Gibbs sampling is a form of Markov chain Monte Carlo (MCMC) sampling. MCMC has opened up the power of Bayesian statistics and thus has become very popular in the field of statistics; it is particularly applicable to genomics applications.
Gibbs Sampling and Bayesian Inference
CE Lawrence, Wadsworth Center, Albany, New York, USA
Published online: January 2006
DOI: 10.1038/npg.els.0005848
| References | |
| Churchill GA and Lazareva B (1999) Bayesian restoration of a hidden Markov chain with applications to DNA sequencing. Journal of Computational Biology 6: 261–277. | |
| Fickett JW (1996) Quantitative discrimination of MEF2 sites. Molecular and Cellular Biology 16: 437–441. | |
| Lawrence CE, Altschul S, Boguski M, et al. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262: 208–214. | |
| Lawrence CE and Reilly AA (1990) An EM algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins: Structure, Function and Genetics 7: 41–51. | |
| Lawrence CE and Reilly AA (1996) Likelihood inference for permuted data with application to gene regulation. Journal of the American Statistical Association 91(433): 76–85. | |
| Liu J (1994) The collapse gibbs sampler in bayesian computations with applications to a gene regulation problem. Journal of the American Statistical Association 89(427): 958. | |
| Liu J and Lawrence CE (1999) Bayesian inference on biopolymer models. Bioinformatics 15: 38–52. | |
| Liu J, Neuwald A and Lawrence CE (1995) Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. Journal of the American Statistical Association 90(432): 1156–1170. | |
| Liu J, Neuwald A and Lawrence CE (1999) Markovian structures in biological sequence alignments. Journal of the American Statistical Association 94: 1–15. | |
| McCue LA, Thompson W, Carmack CS, et al. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Research 29: 774–782. | |
| Neuwald AF, Liu J and Lawrence CE (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Science 4: 1618–1632. | |
| Neuwald AF, Liu J, Lipman D and Lawrence CE (1997) Extracting protein alignment models from the sequence database. Nucleic Acids Research 25: 1665–1677. | |
| Roth FP, Hughes JD, Estep PW and Church GM (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology 16: 939–945. | |
| Wasserman WW, Palumbo M, Thompson W, Fickett JW and Lawrence CE (2000) Human–mouse genome comparison to locate human regulatory sites. Nature Genetics 26: 225–228. | |
| Web Links | |
| ePath Web servers and software for Gibbs sampling algorithms of this type are available from the following websites www.wadsworth.org/res&res/bioinfo | |
| ePath ftp.ncbi.nlm.nih.gov/pub/neuwald/ | |
| ePath atlas.med.harvard.edu | |
| ePath copan.unam.mx/~jvanheld/rsa-tools/boiweb.pasteur.fr/ | |
| ePath seqannal/interfaces/gibbs.html | |
