Research Topics
| Mikko J SillanpääSummaryAffiliation: University of Helsinki Country: Finland Publications
| Collaborators
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Detail Information
Publications
Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical Bayesian modelingM J Sillanpää
Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
Heredity (Edinb) 108:134-46. 2012....- On statistical methods for estimating heritability in wild populationsMikko J Sillanpää
Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
Mol Ecol 20:1324-32. 2011..Also computational issues and hypothetical example applications for ecologists are considered... - Overview of techniques to account for confounding due to population stratification and cryptic relatedness in genomic data association analysesM J Sillanpää
Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
Heredity (Edinb) 106:511-9. 2011..Even though many of these techniques have originally been developed in the context of human genetics, most of them are also applicable to model organisms and breeding populations... - Hierarchical modeling of clinical and expression quantitative trait lociM J Sillanpää
Department of Mathematics and Statistics, Rolf Nevanlinna Institute, University of Helsinki, Helsinki, Finland
Heredity 101:271-84. 2008..The method is illustrated using both simulated and real data... - Mapping quantitative trait loci from a single-tail sample of the phenotype distribution including survival dataMikko J Sillanpää
Department of Mathematics and Statistics, University of Helsinki, Finland
Genetics 177:2361-77. 2007..The benefits of the approach are illustrated using simulated data sets and a real data set on the survival of F(2) mice following infection with Listeria monocytogenes... - Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross dataM J Sillanpää
Rolf Nevanlinna Institute, University of Helsinki, Finland
Genetics 148:1373-88. 1998..It is implemented as a software package. Its initial version is freely available for research purposes under the name Multimapper at URL http://www.rni.helsinki.fi/mjs... - Association mapping of complex trait loci with context-dependent effects and unknown context variableMikko J Sillanpää
Rolf Nevanlinna Institute, University of Helsinki, Finland
Genetics 174:1597-611. 2006..The implementation (written in WinBUGS) is freely available for research purposes from http://www.rni.helsinki.fi/ approximately mjs/... - Replication in genetic studies of complex traitsM J Sillanpää
Rolf Nevanlinna Institute, Department of Mathematics and Statistics, P O Box 68, FIN 00014 University of Helsinki, Finland
Ann Hum Genet 68:646-57. 2004..There are also other reasons related to the data collection and analysis. Replication may remain a source of frustration unless more emphasis is put on controlling these sources of heterogeneity between studies... - Bayesian association-based fine mapping in small chromosomal segmentsMikko J Sillanpää
Rolf Nevanlinna Institute, University of Helsinki, FIN 00014 Helsinki, Finland
Genetics 169:427-39. 2005..Estimation of model parameters is based on Markov chain Monte Carlo (MCMC) sampling and is implemented using WinBUGS. The model specification code is freely available for research purposes from http://www.rni.helsinki.fi/~mjs/... - Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring dataM J Sillanpää
Rolf Nevanlinna Institute, FIN 00014 University of Helsinki, Finland
Genetics 151:1605-19. 1999..The method is implemented as a software package and is freely available under the name Multimapper/outbred at URL http://www.rni.helsinki.fi/mjs/... - Mathematics-assisted mapping in analysis of medical diseaseMikko J Sillanpää
Rolf Nevanlinna Institute, University of Helsinki, Finland
Ann Med 34:291-8. 2002..We also illustrate how to proceed and what kind of possibilities the statistical analysis may provide to medical scientists... - Model choice in gene mapping: what and whyMikko J Sillanpää
Rolf Nevanlinna Institute, FIN 00014 University of Helsinki, Finland
Trends Genet 18:301-7. 2002..Our aim here is to give an overview of the most popular statistical criteria and to present principles behind them. Bayesian model averaging is suggested as a robust alternative for such methods... - Estimating genealogies from linked marker data: a Bayesian approachDario Gasbarra
Department of Mathematics and Statistics, University of Helsinki, Finland
BMC Bioinformatics 8:411. 2007..A few examples of such questions are haplotype estimation, relatedness and relationship estimation, gene mapping by combining pedigree and linkage disequilibrium information, and estimation of population structure... - Bayesian quantitative trait locus mapping based on reconstruction of recent genetic historiesDario Gasbarra
Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
Genetics 183:709-21. 2009..The method is tested on two simulated data sets. Comparisons with traditional variance component linkage analysis and association analysis demonstrate the benefits of our approach in a gene mapping context... - Estimating population haplotype frequencies from pooled DNA samples using PHASE algorithmMatti Pirinen
Department of Mathematics and Statistics, University of Helsinki, PO Box 68, FIN 00014 University of Helsinki, Finland
