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TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei

Research output: Contribution to Journal/Magazine › Journal article › peer-review

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TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. / Shameer, Sanu; Logan-Klumpler, Flora J.; Vinson, Florence et al.
In: Nucleic Acids Research, Vol. 43, No. D1, 28.01.2015, p. D637-D644.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Harvard

Shameer, S, Logan-Klumpler, FJ, Vinson, F, Cottret, L, Merlet, B, Achcar, F, Boshart, M, Berriman, M, Breitling, R, Bringaud, F, Bütikofer, P, Cattanach, AM, Bannerman-Chukualim, B, Creek, DJ, Crouch, K, de Koning, HP, Denise, H, Ebikeme, C, Fairlamb, AH, Ferguson, MAJ, Ginger, ML, Hertz-Fowler, C, Kerkhoven, EJ, Mäser, P, Michels, PAM, Nayak, A, Nes, DW, Nolan, DP, Olsen, C, Silva-Franco, F, Smith, TK, Taylor, MC, Tielens, AGM, Urbaniak, MD, van Hellemond, JJ, Vincent, IM, Wilkinson, SR, Wyllie, S, Opperdoes, FR, Barrett, MP & Jourdan, F 2015, 'TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei', Nucleic Acids Research, vol. 43, no. D1, pp. D637-D644. https://doi.org/10.1093/nar/gku944

APA

Shameer, S., Logan-Klumpler, F. J., Vinson, F., Cottret, L., Merlet, B., Achcar, F., Boshart, M., Berriman, M., Breitling, R., Bringaud, F., Bütikofer, P., Cattanach, A. M., Bannerman-Chukualim, B., Creek, D. J., Crouch, K., de Koning, H. P., Denise, H., Ebikeme, C., Fairlamb, A. H., ... Jourdan, F. (2015). TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, 43(D1), D637-D644. https://doi.org/10.1093/nar/gku944

Vancouver

Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F et al. TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research. 2015 Jan 28;43(D1):D637-D644. Epub 2014 Oct 9. doi: 10.1093/nar/gku944

Author

Shameer, Sanu ; Logan-Klumpler, Flora J. ; Vinson, Florence et al. / TrypanoCyc : a community-led biochemical pathways database for Trypanosoma brucei. In: Nucleic Acids Research. 2015 ; Vol. 43, No. D1. pp. D637-D644.

Bibtex

@article{d2a44b71c7994e4ab5497ecb87724571,
title = "TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei",
abstract = "The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.",
author = "Sanu Shameer and Logan-Klumpler, {Flora J.} and Florence Vinson and Ludovic Cottret and Benjamin Merlet and Fiona Achcar and Michael Boshart and Matthew Berriman and Rainer Breitling and Fr{\'e}d{\'e}ric Bringaud and Peter B{\"u}tikofer and Cattanach, {Amy M.} and Bridget Bannerman-Chukualim and Creek, {Darren J.} and Kathryn Crouch and {de Koning}, {Harry P.} and Hubert Denise and Charles Ebikeme and Fairlamb, {Alan H.} and Ferguson, {Michael A. J.} and Ginger, {Michael L.} and Christiane Hertz-Fowler and Kerkhoven, {Eduard J.} and Pascal M{\"a}ser and Michels, {Paul A. M.} and Archana Nayak and Nes, {David W.} and Nolan, {Derek P.} and Christian Olsen and Fatima Silva-Franco and Smith, {Terry K.} and Taylor, {Martin C.} and Tielens, {Aloysius G. M.} and Urbaniak, {Michael D.} and {van Hellemond}, {Jaap J.} and Vincent, {Isabel M.} and Wilkinson, {Shane R.} and Susan Wyllie and Opperdoes, {Fred R.} and Barrett, {Michael P.} and Fabien Jourdan",
note = "C The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com ",
year = "2015",
month = jan,
day = "28",
doi = "10.1093/nar/gku944",
language = "English",
volume = "43",
pages = "D637--D644",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "D1",

}

RIS

TY - JOUR

T1 - TrypanoCyc

T2 - a community-led biochemical pathways database for Trypanosoma brucei

AU - Shameer, Sanu

AU - Logan-Klumpler, Flora J.

AU - Vinson, Florence

AU - Cottret, Ludovic

AU - Merlet, Benjamin

AU - Achcar, Fiona

AU - Boshart, Michael

AU - Berriman, Matthew

AU - Breitling, Rainer

AU - Bringaud, Frédéric

AU - Bütikofer, Peter

AU - Cattanach, Amy M.

AU - Bannerman-Chukualim, Bridget

AU - Creek, Darren J.

AU - Crouch, Kathryn

AU - de Koning, Harry P.

AU - Denise, Hubert

AU - Ebikeme, Charles

AU - Fairlamb, Alan H.

AU - Ferguson, Michael A. J.

AU - Ginger, Michael L.

AU - Hertz-Fowler, Christiane

AU - Kerkhoven, Eduard J.

AU - Mäser, Pascal

AU - Michels, Paul A. M.

AU - Nayak, Archana

AU - Nes, David W.

AU - Nolan, Derek P.

AU - Olsen, Christian

AU - Silva-Franco, Fatima

AU - Smith, Terry K.

AU - Taylor, Martin C.

AU - Tielens, Aloysius G. M.

AU - Urbaniak, Michael D.

AU - van Hellemond, Jaap J.

AU - Vincent, Isabel M.

AU - Wilkinson, Shane R.

AU - Wyllie, Susan

AU - Opperdoes, Fred R.

AU - Barrett, Michael P.

AU - Jourdan, Fabien

N1 - C The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

PY - 2015/1/28

Y1 - 2015/1/28

N2 - The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.

AB - The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.

U2 - 10.1093/nar/gku944

DO - 10.1093/nar/gku944

M3 - Journal article

C2 - 25300491

VL - 43

SP - D637-D644

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - D1

ER -