Mikko Sillanpää
Mikko J. Sillanpää, Ph.D.
Senior Research Scientist3
Associate Editor of
Theoretical and Applied Genetics
2006 - present
SOFTWARE:
Multimapper / Bayesian QTL mapping software for analysing backcross, double haploid, and F2 data from designed crossing experiments of inbred lines (initial version)
(C source codes) .
(reference manual in PS) .
(reference manual in PDF) .
(simulated test data set) .
(simulated test data set with missing values) .
Multimapper (Version 1.0) with environmental covariates
(info) .
(updated codes) . .
This sofware is made for Linux but can also be used under Windows through Cygwin (which provides linux-like environment for Windows).
MULTIMAPPER was presented in the papers :
Sillanpää, M. J. and E. Arjas (1998) Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373-1388.
Martinez, V., G. Thorgaard, B. Robison, and M. J. Sillanpää (2005) An application of Bayesian QTL mapping to early development in double haploid lines of rainbow trout including environmental effects. Genetical Research 86: 209-221.
Multimapper/OUTBRED
Bayesian QTL mapping software for analysing backcross and F2 data from designed crossing experiments of outbred lines (Version 1.1)
(C source codes for MM/OUTBRED) .
(C source codes for preprocessor) .
(reference manual in PS) .
(reference manual in PDF) .
(simulated test data set) .
This sofware is made for Linux but can also be used under Windows through Cygwin (which provides linux-like environment for Windows).
MULTIMAPPER/OUTBRED was presented in the paper :
Sillanpää, M. J. and E. Arjas (1999) Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. Genetics 151: 1605-1619.
BAPS / Windows software for Bayesian analysis of population structure
winzip-file containing executable program, dll-files, manual, and test data set can be found in
The population structure estimation work that we initially started as methodological project to correct for unobserved counfounders in association analysis (Sillanpää et al. 2001; Ripatti et al. 2001) later on culminated in development of BAPS (Corander et al. 2003, 2004). Our new development of population structure estimation work is represented by Gasbarra et al. (2007a,b) where the unknown relatedness structure (pedigree and geneflow) are simultaneously estimated and different degrees of relationships are allowed among the study individuals.
BAPS versions are implemented using MATLAB and are then converted to C-language, where only executable programs are distributed. For user information and installation details, see the manual. Details of the method are presented in the papers :
Corander, J., P. Waldmann, and M. J. Sillanpää (2003) Bayesian analysis of genetic differentiation between populations. Genetics 163: 367-374.
Corander, J., P. Waldmann, P. Marttinen, and M. J. Sillanpää (2004) BAPS 2: enhanced possibilities for the analysis of the genetic population structure. Bioinformatics 20: 2363-2469.
BAMA / Software for Bayesian analysis of multilocus association (initial version)
(C source codes) bama.c.Z.
(reference manual in PS) .
(reference manual in PDF) .
(simulated test data sets) .
This sofware is made for Linux but can also be used under Windows through Cygwin (which provides linux-like environment for Windows).
BAMA was presented in the paper :
Kilpikari, R. and M. J. Sillanpää (2003) Bayesian analysis of multilocus association in quantitative and qualitative traits. Genetic Epidemiology 25: 122-135.
For epistasis and interaction searches using BAMA, see :
Sillanpää, M. J. (2009) Detecting interactions in association studies by using simple allele recoding. Human Heredity 67: 69-75.
Bayesian association-based fine mapping in small chromosomal segments
(WinBUGS model specification code in ASCII)
()
The method is presented in the paper :
Sillanpää, M. J. and M. Bhattacharjee (2005) Bayesian association-based fine mapping in small chromosomal segments. Genetics 169: 427-439.
Hierarchical modeling of clinical and expression QTLs
(Instructions)
(OpenBUGS model specification codes)
The method is presented in the paper :
Sillanpää, M. J., and N. Noykova (2008) Hierarchical modeling of clinical and expression quantitative trait loci. Heredity 101: 271-284.
