Data mining in genetics

Publications

• An empirical comparison of case-control and trio-based study designs in high-throughput association mapping by Petteri Hintsanen, Petteri Sevon, Päivi Onkamo, Lauri Eronen, and Hannu Toivonen. Journal of Medical Genetics 43: 617-624, 2006. (data sets are available in bzip2-compressed tar file, approx. 1GB compressed, 19GB uncompressed).
• HaploRec: Efficient and accurate large-scale reconstruction of haplotypes by Lauri Eronen, Floris Geerts and Hannu Toivonen. BMC Bioinformatics 7:542, 2006.
• Visualisation of Associations Between Nucleotides in SNP Neighbourhoods by Kimmo Kulovesi, Juho Muhonen, Ilkka Lappalainen, Pentti T. Riikonen, Mauno Vihinen, Hannu Toivonen and Tomi A. Pasanen. Workshop on Intelligent Data Analysis in bioMedicine and Pharmacology (IDAMAP 06), Verona, Italy, August 2006, to appear.
• Link discovery in graphs derived from biological databases by Petteri Sevon, Lauri Eronen, Petteri Hintsanen, Kimmo Kulovesi, Hannu Toivonen. 3rd International Workshop on Data Integration in the Life Sciences 2006 (DILS'06), Hinxton, UK, July 2006, to appear.
• Constrained Hidden Markov Models for Population-based Haplotyping by Niels Landwehr, Taneli Mielikainen, Lauri Eronen, Hannu Toivonen, Heikki Mannila. Workshop on Probabilistic Modeling and Machine Learning in Structural and Systems Biology, Tuusula, Finland, June 2006.
• TreeDT: Tree pattern mining for gene mapping by Petteri Sevon, Hannu Toivonen, Vesa Ollikainen. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3 (2): 174-185, April-June 2006.
• A survey of data mining methods for linkage disequilibrium mapping by Päivi Onkamo and Hannu Toivonen. Human Genomics, 2 (5): 336-340, 2006.

• Combining phenotypic and genotypic data to discover multiple disease genes by Hannu Toivonen, Saara Hyvönen, Petteri Sevon. Symposium on Knowledge Representation in Bioinformatics (KRBIO'05), 7-14, Espoo, Finland, June 2005.
• Data Mining in Bioinformatics by Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer, 2005. ISBN 1-85233-671-4.
• Data Mining for Gene Mapping by Hannu Toivonen, Päivi Onkamo, Petteri Hintsanen, Evimaria Terzi, and Petteri Sevon. In Next Generation of Data Mining Applications by Mehmed Kantardzic and Jozef Zurada (Eds.), 263-293. Wiley-IEEE Press, 2005. (manuscript)
• Gene Mapping by Pattern Discovery by Petteri Sevon, Hannu T.T. Toivonen, and Päivi Onkamo. In J. Wang et al (Eds.), Data Mining in Bioinformatics, 105-126. Springer, 2005. (manuscript)

• A Markov Chain Approach to Reconstruction of Long Haplotypes Eronen L, Geerts F and Toivonen H. Proceedings of the 9th Pacific Symposium on Biocomputing (PSB'04), 104-115, Hawaii, USA, January 2004. World Scientific.
• Algorithms for Association-Based Gene mapping, PhD thesis, Petteri Sevon. Department of Computer Science, Report A-2004-4.
• Increasing incidence of Type 1 diabetes -- a role for genes?, Pitkäniemi J, Onkamo P, Tuomilehto J, Arjas E. BMC Genetics, 2004.
• Fine mapping of the 2p12-p11 dyslexia candidate region and exclusion of TACR1 as a candidate gene, Peyrard-Janvid M, Anthoni H, Onkamo P, Lahermo P, Zucchelli M, Kaminen N, Hannula-Jouppi K, Lyytinen H, Muller K, Kaaranen M, Nopola-Hemmi J, Voutilainen A and Kere J. Human Genetics, 114:510-516, 2004.
• Haplotype associations define target regions for susceptibility loci in Systemic lupus erythematosus, Koskenmies S, Widén E, Onkamo P, Sevón P, Julkunen H, Kere J. Eur J Hum Genetics, 12:489-494, 2004.

