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  • 201.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Haplotype inference based on hidden Markov models in the QTL–MAS 2010 multigenerational dataset2011In: Proc. 14th European Workshop on QTL Mapping and Marker Assisted Selection, London: BioMed Central , 2011, p. S10:1-7Conference paper (Refereed)
  • 202.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data2012Report (Other academic)
  • 203.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data2012In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 13, p. 85:1-13Article in journal (Refereed)
  • 204.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Two Optimization Problems in Genetics: Multi-dimensional QTL Analysis and Haplotype Inference2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The existence of new technologies, implemented in efficient platforms and workflows has made massive genotyping available to all fields of biology and medicine. Genetic analyses are no longer dominated by experimental work in laboratories, but rather the interpretation of the resulting data. When billions of data points representing thousands of individuals are available, efficient computational tools are required. The focus of this thesis is on developing models, methods and implementations for such tools.

    The first theme of the thesis is multi-dimensional scans for quantitative trait loci (QTL) in experimental crosses. By mating individuals from different lines, it is possible to gather data that can be used to pinpoint the genetic variation that influences specific traits to specific genome loci. However, it is natural to expect multiple genes influencing a single trait to interact. The thesis discusses model structure and model selection, giving new insight regarding under what conditions orthogonal models can be devised. The thesis also presents a new optimization method for efficiently and accurately locating QTL, and performing the permuted data searches needed for significance testing. This method has been implemented in a software package that can seamlessly perform the searches on grid computing infrastructures.

    The other theme in the thesis is the development of adapted optimization schemes for using hidden Markov models in tracing allele inheritance pathways, and specifically inferring haplotypes. The advances presented form the basis for more accurate and non-biased line origin probabilities in experimental crosses, especially multi-generational ones. We show that the new tools are able to reconstruct haplotypes and even genotypes in founder individuals and offspring alike, based on only unordered offspring genotypes. The tools can also handle larger populations than competing methods, resolving inheritance pathways and phase in much larger and more complex populations. Finally, the methods presented are also applicable to datasets where individual relationships are not known, which is frequently the case in human genetics studies. One immediate application for this would be improved accuracy for imputation of SNP markers within genome-wide association studies (GWAS).

    List of papers
    1. Coherent estimates of genetic effects with missing information
    Open this publication in new window or tab >>Coherent estimates of genetic effects with missing information
    2012 (English)In: Open Journal of Genetics, ISSN 2162-4453, E-ISSN 2162-4461, Vol. 2, p. 31-38Article in journal (Refereed) Published
    Keywords
    genetic effects, missing genotypes, orthogonal estimation, QTL analysis
    National Category
    Bioinformatics and Systems Biology Genetics Probability Theory and Statistics Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-180915 (URN)10.4236/ojgen.2012.21003 (DOI)
    Projects
    eSSENCE
    Available from: 2012-03-02 Created: 2012-09-12 Last updated: 2017-12-07Bibliographically approved
    2. Fast and accurate detection of multiple quantitative trait loci
    Open this publication in new window or tab >>Fast and accurate detection of multiple quantitative trait loci
    2013 (English)In: Journal of Computational Biology, ISSN 1066-5277, E-ISSN 1557-8666, Vol. 20, p. 687-702Article in journal (Refereed) Published
    National Category
    Bioinformatics and Systems Biology Genetics Computational Mathematics Probability Theory and Statistics
    Identifiers
    urn:nbn:se:uu:diva-180916 (URN)10.1089/cmb.2012.0242 (DOI)000323822000006 ()
    Projects
    eSSENCE
    Available from: 2013-08-06 Created: 2012-09-13 Last updated: 2017-12-07Bibliographically approved
    3. A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Open this publication in new window or tab >>A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Show others...
