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Johan Trygg - Combined Profiling in Poplar using a Systems Biology Approach Print E-mail

info_16x16We use and develop chemometrics tools and strategies for global phenotyping of transgenic and wild type Poplar trees. Chemometrics represents a key philosophy and technology, since it is used for planning experiments to maximise information, to obtain good predictions and to visualize collected complex data. We apply a systems biology approach, in which multiple profiling techniques, e.g. metabolomics and proteomics, are combined to elucidate biochemical mechanisms and pathways at different organization levels.
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Overview of O2PLS modeling based on combined profiling using transcriptomics, proteomics and metabolomics data from Poplar trees. [See Ref Bylesjö et al 2009]
Experimental sciences, e.g. biology, chemistry and medicine, have to a large extent become information sciences and, in turn, bioinformatics and chemometrics are now prerequisites for experimental and applied research. Our aim is to develop and apply a systems biology approach to study growth and development in Poplar (the tree model) and Arabidopsis (the universal plant model) - all this in collaboration with Umeå Plant Science Centre and the Computational Life Science Cluster at Umeå University. We have already developed and optimized experimental protocols and data modelling tools to enable global phenotyping of thousands of plants using low-, semi- and high-throughput molecular profiling techniques for both Poplar and Arabidopsis. We have also developed novel strategies for generating and combining transcriptomic, proteomic and metabolomic profile data acquired from parallel analyses of hybrid aspen (Populus tremula × P. tremuloides). However, further research is needed to develop systems informatics tools and existing databases and statistical modeling to ‘catch up’ with the challenges that new experimental technologies provide.
Computational Life Science cluster (CLiC)
www.kbc.umu.se/clic
In our multidisciplinary approach, we integrate the fields of biology, mathematics, chemistry, physics and informatics. As a result, we have established a unique bioinformatics cluster, the Computational Life Science cluster (CLiC) at the Chemical Biology Centre (KBC), which encompass more than 30 researchers working together from six different departments. CLiC will stimulate and advance our already world-leading experimental research in forest biotechnology, by providing the missing link in informatics and modelling.
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Key publications

Trygg, J. and S. Wold, Orthogonal projections to latent structures (O-PLS), Journal of Chemometrics, 2002 16(3), p:119-128.

Trygg J, Holmes E, Lundstedt T, Chemometrics in metabonomics. J. Proteome Res 6 (2): 469-479, 2007

Bylesjö, M., D. Eriksson, M. Kusano, T. Moritz and J. Trygg, Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data, Plant Journal, 2007 52(6), p:1181-1191.

Bylesjö M, Nilsson R, Srivastava V, Grönlund A, Johansson, AI, Jansson S, Karlsson J, Moritz T, Wingsle G, Trygg J, Integrated Analysis of Transcript, Protein and Metabolite Data to Study Lignin Biosynthesis in Hybrid Aspen, J. Proteome Res. 2009, 8, 199-210

