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For: Keith JM. Segmenting Eukaryotic Genomes with the Generalized Gibbs Sampler. J Comput Biol 2006;13:1369-83. [PMID: 17037964 DOI: 10.1089/cmb.2006.13.1369] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Burks DJ, Azad RK. Mapping Strengths and Weaknesses of Different Clustering Approaches to Deciphering Bacterial Chimerism. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022;26:422-439. [PMID: 35925817 DOI: 10.1089/omi.2022.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
2
Maderazo D, Flegg JA, Algama M, Ramialison M, Keith J. Detection and identification of cis-regulatory elements using change-point and classification algorithms. BMC Genomics 2022;23:78. [PMID: 35078412 PMCID: PMC8790847 DOI: 10.1186/s12864-021-08190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022]  Open
3
Sadia F, Boyd S, Keith JM. Bayesian change-point modeling with segmented ARMA model. PLoS One 2019;13:e0208927. [PMID: 30596668 PMCID: PMC6312324 DOI: 10.1371/journal.pone.0208927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/26/2018] [Indexed: 11/18/2022]  Open
4
Sequence Segmentation with changeptGUI. Methods Mol Biol 2018;1525:293-312. [PMID: 27896726 DOI: 10.1007/978-1-4939-6622-6_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
5
Algama M, Tasker E, Williams C, Parslow AC, Bryson-Richardson RJ, Keith JM. Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach. BMC Genomics 2017;18:259. [PMID: 28347272 PMCID: PMC5369223 DOI: 10.1186/s12864-017-3645-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/18/2017] [Indexed: 11/17/2022]  Open
6
Hybrid algorithms for multiple change-point detection in biological sequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015;823:41-61. [PMID: 25381101 DOI: 10.1007/978-3-319-10984-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
7
Discovery of putative small non-coding RNAs from the obligate intracellular bacterium Wolbachia pipientis. PLoS One 2015;10:e0118595. [PMID: 25739023 PMCID: PMC4349823 DOI: 10.1371/journal.pone.0118595] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/21/2015] [Indexed: 12/18/2022]  Open
8
Algama M, Keith JM. Investigating genomic structure using changept: A Bayesian segmentation model. Comput Struct Biotechnol J 2014;10:107-15. [PMID: 25349679 PMCID: PMC4204429 DOI: 10.1016/j.csbj.2014.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
9
Algama M, Oldmeadow C, Tasker E, Mengersen K, Keith JM. Drosophila 3' UTRs are more complex than protein-coding sequences. PLoS One 2014;9:e97336. [PMID: 24824035 PMCID: PMC4019593 DOI: 10.1371/journal.pone.0097336] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 04/18/2014] [Indexed: 01/03/2023]  Open
10
Futschik A, Hotz T, Munk A, Sieling H. Multiscale DNA partitioning: statistical evidence for segments. Bioinformatics 2014;30:2255-62. [PMID: 24753487 DOI: 10.1093/bioinformatics/btu180] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
11
Azad RK, Li J. Interpreting genomic data via entropic dissection. Nucleic Acids Res 2012;41:e23. [PMID: 23036836 PMCID: PMC3592408 DOI: 10.1093/nar/gks917] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
12
Felicioli C, Marangoni R. BpMatch: an efficient algorithm for a segmental analysis of genomic sequences. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012;9:1120-1127. [PMID: 22350206 DOI: 10.1109/tcbb.2012.30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
13
Boyd SE, Nair B, Ng SW, Keith JM, Orian JM. Computational characterization of 3' splice variants in the GFAP isoform family. PLoS One 2012;7:e33565. [PMID: 22479412 PMCID: PMC3316583 DOI: 10.1371/journal.pone.0033565] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 02/16/2012] [Indexed: 12/26/2022]  Open
14
Oldmeadow C, Keith JM. Model selection in Bayesian segmentation of multiple DNA alignments. ACTA ACUST UNITED AC 2011;27:604-10. [PMID: 21208984 DOI: 10.1093/bioinformatics/btq716] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
15
Stochastic models for large interacting systems and related correlation inequalities. Proc Natl Acad Sci U S A 2010;107:16413-9. [PMID: 20826441 DOI: 10.1073/pnas.1011270107] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
16
Oldmeadow C, Mengersen K, Mattick JS, Keith JM. Multiple evolutionary rate classes in animal genome evolution. Mol Biol Evol 2009;27:942-53. [PMID: 19955480 DOI: 10.1093/molbev/msp299] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
17
Zhou Q, Wong WH. Reconstructing the energy landscape of a distribution from Monte Carlo samples. Ann Appl Stat 2008. [DOI: 10.1214/08-aoas196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
18
Keith JM, Adams P, Stephen S, Mattick JS. Delineating slowly and rapidly evolving fractions of the Drosophila genome. J Comput Biol 2008;15:407-30. [PMID: 18435570 DOI: 10.1089/cmb.2007.0173] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
19
Sequence segmentation. Methods Mol Biol 2008;452:207-29. [PMID: 18566767 DOI: 10.1007/978-1-60327-159-2_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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