13.07.2015 Views

BigFoot: Bayesian Alignment and Phylogenetic Footprinting with ...

BigFoot: Bayesian Alignment and Phylogenetic Footprinting with ...

BigFoot: Bayesian Alignment and Phylogenetic Footprinting with ...

SHOW MORE
SHOW LESS

Create successful ePaper yourself

Turn your PDF publications into a flip-book with our unique Google optimized e-Paper software.

22. Durbin R, et al.: Biological sequence analysis. Cambridge University Press New York 1998.23. Eddy S: A model of the statistical power of comparative genome sequence analysis. PLoS Biol 2005,3:e10.24. Karolchik D, Kuhn R, Baertsch R, Barber G, Clawson H, Diekhans M, Giardine B, Harte R, Hinrichs A, Hsu F,et al.: The UCSC Genome Browser Database: 2008 update. Nucleic Acids Research 2008, 36(Databaseissue):D773.25. Metropolis N, Rosenbluth A, Rosenbluth M, Teller A, Teller E: Equation of State Calculations by FastComputing Machines. The Journal of Chemical Physics 1953, 21(6):1087.26. Hastings W: Monte Carlo simulation methods using Markov chains <strong>and</strong> their applications. Biometrika1970, 57:97–109.27. Holmes I, Bruno W: Evolutionary HMMs: a <strong>Bayesian</strong> approach to multiple alignment. Bioinformatics2001, 17(9):803–820.28. Novak A, Miklos I, Lyngso R, Hein J: StatAlign: An Extendable Software Package for Joint <strong>Bayesian</strong>Estimation of <strong>Alignment</strong>s <strong>and</strong> Evolutionary Trees. Bioinformatics 2008, :btn457, [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn457v1].29. Holmes I: Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics 2003,19(90001):147–157.30. Bradley R, Holmes I: Transducers: An Emerging Probabilistic Framework for Modeling Indels onTrees. Bioinformatics 2007.31. Miklós I, Novák Á, Dombai B, Hein J: How reliably can we predict the reliability of protein structurepredictions? BMC Bioinformatics 2008, 9:137.32. Holmes I, Durbin R: Dynamic programming alignment accuracy. Proceedings of the second annual internationalconference on Computational molecular biology 1998, :102–108.33. Ludwig M: Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governingconservation <strong>and</strong> change. Development 1998, 125(5):949–958.34. Gallo S, Li L, Hu Z, Halfon M: REDfly: a Regulatory Element Database for Drosophila. Bioinformatics2006, 22(3):381–383.35. Bergman C, Carlson J, Celniker S: Drosophila DNase I footprint database: a systematic genome annotationof transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics2005, 21(8):1747–1749.36. Stanojevic D, Small S, Levine M: Regulation of a segmentation stripe by overlapping activators <strong>and</strong>repressors in the Drosophila embryo. Science 1991, 254(5036):1385–1387.37. Kreitman M, Ludwig M: Tempo <strong>and</strong> mode of even-skipped stripe 2 enhancer evolution in Drosophila.Seminars in Cell <strong>and</strong> Developmental Biology 1996, 7(4):583–592.38. Drosophila 12 Genomes Consortium: Evolution of genes <strong>and</strong> genomes on the Drosophila phylogeny.Nature 2007, 450:203–218.39. Dewey C, Huggins P, Woods K, Sturmfels B, Pachter L: Parametric alignment of Drosophila genomes.PLoS Computational Biology 2006, 2(6):e73.40. Hughes J, Cheng J, Ventress N, Prabhakar S, Clark K, Anguita E, De Gobbi M, de Jong P, Rubin E, HiggsD: Annotation of cis-regulatory elements by identification, subclassification, <strong>and</strong> functional assessmentof multispecies conserved sequences. Proceedings of the National Academy of Sciences 2005,102(28):9830–9835.41. Onodera K, Takahashi S, Nishimura S, Ohta J, Motohashi H, Yomogida K, Hayashi N, Engel J, YamamotoM: GATA-1 transcription is controlled by distinct regulatory mechanisms during primitive <strong>and</strong>definitive erythropoiesis. Proceedings of the National Academy of Sciences 1997, 94(9):4487–4492.42. Miller W, Rosenbloom K, Hardison R, Hou M, Taylor J, Raney B, Burhans R, King D, Baertsch R, BlankenbergD, et al.: 28-Way vertebrate alignment <strong>and</strong> conservation track in the UCSC Genome Browser.Genome Research 2007, 17(12):1797.15

Hooray! Your file is uploaded and ready to be published.

Saved successfully!

Ooh no, something went wrong!