PUBLICATIONS:
2008
Kulathinal, S., D. Gasbarra, S. Kinra, S. Ebrahim, and M. J. Sillanpää (2008) Estimation of additive genetic and environmental sources of quantitative trait variation using data on married couples and their siblings. Genetics Research 90: 269-279.
Waldmann, P., J. Hallander, F. Hoti, and M. J. Sillanpää (2008) Efficient MCMC implementation of Bayesian analysis of additive and dominance genetic variances in non-inbred pedigrees. Genetics 179: 1101-1112.
Sillanpää, M. J., and N. Noykova (2008) Hierarchical modeling of clinical and expression quantitative trait loci. Heredity 101: 271-284.
Sillanpää, M. J. (2009) Detecting interactions in association studies by using simple allele recoding. Human Heredity 67: 69-75.
Bhattacharjee, M., C. H. Botting, and M. J. Sillanpää (2008) Bayesian biomarker identification based on marker-expression-proteomics data. Genomics (accepted).
Pirinen, M., S. Kulathinal, D. Gasbarra, and M. J. Sillanpää (2008) Estimating population haplotype frequencies from pooled DNA samples using PHASE algorithm. Genetics Research (accepted).
2007
Sillanpää, M. J. and F. Hoti (2007) Mapping quantitative trait loci from a single tail sample of the phenotype distribution including survival data. Genetics 177: 2361-2377.
Gasbarra, D., M. Pirinen, M. J. Sillanpää, E. Salmela, and E. Arjas (2007) Estimating genealogies from unlinked marker data: a Bayesian approach. Theoretical Population Biology 72: 305-322.
Gasbarra, D., M. Pirinen, M. J. Sillanpää, and E. Arjas (2007) Estimating genealogies from linked marker data: a Bayesian approach. BMC Bioinformatics 8: 411.
2006
Sillanpää, M. J. and M. Bhattacharjee (2006) Association mapping of complex trait loci with context-dependent effects and unknown context-variable. Genetics 174: 1597-1611.
Hoti, F. and M. J. Sillanpää (2006) Bayesian mapping of genotype × expression interactions in quantitative and qualitative traits. Heredity 97: 4-18.
Gasbarra, D. and M. J. Sillanpää (2006) Constructing parental linkage phase and genetic map over distances < 1 cM using pooled haploid DNA. Genetics 172: 1325-1335.
2005
Sillanpää, M. J. and M. Bhattacharjee (2005) Bayesian association-based fine mapping in small chromosomal segments. Genetics 169: 427-439.
Gasbarra, D., M. J. Sillanpää, and E. Arjas (2005) Backward simulation of ancestors of sampled individuals. Theoretical Population Biology 67: 75-83.
Waldmann, P., M. R. Garcia-Gil, and M. J. Sillanpää (2005) Comparing Bayesian estimates of genetic differentiation of molecular markers and quantitative traits: An application to Pinus sylvestris. Heredity 94: 623-629.
Pekkinen, M., S. Varvio, K. K. M. Kulju, H. Kärkkäinen, S. Smolander, A. Viherä-Aarnio, V. Koski, and M. J. Sillanpää (2005) Linkage map of birch, Betula pendula Roth, based on microsatellites and amplified fragment length polymorphisms. Genome 48: 619-625.
Martinez, V., G. Thorgaard, B. Robison, and M. J. Sillanpää (2005) An application of Bayesian QTL mapping to early development in double haploid lines of rainbow trout including environmental effects. Genetical Research 86: 209-221.
Martinez, V., G. Thorgaard, B. Robinson, and M. J. Sillanpää (2005) Posterior evidence of multiple QTL influencing early development in double haploid lines of rainbow trout, Oncorhynchus mykiss. Aquaculture 247: 25-25. (Meeting Abstract).
2004
Corander, J., P. Waldmann, P. Marttinen, and M. J. Sillanpää (2004) BAPS 2: enhanced possibilities for the analysis of the genetic population structure. Bioinformatics 20: 2363-2469.
Sillanpää, M. J., D. Gasbarra, and E. Arjas (2004) Comment on the "On the Metropolis-Hastings acceptance probability to add or drop a quantitative trait locus in Markov Chain Monte Carlo-based Bayesian analyses". Genetics 167: 1037-1037.
Sillanpää, M. J. and K. Auranen (2004) Replication in genetic studies of complex traits. Annals of Human Genetics 68: 646-657.
Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, Beavis WD, Belknap JK, Bennett B, Berrettini W, Bleich A, Bogue M, Broman KW, Buck KJ, Buckler E, Burmeister M, Chesler EJ, Cheverud JM, Clapcote S, Cook MN, Cox RD, Crabbe JC, Crusio WE, Darvasi A, Deschepper CF, Doerge RW, Farber CR, Forejt J, Gaile D, Garlow SJ, Geiger H, Gershenfeld H, Gordon T, Gu J, Gu W, de Haan G, Hayes NL, Heller C, Himmelbauer H, Hitzemann R, Hunter K, Hsu HC, Iraqi FA, Ivandic B, Jacob HJ, Jansen RC, Jepsen KJ, Johnson DK, Johnson TE, Kempermann G, Kendziorski C, Kotb M, Kooy RF, Llamas B, Lammert F, Lassalle JM, Lowenstein PR, Lu L, Lusis A, Manly KF, Marcucio R, Matthews D, Medrano JF, Miller DR, Mittleman G, Mock BA, Mogil JS, Montagutelli X, Morahan G, Morris DG, Mott R, Nadeau JH, Nagase H, Nowakowski RS, O'hara BF, Osadchuk AV, Page GP, Paigen B, Paigen K, Palmer AA, Pan HJ, Peltonen-Palotie L, Peirce J, Pomp D, Pravenec M, Prows DR, Qi Z, Reeves RH, Roder J, Rosen GD, Schadt EE, Schalkwyk LC, Seltzer Z, Shimomura K, Shou S, Sillanpaa MJ, Siracusa LD, Snoeck HW, Spearow JL, Svenson K, Tarantino LM, Threadgill D, Toth LA, Valdar W, de Villena FP, Warden C, Whatley S, Williams RW, Wiltshire T, Yi N, Zhang D, Zhang M, Zou F. (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nature Genetics 36: 1133-1137.
2003
Corander, J., P. Waldmann, and M. J. Sillanpää (2003) Bayesian analysis of genetic differentiation between populations. Genetics 163: 367-374.
Kilpikari, R. and M. J. Sillanpää (2003) Bayesian analysis of multilocus association in quantitative and qualitative traits. Genetic Epidemiology 25: 122-135.
Bhattacharjee, M., C. Pritchard, M. J. Sillanpää, and E. Arjas (2003) Bayesian characterization of natural variation in gene expression. In: Methods of Microarray Data Analysis III. Eds. K. F. Johnson and S. M. Lin. Kluwer Academic Publishers, Boston, pp. 155-172.
2002
Bink, M. C. A. M, P. Uimari, M. J. Sillanpää, L. L. G. Janss, and R. C. Jansen (2002) Multiple QTL mapping in related plant populations via a pedigree-analysis approach. {Theoretical and Applied Genetics 104: 751-762|http://link.springer.de/link/service/journals/00122/contents/01/00796/].
Hoti, F. J., M. J. Sillanpää, and L. Holmström (2002) A note on estimating the posterior density of a quantitative trait locus from a Markov chain Monte Carlo sample.
Genetic Epidemiology 22: 369-376.
Sillanpää, M. J. and J. Corander (2002) Model choice in gene mapping: what and why. Trends in Genetics 18: 301-307.
Sillanpää, M. J. (2002) Mathematics-assisted mapping in analysis of medical disease. Annals of Medicine 34: 291-298.
Corander, J. and M. J. Sillanpää (2002) A unified approach to joint modeling of multiple quantitative and qualitative traits in gene mapping. Journal of Theoretical Biology 218: 435-446.
