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For: Nicolas P, Bize L, Muri F, Hoebeke M, Rodolphe F, Ehrlich SD, Prum B, Bessières P. Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Res 2002;30:1418-26. [PMID: 11884641 PMCID: PMC101363 DOI: 10.1093/nar/30.6.1418] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2001] [Revised: 01/24/2002] [Accepted: 01/24/2002] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Erkelens AM, van Erp B, Meijer WJJ, Dame RT. Rok from B. subtilis: Bridging genome structure and transcription regulation. Mol Microbiol 2025;123:109-123. [PMID: 38511404 PMCID: PMC11841835 DOI: 10.1111/mmi.15250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
2
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]
3
Pandey RS, Azad RK. Factors That Influence the Choice of Markov Model Order in Discriminating DNA Sequences from Different Sources. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022;26:348-355. [PMID: 35648077 DOI: 10.1089/omi.2022.0043] [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]
4
Multi-omics Approach Reveals How Yeast Extract Peptides Shape Streptococcus thermophilus Metabolism. Appl Environ Microbiol 2020;86:AEM.01446-20. [PMID: 32769193 DOI: 10.1128/aem.01446-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022]  Open
5
Lingeswaran A, Metton C, Henry C, Monnet V, Juillard V, Gardan R. Export of Rgg Quorum Sensing Peptides is Mediated by the PptAB ABC Transporter in Streptococcus Thermophilus Strain LMD-9. Genes (Basel) 2020;11:genes11091096. [PMID: 32961685 PMCID: PMC7564271 DOI: 10.3390/genes11091096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/10/2020] [Accepted: 09/17/2020] [Indexed: 12/26/2022]  Open
6
Arndt D, Marcu A, Liang Y, Wishart DS. PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes. Brief Bioinform 2020;20:1560-1567. [PMID: 29028989 DOI: 10.1093/bib/bbx121] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/31/2017] [Indexed: 11/13/2022]  Open
7
Tang K, Lu YY, Sun F. Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer. Front Microbiol 2018;9:711. [PMID: 29713314 PMCID: PMC5911508 DOI: 10.3389/fmicb.2018.00711] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/27/2018] [Indexed: 11/20/2022]  Open
8
Duchaud E, Rochat T, Habib C, Barbier P, Loux V, Guérin C, Dalsgaard I, Madsen L, Nilsen H, Sundell K, Wiklund T, Strepparava N, Wahli T, Caburlotto G, Manfrin A, Wiens GD, Fujiwara-Nagata E, Avendaño-Herrera R, Bernardet JF, Nicolas P. Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum. Front Microbiol 2018;9:138. [PMID: 29467746 PMCID: PMC5808330 DOI: 10.3389/fmicb.2018.00138] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/22/2018] [Indexed: 12/04/2022]  Open
9
Lapuyade-Lahorgue J, Xue JH, Ruan S. Segmenting Multi-Source Images Using Hidden Markov Fields With Copula-Based Multivariate Statistical Distributions. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2017;26:3187-3195. [PMID: 28333631 DOI: 10.1109/tip.2017.2685345] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
10
Jani M, Mathee K, Azad RK. Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering. Front Microbiol 2016;7:1210. [PMID: 27536294 PMCID: PMC4971588 DOI: 10.3389/fmicb.2016.01210] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/20/2016] [Indexed: 02/03/2023]  Open
11
Caprari S, Metzler S, Lengauer T, Kalinina OV. Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses. Viruses 2015;7:5388-409. [PMID: 26492264 PMCID: PMC4632390 DOI: 10.3390/v7102882] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 12/20/2022]  Open
12
Rey J, Deschavanne P, Tuffery P. BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014;2014:bau106. [PMID: 25377257 PMCID: PMC4221844 DOI: 10.1093/database/bau106] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
13
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
14
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
15
Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RAT, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 2012;335:1103-6. [PMID: 22383849 DOI: 10.1126/science.1206848] [Citation(s) in RCA: 690] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
16
Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. Appl Environ Microbiol 2011;77:7656-62. [PMID: 21926215 DOI: 10.1128/aem.05625-11] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
17
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011;39:W347-52. [PMID: 21672955 PMCID: PMC3125810 DOI: 10.1093/nar/gkr485] [Citation(s) in RCA: 1656] [Impact Index Per Article: 118.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
18
