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Items: 1 to 20 of 27

1.

Representation and inference of cellular architecture for metabolic reconstruction and modeling.

Paley S, Krummenacker M, Karp PD.

Bioinformatics. 2016 Apr 1;32(7):1074-9. doi: 10.1093/bioinformatics/btv702. Epub 2015 Dec 1.

PMID:
26628588
2.

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

Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Karp PD.

Nucleic Acids Res. 2016 Jan 4;44(D1):D471-80. doi: 10.1093/nar/gkv1164. Epub 2015 Nov 2.

3.

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R.

Brief Bioinform. 2015 Oct 10. pii: bbv079. [Epub ahead of print]

PMID:
26454094
4.

Computational Metabolomics Operations at BioCyc.org.

Karp PD, Billington R, Holland TA, Kothari A, Krummenacker M, Weaver D, Latendresse M, Paley S.

Metabolites. 2015 May 22;5(2):291-310. doi: 10.3390/metabo5020291.

5.

The EcoCyc Database.

Karp PD, Weaver D, Paley S, Fulcher C, Kubo A, Kothari A, Krummenacker M, Subhraveti P, Weerasinghe D, Gama-Castro S, Huerta AM, Muñiz-Rascado L, Bonavides-Martinez C, Weiss V, Peralta-Gil M, Santos-Zavaleta A, Schröder I, Mackie A, Gunsalus R, Collado-Vides J, Keseler IM, Paulsen I.

EcoSal Plus. 2014 May;6(1). doi: 10.1128/ecosalplus.ESP-0009-2013.

6.

Optimal metabolic route search based on atom mappings.

Latendresse M, Krummenacker M, Karp PD.

Bioinformatics. 2014 Jul 15;30(14):2043-50. doi: 10.1093/bioinformatics/btu150. Epub 2014 Mar 17.

7.

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

Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD.

Nucleic Acids Res. 2014 Jan;42(Database issue):D459-71. doi: 10.1093/nar/gkt1103. Epub 2013 Nov 12.

8.

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.

9.

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.

10.

Construction and completion of flux balance models from pathway databases.

Latendresse M, Krummenacker M, Trupp M, Karp PD.

Bioinformatics. 2012 Feb 1;28(3):388-96. doi: 10.1093/bioinformatics/btr681. Epub 2012 Jan 18.

11.

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.

12.

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.

13.

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.

Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R.

Brief Bioinform. 2010 Jan;11(1):40-79. doi: 10.1093/bib/bbp043. Epub 2009 Dec 2.

14.

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.

15.

What we can learn about Escherichia coli through application of Gene Ontology.

Hu JC, Karp PD, Keseler IM, Krummenacker M, Siegele DA.

Trends Microbiol. 2009 Jul;17(7):269-78. doi: 10.1016/j.tim.2009.04.004. Epub 2009 Jul 1. Review.

16.

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.

17.

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.

18.

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.

19.

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.

Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ.

Mol Syst Biol. 2007;3:121. Epub 2007 Jun 26.

20.

MetaCyc: a multiorganism database of metabolic pathways and enzymes.

Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, Karp PD.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D511-6.

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