    2010 (English)In: Proc. 2nd International Conference on Bioinformatics and Computational Biology, Cary, NC: ISCA , 2010, p. 202-209Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Cary, NC: ISCA, 2010
    National Category
    Software Engineering Genetics
    Identifiers
    urn:nbn:se:uu:diva-111594 (URN)978-1-880843-76-5 (ISBN)
    Projects
    eSSENCE
    Available from: 2010-01-12 Created: 2009-12-17 Last updated: 2018-01-12Bibliographically approved
    4. cnF2freq: Efficient determination of genotype and haplotype probabilities in outbred populations using Markov models
    Open this publication in new window or tab >>cnF2freq: Efficient determination of genotype and haplotype probabilities in outbred populations using Markov models
    2009 (English)In: Bioinformatics and Computational Biology, Berlin: Springer-Verlag , 2009, p. 307-319Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2009
    Series
    Lecture Notes in Computer Science ; 5462
    National Category
    Computational Mathematics Genetics
    Identifiers
    urn:nbn:se:uu:diva-103916 (URN)10.1007/978-3-642-00727-9_29 (DOI)000265785800029 ()978-3-642-00726-2 (ISBN)
    Available from: 2009-05-25 Created: 2009-05-25 Last updated: 2017-01-25Bibliographically approved
    5. An improved method for estimating chromosomal line origin in QTL analysis of crosses between outbred lines
    Open this publication in new window or tab >>An improved method for estimating chromosomal line origin in QTL analysis of crosses between outbred lines
    2011 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 1, p. 57-64Article in journal (Refereed) Published
    National Category
    Computational Mathematics Genetics
    Identifiers
    urn:nbn:se:uu:diva-156197 (URN)10.1534/g3.111.000109 (DOI)000312405400007 ()
    Projects
    eSSENCE
    Available from: 2011-06-01 Created: 2011-07-15 Last updated: 2017-12-08Bibliographically approved
    6. MAPfastR: Quantitative trait loci mapping in outbred line crosses
    Open this publication in new window or tab >>MAPfastR: Quantitative trait loci mapping in outbred line crosses
    Show others...
    2013 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 3, p. 2147-2149Article in journal (Refereed) Published
    National Category
    Computational Mathematics Genetics Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-180917 (URN)10.1534/g3.113.008623 (DOI)000328334500005 ()
    Projects
    eSSENCE
    Available from: 2013-10-11 Created: 2012-09-13 Last updated: 2017-12-07Bibliographically approved
    7. Haplotype inference based on hidden Markov models in the QTL–MAS 2010 multigenerational dataset
    Open this publication in new window or tab >>Haplotype inference based on hidden Markov models in the QTL–MAS 2010 multigenerational dataset
    2011 (English)In: Proc. 14th European Workshop on QTL Mapping and Marker Assisted Selection, London: BioMed Central , 2011, p. S10:1-7Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    London: BioMed Central, 2011
    Series
    BMC Proceedings, ISSN 1753-6561 ; 5:3
    National Category
    Computational Mathematics Genetics
    Identifiers
    urn:nbn:se:uu:diva-153449 (URN)10.1186/1753-6561-5-S3-S10 (DOI)
    Projects
    eSSENCE
    Available from: 2010-05-17 Created: 2011-05-12 Last updated: 2017-01-25Bibliographically approved
    8. Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data
    Open this publication in new window or tab >>Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data
    2012 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 13, p. 85:1-13Article in journal (Refereed) Published
    Keywords
    haplotyping, phasing, genotype inference, nuclear family data, hidden Markov models
    National Category
    Probability Theory and Statistics Computational Mathematics Genetics Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-182488 (URN)10.1186/1471-2156-13-85 (DOI)000314354600001 ()
    Projects
    eSSENCE
    Available from: 2012-10-10 Created: 2012-10-10 Last updated: 2017-12-07Bibliographically approved
    9. Breakdown of methods for phasing and imputation in the presence of double genotype sharing
    Open this publication in new window or tab >>Breakdown of methods for phasing and imputation in the presence of double genotype sharing
    2012 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2012-027
    National Category
    Probability Theory and Statistics Computational Mathematics Genetics Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-181598 (URN)
    Projects
    eSSENCE
    Available from: 2012-09-25 Created: 2012-09-26 Last updated: 2017-01-25Bibliographically approved
  • 205.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Using Markov models and a stochastic Lipschitz condition for genetic analyses2010Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    A proper understanding of biological processes requires an understanding of genetics and evolutionary mechanisms. The vast amounts of genetical information that can routinely be extracted with modern technology have so far not been accompanied by an equally extended understanding of the corresponding processes.

