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Items: 16

1.

Finding sequences for over 270 orphan enzymes.

Shearer AG, Altman T, Rhee CD.

PLoS One. 2014 May 14;9(5):e97250. doi: 10.1371/journal.pone.0097250. eCollection 2014.

2.

Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

Ramkissoon KR, Miller JK, Ojha S, Watson DS, Bomar MG, Galande AK, Shearer AG.

PLoS One. 2013 Dec 30;8(12):e84508. doi: 10.1371/journal.pone.0084508. eCollection 2013.

3.

Addition of Escherichia coli K-12 growth observation and gene essentiality data to the EcoCyc database.

Mackie A, Paley S, Keseler IM, Shearer A, Paulsen IT, Karp PD.

J Bacteriol. 2014 Mar;196(5):982-8. doi: 10.1128/JB.01209-13. Epub 2013 Dec 20.

4.

Computing minimal nutrient sets from metabolic networks via linear constraint solving.

Eker S, Krummenacker M, Shearer AG, Tiwari A, Keseler IM, Talcott C, Karp PD.

BMC Bioinformatics. 2013 Mar 27;14:114. doi: 10.1186/1471-2105-14-114.

5.

EcoCyc: fusing model organism databases with systems biology.

Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD.

Nucleic Acids Res. 2013 Jan;41(Database issue):D605-12. doi: 10.1093/nar/gks1027. Epub 2012 Nov 9.

6.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD.

Nucleic Acids Res. 2012 Jan;40(Database issue):D742-53. doi: 10.1093/nar/gkr1014. Epub 2011 Nov 18.

7.

Discovering novel subsystems using comparative genomics.

Ferrer L, Shearer AG, Karp PD.

Bioinformatics. 2011 Sep 15;27(18):2478-85. doi: 10.1093/bioinformatics/btr428. Epub 2011 Jul 19.

8.

EcoCyc: a comprehensive database of Escherichia coli biology.

Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD.

Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21.

9.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Paley S, Popescu L, Pujar A, Shearer AG, Zhang P, Karp PD.

Nucleic Acids Res. 2010 Jan;38(Database issue):D473-9. doi: 10.1093/nar/gkp875. Epub 2009 Oct 22.

10.

EcoCyc: a comprehensive view of Escherichia coli biology.

Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD.

Nucleic Acids Res. 2009 Jan;37(Database issue):D464-70. doi: 10.1093/nar/gkn751. Epub 2008 Oct 30.

11.

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD.

Nucleic Acids Res. 2008 Jan;36(Database issue):D623-31. Epub 2007 Oct 27.

12.

Multidimensional annotation of the Escherichia coli K-12 genome.

Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spínola MI, Bonavides-Martinez C, Ingraham J.

Nucleic Acids Res. 2007;35(22):7577-90. Epub 2007 Oct 16.

13.

INSIG: a broadly conserved transmembrane chaperone for sterol-sensing domain proteins.

Flury I, Garza R, Shearer A, Rosen J, Cronin S, Hampton RY.

EMBO J. 2005 Nov 16;24(22):3917-26. Epub 2005 Nov 3.

14.

Lipid-mediated, reversible misfolding of a sterol-sensing domain protein.

Shearer AG, Hampton RY.

EMBO J. 2005 Jan 12;24(1):149-59. Epub 2005 Jan 6.

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