BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry

Hoffmann N, Wilhelm M, Doebbe A, Niehaus K, Stoye J (2014)
Bioinformatics 30(7): 988-995.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
Hoffmann, NilsUniBi ; Wilhelm, Mathias; Doebbe, AnjaUniBi; Niehaus, KarstenUniBi; Stoye, JensUniBi
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe O. Kruse
Centrum für Biotechnologie > Arbeitsgruppe K. Niehaus
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Institut für Biochemie und Biotechnik
Fakultät für Biologie > Algenbiotechnologie
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Fakultät für Biologie > Proteom- und Metabolomforschung
Erscheinungsjahr
2014
Zeitschriftentitel
Bioinformatics
Band
30
Ausgabe
7
Seite(n)
988-995
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/2643941

Zitieren

Hoffmann N, Wilhelm M, Doebbe A, Niehaus K, Stoye J. BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry. Bioinformatics. 2014;30(7):988-995.
Hoffmann, N., Wilhelm, M., Doebbe, A., Niehaus, K., & Stoye, J. (2014). BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry. Bioinformatics, 30(7), 988-995. https://doi.org/10.1093/bioinformatics/btt738
Hoffmann, Nils, Wilhelm, Mathias, Doebbe, Anja, Niehaus, Karsten, and Stoye, Jens. 2014. “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”. Bioinformatics 30 (7): 988-995.
Hoffmann, N., Wilhelm, M., Doebbe, A., Niehaus, K., and Stoye, J. (2014). BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry. Bioinformatics 30, 988-995.
Hoffmann, N., et al., 2014. BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry. Bioinformatics, 30(7), p 988-995.
N. Hoffmann, et al., “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”, Bioinformatics, vol. 30, 2014, pp. 988-995.
Hoffmann, N., Wilhelm, M., Doebbe, A., Niehaus, K., Stoye, J.: BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry. Bioinformatics. 30, 988-995 (2014).
Hoffmann, Nils, Wilhelm, Mathias, Doebbe, Anja, Niehaus, Karsten, and Stoye, Jens. “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”. Bioinformatics 30.7 (2014): 988-995.

3 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Updates in metabolomics tools and resources: 2014-2015.
Misra BB, van der Hooft JJ., Electrophoresis 37(1), 2016
PMID: 26464019
A peaklet-based generic strategy for the untargeted analysis of comprehensive two-dimensional gas chromatography mass spectrometry data sets.
Egert B, Weinert CH, Kulling SE., J Chromatogr A 1405(), 2015
PMID: 26074098
Maui-VIA: A User-Friendly Software for Visual Identification, Alignment, Correction, and Quantification of Gas Chromatography-Mass Spectrometry Data.
Kuich PH, Hoffmann N, Kempa S., Front Bioeng Biotechnol 2(), 2014
PMID: 25654076

34 References

Daten bereitgestellt von Europe PubMed Central.

