Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm)

http://www.nobel.se/chemistry/laureates/2002/chemadv02.pdf (Cited 5 December 2003) Lockhart DJ, Winzeler EA (2000) Nature 405:827–836 Nicholson JK, Connelly J, Lindon JC, Holmes E (2002) Metabonomics: A Platform for Studying Drug Toxicity and Gene Function. Nat Rev 1:153–161 Jackson JE (1991) A user’s guide to principal components. Wiley, New York (ISBN 0-471-62267-2) Martens H, Naes T (1989) Multivariate calibration. Wiley, NY, ISBN 0-471-90979-3 Wold S, Esbensen K, Geladi P (1987) Chemom Intel Lab Syst 2:37–52 Wold S, Albano C, Dunn WJ, Edlund U, Esbensen K, Geladi P, Hellberg S, Johansson E, Lindberg W, Sjöström M (1984) In: Kowalski BR (ed) Chemometrics: mathematics and statistics in chemistry, D. Reidel Publishing Company, Dordrecht Sjöström M, Wold S, Söderström B (1985) PLS Discriminant Plots. In: Proceedings of PARC in Practice, Amsterdam Kalivas JH (1999) J Chemom 13:111–132 Wold S, Johansson E, Cocchi M (1993) In: Kubinyi H (ed) 3D-QSAR in drug design, theory, methods, and applications. ESCOM Science Publishers, Leiden, pp 523–550 Burnham, AJ, Viveros R, MacGregor JF (1996) J Chemom 10:31–45 Burnham, AJ, MacGregor JF, Viveros R (1999) Chemom Intel Lab Syst 48:167–180 Eriksson L, Johansson E, Kettaneh-Wold N, Wold S (2001) Multi- and megavariate data analysis—principles and applications. Umetrics AB. ISBN 91-973730-1-X Berglund A, De Rosa MC, Wold S (1997) J Comput Aid Mol Des 11:601–612 Westerhuis J, Kourti T, MacGregor JF (1998) J Chemom 12:301–321 Wold S, Kettaneh N, Tjessem K (1996) J Chemom 10:463–482 Janné K, Pettersen J, Lindberg NO, Lundstedt T (2001) J Chemom 15:203–213 Eriksson L, Johansson E, Lindgren F, Sjöström M, Wold S (2002) J Comput Aided Mol Des 16:711–726 The data are taken from the web-site http://cellcycle-www.stanford.edu. Cited 25 March 2003 Spellman et al. (1998) Mol Biol Cell 9:3273–3297. Cho RJ et al. (1998) Mol Cell 2:65–73 Johansson D, Lindgren P (2002) Masters Thesis in Bioinformatics, Umeå University, Espina JR, Shockcor JP, Herron WJ, Car BD, Contel NR, Ciaccio PJ, Lindon JC, Holmes E, Nicholson JK (2001) Magn Reson Chem 39:559–565 Eriksson L, Antti H, Holmes E, Johansson E Multi- and Megavariate Data Analysis: Finding and Using Regularities in Metabonomics Data. In: Robertson DG (Ed) Toxicological metabonomics: the use of NMR spectroscopy and multivariate statistics in drug safety evaluation. Kluwer, Dordrecht Gunnarsson I, Andersson PM, Wikberg J, Lundstedt T (2003) J Chemom 17:82–92 Sandberg M, Eriksson L, Jonsson J, Sjöström M, Wold S (1988) J Med Chem 41:2481–2491 Eriksson L, Andersson PM, Johansson E, Lundstedt T (2002) Statistical molecular design—a core concept in multivariate qsar and combinatorial technologies. Part I—Basic principles and application to lead optimization. Part II—QSAR applications. Part III—QSAR-directed virtual screening. Part IV—SMD: an integral part of combC and HTS. Part V—Some extensions and recent developments. http://www.acc.umu.se/%7Etnkjtg/chemometrics/editorial/. cited 19 December 2003 http://www.umetrics.com Wold S (1978) Technometrics 20:397–405 Trygg J (2001) PhD Thesis. Umeå University, Ståhle L, Wold S (1987) J Chemom 1:185–196 Barker M, Rayens W (2003) J Chemom 17:166–173 Atif U, Earll, Eriksson L, Johansson E, Lord P, Margrett S (2002) Analysis of gene expression datasets using partial least-squares discriminant analysis and principal-component analysis. In: Martyn Ford, David Livingstone, John Dearden and Han Van de Waterbeemd (eds) Euro QSAR 2002 designing drugs and crop protectants: processes, problems and solutions. Blackwell, Oxford, pp 369–373 ISBN 1-4051-2561-0. Wold S, Trygg J, Berglund A, Antti H (2001) Chemom Intell Lab Syst 58:131–150 Kristal BS (2002) Practical considerations and approaches for entry-level megavariate analysis. http://mickey.utmem.edu/papers/bioinformatics_02/pdfs/Kristal.pdf. cited 5 February 2004 Box GEP, Hunter WG, Hunter JS (1978) Statistics for experimenters. Wiley, New York Eriksson L, Johansson E, Kettaneh-Wold N, Wikström C, Wold S (2000) Design of experiments—principles and applications. Umetrics AB, 2000. ISBN 91-973730-0-1 Olsson I, Gottfries J, Wold S, D-optimal onion design (DOOD) in statistical molecular design, chemometrics and intelligent laboratory systems. Chemom Intell Lab Syst 73:37–46 Eriksson L, Arnhold T, Beck B, Fox T, Johansson E, Kriegl JM (2004) Onion design and its application to a pharmaceutical QSAR problem. J Chemom 18:188–202 Wold S, Antti H, Lindgren F, Öhman J (1998) Chemom Intell Lab Syst 44:175–185 Trygg J, Wold S (1998) Chemom Intell Lab Syst 42:209–220 Wold S, Kettaneh-Wold N, Skagerberg B (1989) Chemom Intell Lab Syst 7:53–65 Wold S (1992) Chemom Intell Lab Syst 14:71–84 Eriksson L, Johansson E, Lindgren F, Wold S (2000) Quant Struct Act Relat 19:345–355 Berglund A, Wold S (1997) J Chemom 11:141–156 Wold S, Hellberg S, Lundstedt T, Sjöström M, Wold H (1987) PLS modeling with latent variables in two or more dimensions. In: Proceedings Frankfurt PLS-meeting, September Eriksson L, Damborsky J, Earll M, Johansson E, Trygg J, Wold S (2004) SAR & QSAR Env. Res. 15 ( In press) Wold S, Kettaneh N, Fridén H, Holmberg A (1998) Chemom Intell Lab Syst 44:331–340 Antti H, Bollard ME, Ebbels T, Keun H, Lindon JC, Nicholson JK, Holmes E (2002) J Chemom 16:461–468 Wold S, Geladi P, Esbensen K, Öhman J (1987) J Chemom 1:41–56 Nomikos P, MacGregor JF (1995) Chemom Intell Lab Syst 30:97–108