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Items: 1 to 20 of 113

1.

The landscape of microbial phenotypic traits and associated genes.

Brbić M, Piškorec M, Vidulin V, Kriško A, Šmuc T, Supek F.

Nucleic Acids Res. 2016 Dec 1;44(21):10074-10090. Epub 2016 Oct 24.

2.

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.

Vallenet D, Calteau A, Cruveiller S, Gachet M, Lajus A, Josso A, Mercier J, Renaux A, Rollin J, Rouy Z, Roche D, Scarpelli C, Médigue C.

Nucleic Acids Res. 2017 Jan 4;45(D1):D517-D528. doi: 10.1093/nar/gkw1101. Epub 2016 Nov 29.

3.

Characterization of Outer Membrane Proteome of Akkermansia muciniphila Reveals Sets of Novel Proteins Exposed to the Human Intestine.

Ottman N, Huuskonen L, Reunanen J, Boeren S, Klievink J, Smidt H, Belzer C, de Vos WM.

Front Microbiol. 2016 Jul 26;7:1157. doi: 10.3389/fmicb.2016.01157. eCollection 2016.

4.

Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem.

Asplund-Samuelsson J, Sundh J, Dupont CL, Allen AE, McCrow JP, Celepli NA, Bergman B, Ininbergs K, Ekman M.

Front Microbiol. 2016 Jul 6;7:1043. doi: 10.3389/fmicb.2016.01043. eCollection 2016.

5.

The Ensembl gene annotation system.

Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, Nag R, Ruffier M, Schuster M, Tang YA, Vogel JH, White S, Zadissa A, Flicek P, Searle SM.

Database (Oxford). 2016 Jun 23;2016. pii: baw093. doi: 10.1093/database/baw093. Print 2016.

6.

Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system.

Chen IM, Markowitz VM, Palaniappan K, Szeto E, Chu K, Huang J, Ratner A, Pillay M, Hadjithomas M, Huntemann M, Mikhailova N, Ovchinnikova G, Ivanova NN, Kyrpides NC.

BMC Genomics. 2016 Apr 26;17:307. doi: 10.1186/s12864-016-2629-y.

7.

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Palaniappan K, Szeto E, Pillay M, Chen IM, Pati A, Nielsen T, Markowitz VM, Kyrpides NC.

Stand Genomic Sci. 2015 Oct 26;10:86. doi: 10.1186/s40793-015-0077-y. eCollection 2015. Erratum in: Stand Genomic Sci. 2016;11:27.

8.

Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology.

Ufarté L, Potocki-Veronese G, Laville É.

Front Microbiol. 2015 Jun 5;6:563. doi: 10.3389/fmicb.2015.00563. eCollection 2015. Review.

9.

Label-free Quantitative Proteomics Reveals a Role for the Mycobacterium tuberculosis SecA2 Pathway in Exporting Solute Binding Proteins and Mce Transporters to the Cell Wall.

Feltcher ME, Gunawardena HP, Zulauf KE, Malik S, Griffin JE, Sassetti CM, Chen X, Braunstein M.

Mol Cell Proteomics. 2015 Jun;14(6):1501-16. doi: 10.1074/mcp.M114.044685. Epub 2015 Mar 26.

10.

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

Bertelli C, Aeby S, Chassot B, Clulow J, Hilfiker O, Rappo S, Ritzmann S, Schumacher P, Terrettaz C, Benaglio P, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, van der Meer JR, Greub G.

Front Microbiol. 2015 Feb 19;6:101. doi: 10.3389/fmicb.2015.00101. eCollection 2015.

11.

New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”.

Lang K, Schuldes J, Klingl A, Poehlein A, Daniel R, Brunea A.

Appl Environ Microbiol. 2015 Feb;81(4):1338-52.

12.

Expanded microbial genome coverage and improved protein family annotation in the COG database.

Galperin MY, Makarova KS, Wolf YI, Koonin EV.

Nucleic Acids Res. 2015 Jan;43(Database issue):D261-9. doi: 10.1093/nar/gku1223. Epub 2014 Nov 26.

13.

Insect gut microbiome - An unexploited reserve for biotechnological application.

Krishnan M, Bharathiraja C, Pandiarajan J, Prasanna VA, Rajendhran J, Gunasekaran P.

Asian Pac J Trop Biomed. 2014 May;4(Suppl 1):S16-21. doi: 10.12980/APJTB.4.2014C95. Review.

14.

Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow.

Bachmann NL, Petty NK, Ben Zakour NL, Szubert JM, Savill J, Beatson SA.

BMC Genomics. 2014 May 21;15:389. doi: 10.1186/1471-2164-15-389.

15.

The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments.

Xu F, Jerlström-Hultqvist J, Einarsson E, Astvaldsson A, Svärd SG, Andersson JO.

PLoS Genet. 2014 Feb 6;10(2):e1004053. doi: 10.1371/journal.pgen.1004053. eCollection 2014 Feb.

16.

New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis.

Wright MS, Haft DH, Harkins DM, Perez F, Hujer KM, Bajaksouzian S, Benard MF, Jacobs MR, Bonomo RA, Adams MD.

MBio. 2014 Jan 21;5(1):e00963-13. doi: 10.1128/mBio.00963-13. Erratum in: MBio. 2015;6(3):e00585.

17.

Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation.

Olson AB, Kent H, Sibley CD, Grinwis ME, Mabon P, Ouellette C, Tyson S, Graham M, Tyler SD, Van Domselaar G, Surette MG, Corbett CR.

BMC Genomics. 2013 Dec 17;14:895. doi: 10.1186/1471-2164-14-895.

18.

IMG 4 version of the integrated microbial genomes comparative analysis system.

Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2014 Jan;42(Database issue):D560-7. doi: 10.1093/nar/gkt963. Epub 2013 Oct 27.

19.

Quantification of endospore-forming firmicutes by quantitative PCR with the functional gene spo0A.

Bueche M, Wunderlin T, Roussel-Delif L, Junier T, Sauvain L, Jeanneret N, Junier P.

Appl Environ Microbiol. 2013 Sep;79(17):5302-12. doi: 10.1128/AEM.01376-13. Epub 2013 Jun 28.

20.

Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments.

Klatt CG, Inskeep WP, Herrgard MJ, Jay ZJ, Rusch DB, Tringe SG, Niki Parenteau M, Ward DM, Boomer SM, Bryant DA, Miller SR.

Front Microbiol. 2013 Jun 3;4:106. doi: 10.3389/fmicb.2013.00106. eCollection 2013.

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