Quantification in comprehensive two-dimensional gas chromatography and a model of quantification based on selected summed modulated peaks.
Amador-Munoz O, Marriott PJ., J Chromatogr A 1184(1-2), 2007
PMID: 17996244
Using comprehensive two-dimensional gas chromatography retention indices to estimate environmental partitioning properties for a complete set of diesel fuel hydrocarbons.
Arey JS, Nelson RK, Xu L, Reddy CM., Anal. Chem. 77(22), 2005
PMID: 16285663
Data analysis tool for comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry.
Castillo S, Mattila I, Miettinen J, Oresic M, Hyotylainen T., Anal. Chem. 83(8), 2011
PMID: 21434611
The interplay of proton, electron, and metabolite supply for photosynthetic H2 production in Chlamydomonas reinhardtii.
Doebbe A, Keck M, La Russa M, Mussgnug JH, Hankamer B, Tekce E, Niehaus K, Kruse O., J. Biol. Chem. 285(39), 2010
PMID: 20581114
Comprehensive two-dimensional gas chromatography and chemometrics for the high-speed quantitative analysis of aromatic isomers in a jet fuel using the standard addition method and an objective retention time alignment algorithm
Fraga CG, Prazen BJ, Synovec RE., Anal. Chem. 72(17), 2000
PMID: 10994978
MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.
Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, Gonzalez-Beltran A, Sansone SA, Griffin JL, Steinbeck C., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23109552
Generic software frameworks for GC-MS based metabolomics
Hoffmann, 2012
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets.
Hoffmann N, Keck M, Neuweger H, Wilhelm M, Hogy P, Niehaus K, Stoye J., BMC Bioinformatics 13(), 2012
PMID: 22920415
The Golm metabolome database: a database for GC-MS based metabolite profiling
Hummel, 2007
Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry.
Jeong J, Shi X, Zhang X, Kim S, Shen C., BMC Bioinformatics 13(), 2012
PMID: 22316124
Quantification of naphthalenes in jet fuel with GC x GC/Tri-PLS and windowed rank minimization retention time alignment.
Johnson KJ, Prazen BJ, Young DC, Synovec RE., J Sep Sci 27(5-6), 2004
PMID: 15335076
Data analysis programs for comprehensive two-dimensional chromatography.
Kallio M, Kivilompolo M, Varjo S, Jussila M, Hyotylainen T., J Chromatogr A 1216(14), 2008
PMID: 19054522
Reducibility among combinatorial problems
Karp, 1972
Comparative analysis of mass spectral similarity measures on peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry.
Kim S, Zhang X., Comput Math Methods Med 2013(), 2013
PMID: 24151524
An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure.
Kim S, Fang A, Wang B, Jeong J, Zhang X., Bioinformatics 27(12), 2011
PMID: 21493650
Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography-mass spectrometry.
Kim S, Koo I, Fang A, Zhang X., BMC Bioinformatics 12(), 2011
PMID: 21676240
Semi-automated non-target processing in GC × GC-MS metabolomics analysis: applicability for biomedical studies.
Koek MM, van der Kloet FM, Kleemann R, Kooistra T, Verheij ER, Hankemeier T., Metabolomics 7(1), 2010
PMID: 21461033
mzML--a community standard for mass spectrometry data.
Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Rompp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW., Mol. Cell Proteomics 10(1), 2010
PMID: 20716697
Trends in data processing of comprehensive two-dimensional chromatography: state of the art.
Matos JT, Duarte RM, Duarte AC., J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 910(), 2012
PMID: 22819203
Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry peak sorting algorithm.
Oh C, Huang X, Regnier FE, Buck C, Zhang X., J Chromatogr A 1179(2), 2007
PMID: 18093607
The use of gene clusters to infer functional coupling.
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N., Proc. Natl. Acad. Sci. U.S.A. 96(6), 1999
PMID: 10077608
Fisher ratio method applied to third-order separation data to identify significant chemical components of metabolite extracts.
Pierce KM, Hoggard JC, Hope JL, Rainey PM, Hoofnagle AN, Jack RM, Wright BW, Synovec RE., Anal. Chem. 78(14), 2006
PMID: 16841931
Analysis of four-way two-dimensional liquid chromatography-diode array data: application to metabolomics.
Porter SE, Stoll DR, Rutan SC, Carr PW, Cohen JD., Anal. Chem. 78(15), 2006
PMID: 16878896
Features for non-targeted cross-sample analysis with comprehensive two-dimensional chromatography.
Reichenbach SE, Tian X, Cordero C, Tao Q., J Chromatogr A 1226(), 2011
PMID: 21855071
NetCDF: an interface for scientific data access
Rew, IEEE Comput. Graph. Appl. 10(), 1990
A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments.
Robinson MD, De Souza DP, Keen WW, Saunders EC, McConville MJ, Speed TP, Likic VA., BMC Bioinformatics 8(), 2007
PMID: 17963529
Complexity results on graphs with few cliques
Rosgen, Discrete Math. Theor. Comput. Sci. 9(), 2007
An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data
Stein, J. Am. Soc. Mass Spectrom. 10(), 1999
Optimization and testing of mass spectral library search algorithms for compound identification.
Stein SE, Scott DR., J. Am. Soc. Mass Spectrom. 5(9), 1994
PMID: 24222034
Analysis of petroleum compositional similarity using multiway principal components analysis (MPCA) with comprehensive two-dimensional gas chromatographic data.
Ventura GT, Hall GJ, Nelson RK, Frysinger GS, Raghuraman B, Pomerantz AE, Mullins OC, Reddy CM., J Chromatogr A 1218(18), 2011
PMID: 21450298
Combination of dynamic time warping and multivariate analysis for the comparison of comprehensive two-dimensional gas chromatograms: application to plant extracts.
Vial J, Nocairi H, Sassiat P, Mallipatu S, Cognon G, Thiebaut D, Teillet B, Rutledge DN., J Chromatogr A 1216(14), 2008
PMID: 18834592
Applications of comprehensive two-dimensional gas chromatography to the characterization of petrochemical and related samples.
von Muhlen C, Zini CA, Caramao EB, Marriott PJ., J Chromatogr A 1105(1-2), 2005
PMID: 16197956
DISCO: distance and spectrum correlation optimization alignment for two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics.
Wang B, Fang A, Heim J, Bogdanov B, Pugh S, Libardoni M, Zhang X., Anal. Chem. 82(12), 2010
PMID: 20476746
MetPP: a computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics.
Wei X, Shi X, Koo I, Kim S, Schmidt RH, Arteel GE, Watson WH, McClain C, Zhang X., Bioinformatics 29(14), 2013
PMID: 23665844
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