Mikko J. Sillanpää
[| University of Oulu | Funet]

Mikko J. Sillanpää, Ph.D.

Professor, Genetics and Biometry, University of Oulu; email: mjs [at] rolf.helsinki.fi

Mobile : (358) 040-6734474
2012 2012 picture

PUBLICATIONS

SOFTWARE


Associate Editor of Theoretical and Applied Genetics, 2006-present

Associate Editor of BMC Genetics, 2009-present

Review Editor of Frontier in Genetics / section Frontiers in Livestock Genomics, 2010-present

Review Editor of Frontier in Genetics /section Frontiers in Genetic Architecture, 2011-present


Project Leader in Biocenter Oulu research project (2012-2015) Genetical and Statistical Evolutionary Genetics: Analyses of Adaptive Phenotypic Variation



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) MM.tar.Z.
(reference manual in PS) MMmanual.ps.Z.
(reference manual in PDF) MMmanual.pdf.
(simulated test data set) MMtestdata.tar.Z.
(simulated test data set with missing values) MMtest30.cro.

Multimapper (Version 1.0) with environmental covariates

(info) MM_info.txt.
(updated codes) metropolis.c. data_structure.h.

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) MM_outbred.tar.Z.
(C source codes for preprocessor) MMo_prepro.tar.Z.
(reference manual in PS) MMo_manual.ps.Z.
(reference manual in PDF) MMo_manual.pdf.
(simulated test data set) o_testdata.tar.Z.

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 BAPS

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) BAMAmanual.ps.
(reference manual in PDF) BAMAmanual.pdf.
(simulated test data sets) BAMAtestdata.tar.Z.

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) Assoc_Map_WinBUGS_1.txt
(Tiny help: How to read genetic data into the WinBUGS)

(WinBUGS code for predicting complex binary trait) Bhattacharjee_code.doc

The method for association mapping 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) eQTLcQTL.pdf

(OpenBUGS model specification codes) eQTL.tar

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.



QTL mapping using hierarchical modeling of functional traits

Explanations of notations in WinBUGS code) code_and_notation.pdf

(WinBUGS model specification code) functional_code.txt

The method is presented in the paper :

Sillanpää, M. J., P. Pikkuhookana, S. Abrahamsson, T. Knürr, A. Fries, E. Lerceteau, P. Waldmann, and M. R. Garcia-Gil (2012) Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical Bayesian modeling. Heredity 108: 135-146.



BMRV / R-package for Hierarchical Bayesian Multiple Regression model for rare variant association test and for detecting rare variant interaction effect in twin study

(BMRV 1.0. R-package - Linux version) BMRV_1.0.tar.gz.
(BMRV 1.0. R-package - Windows version) BMRV_1.0.zip.
(reference manual in PDF) BMRV-manual.pdf.

The methods implemented in the BMRV 1.0. R-package are presented in the papers :

He, L., M. J. Sillanpää, S. Ripatti, and J. Pitkäniemi (2014) Bayesian latent variable collapsing model for detecting rare variant interaction effect in twin study. Genetic Epidemiology 38: 310-324.

He, L., J. Pitkäniemi, A-P. Sarin, V. Salomaa, M. J. Sillanpää, and S. Ripatti (2014) Hierarchical Bayesian model for rare variant association analysis integrating genotype uncertainty in human sequence data. Genetic Epidemiology (accepted).


PUBLICATIONS:

2014

Khazaei, H., D. M. O'Sullivan, H. Jones, M. J. Sillanpää, P. Pärssinen, O. Manninen and F. L. Stoddard (2014) Flanking SNP markers for vicine-convicine concentration in faba bean (Vicia faba L.). Molecular Breeding (accepted).

He, L., J. Pitkäniemi, A-P. Sarin, V. Salomaa, M. J. Sillanpää, and S. Ripatti (2014) Hierarchical Bayesian model for rare variant association analysis integrating genotype uncertainty in human sequence data. Genetic Epidemiology (accepted).

Li, Z., H. R. Hallingbäck, S. Abrahamsson, A. Fries, B. Andersson Gull, M. J. Sillanpää, and M. R. Garcia-Gil (2014) Functional multi-locus QTL mapping of temporal trends in Scots pine wood traits. G3: Genes, Genomes, Genetics 4: 2365-2379.

Mathew, B., J. Leon, and M. J. Sillanpää (2014) INLA inference and cross-validation to learn variance components in breeding value estimation. Molecular Breeding (accepted).

Khazaei, H., D. M. O'Sullivan, M. J. Sillanpää, and F. L. Stoddard (2014) Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.). Theoretical and Applied Genetics 127: 2371-2385.

Khazaei, H., D. M. O'Sullivan, M. J. Sillanpää, and F. L. Stoddard (2014) Genetic analysis reveals a novel locus in Vicia faba L. decoupling pigmentation in the flower from that in the extra-floral nectaries. Molecular Breeding 34: 1507-1513.