Eng C, Thibessard A, Danielsen M, Rasmussen TB, Mari JF, Leblond P. In silico prediction of horizontal gene transfer in Streptococcus thermophilus. Arch Microbiol 2011;193:287-97. [DOI: 10.1007/s00203-010-0671-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 12/20/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022]
19
Akakpo N. Estimating a discrete distributionviahistogram selection. ESAIM-PROBAB STAT 2011. [DOI: 10.1051/ps/2009007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
20
Smits WK, Grossman AD. The transcriptional regulator Rok binds A+T-rich DNA and is involved in repression of a mobile genetic element in Bacillus subtilis. PLoS Genet 2010;6:e1001207. [PMID: 21085634 PMCID: PMC2978689 DOI: 10.1371/journal.pgen.1001207] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 10/13/2010] [Indexed: 11/25/2022]  Open
21
Irnov I, Sharma CM, Vogel J, Winkler WC. Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 2010;38:6637-51. [PMID: 20525796 PMCID: PMC2965217 DOI: 10.1093/nar/gkq454] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 04/27/2010] [Accepted: 05/10/2010] [Indexed: 01/05/2023]  Open
22
Wu H, Caffo B, Jaffee HA, Irizarry RA, Feinberg AP. Redefining CpG islands using hidden Markov models. Biostatistics 2010;11:499-514. [PMID: 20212320 PMCID: PMC2883304 DOI: 10.1093/biostatistics/kxq005] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 01/14/2010] [Accepted: 01/15/2010] [Indexed: 11/13/2022]  Open
23
Mallet LV, Becq J, Deschavanne P. Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus. BMC Genomics 2010;11:171. [PMID: 20226043 PMCID: PMC2848249 DOI: 10.1186/1471-2164-11-171] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 03/12/2010] [Indexed: 12/14/2022]  Open
24
Nuel G, Regad L, Martin J, Camproux AC. Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data. Algorithms Mol Biol 2010;5:15. [PMID: 20205909 PMCID: PMC2828453 DOI: 10.1186/1748-7188-5-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 01/26/2010] [Indexed: 11/18/2022]  Open
25
Rasmussen S, Nielsen HB, Jarmer H. The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 2009;73:1043-57. [PMID: 19682248 PMCID: PMC2784878 DOI: 10.1111/j.1365-2958.2009.06830.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2009] [Indexed: 12/29/2022]
26
Eng C, Asthana C, Aigle B, Hergalant S, Mari JF, Leblond P. A New Data Mining Approach for the Detection of Bacterial Promoters Combining Stochastic and Combinatorial Methods. J Comput Biol 2009;16:1211-25. [DOI: 10.1089/cmb.2008.0122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]  Open
27
Barbe V, Cruveiller S, Kunst F, Lenoble P, Meurice G, Sekowska A, Vallenet D, Wang T, Moszer I, Médigue C, Danchin A. From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. MICROBIOLOGY (READING, ENGLAND) 2009;155:1758-1775. [PMID: 19383706 PMCID: PMC2885750 DOI: 10.1099/mic.0.027839-0] [Citation(s) in RCA: 266] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 02/25/2009] [Accepted: 02/25/2009] [Indexed: 11/18/2022]
28
Chambaz A, Matias C. Number of hidden states and memory: a joint order estimation problem for Markov chains with Markov regime. ESAIM-PROBAB STAT 2009. [DOI: 10.1051/ps:2007048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
29
Ibrahim M, Nicolas P, Bessières P, Bolotin A, Monnet V, Gardan R. A genome-wide survey of short coding sequences in streptococci. MICROBIOLOGY-SGM 2008;153:3631-3644. [PMID: 17975071 DOI: 10.1099/mic.0.2007/006205-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
30
Pieczynski W. Multisensor triplet Markov chains and theory of evidence. Int J Approx Reason 2007. [DOI: 10.1016/j.ijar.2006.05.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
31
In silico segmentations of lentivirus envelope sequences. BMC Bioinformatics 2007;8:99. [PMID: 17376229 PMCID: PMC1847453 DOI: 10.1186/1471-2105-8-99] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 03/21/2007] [Indexed: 11/20/2022]  Open
32
Thakur V, Azad RK, Ramaswamy R. Markov models of genome segmentation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007;75:011915. [PMID: 17358192 DOI: 10.1103/physreve.75.011915] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Revised: 06/19/2006] [Indexed: 05/14/2023]
33
Bryson K, Loux V, Bossy R, Nicolas P, Chaillou S, van de Guchte M, Penaud S, Maguin E, Hoebeke M, Bessières P, Gibrat JF. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res 2006;34:3533-45. [PMID: 16855290 PMCID: PMC1524909 DOI: 10.1093/nar/gkl471] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
34
Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 2006;7:142. [PMID: 16542435 PMCID: PMC1489950 DOI: 10.1186/1471-2105-7-142] [Citation(s) in RCA: 279] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 03/16/2006] [Indexed: 01/25/2023]  Open
35
Bekaert M, Richard H, Prum B, Rousset JP. Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae. Genome Res 2006;15:1411-20. [PMID: 16204194 PMCID: PMC1240084 DOI: 10.1101/gr.4258005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
36
Merkl R. A comparative categorization of protein function encoded in bacterial or archeal genomic islands. J Mol Evol 2005;62:1-14. [PMID: 16341468 DOI: 10.1007/s00239-004-0311-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Accepted: 06/14/2005] [Indexed: 01/11/2023]
37
Carbone A, Madden R. Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis. J Mol Evol 2005;61:456-69. [PMID: 16187158 DOI: 10.1007/s00239-004-0317-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2004] [Accepted: 04/20/2005] [Indexed: 11/27/2022]
38
Calteau A, Gouy M, Perrière G. Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea. J Mol Evol 2005;60:557-65. [PMID: 15983865 DOI: 10.1007/s00239-004-0094-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Accepted: 11/19/2004] [Indexed: 11/27/2022]
39
Ledent S, Robin S. Checking homogeneity of motifs' distribution in heterogenous sequences. J Comput Biol 2005;12:672-85. [PMID: 16108710 DOI: 10.1089/cmb.2005.12.672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
40
Fertil B, Massin M, Lespinats S, Devic C, Dumee P, Giron A. GENSTYLE: exploration and analysis of DNA sequences with genomic signature. Nucleic Acids Res 2005;33:W512-5. [PMID: 15980524 PMCID: PMC1160249 DOI: 10.1093/nar/gki489] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
41
Guéguen L. Sarment: Python modules for HMM analysis and partitioning of sequences. Bioinformatics 2005;21:3427-8. [PMID: 15947017 DOI: 10.1093/bioinformatics/bti533] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
42
Dufraigne C, Fertil B, Lespinats S, Giron A, Deschavanne P. Detection and characterization of horizontal transfers in prokaryotes using genomic signature. Nucleic Acids Res 2005;33:e6. [PMID: 15653627 PMCID: PMC546175 DOI: 10.1093/nar/gni004] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
43
Qiu D, Fujita K, Sakuma Y, Tanaka T, Ohashi Y, Ohshima H, Tomita M, Itaya M. Comparative analysis of physical maps of four Bacillus subtilis (natto) genomes. Appl Environ Microbiol 2004;70:6247-56. [PMID: 15466572 PMCID: PMC522138 DOI: 10.1128/aem.70.10.6247-6256.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Accepted: 06/10/2004] [Indexed: 11/20/2022]  Open
44
Speed T. Discussions on “A Bayesian Approach to DNA Sequence Segmentation”. Biometrics 2004. [DOI: 10.1111/j.0006-341x.2004.206_4.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Boys RJ, Henderson DA. A Bayesian Approach to DNA Sequence Segmentation. Biometrics 2004;60:573-81; discussion 581-8. [PMID: 15339274 DOI: 10.1111/j.0006-341x.2004.00206.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Merkl R. SIGI: score-based identification of genomic islands. BMC Bioinformatics 2004;5:22. [PMID: 15113412 PMCID: PMC394314 DOI: 10.1186/1471-2105-5-22] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Accepted: 03/03/2004] [Indexed: 01/03/2023]  Open
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Samuels DC, Boys RJ, Henderson DA, Chinnery PF. A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate. Nucleic Acids Res 2003;31:6043-52. [PMID: 14530452 PMCID: PMC219467 DOI: 10.1093/nar/gkg784] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2003] [Revised: 08/01/2003] [Accepted: 08/20/2003] [Indexed: 11/12/2022]  Open
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Sandberg R, Bränden CI, Ernberg I, Cöster J. Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content. Gene 2003;311:35-42. [PMID: 12853136 DOI: 10.1016/s0378-1119(03)00581-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Liò P. Statistical bioinformatic methods in microbial genome analysis. Bioessays 2003;25:266-73. [PMID: 12596231 DOI: 10.1002/bies.10231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Klaenhammer T, Altermann E, Arigoni F, Bolotin A, Breidt F, Broadbent J, Cano R, Chaillou S, Deutscher J, Gasson M, van de Guchte M, Guzzo J, Hartke A, Hawkins T, Hols P, Hutkins R, Kleerebezem M, Kok J, Kuipers O, Lubbers M, Maguin E, McKay L, Mills D, Nauta A, Overbeek R, Pel H, Pridmore D, Saier M, van Sinderen D, Sorokin A, Steele J, O'Sullivan D, de Vos W, Weimer B, Zagorec M, Siezen R. Discovering lactic acid bacteria by genomics. Antonie Van Leeuwenhoek 2002;82:29-58. [PMID: 12369195 DOI: 10.1007/978-94-017-2029-8_3] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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