Balding DJ, Carothers AD, Marchini JL, Cardon LR, Vetta A, Griffiths B, Weir BS, Hill WG, Goldstein D, Strimmer K, Myers S, Beaumont MA, Glasbey CA, Mayer CD, Richardson S, Marshall C, Durrett R, Nielsen R, Visscher PM, Knott SA, Haley CS, Ball RD, Hackett CA, Holmes S, Husmeier D, Jansen RC, ter Braak CJF, Maliepaard CA, Boer MP, Joyce P, Li N, Stephens M, Marcoulides GA, Drezner Z, Mardia K, McVean G, Meng XL, Ochs MF, Pagel M, Sha N, Vannucci M, Sillanpaa MJ, Sisson S, Yandell BS, Jin CF, Satagopan JM, Gaffney PJ, Zeng ZB, Broman KW, Speed TP, Fearnhead P, Donnelly P, Larget B, Simon DL, Kadane JB, Nicholson G, Smith AV, Jonsson F, Gustafsson O, Stefansson K, Donnelly P, Parmigiani G, Garrett ES, Anbazhagan R, Gabrielson E (2002) Discussion on the meeting on 'Statistical modelling and analysis of genetic data'. Journal of Royal Statistical Society, Series B 64: 735-775.
Martinez, V., M. Sillanpää, G. Thorgaard, B. Robinson, J. Woolliams, and S. Knott (2002) Evidence of a pleiotropic QTL influencing components of early development in double haploid lines of rainbow trout. 7th World Congress on Genetics Applied to Livestock Production. CD-ROM. communication N° 06-08.
2001
Uimari, P. and M. J. Sillanpää (2001) Bayesian oligogenic analysis of quantitative and qualitative traits in general pedigrees. Genetic Epidemiology 21: 224-242.
Ripatti, S., J. Pitkäniemi, and M. J. Sillanpää (2001) Joint modeling of genetic association and population stratification using latent class models. Genetic Epidemiology 21 Suppl 1: S409-S414.
Sillanpää, M. J., R. Kilpikari, S. Ripatti, P. Onkamo, and P. Uimari (2001) Bayesian association mapping for quantitative traits in a mixture of two populations.
Genetic Epidemiology 21 Suppl 1: S692-S699.
Maliepaard, C., M. J. Sillanpää, J. Van Ooijen, R. C. Jansen, and E. Arjas (2001) Bayesian versus frequentist analysis of multiple quantitative trait loci with an application to an outbred apple cross. Theoretical and Applied Genetics 103: 1243-1253.
2000-1997
Hurme, P., M. J. Sillanpää, E. Arjas, T. Repo, and O. Savolainen (2000) Genetic basis of climatic adaptation in Scots Pine by Bayesian quantitative trait locus analysis. Genetics 156: 1309-1322.
Sillanpää, M. J. (1999) Bayesian QTL mapping in inbred and outbred experimental designs. Ph.D. thesis. University of Helsinki. Rolf Nevanlinna Institute Reasearch Reports A30. Yliopistopaino, Helsinki. ISBN 952-9528-56-6. ISSN 0787-8338. Reprint (PDF) Version of Ph.D. Thesis
Sillanpää, M. J. and E. Arjas (1999) Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. Genetics 151: 1605-1619.
Sillanpää, M. J. and E. Arjas (1998) Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373-1388.
Kuittinen, H., M. J. Sillanpää, and O. Savolainen (1997) Genetic basis of adaptation: flowering time in Arabidopsis thaliana. Theoretical and Applied Genetics 95: 573-583.
Other reports :
Sillanpää M. ja P. Uimari (1998) Geenikartoitusmenetelmien kehitystyötä.1 Kansanterveys 4/98 s. 9-10.
Sillanpää M. J. and E. Arjas (2001) Statistical methods for the genetic mapping of complex traits in
CSC Report on Scientific Computing 1999-2000, pp. 138-140.
Sirpa Kotila and Juha Haataja (eds.)