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Items: 28

1.

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.

Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. No abstract available.

2.

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.

PMID:
26791506
3.

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.

4.

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.

PMID:
24628880
5.

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.

PMID:
24590707
6.

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.

7.

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.

PMID:
24060134
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.

9.

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.

10.

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.

PMID:
22227326
11.

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.

12.

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.

PMID:
20150127
13.

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.

14.

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.

PMID:
18392963
15.

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.

16.

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.

17.

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.

18.

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.

PMID:
16530833
19.

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.

PMID:
16252283
20.

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.

21.

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.

22.

Molecular mechanisms involved in robustness of yeast central metabolism against null mutations.

Maltsev N, Glass EM, Ovchinnikova G, Gu Z.

J Biochem. 2005 Feb;137(2):177-87.

PMID:
15749832
23.

Staphylococcus aureus virulence genes identified by bursa aurealis mutagenesis and nematode killing.

Bae T, Banger AK, Wallace A, Glass EM, Aslund F, Schneewind O, Missiakas DM.

Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12312-7. Epub 2004 Aug 10.

24.

Transitional cell hyperplasia in the bladders of dogs fed DL-tryptophan.

Radomski JL, Glass EM, Deichmann WB.

Cancer Res. 1971 Nov;31(11):1690-4. No abstract available.

25.

Carcinogenicity testing of N-hydroxy and other oxidation and decomposition products of 1- and 2-naphthylamine.

Radomski JL, Brill E, Deichmann WB, Glass EM.

Cancer Res. 1971 Oct;31(10):1461-7. No abstract available.

26.

Induction of bladder tumors and other malignancies in rats with 2-methoxy-3-aminodibenzofuran.

Radomski JL BRILL E, Glass EM.

J Natl Cancer Inst. 1967 Dec;39(6):1069-80. No abstract available.

PMID:
6079861
27.

[Synergism between orally active carcinogens. IV. Results of simultaneous feeding of 4 carcinogens in rats].

Deichmann WB, Keplinger ML, Glass EM.

Naunyn Schmiedebergs Arch Exp Pathol Pharmakol. 1967;257(1):12. German. No abstract available.

PMID:
4231827
28.

Synergism among oral carcinogens. I. Results of the simultaneous feeding of four tumorigens to rats.

Radomski JL, Deichmann WB, MacDonald WE, Glass EM.

Toxicol Appl Pharmacol. 1965 Sep;7(5):652-6. No abstract available.

PMID:
5866802

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