    The relationship between a single gene and the resulting properties, phenotype of an individual is rarely clear. This thesis addresses several computational challenges regarding identifying and assessing the effects of quantitative trait loci (QTL), genomic positions where variation is affecting a trait. The genetic information available for each individual is rarely complete, meaning that the unknown variable of the genotype in the loci modelled also needs to be addressed. This thesis contains the presentation of new tools for employing the information that is available in a way that maximizes the information used, by using hidden Markov models (HMMs), resulting in a change in algorithm runtime complexity from exponential to log-linear, in terms of the number of markers. It also proposes the introduction of inferred haplotypes to further increase the power to assess these unknown variables for pedigrees of related genetically diverse individuals. Modelling consequences of partial genetic information are also treated.

    Furthermore, genes are not directly affecting traits, but are rather expressed in the environment of and in concordance with other genes. Therefore, significant interactions can be expected within genes, where some combination of genetic variation gives a pronounced, or even opposite, effect, compared to when occurring separately. This thesis addresses how to perform efficient scans for multiple interacting loci, as well as how to derive highly accurate empirical significance tests in these settings. This is done by analyzing the mathematical properties of the objective function describing the quality of model fits, and reformulating it through a simple transformation. Combined with the presented prototype of a problem-solving environment, these developments can make multi-dimensional searches for QTL routine, allowing the pursuit of new biological insight.

  • 206.
    Nettelblad, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Pino-Querido, Ania
    University of Santiago de Compostela, Department of Genetics.
    Álvarez-Castro, José M.
    University of Santiago de Compostela, Department of Genetics.
    Coherent estimates of genetic effects with missing information2012In: Open Journal of Genetics, ISSN 2162-4453, E-ISSN 2162-4461, Vol. 2, p. 31-38Article in journal (Refereed)
  • 207.
    Nettelblad, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Álvarez-Castro, José M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Assessing orthogonality and statistical properties of linear regression methods for interval mapping with partial information2010Report (Other academic)
  • 208.
    Nettelblad, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Stochastically guaranteed global optima in multi-dimensional QTL searches2010Report (Other academic)
  • 209.
    Nettelblad, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Crooks, Lucy
    Carlborg, Örjan
    cnF2freq: Efficient determination of genotype and haplotype probabilities in outbred populations using Markov models2009In: Bioinformatics and Computational Biology, Berlin: Springer-Verlag , 2009, p. 307-319Conference paper (Refereed)
  • 210.
    Nettelblad, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Mahjani, Behrang
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Fast and accurate detection of multiple quantitative trait loci2013In: Journal of Computational Biology, ISSN 1066-5277, E-ISSN 1557-8666, Vol. 20, p. 687-702Article in journal (Refereed)
  • 211.
    Neytcheva, Maya
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Bull, Jonathan R.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Dorostkar, Ali
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Kruchinina, Anastasia
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nikitenko, Dmitry
    Popova, Nina
    Shvets, Pavel
    Teplov, Alexey
    Voevodin, Vadim
    Voevodin, Vladimir
    Multidimensional performance and scalability analysis for diverse applications based on system monitoring data2018In: Parallel Processing and Applied Mathematics: Part I, Springer, 2018, p. 417-431Conference paper (Refereed)
  • 212. Niklasson, Anders M. N.
    et al.
    Cawkwell, Marc J.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Canonical density matrix perturbation theory2015In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 92, p. 063301:1-8, article id 063301Article in journal (Refereed)
  • 213. Niklasson, Anders M. N.
    et al.
    Mniszewski, Susan M.
    Negre, Christian F. A.
    Cawkwell, Marc J.
    Swart, Pieter J.
    Mohd-Yusof, Jamal
    Germann, Timothy C.
    Wall, Michael E.
