, S. P. Bell and R. A. Young (2000): “Genome-wide location and function of DNA binding proteins,” Science, 290(5500), 2306–2309.
Renthal, W., A. Kumar, G. Xiao, M. Wilkinson, R. H. E. Covington, I. Maze, D. Sikder, A. J. Robison, Q. LaPlant, D. M. Dietz, S. J. Russo, V. Vialou, S. Chakravarty, T. J. Kodadek, A. Stack, M. Kabbaj and E. J. Nestler (2009): “Genome-wide analysis of chromatin regulation by cocaine reveals a role for sirtuins,” Neuron, 62(3), 335–348. [PubMed] [Crossref] [Web of Science]
Song, J. S., W. E. Johnson, X. Zhu, X. Zhang, W. Li, A. K. Manrai, J. S. Liu, R. Chen and X. S. Liu (2007): “Model-based analysis of two-color arrays (ma2c),” Genome Biol., 8(8), R178. [Web of Science] [Crossref]
Song, J. S., W. E. Johnson, X. Zhu, X. Zhang, W. Li, A. K. Manrai, J. S. Liu, R. Chen and X. S. Liu (2007): “1R01 HG004069-01/HG/NHGRI NIH HHS/United States 1U01 HG004270-01/HG/NHGRI NIH HHS/United States R01 HG004069-02/HG/NHGRI NIH HHS/United States Research Support, N.I.H,” Extramural England Genome biology Genome Biol., 8(8), R178.
Taslim, C., J. Wu, P. Yan, G. Singer, J. Parvin, T. Huang, S. Lin and K. Huang (2009): “Comparative study on ChIP-seq data: normalization and binding pattern characterization,” Bioinformatics, 25(18), 2334–2340. [Web of Science] [PubMed] [Crossref]
Tsankova, N, W. Renthal, A. Kumar and E. J. Nestler (2007): “Epigenetic regulation in psychiatric disorders,” Nat. Rev. Neurosci., 8, 355–367.
Tsankova, N. M., O. Berton, W. Renthal, A. Kumar, R. L. Neve and E. J. Nestler (2006): “Sustained hippocampal chromatin regulation in a mouse model of depression and antidepressant action,” Nat. Neurosci., 9, 519–525.
Tusher, V.G., R. Tibshirani and G. Chu (2001): “Significance analysis of microarrays applied to the ionizing radiation response,” Proc. Natl. Acad. Sci. USA, 98, 5116–5121. [Crossref]
Valouev, A., D. S. Johnson, A. Sundquist, C. Medina, E. Anton, S. Batzoglou, R. M. Myers and A. Sidow (2008): “Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data,” Nat. Methods, 5, 829–834.
van den Oord, E.J., P. H. Kuo, A. M. Hartmann, B. T. Webb, H. J. Moller, J. M. Hettema, I. Giegling, J. Bukszar and D. Rujescu (2008): “Genomewide association analysis followed by a replication study implicates a novel candidate gene for neuroticism,” Arch. Gen. Psychiatry, 65, 1062–1071. [PubMed] [Web of Science]
Wang, X., M. Zang and G. Xiao (2012): “Epigenetic change detection and pattern recognition via Bayesian hierarchical hidden Markov models,” Stat. Med., doi: 10.1002/sim.5658. [Epub ahead of print]. [Web of Science] [PubMed] [Crossref]
Wemmie, J. A., M. W. Coryell, C. C. Askwith, E. Lamani, A. S. Leonard, C. D. Sigmund and M. J. Welsh (2004): “Overexpression of acid-sensing ion channel 1a in transgenic mice increases acquired fear-related behavior,” Proc. Nat. Acad. Sci. USA, 101(10), 3621–3626. doi:10.1073/pnas.0308753101. [Crossref]
Wilkinson, M. B., G. Xiao, A. Kumar, Q. LaPlant, W. Renthal, D. Sikder, T. J. Ko-dadek and E. J. Nestler (2009): “Imipramine treatment and resiliency exhibit similar chromatin regulation in the mouse nucleus accumbens in depression models,” J. Neurosci., 29(24), 7820–7832. [Crossref] [Web of Science]
Xu, H., C. L. Wei, F. Lin and W. K. Sung (2008): “An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data,” Bioinformatics, 24(20), 2344–2349. [Web of Science] [Crossref] [PubMed]
Zhang, Y., T. Liu, C. A. Meyer, J. Eeckhoute, D. S. Johnson, B. E. Bernstein, C. Nusbaum, R. M. Myers, M. Brown, W. Li and X. S. Liu (2008): “Model-based analysis of ChIP-Seq (MACS),” Genome Biol., 9, R137. [Crossref] [Web of Science]