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  1. Madsen R, Rantapää-Dahlqvist S, Lundstedt T, Moritz T, Trygg J
    Metabolic responses to change in disease activity during tumor necrosis factor inhibition in patients with rheumatoid arthritis
    J Proteome Res. 2012 11(7):3796-804
  2. Gerber L, Eliasson M, Trygg J, Moritz T, Sundberg B
    Multivariate curve resolution provides a high-throughput data processing pipeline for pyrolysis-gas chromatography/mass spectrometry
    JOURNAL OF ANALYTICAL AND APPLIED PYROLYSIS 2012 95:95-100
  3. Madsen R, Banday VS, Moritz T, Trygg J, Lejon K
    Altered metabolic signature in pre-diabetic NOD mice
    PLoS One. 20127(4):e35445. Epub 2012 Apr 13
  4. Gorzsás A, Stenlund H, Persson P, Trygg J, Sundberg B
    Cell-specific chemotyping and multivariate imaging by combined FT-IR microspectroscopy and orthogonal projections to latent structures (OPLS) analysis reveals the chemical landscape of secondary xylem
    The Plant Journal: 2011 66:903-914
  5. Madsen RK, Lundstedt T, Gabrielsson J, Sennbro CJ, Alenius GM, Moritz T, Rantapaa-Dahlqvist S, Trygg J
    Diagnostic properties of metabolic perturbations in rheumatoid arthritis
    Arthritis Research: 2011 13:R19
  6. Hoffman DE, Jonsson P, Bylesjö M, Trygg J, Antti H, Eriksson ME, Moritz T
    Changes in diurnal patterns within the Populus transcriptome and metabolome in response to photoperiod variation
    Plant, Cell & Environment: 2010 33:1298-1313
  7. Fahlén J, Landfors M, Freyhult E, Bylesjö M, Trygg J, Hvidsten TR, Rydén P
    Bioinformatic strategies for cDNA-microarray data processing
    In: Batch Effects and Noise in Microarray Experiments: Sources and Solutions, Edited by A. Scherer, John Wiley & Sons 2009, 61-74
  8. Bylesjö M, Rantalainen M, Nicholson JK, Holmes E, Trygg J
    K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space
    BMC Bioinformatics 2008 9, 106:1-7
  9. Rantalainen M, Cloare O, Ebbels TMD, Lundstedt T, Nicholson JK, Holmes E, Trygg J
    Piecewise multivariate modelling of sequential metabolic profiling data
    BMC Bioinformatics 2008 9, 105:1-13
  10. Stenlund H, Gorzsás A, Persson P, Sundberg B, Trygg J
    Orthogonal projections to latent structures discriminant analysis modeling on in situ FT-IR spectral imaging of liver tissue for identifying sources of variability
    Analytical Chemistry: 2008 80:6898-6906
  11. Stenlund H, Johansson E, Gottfries J, Trygg J
    Unlocking interpretation in near infrared multivariate calibrations by orthogonal partial least squares
    Analytical chemistry: 2009 81:203-209
  12. Street NR, Sjödin A, Bylesjö M, Gustafsson P, Trygg J, Jansson S
    A cross-species transcriptomics approach to identify genes involved in leaf development
    BMC Genomics: 2008 9:589
  13. Bylesjö M, Nilsson R, Srivastava V, Grönlund A, Johansson AI, Jansson S, Karlsson J, Moritz T, Wingsle G, Trygg J
    Integrated Analysis of Transcript, Protein and Metabolite Data To Study Lignin Biosynthesis in Hybrid Aspen
    Journal of Proteome Research: 2009 8:199-210
  14. Bylesjö M, Segura V, Soolanayakanahally RY, Rae AM, Trygg J, Gustafsson P, Jansson S, Street NR
    LAMINA: a tool for rapid quantification of leaf size and shape parameters
    BMC Plant Biology: 2008 8:82
  15. Sjödin A, Wissel K, Bylesjö M, Trygg J, Jansson S
    Global expression profiling in leaves of free-growing aspen
    BMC Plant Biology: 2008 8:61
  16. Bruce SJ, Jonsson P, Antti H., Cioarec O, Trygg J, Marklund SL, Moritz T
    Evaluation of a protocol for metabolic prifiling studies on human blood plasma by combined ultra-performance liquid chromatography/mass spectrometry: From extraction to data analysis
    Analytical Biochemistry: 2008 372: 237-249
  17. Wiklund S, Johansson E, Sjöström L, Mellerowicz EJ, Edlund U, Shockcor JP, Gottfries J, Moritz T, Trygg J
    Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models
    Analytical Chemistry: 2008 80: 115-122
  18. Bylesjö M, Eriksson D, Kusano M, Moritz T, Trygg J
    Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data
    Plant Journal: 2008 52:1181-1191
  19. Bylesjo M, Eriksson D, Sjodin A, Jansson S, Moritz T, Trygg J
    Orthogonal projections to latent structures as a strategy for microarray data normalization.
    BMC Bioinformatics 2007, 8:207.
  20. Druart N, Johansson A, Baba K, Schrader J, Sjödin A, Bhalerao RR, Resman L, Trygg J, Moritz T, Bhallerao RP
    Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks
    The Plant Journal: 2007 50:557-573
  21. Benedict C, Geisler M, Trygg J, Huner N, Hurry V
    Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis
