Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 119

1.

Metabolic route computation in organism communities.

Krummenacker M, Latendresse M, Karp PD.

Microbiome. 2019 Jun 7;7(1):89. doi: 10.1186/s40168-019-0706-6.

2.

Using Pathway Covering to Explore Connections among Metabolites.

Midford PE, Latendresse M, O'Maille PE, Karp PD.

Metabolites. 2019 May 2;9(5). pii: E88. doi: 10.3390/metabo9050088.

3.

A Comparison of Microbial Genome Web Portals.

Karp PD, Ivanova N, Krummenacker M, Kyrpides N, Latendresse M, Midford P, Ong WK, Paley S, Seshadri R.

Front Microbiol. 2019 Feb 22;10:208. doi: 10.3389/fmicb.2019.00208. eCollection 2019. Review.

4.

The EcoCyc Database.

Karp PD, Ong WK, Paley S, Billington R, Caspi R, Fulcher C, Kothari A, Krummenacker M, Latendresse M, Midford PE, Subhraveti P, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Collado-Vides J, Keseler IM, Paulsen I.

EcoSal Plus. 2018 Nov;8(1). doi: 10.1128/ecosalplus.ESP-0006-2018. Review.

5.

How accurate is automated gap filling of metabolic models?

Karp PD, Weaver D, Latendresse M.

BMC Syst Biol. 2018 Jun 19;12(1):73. doi: 10.1186/s12918-018-0593-7.

6.

The BioCyc collection of microbial genomes and metabolic pathways.

Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, Keseler IM, Krummenacker M, Midford PE, Ong Q, Ong WK, Paley SM, Subhraveti P.

Brief Bioinform. 2017 Aug 17. doi: 10.1093/bib/bbx085. [Epub ahead of print]

PMID:
29447345
7.

Evaluation of reaction gap-filling accuracy by randomization.

Latendresse M, Karp PD.

BMC Bioinformatics. 2018 Feb 14;19(1):53. doi: 10.1186/s12859-018-2050-4.

8.

Update notifications for the BioCyc collection of databases.

Paley S, Karp PD.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax086.

9.

The MetaCyc database of metabolic pathways and enzymes.

Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD.

Nucleic Acids Res. 2018 Jan 4;46(D1):D633-D639. doi: 10.1093/nar/gkx935.

10.

The Omics Dashboard for interactive exploration of gene-expression data.

Paley S, Parker K, Spaulding A, Tomb JF, O'Maille P, Karp PD.

Nucleic Acids Res. 2017 Dec 1;45(21):12113-12124. doi: 10.1093/nar/gkx910.

11.

How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications.

Khomtchouk BB, Weitz E, Karp PD, Wahlestedt C.

Brief Bioinform. 2017 Sep 1;18(5):905. doi: 10.1093/bib/bbx016. No abstract available.

12.

How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications.

Khomtchouk BB, Weitz E, Karp PD, Wahlestedt C.

Brief Bioinform. 2018 May 1;19(3):537-543. doi: 10.1093/bib/bbw130. Erratum in: Brief Bioinform. 2017 Sep 1;18(5):905.

13.

Can we replace curation with information extraction software?

Karp PD.

Database (Oxford). 2016 Dec 26;2016. pii: baw150. doi: 10.1093/database/baw150. Print 2016. Review.

14.

Crowd-sourcing and author submission as alternatives to professional curation.

Karp PD.

Database (Oxford). 2016 Dec 26;2016. pii: baw149. doi: 10.1093/database/baw149. Print 2016.

15.

Pathway collages: personalized multi-pathway diagrams.

Paley S, O'Maille PE, Weaver D, Karp PD.

BMC Bioinformatics. 2016 Dec 13;17(1):529.

16.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.

Keseler IM, Mackie A, Santos-Zavaleta A, Billington R, Bonavides-Martínez C, Caspi R, Fulcher C, Gama-Castro S, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Peralta-Gil M, Subhraveti P, Velázquez-Ramírez DA, Weaver D, Collado-Vides J, Paulsen I, Karp PD.

Nucleic Acids Res. 2017 Jan 4;45(D1):D543-D550. doi: 10.1093/nar/gkw1003. Epub 2016 Nov 28.

17.

How much does curation cost?

Karp PD.

Database (Oxford). 2016 Aug 7;2016. pii: baw110. doi: 10.1093/database/baw110. Print 2016.

18.

The Time Is Right to Focus on Model Organism Metabolomes.

Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR.

Metabolites. 2016 Feb 15;6(1). pii: E8. doi: 10.3390/metabo6010008.

19.

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.

20.

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.

21.

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. 2016 Sep;17(5):877-90. doi: 10.1093/bib/bbv079. Epub 2015 Oct 10.

22.

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.

F1000Res. 2015 Jan 15;4:12. doi: 10.12688/f1000research.6038.1. eCollection 2015.

23.

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.

24.

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
25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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
31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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
43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

A survey of metabolic databases emphasizing the MetaCyc family.

Karp PD, Caspi R.

Arch Toxicol. 2011 Sep;85(9):1015-33. doi: 10.1007/s00204-011-0705-2. Epub 2011 Apr 27. Review.

Supplemental Content

Support Center