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Items: 17

1.

Genomic insights into bifidobacteria.

Lee JH, O'Sullivan DJ.

Microbiol Mol Biol Rev. 2010 Sep;74(3):378-416. doi: 10.1128/MMBR.00004-10. Review.

2.

Selection of bifidobacteria based on adhesion and anti-inflammatory capacity in vitro for amelioration of murine colitis.

Preising J, Philippe D, Gleinser M, Wei H, Blum S, Eikmanns BJ, Niess JH, Riedel CU.

Appl Environ Microbiol. 2010 May;76(9):3048-51. doi: 10.1128/AEM.03127-09. Epub 2010 Mar 12.

3.

Prodigal: prokaryotic gene recognition and translation initiation site identification.

Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ.

BMC Bioinformatics. 2010 Mar 8;11:119. doi: 10.1186/1471-2105-11-119.

4.

The Pfam protein families database.

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. doi: 10.1093/nar/gkp985. Epub 2009 Nov 17.

5.

Frameshift detection in prokaryotic genomic sequences.

Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M.

Int J Bioinform Res Appl. 2009;5(4):458-77.

PMID:
19640832
6.

Genome-scale analyses of health-promoting bacteria: probiogenomics.

Ventura M, O'Flaherty S, Claesson MJ, Turroni F, Klaenhammer TR, van Sinderen D, O'Toole PW.

Nat Rev Microbiol. 2009 Jan;7(1):61-71. doi: 10.1038/nrmicro2047. Epub 2008 Nov 24. Review.

PMID:
19029955
7.

InterPro: the integrative protein signature database.

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.

Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5. doi: 10.1093/nar/gkn785. Epub 2008 Oct 21.

8.

KEGG for linking genomes to life and the environment.

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y.

Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4. Epub 2007 Dec 12.

9.

Anti-inflammatory effects of bifidobacteria by inhibition of LPS-induced NF-kappaB activation.

Riedel CU, Foata F, Philippe D, Adolfsson O, Eikmanns BJ, Blum S.

World J Gastroenterol. 2006 Jun 21;12(23):3729-35.

10.

Interaction of bifidobacteria with Caco-2 cells-adhesion and impact on expression profiles.

Riedel CU, Foata F, Goldstein DR, Blum S, Eikmanns BJ.

Int J Food Microbiol. 2006 Jul 1;110(1):62-8. Epub 2006 May 19.

PMID:
16713644
11.

Getting better with bifidobacteria.

Leahy SC, Higgins DG, Fitzgerald GF, van Sinderen D.

J Appl Microbiol. 2005;98(6):1303-15. Review. No abstract available.

12.

The TIGRFAMs database of protein families.

Haft DH, Selengut JD, White O.

Nucleic Acids Res. 2003 Jan 1;31(1):371-3.

13.

Artemis: sequence visualization and annotation.

Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B.

Bioinformatics. 2000 Oct;16(10):944-5.

PMID:
11120685
14.

The COG database: a tool for genome-scale analysis of protein functions and evolution.

Tatusov RL, Galperin MY, Natale DA, Koonin EV.

Nucleic Acids Res. 2000 Jan 1;28(1):33-6.

15.

The Staden package, 1998.

Staden R, Beal KF, Bonfield JK.

Methods Mol Biol. 2000;132:115-30. No abstract available.

PMID:
10547834
16.
17.

Basic local alignment search tool.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ.

J Mol Biol. 1990 Oct 5;215(3):403-10.

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