    Bock, Nicolas
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Djidjev, Hristo
    Graph-based linear scaling electronic structure theory2016In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 144, p. 234101:1-8, article id 234101Article in journal (Refereed)
  • 214. Nilsen, Jon K.
    et al.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nagy, Zsombor
    Mohn, Bjarte
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Chelonia — a self-healing storage cloud2010In: Proc. 9th Cracow Grid Workshop, Kraków, Poland: ACC Cyfronet AGH , 2010, p. 5-12Conference paper (Refereed)
  • 215. Nilsen, Jon Kerr
    et al.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nagy, Zsombor
    Mohn, Bjarte
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Read, Alex
    Performance and stability of the Chelonia storage system2012In: Proc. International Symposium on Grids and Clouds 2012, Trieste, Italy: SISSA , 2012, p. 009:1-14Conference paper (Refereed)
  • 216. Nilsen, Jon Kerr
    et al.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nagy, Zsombor
    Read, Alex
    Chelonia: A self-healing, replicated storage system2011In: Computing in High Energy and Nuclear Physics: CHEP 2010, Bristol, UK: Institute of Physics Publishing (IOPP), 2011, p. 062019:1-6Conference paper (Refereed)
  • 217. Nissen, Anna
    et al.
    Kormann, Katharina
    Grandin, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Virta, Kristoffer
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Stable difference methods for block-oriented adaptive grids2015In: Journal of Scientific Computing, ISSN 0885-7474, E-ISSN 1573-7691, Vol. 65, p. 486-511Article in journal (Refereed)
  • 218.
    Nordén, Markus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Löf, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Rantakokko, Jarmo
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Dynamic data migration for structured AMR solvers2007In: International journal of parallel programming, ISSN 0885-7458, E-ISSN 1573-7640, Vol. 35, p. 477-491Article in journal (Refereed)
  • 219.
    Nordén, Markus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Löf, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Rantakokko, Jarmo
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Geographical locality and dynamic data migration for OpenMP implementations of adaptive PDE solvers2008In: OpenMP Shared Memory Parallel Programming, Berlin: Springer-Verlag , 2008, p. 382-393Conference paper (Refereed)
  • 220. Normann, Per
    et al.
    Öfverstedt, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Deterministic parallel graph coloring with hashing2015Report (Other academic)
  • 221. Normann, Per
    et al.
    Öfverstedt, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Deterministic parallel graph coloring with symmetry breaking2015Report (Other academic)
  • 222.
    Novella, Jon Ander
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Emami Khoonsari, Payam
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Chemistry.
    Herman, Stephanie
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Chemistry. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Whitenack, Daniel
    Capuccini, Marco
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Burman, Joachim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Neurology.
    Kultima, Kim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Chemistry.
    Spjuth, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Container-based bioinformatics with Pachyderm2019In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 35, p. 839-846Article in journal (Refereed)
  • 223.
    Nylén, Aletta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Thota, Neena
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Kinnunen, Päivi
    Butler, Matthew
    Morgan, Michael
    Multidimensional analysis of creative coding MOOC forums: a methodological discussion2015In: Proc. 15th International Conference on Computing Education Research: Koli Calling, New York: ACM Press, 2015, p. 137-141Conference paper (Refereed)
  • 224.
    Peters, Anne-Kathrin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Identity development of CS and IT students: What's the role of higher education?2013In: Proc. 9th International Computing Education Research Conference, New York: ACM Press, 2013, p. 187-188Conference paper (Refereed)
  • 225.
    Peters, Anne-Kathrin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computer Systems. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    The role of students' identity development in higher education in computing2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Higher Education Research in science, technology, engineering, and mathematics (STEM) indicates that students are not well supported in the process of integrating their educational experience with their perception of who they are and want to become. This is associated with drop-out and also has consequences for student learning. Here, learning is defined in the broad sense of personal and professional development.

    This thesis presents results from a research project that explores students' identity development during their first three years of studies. The analysis and results build on interview and essay data collected during a longitudinal study of students in two study programmes at Uppsala University, Computer and Information Engineering (IT) and Computer Science (CS). The main body of data analysed for this thesis was collected from the students at the beginning and end of their first study year.

    A research framework to study identity has been developed. The notion of identity used in this work has been inspired by Lave and Wenger's social theory of learning, and theory of situated learning. Identity, in this work, refers to students' histories of experiences with a focus on how they negotiate meaning within the discipline of CS/IT.

