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Items: 1 to 20 of 67

1.

Simplivariate models: uncovering the underlying biology in functional genomics data.

Saccenti E, Westerhuis JA, Smilde AK, van der Werf MJ, Hageman JA, Hendriks MM.

PLoS One. 2011;6(6):e20747. doi: 10.1371/journal.pone.0020747.

2.

Simplivariate models: ideas and first examples.

Hageman JA, Hendriks MM, Westerhuis JA, van der Werf MJ, Berger R, Smilde AK.

PLoS One. 2008 Sep 23;3(9):e3259. doi: 10.1371/journal.pone.0003259.

3.

Integrating functional genomics data using maximum likelihood based simultaneous component analysis.

van den Berg RA, Van Mechelen I, Wilderjans TF, Van Deun K, Kiers HA, Smilde AK.

BMC Bioinformatics. 2009 Oct 16;10:340. doi: 10.1186/1471-2105-10-340.

4.

New figures of merit for comprehensive functional genomics data: the metabolomics case.

Van Batenburg MF, Coulier L, van Eeuwijk F, Smilde AK, Westerhuis JA.

Anal Chem. 2011 May 1;83(9):3267-74. doi: 10.1021/ac102374c.

PMID:
21391558
5.

Filtering genes for cluster and network analysis.

Tritchler D, Parkhomenko E, Beyene J.

BMC Bioinformatics. 2009 Jun 23;10:193. doi: 10.1186/1471-2105-10-193.

6.

Generic framework for high-dimensional fixed-effects ANOVA.

Smilde AK, Timmerman ME, Hendriks MM, Jansen JJ, Hoefsloot HC.

Brief Bioinform. 2012 Sep;13(5):524-35. doi: 10.1093/bib/bbr071. Review.

PMID:
22199378
7.

Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data.

Boyer F, Morgat A, Labarre L, Pothier J, Viari A.

Bioinformatics. 2005 Dec 1;21(23):4209-15.

PMID:
16216829
8.

GRAST: a new way of genome reduction analysis using comparative genomics.

Toft C, Fares MA.

Bioinformatics. 2006 Jul 1;22(13):1551-61.

PMID:
16601001
9.

Comparison of two algorithmic data processing strategies for metabolic fingerprinting by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry.

Almstetter MF, Appel IJ, Dettmer K, Gruber MA, Oefner PJ.

J Chromatogr A. 2011 Sep 28;1218(39):7031-8. doi: 10.1016/j.chroma.2011.08.006.

PMID:
21871627
10.

CLEAN: CLustering Enrichment ANalysis.

Freudenberg JM, Joshi VK, Hu Z, Medvedovic M.

BMC Bioinformatics. 2009 Jul 29;10:234. doi: 10.1186/1471-2105-10-234.

11.
12.

Plant metabolomics: large-scale phytochemistry in the functional genomics era.

Sumner LW, Mendes P, Dixon RA.

Phytochemistry. 2003 Mar;62(6):817-36. Review.

PMID:
12590110
13.

Genome-scale gene/reaction essentiality and synthetic lethality analysis.

Suthers PF, Zomorrodi A, Maranas CD.

Mol Syst Biol. 2009;5:301. doi: 10.1038/msb.2009.56.

14.

An integrative approach towards completing genome-scale metabolic networks.

Christian N, May P, Kempa S, Handorf T, Ebenhöh O.

Mol Biosyst. 2009 Dec;5(12):1889-903. doi: 10.1039/B915913b.

PMID:
19763335
15.

coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics.

Chaudhuri RR, Khan AM, Pallen MJ.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D296-9.

16.

Comparative microbial modules resource: generation and visualization of multi-species biclusters.

Kacmarczyk T, Waltman P, Bate A, Eichenberger P, Bonneau R.

PLoS Comput Biol. 2011 Dec;7(12):e1002228. doi: 10.1371/journal.pcbi.1002228.

17.

Functional genomics of Escherichia coli in Japan.

Mori H, Isono K, Horiuchi T, Miki T.

Res Microbiol. 2000 Mar;151(2):121-8. Review.

PMID:
10865957
18.

Equating, or correction for between-block effects with application to body fluid LC-MS and NMR metabolomics data sets.

Draisma HH, Reijmers TH, van der Kloet F, Bobeldijk-Pastorova I, Spies-Faber E, Vogels JT, Meulman JJ, Boomsma DI, van der Greef J, Hankemeier T.

Anal Chem. 2010 Feb 1;82(3):1039-46. doi: 10.1021/ac902346a.

PMID:
20052990
19.

Development of a target component extraction method from GC-MS data with an in-house program for metabolite profiling.

Choe S, Woo SH, Kim DW, Park Y, Choi H, Hwang BY, Lee D, Kim S.

Anal Biochem. 2012 Jul 15;426(2):94-102. doi: 10.1016/j.ab.2012.04.010.

PMID:
22507375
20.

Challenges in mass spectrometry based targeted metabolomics.

Koal T, Deigner HP.

Curr Mol Med. 2010 Mar;10(2):216-26. Review.

PMID:
20196726

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