He, L., M. J. Sillanpää, S. Ripatti, and J. Pitkäniemi (2014) Bayesian latent variable collapsing model for detecting rare variant interaction effect in twin study. Genetic Epidemiology 38: 310-324.

Pikkuhookana, P., and M. J. Sillanpää (2014) Combined linkage disequilibrium and linkage mapping: Bayesian multilocus approach. Heredity 112: 351-360.

Makgahlela, M. L., I. Strandén, U. S. Nielsen, M. J. Sillanpää, and E. A. Mäntysaari (2014) Using the unified relationship matrix adjusted by breed-wise allele frequencies in genomic evaluation of a cross-breed population. Journal of Dairy Science 97: 1117-1127.

2013

Ahlinder, J., and M. J. Sillanpää (2013) Rapid Bayesian inference of heritability in animal models without convergence problems. Methods in Ecology and Evolution 4: 1037-1046.

Kärkkäinen, H. P., and M. J. Sillanpää (2013) Fast genomic predictions via Bayesian G-BLUP and multilocus models of threshold traits including censored Gaussian data. G3: Genes, Genomes, Genetics 3: 1511-1523.

Knürr, T., E. Läärä, and M. J. Sillanpää (2013) Impact of prior specifications in a shrinkage-inducing Bayesian model for quantitative trait mapping and genomic prediction. Genetics Selection Evolution 45: 24.

Li, Z., and M. J. Sillanpää (2013) A Bayesian non-parametric approach for mapping dynamic quantitative traits. Genetics 194: 997-1016.

Häggman, J., J. Juga, M. J. Sillanpää, and R. Thompson (2013) Genetic parameters for claw health and feet and leg conformation traits in Finnish Ayrshire cows. Journal of Animal Breeding and Genetics 130: 89-97.

Makgahlela, M. L., E. A. Mäntysaari, I. Stranden, M. Koivula, U. S. Nielsen, M. J. Sillanpää, and J. Juga (2013) Across breed multi-trait random regression genomic predictions in the Nordic Red dairy cattle. Journal of Animal Breeding and Genetics 130: 10-19.

Makgahlela, M. L., I. Strandén, U. S. Nielsen, M. J. Sillanpää, and E. A. Mäntysaari (2013) The estimation of genomic relationships using breedwise allele frequencies among animals in multibreed populations. Journal of Dairy Science 98: 5364-5375.

Meyer P, Siwo G, Zeevi D, Sharon E, Norel R, DREAM6 Promoter Prediction Consortium (including Sillanpää MJ), Segal E, Stolovitzky G (2013) Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. Genome Research 23: 1928-1937.

2012

Li, Z., and M. J. Sillanpää (2012) Estimation of quantitative trait locus effects with epistasis by variational Bayes algorithms. Genetics 190: 231-249.

Sillanpää, M. J., P. Pikkuhookana, S. Abrahamsson, T. Knürr, A. Fries, E. Lerceteau, P. Waldmann, and M. R. Garcia-Gil (2012) Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical Bayesian modeling. Heredity 108: 134-146.

Kärkkäinen, H. P., and M. J. Sillanpää (2012) Back to basics for Bayesian model building in genomic selection. Genetics 191: 969-987.

Li, Z., and M. J. Sillanpää (2012) Overview of LASSO-related penalized regression methods for quantitative trait mapping and genomic selection. Theoretical and Applied Genetics 125: 419-435.

Mutshinda, C. M., N. Noykova, and M. J. Sillanpää (2012) A hierarchical Bayesian approach to multi-trait clinical quantitative trait locus modeling. Frontiers in Genetics 3: 97.

Mathew, B., A. M. Bauer, P. Koistinen, T. C. Reetz, J. Leon, and M. J. Sillanpää (2012) Bayesian adaptive Markov Chain Monte Carlo estimation of genetic parameters. Heredity 109: 235-245.

Mutshinda, C. M., and M. J. Sillanpää (2012) Swift block-updating EM and pseudo-EM procedures for Bayesian shrinkage analysis of quantitative trait loci. Theoretical and Applied Genetics 125: 1575-1587.

Kärkkäinen, H. P., and M. J. Sillanpää (2012) Robustness of Bayesian multilocus association models to cryptic relatedness. Annals of Human Genetics 76: 510-523.

Mutshinda, C. M., and M. J. Sillanpää (2012) A decision rule for quantitative trait locus detection under the extended Bayesian LASSO model. Genetics 192: 1483-1491.

Kaakinen, M., F. Ducci, M. J. Sillanpää, E. Läärä, and M.-R. Järvelin (2012) Associations between variation in CHRNA5-CHRNA3-CHRNB4, body mass index and blood pressure in the northern Finland birth cohort 1966. PLoS ONE 7: e46557.