    The results describe aspects of CS/IT students' identities and provide a basis from which to discuss the implications of identity for learning and education, as well as to reason about how identity development can be supported in CS/IT education.

    List of papers
    1. Students' experiences and attitudes towards learning Computer Science
    Open this publication in new window or tab >>Students' experiences and attitudes towards learning Computer Science
    2012 (English)In: Proc. 42nd ASEE/IEEE Frontiers in Education Conference, Piscataway, NJ: IEEE , 2012, p. 88-93Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Piscataway, NJ: IEEE, 2012
    National Category
    Computer Sciences Educational Sciences
    Identifiers
    urn:nbn:se:uu:diva-184605 (URN)10.1109/FIE.2012.6462238 (DOI)000356489200033 ()978-1-4673-1353-7 (ISBN)
    Available from: 2012-10-06 Created: 2012-11-09 Last updated: 2018-01-12Bibliographically approved
    2. Engagement in Computer Science and IT — What!: A matter of identity?
    Open this publication in new window or tab >>Engagement in Computer Science and IT — What!: A matter of identity?
    2013 (English)In: Proc. 1st International Conference on Learning and Teaching in Computing and Engineering, Los Alamitos, CA: IEEE Computer Society, 2013, p. 114-121Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2013
    National Category
    Computer Sciences Educational Sciences
    Identifiers
    urn:nbn:se:uu:diva-202686 (URN)10.1109/LaTiCE.2013.42 (DOI)000324484000016 ()978-1-4673-5627-5 (ISBN)
    Conference
    LaTiCE 2013
    Available from: 2013-06-22 Created: 2013-06-25 Last updated: 2018-01-11Bibliographically approved
    3. First year Computer Science and IT students' experience of participation in the discipline
    Open this publication in new window or tab >>First year Computer Science and IT students' experience of participation in the discipline
    2014 (English)In: Proc. 2nd International Conference on Learning and Teaching in Computing and Engineering, Los Alamitos, CA: IEEE Computer Society, 2014, p. 1-8Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2014
    National Category
    Computer Sciences Educational Sciences
    Identifiers
    urn:nbn:se:uu:diva-224653 (URN)10.1109/LaTiCE.2014.9 (DOI)000355978500001 ()978-1-4799-3591-8 (ISBN)
    Conference
    LaTiCE 2014
    Available from: 2014-06-10 Created: 2014-05-16 Last updated: 2018-01-11Bibliographically approved
  • 226.
    Peters, Anne-Kathrin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Berglund, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Pears, Arnold
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    First year Computer Science and IT students' experience of participation in the discipline2014In: Proc. 2nd International Conference on Learning and Teaching in Computing and Engineering, Los Alamitos, CA: IEEE Computer Society, 2014, p. 1-8Conference paper (Refereed)
  • 227.
    Peters, Anne-Kathrin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Berglund, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Pears, Arnold
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Second year Computer Science and IT students' experience of participation in the discipline2015In: Proc. 15th International Conference on Computing Education Research: Koli Calling, New York: ACM Press, 2015, p. 68-76Conference paper (Refereed)
  • 228.
    Peters, Anne-Kathrin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Pears, Arnold
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Engagement in Computer Science and IT — What!: A matter of identity?2013In: Proc. 1st International Conference on Learning and Teaching in Computing and Engineering, Los Alamitos, CA: IEEE Computer Society, 2013, p. 114-121Conference paper (Refereed)
  • 229.
    Peters, Anne-Kathrin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Pears, Arnold
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Students' experiences and attitudes towards learning Computer Science2012In: Proc. 42nd ASEE/IEEE Frontiers in Education Conference, Piscataway, NJ: IEEE , 2012, p. 88-93Conference paper (Refereed)
  • 230.
    Pietrini, Alberto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sébastien
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A statistical approach to detect protein complexes at X-ray free electron laser facilities2018In: Communications Physics, E-ISSN 2399-3650, Vol. 1, p. 92:1-11, article id 92Article in journal (Refereed)
  • 231.
    Pietrini, Alberto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Artifact reduction in the CSPAD detectors used for LCLS experiments2017In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 24, p. 1092-1097Article in journal (Refereed)
  • 232.
