Computational Genomics

Articles and Refereed Conference Contributions

• Imputation of single nucleotide polymorphism genotypes in biparental, backcross, and topcross populations with a hidden Markov model. John M. Hickey, Gregor Gorjanc, Rajeev K. Varshney, and Carl Nettelblad. In Crop science, volume 55, pp 1934-1946, 2015. (DOI, Fulltext).
• MAPfastR: Quantitative trait loci mapping in outbred line crosses. Ronald M. Nelson, Carl Nettelblad, Mats E. Pettersson, Xia Shen, Lucy Crooks, François Besnier, José Álvarez-Castro, Lars Rönnegård, Weronica Ek, Zheya Sheng, Marcin Kierczak, Sverker Holmgren, and Örjan Carlborg. In G3: Genes, Genomes, Genetics, volume 3, pp 2147-2149, 2013. (DOI, Fulltext).
• Fast and accurate detection of multiple quantitative trait loci. Carl Nettelblad, Behrang Mahjani, and Sverker Holmgren. In Journal of Computational Biology, volume 20, pp 687-702, 2013. (DOI).
• Breakdown of methods for phasing and imputation in the presence of double genotype sharing. Carl Nettelblad. In PLOS ONE, volume 8, pp e60354:1-5, 2013. (DOI, fulltext:print).
• Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data. Carl Nettelblad. In BMC Genetics, volume 13, pp 85:1-13, 2012. (DOI, fulltext:print).
• Coherent estimates of genetic effects with missing information. Carl Nettelblad, Örjan Carlborg, Ania Pino-Querido, and José M. Álvarez-Castro. In Open Journal of Genetics, volume 2, pp 31-38, 2012. (DOI, Fulltext).
• An improved method for estimating chromosomal line origin in QTL analysis of crosses between outbred lines. Lucy Crooks, Carl Nettelblad, and Örjan Carlborg. In G3: Genes, Genomes, Genetics, volume 1, pp 57-64, 2011. (DOI).
• Haplotype inference based on hidden Markov models in the QTL–MAS 2010 multigenerational dataset. Carl Nettelblad. 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).
• Assessing a multiple QTL search using the variance component model. Kateryna Mishchenko, Lars Rönnegård, Sverker Holmgren, and Volodymyr Mishchenko. In Computational biology and chemistry (Print), volume 34, pp 34-41, 2010. (DOI).
• A Grid-Enabled Problem Solving Environment for QTL Analysis in R. Mahen Jayawardena, Carl Nettelblad, Salman Toor, Per-Olov Östberg, Erik Elmroth, and Sverker Holmgren. In Proc. 2nd International Conference on Bioinformatics and Computational Biology, pp 202-209, ISCA, Cary, NC, 2010.
• Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits. Kajsa Ljungberg, Kateryna Mishchenko, and Sverker Holmgren. In Advances and Applications in Bioinformatics and Chemistry, volume 3, pp 75-88, 2010. (DOI).
• A grid portal for genetic analysis of complex traits. Mahen Jayawardena, Salman Toor, and Sverker Holmgren. In Proc. 32nd International Convention on Information and Communication Technology, Electronics and Microelectronics: Volume I, pp 281-284, MIPRO, Rijeka, Croatia, 2009.
• cnF2freq: Efficient determination of genotype and haplotype probabilities in outbred populations using Markov models. Carl Nettelblad, Sverker Holmgren, Lucy Crooks, and Örjan Carlborg. In Bioinformatics and Computational Biology, volume 5462 of Lecture Notes in Computer Science, pp 307-319, Springer-Verlag, Berlin, 2009. (DOI).
• New algorithms for evaluating the log-likelihood function derivatives in the AI-REML method. Kateryna Mishchenko and Maya Neytcheva. In Communications in statistics. Simulation and computation, volume 38, pp 1348-1364, 2009. (DOI).
• Newton-type methods for REML estimation in genetic analysis of quantitative traits. Kateryna Mishchenko, Sverker Holmgren, and Lars Rönnegård. In Journal of Computational Methods in Sciences and Engineering, volume 8, pp 53-67, 2008.
• Grid-enabling an efficient algorithm for demanding global optimization problems in genetic analysis. Mahen Jayawardena and Sverker Holmgren. In Proc. 3rd International Conference on e-Science and Grid Computing, pp 205-212, IEEE Computer Society, Los Alamitos, CA, 2007. (DOI).
• Using parallel computing and grid systems for genetic mapping of quantitative traits. Mahen Jayawardena, Kajsa Ljungberg, and Sverker Holmgren. 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).
• Increasing the efficiency of variance component quantitative trait loci analysis by using reduced-rank identity-by-descent matrices. Lars Rönnegård, Kateryna Mishchenko, Sverker Holmgren, and Örjan Carlborg. In Genetics, volume 176, pp 1935-1938, 2007. (DOI).
• Simultaneous search for multiple QTL using the global optimization algorithm DIRECT. Kajsa Ljungberg, Sverker Holmgren, and Örjan Carlborg. In Bioinformatics, volume 20, pp 1887-1895, 2004. (DOI).
• Efficient algorithms for quantitative trait loci mapping problems. Kajsa Ljungberg, Sverker Holmgren, and Örjan Carlborg. In Journal of Computational Biology, volume 9, pp 793-804, 2002. (DOI).

Technical Reports and Preprints

• Stochastically Guaranteed Global Optimums Achievable with a Divide-and-Conquer Approach to Multidimensional QTL Searches. Carl Nettelblad and Sverker Holmgren. Technical report / Department of Information Technology, Uppsala University nr 2010-006, 2010. (fulltext).
• Assessing orthogonality and statistical properties of linear regression methods for interval mapping with partial information. Carl Nettelblad, Örjan Carlborg, and José M. Álvarez-Castro. Technical report / Department of Information Technology, Uppsala University nr 2010-005, 2010. (External link, fulltext).
• Computational and visualization tools for genetic analysis of complex traits. Mahen Jayawardena, Salman Toor, and Sverker Holmgren. Technical report / Department of Information Technology, Uppsala University nr 2010-001, 2010. (External link, fulltext).
• Efficient optimization algorithms and implementations for genetic analysis of complex traits on a grid system with multicore nodes. Mahen Jayawardena, Henrik Löf, and Sverker Holmgren. PARA 2008: State of the Art in Scientific and Parallel Computing, Norwegian University of Science and Technology, Trondheim, Norway, 2008.

Theses

• Methods from Statistical Computing for Genetic Analysis of Complex Traits. Behrang Mahjani. 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).
• Two Optimization Problems in Genetics: Multi-dimensional QTL Analysis and Haplotype Inference. Carl Nettelblad. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 973, Acta Universitatis Upsaliensis, Uppsala, 2012. (fulltext).
• Using Markov models and a stochastic Lipschitz condition for genetic analyses. Carl Nettelblad. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2010-002, Uppsala University, 2010. (fulltext).
• An e-Science Approach to Genetic Analysis of Quantitative Traits. Mahen Jayawardena. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 708, Acta Universitatis Upsaliensis, Uppsala, 2010. (fulltext).
• Parallel algorithms and implementations for genetic analysis of quantitative traits. Mahen Jayawardena. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2007-005, Uppsala University, 2007. (fulltext).
• Numerical Algorithms for Mapping of Multiple Quantitative Trait Loci in Experimental Populations. Kajsa Ljungberg. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 133, Acta Universitatis Upsaliensis, Uppsala, 2005. (fulltext).
• Numerical methods for mapping of multiple QTL. Kajsa Ljungberg. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2003-014, Uppsala University, 2003. (fulltext).

• 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)