2011

Sillanpää, M. J. (2011) Overview of techniques to account for confounding due to population stratification and cryptic relatedness in genomic data association analyses. Heredity 106: 511-519.

Sillanpää, M. J. (2011) On statistical methods for estimating heritability in wild populations. Molecular Ecology 20: 1324-1332.

Gasbarra, D., M. Pirinen, S. Kulathinal, and M. J. Sillanpää (2011) Estimating haplotype frequencies by combining data from large DNA pools with database information. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8: 36-44.

Mutshinda, C. M., and M. J. Sillanpää (2011) Bayesian shrinkage analysis of QTLs under shape-adaptive shrinkage priors, and accurate re-estimation of genetic effects. Heredity 107: 405-412.

Knürr, T., E. Läärä, and M. J. Sillanpää (2011) Genetic analysis of complex traits via Bayesian variable selection: the utility of a mixture of uniform priors. Genetics Research 93: 303-318.

Bhattacharjee, M., and M. J. Sillanpää (2011) A Bayesian mixed regression based prediction of quantitative traits from molecular marker and gene expression data. PLoS ONE 6: e26959.

2010

Mutshinda, C. M., and M. J. Sillanpää (2010) Extended Bayesian LASSO for multiple quantitative trait loci mapping and unobserved phenotype prediction. Genetics 186: 1067-1075.

Hallander J., P. Waldmann, C. Wang, and M. J. Sillanpää (2010) Bayesian inference of genetic parameters based on conditional decompositions of multivariate normal distributions. Genetics 185: 645-654.

Jolma, A., T. Kivioja, J. Toivonen, L. Cheng, G. Wei, M. Enge, M. Taipale, J. M. Vaquerizas, J. Yan, M. J. Sillanpää, M. Bonke, K. Palin, S. Talukder, T. R. Hughes, N. M. Luscombe, E. Ukkonen, and J. Taipale (2010) Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Research 20: 861-873.

2009

Sillanpää, M. J. (2009) Detecting interactions in association studies by using simple allele recoding. Human Heredity 67: 69-75.

O'Hara, R. B., and M. J. Sillanpää (2009) Review of Bayesian variable selection methods: what, how and which. Bayesian Analysis 4: 85-118.

Bhattacharjee, M., and M. J. Sillanpää (2009) Bayesian joint disease-marker-expression analysis applied to clinical characteristics of chronic fatique syndrome. In: Methods of Microarray Data Analysis VI. Eds. P. McConnell, S. Lim, and A. J. Cuticchia. CreateSpace Publishing, Scotts Valley, California, pp.15-34.

Bauer, A., F. Hoti, M. von Korff, K. Pillen, J. Leon, and M. J. Sillanpää (2009) Advanced backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML vs. a Bayesian model in multi-environmental field trials. Theoretical and Applied Genetics 119: 105-123.

Bauer, A., F. Hoti, T. C. Reetz, W.-D. Schuh, J. Leon, and M. J. Sillanpää (2009) Bayesian prediction of breeding values by accounting for genotype-by-environment interaction in self-pollinating crops. Genetics Research 91: 193-207.

Pikkuhookana, P., and M. J. Sillanpää (2009) Correcting for relatedness in Bayesian models for genomic data association analysis. Heredity 103: 223-237.

Gasbarra, D., M. Pirinen, M. J. Sillanpää, and E. Arjas (2009) Bayesian QTL mapping based on reconstruction of recent genetic histories. Genetics 183: 709-721.

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.

Bhattacharjee, M., C. H. Botting, and M. J. Sillanpää (2008) Bayesian biomarker identification based on marker-expression-proteomics data. Genomics 92: 384-392.; commentary links for the paper: [1] CFIDS Association of America, [2] CDC, U.S. Department of Health and Human Services

Pirinen, M., S. Kulathinal, D. Gasbarra, and M. J. Sillanpää (2008) Estimating population haplotype frequencies from pooled DNA samples using PHASE algorithm. Genetics Research 90: 509-524.

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.

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 :

Mikko J. Sillanpää (2013) Mihin tilastollista mallia tarvitaan biologiassa? Dimensio 1/2013 : 37-39.

Mikko J. Sillanpää (2012) Perinnöllisyyttä ja tilastotiedettä. Solmu 3/2012.

Haastattelu (Kaleva, syksy 2011): Matematiikan suosio huolettaa

Tietoa vanhasta huippuyksiköstä

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.)

Helsingin Yliopiston lehdistötiedote: Väitös 31. 1. 2000


Sillanpää M. ja P. Uimari (1998) Geenikartoitusmenetelmien kehitystyötä.1 Kansanterveys 4/98 s. 9-10.

Teaching the courses: Statistical methods in genetics, fall 2008

Genome-wide association mapping, spring 2009



Mikko Sillanpää <mjs@rolf.helsinki.fi> Last modified: Fri Feb 14 15:24:03 2003 #

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