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  • 151.
    Kruchinina, Anastasia
    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.
    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.
    Parameterless stopping criteria for recursive density matrix expansions2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, p. 5788-5802Article in journal (Refereed)
  • 152.
    Källén, Malin
    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.
    Hvannberg, Ebba þóra
    Impact of code refactoring using object-oriented methodology on a scientific computing application2014In: Proc. 14th International Working Conference on Source Code Analysis and Manipulation, Los Alamitos, CA: IEEE Computer Society, 2014, p. 125-134Conference paper (Refereed)
  • 153.
    Källén, Malin
    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.
    Wrigstad, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Performance of an OO compute kernel on the JVM: Revisiting Java as a language for scientific computing applications2019In: Proc. 16th ACM SIGPLAN International Conference on Managed Programming Languages and Runtimes, New York: ACM Press, 2019, p. 144-156Conference paper (Refereed)
  • 154.
    Källén, Malin
    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.
    Wrigstad, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Performance of an OO compute kernel on the JVM: Revisiting Java as a language for scientific computing applications (extended version)2019Report (Other academic)
  • 155. Langtangen, Hans Petter
    et al.
    Thuné, MichaelUppsala 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 Issues in Computational Science and Engineering2009Conference proceedings (editor) (Refereed)
  • 156.
    Larsson, Elisabeth
    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.
    Pålsson, Stefan
    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.
    von Sydow, Lina
    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.
    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.
    Gender-aware course reform in Scientific Computing2013In: International journal of engineering education, ISSN 0949-149X, Vol. 29, no 2, p. 403-414Article in journal (Refereed)
  • 157.
    Larsson, Elisabeth
    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.
    Zafari, Afshin
    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.
    Righero, Marco
    Francavilla, M. Alessandro
    Giordanengo, Giorgio
    Vipiana, Francesca
    Vecchi, Giuseppe
    Kessler, Christoph
    Ancourt, Corinne
    Grelck, Clemens
    Parallelization of hierarchical matrix algorithms for electromagnetic scattering problems2019In: High-Performance Modelling and Simulation for Big Data Applications, Springer, 2019, p. 36-68Chapter in book (Refereed)
  • 158. Laure, Erwin
    et al.
    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.
    Preface: e-Science Applications and Tools2013In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 29, no 8, p. 2115-2116Article, review/survey (Refereed)
  • 159.
    Lawson, Michael J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Petzold, Linda
    Hellander, Andreas
    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.
    Accuracy of the Michaelis–Menten approximation when analysing effects of molecular noise2015In: Journal of the Royal Society Interface, ISSN 1742-5689, E-ISSN 1742-5662, Vol. 12, no 106, p. 20150054:1-10, article id 20150054Article in journal (Refereed)
  • 160.
    Lindén, Jonatan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Bauer, Pavol
    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.
    Engblom, Stefan
    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.
    Jonsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Exposing inter-process information for efficient parallel discrete event simulation of spatial stochastic systems2017In: Proc. 5th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, New York: ACM Press, 2017, p. 53-64Conference paper (Refereed)
  • 161.
    Lindén, Jonatan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Bauer, Pavol
    Engblom, Stefan
    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.
    Jonsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Exposing inter-process information for efficient PDES of spatial stochastic systems on multicores2019In: ACM Transactions on Modeling and Computer Simulation, ISSN 1049-3301, E-ISSN 1558-1195, Vol. 29, no 2, p. 11:1-25, article id 11Article in journal (Refereed)
  • 162.
    Lindén, Jonatan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Bauer, Pavol
    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.
    Engblom, Stefan
    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.
    Jonsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Fine-grained local dynamic load balancing in PDES2018In: Proc. 6th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, New York: ACM Press, 2018, p. 201-212Conference paper (Refereed)
  • 163. Lister, Raymond
    et al.
    Clear, Tony
    Simon,
    Bouvier, Dennis J.
    Carter, Paul
    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.
    Jacková, Jana
    Lopez, Mike
    McCartney, Robert
    Robbins, Phil
    Seppälä, Otto
    Thompson, Errol
    Naturally Occurring Data as Research Instrument: Analyzing examination responses to study the novice programmer2009In: SIGCSE Bulletin inroads, ISSN 0097-8418, Vol. 41, no 4, p. 156-173Article in journal (Refereed)
  • 164.
    Liu, Jing
    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.
    Engblom, Stefan
    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. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Assessing uncertainties in x-ray single-particle three-dimensional reconstruction2018In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 98, p. 013303:1-12, article id 013303Article in journal (Refereed)
  • 165.
