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MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function.

Keegan KP, Glass EM, Meyer F.

Methods Mol Biol. 2016;1399:207-33. doi: 10.1007/978-1-4939-3369-3_13.


A RESTful API for accessing microbial community data for MG-RAST.

Wilke A, Bischof J, Harrison T, Brettin T, D'Souza M, Gerlach W, Matthews H, Paczian T, Wilkening J, Glass EM, Desai N, Meyer F.

PLoS Comput Biol. 2015 Jan 8;11(1):e1004008. doi: 10.1371/journal.pcbi.1004008. eCollection 2015 Jan.


The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome.

Handley KM, Bartels D, O'Loughlin EJ, Williams KH, Trimble WL, Skinner K, Gilbert JA, Desai N, Glass EM, Paczian T, Wilke A, Antonopoulos D, Kemner KM, Meyer F.

Environ Microbiol. 2014 Nov;16(11):3443-62. doi: 10.1111/1462-2920.12453. Epub 2014 Apr 21.


Target selection for structural genomics of infectious diseases.

Yeats C, Dessailly BH, Glass EM, Fremont DH, Orengo CA.

Methods Mol Biol. 2014;1140:35-51. doi: 10.1007/978-1-4939-0354-2_3.


MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.

Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM.

ISME J. 2014 Jan;8(1):1-3. doi: 10.1038/ismej.2013.176. Epub 2013 Oct 24. No abstract available.


A metagenomics portal for a democratized sequencing world.

Wilke A, Glass EM, Bartels D, Bischof J, Braithwaite D, D'Souza M, Gerlach W, Harrison T, Keegan K, Matthews H, Kottmann R, Paczian T, Tang W, Trimble WL, Yilmaz P, Wilkening J, Desai N, Meyer F.

Methods Enzymol. 2013;531:487-523. doi: 10.1016/B978-0-12-407863-5.00022-8.


The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools.

Wilke A, Harrison T, Wilkening J, Field D, Glass EM, Kyrpides N, Mavrommatis K, Meyer F.

BMC Bioinformatics. 2012 Jun 21;13:141. doi: 10.1186/1471-2105-13-141.


Identification of chromosomal genes in Yersinia pestis that influence type III secretion and delivery of Yops into target cells.

Houppert AS, Kwiatkowski E, Glass EM, DeBord KL, Merritt PM, Schneewind O, Marketon MM.

PLoS One. 2012;7(3):e34039. doi: 10.1371/journal.pone.0034039. Epub 2012 Mar 30.


From genomics to metagenomics.

Desai N, Antonopoulos D, Gilbert JA, Glass EM, Meyer F.

Curr Opin Biotechnol. 2012 Feb;23(1):72-6. doi: 10.1016/j.copbio.2011.12.017. Epub 2012 Jan 5. Review.


Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010.

O'Brien SL, Glass EM, Brulc JM, Gilbert JA, Antonopoulos DA, Meyer F.

Stand Genomic Sci. 2011 Nov 30;5(2):198-202. doi: 10.4056/sigs.1874546. Epub 2011 Nov 15.


Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes.

Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F.

Cold Spring Harb Protoc. 2010 Jan;2010(1):pdb.prot5368. doi: 10.1101/pdb.prot5368. No abstract available.


The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.

Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA.

BMC Bioinformatics. 2008 Sep 19;9:386. doi: 10.1186/1471-2105-9-386.


Generating a collection of insertion mutations in the Staphylococcus aureus genome using bursa aurealis.

Bae T, Glass EM, Schneewind O, Missiakas D.

Methods Mol Biol. 2008;416:103-16. doi: 10.1007/978-1-59745-321-9_7.


The RAST Server: rapid annotations using subsystems technology.

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O.

BMC Genomics. 2008 Feb 8;9:75. doi: 10.1186/1471-2164-9-75.


Identification of Francisella tularensis Himar1-based transposon mutants defective for replication in macrophages.

Maier TM, Casey MS, Becker RH, Dorsey CW, Glass EM, Maltsev N, Zahrt TC, Frank DW.

Infect Immun. 2007 Nov;75(11):5376-89. Epub 2007 Aug 6.


Sentra: a database of signal transduction proteins for comparative genome analysis.

D'Souza M, Glass EM, Syed MH, Zhang Y, Rodriguez A, Maltsev N, Galperin MY.

Nucleic Acids Res. 2007 Jan;35(Database issue):D271-3. Epub 2006 Nov 29.


Transposon mutagenesis of Bacillus anthracis strain Sterne using Bursa aurealis.

Tam C, Glass EM, Anderson DM, Missiakas D.

Plasmid. 2006 Jul;56(1):74-7. Epub 2006 Mar 13.


Knowledge-based voting algorithm for automated protein functional annotation.

Yu GX, Glass EM, Karonis NT, Maltsev N.

Proteins. 2005 Dec 1;61(4):907-17.


The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V.

Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005.


Bacillus anthracis sortase A (SrtA) anchors LPXTG motif-containing surface proteins to the cell wall envelope.

Gaspar AH, Marraffini LA, Glass EM, Debord KL, Ton-That H, Schneewind O.

J Bacteriol. 2005 Jul;187(13):4646-55.

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