• Proceedings of BIOKDD'03, 3rd ACM SIGKDD Workshop on Data Mining in Bioinformatics, Eds. Mohammed Zaki, Jason T.L. Wang, and Hannu Toivonen. Washington DC, August 2003. Report No. 03-11, Rensselaer Polytechnic Institute, Troy, NY. 2003.
• Finding recurrent sources in sequences. Gionis A and Mannila H. ACM ReCOMB 2003. [PS]
• BIOKDD 2002: Recent Advances in Data Mining for Bioinformatics by M.J. Zaki, J.T.L. Wang, and H.T.T.Toivonen. SIGKDD Explorations 4 (2): 112 - 114, January 2003.

• An MDL method for finding haplotype blocks and for estimating the strength of haplotype block boundaries Koivisto M, Perola M, Varilo T, Hennah W, Ekelund J, Lukk M, Peltonen L, Ukkonen E, and Mannila H. In Pacific Symposium on Biocomputing 2003 (PSB'03), R.B. Altman, A.K. Dukner, L. Hunter T.A. Jung and T.E. Klein, eds., World Scientific p. 502-513, 2002. [PDF, PS]
• Association analysis for quantitative traits by data mining: QHPM. Onkamo P, Ollikainen V, Sevon P, Toivonen HTT, Mannila H, Kere J. Ann Hum Genet 66:419-429, 2002.
• Simulation techniques for disease gene localization in isolated populations Ollikainen V, Ph.D thesis, 2002. [PS], Errata (doc, 16K)
• BIOKDD01: Workshop on Data Mining in Bioinformatics by M.J. Zaki, J.T.L. Wang, and H.T.T.Toivonen. SIGKDD Explorations 3 (2): 71 - 73, January 2002.

• Mining associations between genetic markers, phenotypes and covariates. Sevon P, Ollikainen V, Onkamo P, Toivonen HTT, Mannila H, and Kere J. In Wijsman EM, Almasy L, Amos CI, Borecki I, Falk CT, King TM, Martinez MM, Meyers D, Neuman R, Olson JM, Rich S, Spence MA, Thomas DC, Vieland VJ, Witte JS, MacCluer JW. Analysis of complex genetic traits: Applications to asthma and simulated data. In Genetic Epidemiology, Volume 21(Suppl 1), pgs. S588-S593, 2001.
• Association analysis by data mining tools by Päivi Onkamo, Petteri Sevon, Vesa Ollikainen, Hannu TT Toivonen, Heikki Mannila, and Juha Kere. American Journal of Human Genetics 69(4, Suppl. 1): 1320, October 2001.
• Offspring risk and sibling risk for multilocus traits Koivisto M and Mannila H. Human Heredity 51:4:209-216, 2001.
• TreeDT: Gene mapping by tree disequilibrium test by Petteri Sevon, Hannu TT Toivonen, and Vesa Ollikainen. In The Seventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD-2001), 365 - 370, San Francisco, California, August 2001. ACM.
• A second-generation association study of the 5q31 cytokine gene cluster and the interleukin-4 receptor in asthma by Paula Kauppi, Kerstin Lindblad-Toh, Petteri Sevon, Hannu T. T. Toivonen, John D. Rioux, Anu Villapakkam, Lauri A. Laitinen, Thomas J. Hudson, Juha Kere, and Tarja Laitinen. Genomics 77(1-2): 35 - 42, September 2001.
• BIOKDD01 Workshop on Data Mining in Bioinformatics by Mohammed J. Zaki, Hannu T.T. Toivonen, and Jason T.L. Wang, editors. Rensselaer Polytechnic Institute, July 2001. RPI Technical Report 01-8.

• Data mining applied to linkage disequilibrium mapping. Toivonen HTT, Onkamo P, Vasko K, Ollikainen V, Sevon P, Mannila H, Herr M and Kere J. American Journal of Human Genetics 67:133-145, 2000.
• Gene mapping by haplotype pattern mining by Hannu TT Toivonen, Päivi Onkamo, Kari Vasko, Vesa Ollikainen, Petteri Sevon, Heikki Mannila, and Juha Kere. In IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE 2000), 99 - 108, Arlington, Virginia, November 2000. IEEE.

See also the homepages of our group members for additional publications