Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 16

1.

Efficiently gap-filling reaction networks.

Latendresse M.

BMC Bioinformatics. 2014 Jun 28;15:225. doi: 10.1186/1471-2105-15-225.

PMID:
24972703
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24225315
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
23143106
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Regulatory network operations in the Pathway Tools software.

Paley SM, Latendresse M, Karp PD.

BMC Bioinformatics. 2012 Sep 24;13:243. doi: 10.1186/1471-2105-13-243.

PMID:
22998532
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The pathway tools pathway prediction algorithm.

Karp PD, Latendresse M, Caspi R.

Stand Genomic Sci. 2011 Dec 31;5(3):424-9. doi: 10.4056/sigs.1794338. Epub 2011 Dec 23.

PMID:
22675592
[PubMed]
Free PMC Article
6.

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.

PMID:
22262672
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Browsing metabolic and regulatory networks with BioCyc.

Latendresse M, Paley S, Karp PD.

Methods Mol Biol. 2012;804:197-216. doi: 10.1007/978-1-61779-361-5_11.

PMID:
22144155
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22102576
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Web-based metabolic network visualization with a zooming user interface.

Latendresse M, Karp PD.

BMC Bioinformatics. 2011 May 19;12:176. doi: 10.1186/1471-2105-12-176.

PMID:
21595965
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
21097882
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

An advanced web query interface for biological databases.

Latendresse M, Karp PD.

Database (Oxford). 2010 Jul 6;2010:baq006. doi: 10.1093/database/baq006.

PMID:
20624715
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants.

Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY.

Plant Physiol. 2010 Aug;153(4):1479-91. doi: 10.1104/pp.110.157396. Epub 2010 Jun 3.

PMID:
20522724
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
19955237
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
19850718
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
17965431
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
17940092
[PubMed - indexed for MEDLINE]
Free PMC Article

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Loading ...
Write to the Help Desk