This page is a copy of research/scientific_computing/project/genomics/publications (Wed, 31 Aug 2022 15:01:12)
Computational Genomics
Articles and Refereed Conference Contributions
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Imputation of single nucleotide polymorphism genotypes in biparental, backcross, and topcross populations with a hidden Markov model
. In Crop science, volume 55, pp 1934-1946, 2015. (DOI
, Fulltext
).
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MAPfastR: Quantitative trait loci mapping in outbred line crosses
. In G3: Genes, Genomes, Genetics, volume 3, pp 2147-2149, 2013. (DOI
, Fulltext
).
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Fast and accurate detection of multiple quantitative trait loci
. In Journal of Computational Biology, volume 20, pp 687-702, 2013. (DOI
).
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Breakdown of methods for phasing and imputation in the presence of double genotype sharing
. In PLOS ONE, volume 8, pp e60354:1-5, 2013. (DOI
, fulltext:print
).
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Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data
. In BMC Genetics, volume 13, pp 85:1-13, 2012. (DOI
, fulltext:print
).
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Coherent estimates of genetic effects with missing information
. In Open Journal of Genetics, volume 2, pp 31-38, 2012. (DOI
, Fulltext
).
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An improved method for estimating chromosomal line origin in QTL analysis of crosses between outbred lines
. In G3: Genes, Genomes, Genetics, volume 1, pp 57-64, 2011. (DOI
).
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Haplotype inference based on hidden Markov models in the QTL–MAS 2010 multigenerational dataset
. In Proc. 14th European Workshop on QTL Mapping and Marker Assisted Selection, volume 5:3 of BMC Proceedings, pp S10:1-7, BioMed Central, London, 2011. (DOI
).
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Assessing a multiple QTL search using the variance component model
. In Computational biology and chemistry (Print), volume 34, pp 34-41, 2010. (DOI
).
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A Grid-Enabled Problem Solving Environment for QTL Analysis in R
. In Proc. 2nd International Conference on Bioinformatics and Computational Biology, pp 202-209, ISCA, Cary, NC, 2010.
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Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits
. In Advances and Applications in Bioinformatics and Chemistry, volume 3, pp 75-88, 2010. (DOI
).
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A grid portal for genetic analysis of complex traits
. In Proc. 32nd International Convention on Information and Communication Technology, Electronics and Microelectronics: Volume I, pp 281-284, MIPRO, Rijeka, Croatia, 2009.
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cnF2freq: Efficient determination of genotype and haplotype probabilities in outbred populations using Markov models
. In Bioinformatics and Computational Biology, volume 5462 of Lecture Notes in Computer Science, pp 307-319, Springer-Verlag, Berlin, 2009. (DOI
).
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New algorithms for evaluating the log-likelihood function derivatives in the AI-REML method
. In Communications in statistics. Simulation and computation, volume 38, pp 1348-1364, 2009. (DOI
).
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Newton-type methods for REML estimation in genetic analysis of quantitative traits
. In Journal of Computational Methods in Sciences and Engineering, volume 8, pp 53-67, 2008.
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Grid-enabling an efficient algorithm for demanding global optimization problems in genetic analysis
. In Proc. 3rd International Conference on e-Science and Grid Computing, pp 205-212, IEEE Computer Society, Los Alamitos, CA, 2007. (DOI
).
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Using parallel computing and grid systems for genetic mapping of quantitative traits
. In Applied Parallel Computing: State of the Art in Scientific Computing, volume 4699 of Lecture Notes in Computer Science, pp 627-636, Springer-Verlag, Berlin, 2007. (DOI
).
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Increasing the efficiency of variance component quantitative trait loci analysis by using reduced-rank identity-by-descent matrices
. In Genetics, volume 176, pp 1935-1938, 2007. (DOI
).
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Simultaneous search for multiple QTL using the global optimization algorithm DIRECT
. In Bioinformatics, volume 20, pp 1887-1895, 2004. (DOI
).
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Efficient algorithms for quantitative trait loci mapping problems
. In Journal of Computational Biology, volume 9, pp 793-804, 2002. (DOI
).
Technical Reports and Preprints
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Stochastically Guaranteed Global Optimums Achievable with a Divide-and-Conquer Approach to Multidimensional QTL Searches
. Technical report / Department of Information Technology, Uppsala University nr 2010-006, 2010. (fulltext
).
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Assessing orthogonality and statistical properties of linear regression methods for interval mapping with partial information
. Technical report / Department of Information Technology, Uppsala University nr 2010-005, 2010. (External link
, fulltext
).
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Computational and visualization tools for genetic analysis of complex traits
. Technical report / Department of Information Technology, Uppsala University nr 2010-001, 2010. (External link
, fulltext
).
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Efficient optimization algorithms and implementations for genetic analysis of complex traits on a grid system with multicore nodes
. PARA 2008: State of the Art in Scientific and Parallel Computing, Norwegian University of Science and Technology, Trondheim, Norway, 2008.
Theses
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Methods from Statistical Computing for Genetic Analysis of Complex Traits
. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 1373, Acta Universitatis Upsaliensis, Uppsala, 2016. (fulltext
, preview image
, errata
).
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Two Optimization Problems in Genetics: Multi-dimensional QTL Analysis and Haplotype Inference
. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 973, Acta Universitatis Upsaliensis, Uppsala, 2012. (fulltext
).
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Using Markov models and a stochastic Lipschitz condition for genetic analyses
. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2010-002, Uppsala University, 2010. (fulltext
).
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An e-Science Approach to Genetic Analysis of Quantitative Traits
. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 708, Acta Universitatis Upsaliensis, Uppsala, 2010. (fulltext
).
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Parallel algorithms and implementations for genetic analysis of quantitative traits
. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2007-005, Uppsala University, 2007. (fulltext
).
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Numerical Algorithms for Mapping of Multiple Quantitative Trait Loci in Experimental Populations
. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 133, Acta Universitatis Upsaliensis, Uppsala, 2005. (fulltext
).
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Numerical methods for mapping of multiple QTL
. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2003-014, Uppsala University, 2003. (fulltext
).
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Numerical Algorithms for Optimization Problems in Genetical Analysis
. Kateryna Mishchenko. Ph.D. thesis, Mälardalen University Press Dissertations nr 59, Mälardalen University, Västerås, 2008.
Supervised M.Sc. Theses and Project Reports
- S. Toor, A Grid Portal Implementation for Genetic Mapping of Multiple QTL. MSc Thesis in Scientific Computing, Uppsala University, 2007. (Advisor: S. Holmgren)