    Liu, Jing
    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.
    van der Schot, Gijs
    Engblom, Stefan
    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.
    Supervised classification methods for flash X-ray single particle diffraction imaging2019In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 27, p. 3884-3899Article in journal (Refereed)
  • 166.
    Ljungberg, Kajsa
    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.
    Mishchenko, Kateryna
    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.
    Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits2010In: Advances and Applications in Bioinformatics and Chemistry, ISSN 1178-6949, Vol. 3, p. 75-88Article in journal (Refereed)
  • 167.
    Ljungkvist, Karl
    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.
    Finite Element Computations on Multicore and Graphics Processors2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, techniques for efficient utilization of modern computer hardwarefor numerical simulation are considered. In particular, we study techniques for improving the performance of computations using the finite element method.

    One of the main difficulties in finite-element computations is how to perform the assembly of the system matrix efficiently in parallel, due to its complicated memory access pattern. The challenge lies in the fact that many entries of the matrix are being updated concurrently by several parallel threads. We consider transactional memory, an exotic hardware feature for concurrent update of shared variables, and conduct benchmarks on a prototype multicore processor supporting it. Our experiments show that transactions can both simplify programming and provide good performance for concurrent updates of floating point data.

    Secondly, we study a matrix-free approach to finite-element computation which avoids the matrix assembly. In addition to removing the need to store the system matrix, matrix-free methods are attractive due to their low memory footprint and therefore better match the architecture of modern processors where memory bandwidth is scarce and compute power is abundant. Motivated by this, we consider matrix-free implementations of high-order finite-element methods for execution on graphics processors, which have seen a revolutionary increase in usage for numerical computations during recent years due to their more efficient architecture. In the implementation, we exploit sum-factorization techniques for efficient evaluation of matrix-vector products, mesh coloring and atomic updates for concurrent updates, and a geometric multigrid algorithm for efficient preconditioning of iterative solvers. Our performance studies show that on the GPU, a matrix-free approach is the method of choice for elements of order two and higher, yielding both a significantly faster execution, and allowing for solution of considerably larger problems. Compared to corresponding CPU implementations executed on comparable multicore processors, the GPU implementation is about twice as fast, suggesting that graphics processors are about twice as power efficient as multicores for computations of this kind.

    List of papers
    1. Using hardware transactional memory for high-performance computing
    Open this publication in new window or tab >>Using hardware transactional memory for high-performance computing
    Show others...
    2011 (English)In: Proc. 25th International Symposium on Parallel and Distributed Processing Workshops and PhD Forum, Piscataway, NJ: IEEE , 2011, p. 1660-1667Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Piscataway, NJ: IEEE, 2011
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-158551 (URN)10.1109/IPDPS.2011.322 (DOI)978-1-61284-425-1 (ISBN)
    Conference
    IPDPS Workshop on Multi-Threaded Architectures and Applications
    Projects
    eSSENCEUPMARC
    Available from: 2011-09-01 Created: 2011-09-10 Last updated: 2018-01-12Bibliographically approved
    2. Matrix-free finite-element operator application on graphics processing units
    Open this publication in new window or tab >>Matrix-free finite-element operator application on graphics processing units
    2014 (English)In: Euro-Par 2014: Parallel Processing Workshops, Part II, Springer, 2014, p. 450-461Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Springer, 2014
    Series
    Lecture Notes in Computer Science ; 8806
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-238380 (URN)10.1007/978-3-319-14313-2_38 (DOI)000354785000038 ()978-3-319-14312-5 (ISBN)
    Conference
    7th Workshop on Unconventional High-Performance Computing
    Projects
    UPMARCeSSENCE
    Available from: 2014-12-11 Created: 2014-12-11 Last updated: 2018-01-11Bibliographically approved
    3. Matrix-free finite-element computations on graphics processors with adaptively refined unstructured meshes
    Open this publication in new window or tab >>Matrix-free finite-element computations on graphics processors with adaptively refined unstructured meshes
    2017 (English)In: Proc. 25th High Performance Computing Symposium, San Diego, CA: The Society for Modeling and Simulation International, 2017, p. 1-12Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    San Diego, CA: The Society for Modeling and Simulation International, 2017
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-320146 (URN)978-1-5108-3822-2 (ISBN)
    Conference
    HPC 2017, April 23–26, Virginia Beach, VA
    Projects
    UPMARC
    Available from: 2017-04-23 Created: 2017-04-16 Last updated: 2018-01-13Bibliographically approved
    4. Multigrid for matrix-free finite element computations on graphics processors
    Open this publication in new window or tab >>Multigrid for matrix-free finite element computations on graphics processors
    2017 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2017-006
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-320073 (URN)
    Projects
    UPMARCeSSENCE
    Available from: 2017-04-20 Created: 2017-04-13 Last updated: 2018-01-13Bibliographically approved
  • 168.
    Ljungkvist, Karl
    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.
    Matrix-free finite-element computations on graphics processors with adaptively refined unstructured meshes2017In: Proc. 25th High Performance Computing Symposium, San Diego, CA: The Society for Modeling and Simulation International, 2017, p. 1-12Conference paper (Refereed)
  • 169.
    Ljungkvist, Karl
    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.
    Matrix-free finite-element operator application on graphics processing units2014In: Euro-Par 2014: Parallel Processing Workshops, Part II, Springer, 2014, p. 450-461Conference paper (Refereed)
  • 170.
    Ljungkvist, Karl
    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.
    Techniques for finite element methods on modern processors2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, methods for efficient utilization of modern computer hardware for numerical simulation are considered. In particular, we study techniques for speeding up the execution of finite-element methods.

    One of the greatest challenges in finite-element computation is how to efficiently perform the the system matrix assembly efficiently in parallel, due to its complicated memory access pattern. The main difficulty lies in the fact that many entries of the matrix are being updated concurrently by several parallel threads. We consider transactional memory, an exotic hardware feature for concurrent update of shared variables, and conduct benchmarks on a prototype processor supporting it. Our experiments show that transactions can both simplify programming and provide good performance for concurrent updates of floating point data.

    Furthermore, we study a matrix-free approach to finite-element computation which avoids the matrix assembly. Motivated by its computational properties, we implement the matrix-free method for execution on graphics processors, using either atomic updates or a mesh coloring approach to handle the concurrent updates. A performance study shows that on the GPU, the matrix-free method is faster than a matrix-based implementation for many element types, and allows for solution of considerably larger problems. This suggests that the matrix-free method can speed up execution of large realistic simulations.

    List of papers
    1. Using hardware transactional memory for high-performance computing
    Open this publication in new window or tab >>Using hardware transactional memory for high-performance computing
    Show others...
    2011 (English)In: Proc. 25th International Symposium on Parallel and Distributed Processing Workshops and PhD Forum, Piscataway, NJ: IEEE , 2011, p. 1660-1667Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Piscataway, NJ: IEEE, 2011
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-158551 (URN)10.1109/IPDPS.2011.322 (DOI)978-1-61284-425-1 (ISBN)
    Conference
    IPDPS Workshop on Multi-Threaded Architectures and Applications
    Projects
    eSSENCEUPMARC
    Available from: 2011-09-01 Created: 2011-09-10 Last updated: 2018-01-12Bibliographically approved
    2. Matrix-free finite-element operator application on graphics processing units
    Open this publication in new window or tab >>Matrix-free finite-element operator application on graphics processing units
    2014 (English)In: Euro-Par 2014: Parallel Processing Workshops, Part II, Springer, 2014, p. 450-461Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Springer, 2014
    Series
    Lecture Notes in Computer Science ; 8806
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-238380 (URN)10.1007/978-3-319-14313-2_38 (DOI)000354785000038 ()978-3-319-14312-5 (ISBN)
    Conference
    7th Workshop on Unconventional High-Performance Computing
    Projects
    UPMARCeSSENCE
    Available from: 2014-12-11 Created: 2014-12-11 Last updated: 2018-01-11Bibliographically approved
  • 171.
    Ljungkvist, Karl
    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.
    Kronbichler, Martin
    Multigrid for matrix-free finite element computations on graphics processors2017Report (Other academic)
  • 172.
    Ljungkvist, Karl
    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.
    Tillenius, Martin
    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.
    Black-Schaffer, David
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    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.
    Karlsson, Martin
    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.
    Using hardware transactional memory for high-performance computing2011In: Proc. 25th International Symposium on Parallel and Distributed Processing Workshops and PhD Forum, Piscataway, NJ: IEEE , 2011, p. 1660-1667Conference paper (Refereed)
  • 173. Ljungkvist, Karl
    et al.
    Tillenius, Martin
    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.
    Karlsson, Martin
    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.
    Early results using hardware transactional memory for high-performance computing applications2010In: Proc. 3rd Swedish Workshop on Multi-Core Computing, Göteborg, Sweden: Chalmers University of Technology , 2010, p. 93-97Conference paper (Other academic)
  • 174.
    Lukarski, Dimitar
    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.
    Neytcheva, Maya
    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.
    On the impact of the heterogeneous multicore and many-core platforms on iterative solution methods and preconditioning techniques2014In: High-Performance Computing on Complex Environments, Hoboken, NJ: Wiley-Blackwell, 2014, p. 13-32Chapter in book (Refereed)
  • 175.
    Lukarski, Dimitar
    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.
    Skoglund, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    A priori power estimation of linear solvers on multi-core processors2013Report (Other academic)
  • 176.
    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)
  • 177.
    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
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    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.
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    Klei, Lambertus
    Devlin, Bernie
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    Computational challenges in modeling maternal effects in psychiatric disorders2016Manuscript (preprint) (Other academic)
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    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)
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    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.
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    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.
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    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)
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    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)
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    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.
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    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.
    Stable and accurate wave simulations in complex geometries and discontinuous media2013In: Proc. 11th International Conference on Mathematical and Numerical Aspects of Waves, Tunisia: ENIT , 2013, p. 201-202Conference paper (Other academic)
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    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.
    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.
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    Liminal spaces and learning computing2009In: European Journal of Engineering Education, ISSN 0304-3797, E-ISSN 1469-5898, Vol. 34, p. 383-391Article in journal (Refereed)
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    Sanders, Kate
    Thomas, Lynda
    Zander, Carol
    Why computing students learn on their own: Motivation for self-directed learning of computing2016In: ACM Transactions on Computing Education, ISSN 1946-6226, E-ISSN 1946-6226, Vol. 16, no 1, p. 2:1-18, article id 2Article in journal (Refereed)
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    Sanders, Kate
    Zander, Carol
    Can first-year students program yet?: a study revisited2013In: Proc. 9th International Computing Education Research Conference, New York: ACM Press, 2013, p. 91-98Conference paper (Refereed)
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    Folk pedagogy and the geek gene: Geekiness quotient2017In: Proc. 48th SIGCSE Technical Symposium on Computer Science Education, New York: ACM Press, 2017, p. 405-410Conference paper (Refereed)
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    Moström, Jan Erik
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    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.
    Hellander, Andreas
    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.
    Lötstedt, Per
    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.
    Analysis and design of jump coefficients in discrete stochastic diffusion models2016In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 38, p. A55-A83Article in journal (Refereed)
  • 190.
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    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Restrepo, Carlos Ernesto
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Siwani, Samer
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Bauer, Pavol
    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.
    Johann, Stefano Pupe
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Tort, Adriano B. L.
    Kullander, Klas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Leão, Richardson N.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Ventral hippocampal OLM cells control type 2 theta oscillations and response to predator odor2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, p. 3638:1-15, article id 3638Article in journal (Refereed)
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    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.
    Bauer, Pavol
    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.
    Khammash, Mustafa
    Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks2015In: Journal of the Royal Society Interface, ISSN 1742-5689, E-ISSN 1742-5662, Vol. 12, no 113, p. 20150831:1-10, article id 20150831Article in journal (Refereed)
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    Rönnegård, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Newton-type methods for REML estimation in genetic analysis of quantitative traits2008In: Journal of Computational Methods in Sciences and Engineering, ISSN 1472-7978, E-ISSN 1875-8983, Vol. 8, p. 53-67Article in journal (Refereed)
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    New algorithms for evaluating the log-likelihood function derivatives in the AI-REML method2009In: Communications in statistics. Simulation and computation, ISSN 0361-0918, E-ISSN 1532-4141, Vol. 38, p. 1348-1364Article in journal (Refereed)
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    Mishchenko, Volodymyr
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    Linear scaling pseudo Fermi-operator expansion for fractional occupation2019In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, p. 190-200Article in journal (Refereed)
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    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
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    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.
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    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.
    Pettersson, Mats E.
    Shen, Xia
    Crooks, Lucy
    Besnier, François
    Álvarez-Castro, José
    Rönnegård, Lars
    Ek, Weronica
    Sheng, Zheya
    Kierczak, Marcin
    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
    Swedish University of Agricultural Sciences, Division of Computational Genetics.
    MAPfastR: Quantitative trait loci mapping in outbred line crosses2013In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 3, p. 2147-2149Article in journal (Refereed)
  • 199.
    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.
    Breakdown of methods for phasing and imputation in the presence of double genotype sharing2012Report (Other academic)
  • 200.
    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.
    Breakdown of methods for phasing and imputation in the presence of double genotype sharing2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, p. e60354:1-5Article in journal (Refereed)
1234567 151 - 200 of 325
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