    Plant Physiology: 2006 141:1219-1232
  22. Jonsson P, Johansson ES, Wuolikainen A, Lindberg J, Schuppe-Koistinen I, Kusano M, Sjostrom M, Trygg J, Moritz T, Antti H
    Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS datas - A potential tool for multi-parametric diagnosis
    Journal of Proteome Research: 2006 5:1407-1414
  23. Cloarec O, Dumas ME, Trygg J, Craig A, Barton RH, Lindon JC, Nicholson JK, Holmes E
    Evaluation of the orthogonal projection on latent structure model limitations caused by chemical shift variability and improved visualization of biomarker changes in 1H NMR spectroscopic metabonomic studies
    Anal Chem: 2005 77:517-526
  24. Jiye A, Trygg J, Gullberg J, Johansson AI, Jonsson P, Antti H, Marklund SL, Moritz T
    Extraction and GC/MS analysis of the human blood plasma metabolome
    Anal Chem: 2005 77:8086-8094
  25. Jonsson P, Bruce SJ, Moritz T, Trygg J, Sjostrom M, Plumb R, Granger J, Maibaum E, Nicholson JK, Holmes E, Antti H
    Extraction, interpretation and validation of information for comparing samples in metabolic LC/MS data sets
    Analyst: 2005 130:701-707
  26. Jonsson P, Johansson AI, Gullberg J, Trygg J, A J, Grung B, Marklund S, Sjostrom M, Antti H, Moritz T
    High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses
    Anal Chem: 2005 77:5635-5642
  27. Bylesjo M, Eriksson D, Sjodin A, Sjostrom M, Jansson S, Antti H, Trygg J
    MASQOT: a method for cDNA microarray spot quality control
    Bmc Bioinformatics: 2005 6:250
  28. Cloarec O, Dumas M-E, Craig A, Barton RH, Trygg J, Hudson J, Blancher C, Gauguier D, Lindon JC, Holmes E, Nicholson J
    Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets
    Anal Chem: 2005 77:1282-1289
  29. Cloarec O, Dumas ME, Craig A, Barton RH, Trygg J, Hudson J, Blancher C, Gauguier D, Lindon JC, Holmes E, Nicholson J
    Statistical total correlation spectroscopy: An exploratory approach for latent biomarker identification from metabolic H-1 NMR data sets
    Analytical Chemistry: 2005 77:1282-1289
  30. Jiye A, Trygg J, Gullberg J, Moritz T, Marklund S
    Global analysis of low-molecular-weight compounds in human plasma using GC/TOF-MS
    Drug Metabolism Reviews: 2004 36:246-246
  31. Trygg J
    Prediction and spectral profile estimation in multivariate calibration
    Journal of Chemometrics: 2004 18:166-172
  32. Eriksson L, Damborsky J, Earll M, Johansson E, Trygg J, Wold S
    Three-block bi-focal PLS (3BIF-PLS) and its application in QSAR
    SAR QSAR Environ Res: 2004 15:481-499
  33. Eriksson L, Antti H, Gottfries J, Holmes E, Johansson E, Lindgren F, Long I, Lundstedt T, Trygg J, Wold S
    Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm)
    Anal Bioanal Chem: 2004 380:419-429
  34. Trygg J, Wold S
    O2-PLS, a two-block (X-Y) latent variable regression (LVR) method with an integral OSC filter
    Journal of Chemometrics: 2003 17:53-64
  35. Trygg J
    O2-PLS for qualitative and quantitative analysis in multivariate calibration
    Journal of Chemometrics: 2002 16:283-293
  36. Trygg J, Wold S
    Orthogonal projections to latent structures (O-PLS)
    Journal of Chemometrics: 2002 16:119-128
  37. Trygg J, Kettaneh-Wold N, Wallbacks L
    2D wavelet analysis and compression of on-line industrial process data
    Journal of Chemometrics: 2001 15:299-319
  38. Hauksson JB, Edlund U, Trygg J
    NMR processing techniques based on multivariate data analysis and orthogonal signal correction. C-13 CP/MAS NMR spectroscopic characterization of softwood kraft pulp
    Magnetic Resonance in Chemistry: 2001 39:267-275
  39. Wold S, Trygg J, Berglund A, Antti H
    Some recent developments in PLS modeling
    Chemometrics and Intelligent Laboratory Systems: 2001 58:131-150
  40. Eriksson L, Trygg J, Johansson E, Bro R, Wold S
    Orthogonal signal correction, wavelet analysis, and multivariate calibration of complicated process fluorescence data
    Analytica Chimica Acta: 2000 420:181-195
  41. Artursson T, Hagman A, Bjork S, Trygg J, Wold S, Jacobsson SP
    Study of preprocessing methods for the determination of crystalline phases in binary mixtures of drug substances by X-ray powder diffraction and multivariate calibration
    Applied Spectroscopy: 2000 54:1222-1230
  42. Geladi P, Barring H, Dabakk E, Trygg J, Antti H, Wold S, Karlberg B
    Calibration transfer for predicting lake-water pH from near infrared spectra of lake sediments
    Journal of near Infrared Spectroscopy: 1999 7:251-264
  43. Trygg J, Wold S
    PLS regression on wavelet compressed NIR spectra
    Chemometrics and Intelligent Laboratory Systems: 1998 42:209-220
 
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