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Results: 1 to 20 of 96

1.

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.

Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B.

Bioinformatics. 2015 Feb 15;31(4):616-7. doi: 10.1093/bioinformatics/btv019. Epub 2015 Feb 2.

PMID:
25644272
2.

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;2014. doi: 10.1128/ecosalplus.ESP-0009-2013.

3.

Metabolic pathways for the whole community.

Hanson NW, Konwar KM, Hawley AK, Altman T, Karp PD, Hallam SJ.

BMC Genomics. 2014 Jul 22;15:619. doi: 10.1186/1471-2164-15-619.

4.

A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database.

Weaver DS, Keseler IM, Mackie A, Paulsen IT, Karp PD.

BMC Syst Biol. 2014 Jun 30;8:79. doi: 10.1186/1752-0509-8-79.

5.

Curation accuracy of model organism databases.

Keseler IM, Skrzypek M, Weerasinghe D, Chen AY, Fulcher C, Li GW, Lemmer KC, Mladinich KM, Chow ED, Sherlock G, Karp PD.

Database (Oxford). 2014 Jun 12;2014. pii: bau058. doi: 10.1093/database/bau058. Print 2014.

6.

A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs.

Dingerdissen H, Weaver DS, Karp PD, Pan Y, Simonyan V, Mazumder R.

Biol Direct. 2014 Jun 3;9:9. doi: 10.1186/1745-6150-9-9.

7.

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.

PMID:
24642060
8.

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.

9.

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

Hu JC, Sherlock G, Siegele DA, Aleksander SA, Ball CA, Demeter J, Gouni S, Holland TA, Karp PD, Lewis JE, Liles NM, McIntosh BK, Mi H, Muruganujan A, Wymore F, Thomas PD, Altman T.

Nucleic Acids Res. 2014 Jan;42(Database issue):D677-84. doi: 10.1093/nar/gkt1203. Epub 2013 Nov 26. Erratum in: Nucleic Acids Res. 2014 Oct 29;42(19):12330.

10.

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.

11.

Dead end metabolites--defining the known unknowns of the E. coli metabolic network.

Mackie A, Keseler IM, Nolan L, Karp PD, Paulsen IT.

PLoS One. 2013 Sep 23;8(9):e75210. doi: 10.1371/journal.pone.0075210. eCollection 2013.

12.

Groups: knowledge spreadsheets for symbolic biocomputing.

Travers M, Paley SM, Shrager J, Holland TA, Karp PD.

Database (Oxford). 2013 Sep 14;2013:bat061. doi: 10.1093/database/bat061. Print 2013.

13.

The challenge of constructing, classifying, and representing metabolic pathways.

Caspi R, Dreher K, Karp PD.

FEMS Microbiol Lett. 2013 Aug;345(2):85-93. doi: 10.1111/1574-6968.12194. Epub 2013 Jun 27. Review.

14.

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.

15.

A systematic comparison of the MetaCyc and KEGG pathway databases.

Altman T, Travers M, Kothari A, Caspi R, Karp PD.

BMC Bioinformatics. 2013 Mar 27;14:112. doi: 10.1186/1471-2105-14-112.

16.

Data mining in the MetaCyc family of pathway databases.

Karp PD, Paley S, Altman T.

Methods Mol Biol. 2013;939:183-200. doi: 10.1007/978-1-62703-107-3_12.

17.

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.

18.

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.

19.

Accurate atom-mapping computation for biochemical reactions.

Latendresse M, Malerich JP, Travers M, Karp PD.

J Chem Inf Model. 2012 Nov 26;52(11):2970-82. doi: 10.1021/ci3002217. Epub 2012 Oct 15.

PMID:
22963657
20.

Metabolomics reveals amino acids contribute to variation in response to simvastatin treatment.

Trupp M, Zhu H, Wikoff WR, Baillie RA, Zeng ZB, Karp PD, Fiehn O, Krauss RM, Kaddurah-Daouk R.

PLoS One. 2012;7(7):e38386. doi: 10.1371/journal.pone.0038386. Epub 2012 Jul 9.

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