Genet Res (Camb) 90:509-24. 2008..Our results are in line with the earlier findings in that the pool size should be relatively small, only 2-5 individuals in our examples, in order to provide reliable estimates of population haplotype frequencies... - Estimating haplotype frequencies by combining data from large DNA pools with database informationDario Gasbarra
Department of Mathematics and Statistics, University of Helsinki, FIN 00014 Helsinki, Finland
IEEE/ACM Trans Comput Biol Bioinform 8:36-44. 2011..The method has been implemented using Matlab and the code is available upon request from the authors... - BAPS 2: enhanced possibilities for the analysis of genetic population structureJukka Corander
Rolf Nevanlinna Institute, P O Box 4, FIN 00014 University of Helsinki, Finland
Bioinformatics 20:2363-9. 2004..The enhanced features are illustrated by analyses of simulated data and an extensive human molecular dataset. AVAILABILITY: Freely available at http://www.rni.helsinki.fi/~jic/bapspage.html... - Estimating genealogies from unlinked marker data: a Bayesian approachDario Gasbarra
Department of Mathematics and Statistics, University of Helsinki, P O Box 68, FIN 00014, Finland
Theor Popul Biol 72:305-22. 2007..As illustrations of the method, we consider the question of relatedness at the level of genes/genomes (IBD estimation), using both simulated and real data... - Bayesian analysis of multilocus association in quantitative and qualitative traitsRiika Kilpikari
Rolf Nevanlinna Institute, University of Helsinki, Helsinki, Finland
Genet Epidemiol 25:122-35. 2003..The method is implemented as a software package, which is freely available for research purposes under the name BAMA... - Genetic analysis of complex traits via Bayesian variable selection: the utility of a mixture of uniform priorsTimo Knürr
Department of Mathematics and Statistics, P O Box 68, FIN 00014 University of Helsinki, Finland
Genet Res (Camb) 93:303-18. 2011..The sensitivity of MU to the specification of hyperparameters is assessed in one of the data examples... - Extended Bayesian LASSO for multiple quantitative trait loci mapping and unobserved phenotype predictionCrispin M Mutshinda
Department of Agricultural Sciences, University of Helsinki, Helsinki FIN 00014, Finland
Genetics 186:1067-75. 2010..Consequently, the EBL seems to point to a new direction for QTL mapping, phenotype prediction, and GBV estimation... - A note on estimating the posterior density of a quantitative trait locus from a Markov chain Monte Carlo sampleFabian J Hoti
Rolf Nevanlinna Institute, University of Helsinki, Helsinki, Finland
Genet Epidemiol 22:369-76. 2002..Different kernel implementations are available from Rolf Nevanlinna Institute's web page (http://www.rni.helsinki.fi/;fjh)... - A unified approach to joint modeling of multiple quantitative and qualitative traits in gene mappingJukka Corander
Rolf Nevanlinna Institute, University of Helsinki, 4, Finland
J Theor Biol 218:435-46. 2002..Outline of the possible implementation of the Bayesian method is described using the general reversible-jump Markov chain Monte Carlo algorithm. Some future challenges and extensions are also discussed... - Detecting interactions in association studies by using simple allele recodingMikko J Sillanpää
Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
Hum Hered 67:69-75. 2009..Data recoding is illustrated for several interaction models using hypothetical examples and by presenting gene-gene interaction analysis in a real cystic fibrosis dataset using the BAMA software... - Constructing the parental linkage phase and the genetic map over distances <1 cM using pooled haploid DNADario Gasbarra
University of Helsinki, Helsinki FIN 00014, Finland
Genetics 172:1325-35. 2006..The role of segregation distortion as a source of these deviations is also discussed. The software implementing this method is freely available for research purposes from the authors... - Estimation of additive genetic and environmental sources of quantitative trait variation using data on married couples and their siblingsSangita Kulathinal
Department of Mathematics and Statistics, University of Helsinki
Genet Res (Camb) 90:269-79. 2008..Here, these estimates are provided for body height, weight, systolic blood pressure and total serum cholesterol measured from subjects of the Indian Migration Study... - Backward simulation of ancestors of sampled individualsDario Gasbarra
Department of Mathematics and Statistics, Rolf Nevanlinna Institute, University of Helsinki, P.O. Box 68, FIN-00014 Helsinki, Finland
Theor Popul Biol 67:75-83. 2005..The performance of the approach is illustrated with a simulation example. The software (written in C-language) is freely available for research purposes at http://www.rni.helsinki.fi/~dag/... - Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificitiesArttu Jolma
Department of Molecular Medicine, National Public Health Institute KTL and Genome Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
Genome Res 20:861-73. 2010..Our results reveal unexpected dimeric modes of binding for several factors that were thought to preferentially bind DNA as monomers... - Bayesian analysis of genetic differentiation between populationsJukka Corander
Rolf Nevanlinna Institute, FIN-00014, University of Helsinki, Helsinki, Finland
Genetics 163:367-74. 2003..The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/~mjs...