uu.seUppsala University Publications
Change search
Refine search result
1 - 8 of 8
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    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.
    Global optimization algorithm PruneDIRECT as an R package2016Report (Other academic)
  • 2.
    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.
    Methods from Statistical Computing for Genetic Analysis of Complex Traits2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The goal of this thesis is to explore, improve and implement some advanced modern computational methods in statistics, focusing on applications in genetics. The thesis has three major directions.

    First, we study likelihoods for genetics analysis of experimental populations. Here, the maximum likelihood can be viewed as a computational global optimization problem. We introduce a faster optimization algorithm called PruneDIRECT, and explain how it can be parallelized for permutation testing using the Map-Reduce framework. We have implemented PruneDIRECT as an open source R package, and also Software as a Service for cloud infrastructures (QTLaaS).

    The second part of the thesis focusses on using sparse matrix methods for solving linear mixed models with large correlation matrices. For populations with known pedigrees, we show that the inverse of covariance matrix is sparse. We describe how to use this sparsity to develop a new method to maximize the likelihood and calculate the variance components.

    In the final part of the thesis we study computational challenges of psychiatric genetics, using only pedigree information. The aim is to investigate existence of maternal effects in obsessive compulsive behavior. We add the maternal effects to the linear mixed model, used in the second part of this thesis, and we describe the computational challenges of working with binary traits.

    List of papers
    1. 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
    2. Global optimization algorithm PruneDIRECT as an R package
    Open this publication in new window or tab >>Global optimization algorithm PruneDIRECT as an R package
    2016 (English)Report (Other academic)
    National Category
    Computational Mathematics Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-284374 (URN)
    Projects
    eSSENCE
    Available from: 2016-04-24 Created: 2016-04-18 Last updated: 2018-01-10Bibliographically approved
    3. A flexible computational framework using R and Map-Reduce for permutation tests of massive genetic analysis of complex traits
    Open this publication in new window or tab >>A flexible computational framework using R and Map-Reduce for permutation tests of massive genetic analysis of complex traits
    2017 (English)In: IEEE/ACM Transactions on Computational Biology & Bioinformatics, ISSN 1545-5963, E-ISSN 1557-9964, Vol. 14, p. 381-392Article in journal (Refereed) Published
    National Category
    Computational Mathematics Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-284372 (URN)10.1109/TCBB.2016.2527639 (DOI)000399013500017 ()26887003 (PubMedID)
    Projects
    eSSENCE
    Available from: 2016-02-11 Created: 2016-04-18 Last updated: 2018-09-18Bibliographically approved
    4. QTL as a service: PruneDIRECT for multi-dimensional QTL scans in cloud settings
    Open this publication in new window or tab >>QTL as a service: PruneDIRECT for multi-dimensional QTL scans in cloud settings
    2016 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811Article in journal (Other academic) Submitted
    National Category
    Bioinformatics and Systems Biology Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-284376 (URN)
    Projects
    eSSENCE
    Available from: 2016-04-18 Created: 2016-04-18 Last updated: 2018-01-10Bibliographically approved
    5. Software as a service in analysis of quantitative trait loci
    Open this publication in new window or tab >>Software as a service in analysis of quantitative trait loci
    2016 (English)Report (Other academic)
    National Category
    Bioinformatics and Systems Biology Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-284375 (URN)
    Projects
    eSSENCE
    Available from: 2016-04-18 Created: 2016-04-18 Last updated: 2018-01-10Bibliographically approved
    6. Fitting linear mixed models using sparse matrix methods and Lanczos factorization
    Open this publication in new window or tab >>Fitting linear mixed models using sparse matrix methods and Lanczos factorization
    2016 (English)In: Computational Statistics & Data Analysis, ISSN 0167-9473, E-ISSN 1872-7352Article in journal (Other academic) Submitted
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-284373 (URN)
    Projects
    eSSENCE
    Available from: 2016-04-08 Created: 2016-04-18 Last updated: 2017-11-30Bibliographically approved
    7. Computational challenges in modeling maternal effects in psychiatric disorders
    Open this publication in new window or tab >>Computational challenges in modeling maternal effects in psychiatric disorders
    Show others...
    2016 (English)Manuscript (preprint) (Other academic)
    National Category
    Genetics Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-284377 (URN)
    Projects
    eSSENCE
    Available from: 2016-04-18 Created: 2016-04-18 Last updated: 2017-03-06
  • 3.
    Mahjani, Behrang
    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.
    Pawitan, Yudi
    Klei, Lambertus
    Devlin, Bernie
    Buxbaum, Joseph
    Grice, Dorothy
    Reichenberg, Avraham
    Sandin, Sven
    Computational challenges in modeling maternal effects in psychiatric disorders2016Manuscript (preprint) (Other academic)
  • 4.
    Mahjani, Behrang
    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.
    Rönnegård, Lars
    Eldén, Lars
    Fitting linear mixed models using sparse matrix methods and Lanczos factorization2016In: Computational Statistics & Data Analysis, ISSN 0167-9473, E-ISSN 1872-7352Article in journal (Other academic)
  • 5.
    Mahjani, Behrang
    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.
    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.
    Software as a service in analysis of quantitative trait loci2016Report (Other academic)
  • 6.
    Mahjani, Behrang
    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.
    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.
    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.
    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.
    A flexible computational framework using R and Map-Reduce for permutation tests of massive genetic analysis of complex traits2017In: IEEE/ACM Transactions on Computational Biology & Bioinformatics, ISSN 1545-5963, E-ISSN 1557-9964, Vol. 14, p. 381-392Article in journal (Refereed)
  • 7.
    Mahjani, Behrang
    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.
    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.
    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.
    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.
    QTL as a service: PruneDIRECT for multi-dimensional QTL scans in cloud settings2016In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811Article in journal (Other academic)
  • 8.
    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)
1 - 8 of 8
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf