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1:

Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach.

Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D.

Genome Biol. 2003;4(9):R59. Epub 2003 Aug 29.

PMID: 12952538 [PubMed - indexed for MEDLINE]

2:

Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps.

Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D.

Nucleic Acids Res. 2003 Dec 15;31(24):7099-109.

PMID: 14654685 [PubMed - indexed for MEDLINE]

3:

Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis.

Rachman H, Strong M, Ulrichs T, Grode L, Schuchhardt J, Mollenkopf H, Kosmiadi GA, Eisenberg D, Kaufmann SH.

Infect Immun. 2006 Feb;74(2):1233-42.

PMID: 16428773 [PubMed - indexed for MEDLINE]

4:

Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context.

Moreno-Hagelsieb G, Collado-Vides J.

In Silico Biol. 2002;2(2):87-95.

PMID: 12066843 [PubMed - indexed for MEDLINE]

5:

Detection of operons.

Yan Y, Moult J.

Proteins. 2006 Aug 15;64(3):615-28.

PMID: 16755590 [PubMed - indexed for MEDLINE]

6:

Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.

Riley R, Pellegrini M, Eisenberg D.

PLoS Comput Biol. 2008 Sep 12;4(9):e1000174.

PMID: 18787688 [PubMed - indexed for MEDLINE]

7:

Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv.

Camus JC, Pryor MJ, Médigue C, Cole ST.

Microbiology. 2002 Oct;148(Pt 10):2967-73.

PMID: 12368430 [PubMed - indexed for MEDLINE]

8:

Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping.

Fujibuchi W, Ogata H, Matsuda H, Kanehisa M.

Nucleic Acids Res. 2000 Oct 15;28(20):4029-36.

PMID: 11024184 [PubMed - indexed for MEDLINE]

9:

Comparison of predicted and observed properties of proteins encoded in the genome of Mycobacterium tuberculosis H37Rv.

Urquhart BL, Cordwell SJ, Humphery-Smith I.

Biochem Biophys Res Commun. 1998 Dec 9;253(1):70-9.

PMID: 9875222 [PubMed - indexed for MEDLINE]

10:

The minimal genome concept.

Mushegian A.

Curr Opin Genet Dev. 1999 Dec;9(6):709-14. Review.

PMID: 10607608 [PubMed - indexed for MEDLINE]

11:

Macro-array and bioinformatic analyses reveal mycobacterial 'core' genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex.

Marmiesse M, Brodin P, Buchrieser C, Gutierrez C, Simoes N, Vincent V, Glaser P, Cole ST, Brosch R.

Microbiology. 2004 Feb;150(Pt 2):483-96.

PMID: 14766927 [PubMed - indexed for MEDLINE]

12:

Analysis of the proteome of Mycobacterium tuberculosis in silico.

Tekaia F, Gordon SV, Garnier T, Brosch R, Barrell BG, Cole ST.

Tuber Lung Dis. 1999;79(6):329-42.

PMID: 10694977 [PubMed - indexed for MEDLINE]

14:

Deciphering the genes involved in pathogenesis of Mycobacterium tuberculosis.

Singh R, Singh A, Tyagi AK.

Tuberculosis (Edinb). 2005 Sep-Nov;85(5-6):325-35. Epub 2005 Oct 25.

PMID: 16256440 [PubMed - indexed for MEDLINE]

15:

Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis.

Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, Eisen JA, Fraser CM, Fleischmann RD.

J Bacteriol. 2003 Jun;185(11):3392-9.

PMID: 12754238 [PubMed - indexed for MEDLINE]

17:

Computational prediction of operons in Synechococcus sp. WH8102.

Chen X, Su Z, Xu Y, Jiang T.

Genome Inform. 2004;15(2):211-22.

PMID: 15706507 [PubMed - indexed for MEDLINE]

18:

Prediction of operons in microbial genomes.

Ermolaeva MD, White O, Salzberg SL.

Nucleic Acids Res. 2001 Mar 1;29(5):1216-21.

PMID: 11222772 [PubMed - indexed for MEDLINE]

19:

EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance.

Larsen TS, Krogh A.

BMC Bioinformatics. 2003 Jun 3;4:21. Epub 2003 Jun 3.

PMID: 12783628 [PubMed - indexed for MEDLINE]

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