1. Park HS, Galbadrakh B, Kim YM. Recent progresses in the linguistic modeling of biological sequences based on formal language theory. Genomics Inform 2011;9:5–11.
2. Searls DB. The language of genes. Nature 2002;420:211–217. PMID:
12432405.
3. Munch K, Krogh A. Automatic generation of gene finders for eukaryotic species. BMC Bioinformatics 2006;7:263. PMID:
16712739.
4. Durbin R, Eddy SR, Krogh A, Mitchison G. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge: Cambridge University Press, 1998.
5. Pachter L, Alexandersson M, Cawley S. Applications of generalized pair hidden Markov models to alignment and gene finding problems. J Comput Biol 2002;9:389–399. PMID:
12015888.
6. Liang KC, Wang X, Anastassiou D. Bayesian basecalling for DNA sequence analysis using hidden Markov models. IEEE/ACM Trans Comput Biol Bioinform 2007;4:430–440. PMID:
17666762.
7. Lottaz C, Iseli C, Jongeneel CV, Bucher P. Modeling sequencing errors by combining Hidden Markov models. Bioinformatics 2003;19(Suppl 2):ii103–ii112. PMID:
14534179.
8. Won KJ, Hamelryck T, Prugel-Bennett A, Krogh A. An evolutionary method for learning HMM structure: prediction of protein secondary structure. BMC Bioinformatics 2007;8:357. PMID:
17888163.
9. Zhang S, Borovok I, Aharonowitz Y, Sharan R, Bafna V. A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. Bioinformatics 2006;22:e557–e565. PMID:
16873520.
10. Yoon BJ, Vaidyanathan PP. Structural alignment of RNAs using profile-csHMMs and its application to RNA homology search: overview and new results. IEEE Trans Automat Contr 2008;53:10–25.
11. Harmanci AO, Sharma G, Mathews DH. Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinformatics 2007;8:130. PMID:
17445273.
12. Weinberg Z, Ruzzo WL. Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics 2006;22:35–39. PMID:
16267089.
13. Shen L, Waterland RA. Methods of DNA methylation analysis. Curr Opin Clin Nutr Metab Care 2007;10:576–581. PMID:
17693740.
14. Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T,
et al. Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol 2013;9:e1003326. PMID:
24244136.
15. ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004;306:636–640. PMID:
15499007.
17. Li W, Meyer CA, Liu XS. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics 2005;21(Suppl 1):i274–i282. PMID:
15961467.
18. Xu H, Wei CL, Lin F, Sung WK. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics 2008;24:2344–2349. PMID:
18667444.
19. Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 2010;28:817–825. PMID:
20657582.
20. Lieberfarb ME, Lin M, Lechpammer M, Li C, Tanenbaum DM, Febbo PG,
et al. Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP. Cancer Res 2003;63:4781–4785. PMID:
12941794.
21. Baum LE, Petrie T, Soules G, Weiss N. A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann Math Stat 1970;41:164–171.
22. Ji H, Wong WH. TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics 2005;21:3629–3636. PMID:
16046496.
23. Martin-Magniette ML, Mary-Huard T, Bérard C, Robin S. ChIPmix: mixture model of regressions for two-color ChIP-chip analysis. Bioinformatics 2008;24:i181–i186. PMID:
18689822.
24. Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M,
et al. Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics 2010;26:1000–1006. PMID:
20208068.
25. Moghaddam AM, Roudier F, Seifert M, Bérard C, Magniette ML, Ashtiyani RK,
et al. Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids. Plant J 2011;67:691–700. PMID:
21554454.
26. Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V. MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinformatics 2012;28:2930–2939. PMID:
22989518.
27. Arand J, Spieler D, Karius T, Branco MR, Meilinger D, Meissner A,
et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet 2012;8:e1002750. PMID:
22761581.
28. Jaschek R, Tanay A. Spatial clustering of multivariate genomic and epigenomic information. Res Comput Mol Biol 2009;5541:170–183.
29. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB,
et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011;473:43–49. PMID:
21441907.