    Pietrini, Alberto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy2018In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 26, p. 24422-24443Article in journal (Refereed)
  • 233.
    Pålsson, Stefan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Victor, BjörnUppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Proceedings från 5:e utvecklingskonferensen för Sveriges ingenjörsutbildningar2016Conference proceedings (editor) (Other academic)
  • 234. Rached, Imen
    et al.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Tail distribution and extreme quantile estimation using non-parametric approaches2019In: High-Performance Modelling and Simulation for Big Data Applications, Springer, 2019, p. 69-87Chapter in book (Refereed)
  • 235.
    Rantakokko, Jarmo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Thuné, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Parallel Structured Adaptive Mesh Refinement2009In: Parallel Computing: Numerics, Applications, and Trends, London: Springer-Verlag , 2009, p. 147-173Chapter in book (Refereed)
  • 236.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Comment on "On the optimal symmetric purification scheme of the one-particle density matrix" [Chem. Phys. Lett. 511 (2011) 159–160]2012In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 527, p. 84-85Article in journal (Refereed)
  • 237.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Controlling errors in recursive Fermi–Dirac operator expansions with applications in electronic structure theory2012In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 34, p. B1-B23Article in journal (Refereed)
  • 238.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nonmonotonic recursive polynomial expansions for linear scaling calculation of the density matrix2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, p. 1233-1236Article in journal (Refereed)
  • 239.
    Rubensson, Emanuel H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Artemov, Anton G.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Kruchinina, Anastasia
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Localized inverse factorization2018In: Computing Research Repository, no 1812.04919Article in journal (Other academic)
  • 240.
    Rubensson, Emanuel H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Niklasson, Anders M. N.
    Interior eigenvalues from density matrix expansions in quantum mechanical molecular dynamics2014In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 36, p. B147-B170Article in journal (Refereed)
  • 241.
    Rubensson, Emanuel H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Bringing about matrix sparsity in linear-scaling electronic structure calculations2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, p. 1411-1423Article in journal (Refereed)
  • 242.
    Rubensson, Emanuel H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Chunks and Tasks: A programming model for parallelization of dynamic algorithms2014In: Parallel Computing, ISSN 0167-8191, E-ISSN 1872-7336, Vol. 40, p. 328-343Article in journal (Refereed)
  • 243.
    Rubensson, Emanuel H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Locality-aware parallel block-sparse matrix–matrix multiplication using the Chunks and Tasks programming model2016In: Parallel Computing, ISSN 0167-8191, E-ISSN 1872-7336, Vol. 57, p. 87-106Article in journal (Refereed)
  • 244.
    Rubensson, Emanuel H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Salek, Pawel
    Methods for Hartree–Fock and density functional theory electronic structure calculations with linearly scaling processor time and memory usage2011In: Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications, Dordrecht, The Netherlands: Springer , 2011, p. 263-300Chapter in book (Refereed)
  • 245.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Difficulties in applying pure Kohn–Sham density functional theory electronic structure methods to protein molecules2012In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 24, p. 072202:1-7Article in journal (Refereed)
  • 246.
    Rudberg, Elias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Assessment of density matrix methods for electronic structure calculations2010Report (Other academic)
  • 247.
    Rudberg, Elias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Assessment of density matrix methods for linear scaling electronic structure calculations2011In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 23, p. 075502:1-10Article in journal (Refereed)
  • 248.
    Rudberg, Elias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Salek, Pawel
    Kohn–Sham density functional theory electronic structure calculations with linearly scaling computational time and memory usage2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, p. 340-350Article in journal (Refereed)
  • 249.
    Rudberg, Elias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Salek, Pawel
    Kruchinina, Anastasia
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Ergo: An open-source program for linear-scaling electronic structure calculations2018In: SoftwareX, E-ISSN 2352-7110, Vol. 7, p. 107-111Article in journal (Refereed)
  • 250.
    Rönnegård, Lars
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Mishchenko, Kateryna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Increasing the efficiency of variance component quantitative trait loci analysis by using reduced-rank identity-by-descent matrices2007In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 176, p. 1935-1938Article in journal (Refereed)
234567 201 - 250 of 325
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