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Journal Articles

Tomas Johansson, Daniel Lesnic and Thomas Reeve
  The method of fundamental solutions for the two-dimensional inverse Stefan problem
  Inverse Problems in Science and Engineering, 2014, 22(1), 112-129.

 

Roman Chapko, Tomas Johansson and Yuriy Savka
  On the use of an integral equation approach for the numerical solution of a Cauchy problem for Laplace equation in a doubly connected planar domain
  Inverse Problems in Science and Engineering, 2014, 22(1), 130-149.

 

Tomas Johansson, Daniel Lesnic and Thomas Reeve
  A Mesh less Regularization Method for a Two-Dimensional Two-Phase Linear Inverse Stefan Problem
  Advances in Applied Mathematics and Mechanics, 2014, 5(6), 825-845.

 

Tomas Johansson, Daniel Lesnic and Thomas Reeve
  A meshless method for an inverse two-phase one-dimensional nonlinear Stefan problem
  Mathematics and Computers in Simulation, 2014, 101, 61-77.

 

R. Chapko, B.Tomas Johansson and V. Vavrychuk
  Numerical solution of parabolic Cauchy problems in planar corner domains
  Mathematics and Computers in Simulation, 2014, 101, 1-12.

 

Fredrik Berntsson and George Baravdish
  Coefficient identification in PDEs applied to image inpainting
  Applied Mathematics and Computation, 2014, 242, 227-235.

 

M Blaszak and Krzysztof Marciniak
  Invertible Coupled KdV and Coupled Harry Dym Hierarchies
  Studies in applied mathematics (Cambridge), 2013, 131(3), 211-228.

 

Roman Chapko, Tomas Johansson and Vasyl Vavrychuk
  A projected iterative method based on integral equations for inverse heat conduction in domains with a cut
  Inverse Problems, 2013, 29(6), 065003.

 

Thomas Reeve and Tomas Johansson
  The method of fundamental solutions for a time-dependent two-dimensional Cauchy heat conduction problem
  Engineering analysis with boundary elements, 2013, 37(3), 569-578.

 

Berkant Savas and Lars Eldén
  Krylov-type methods for tensor computations I
  Linear Algebra and its Applications, 2013, 438(2), 891-918.
   Fulltext  PDF  
 Web of Science® Times Cited: 4

 

Krzysztof Marciniak and Maciej Blaszak
  On Reciprocal Equivalence of Stäckel Systems
  Studies in applied mathematics (Cambridge), 2012, 129(1), 26-50.
   Fulltext  PDF  
 Web of Science® Times Cited: 1

 

Vishvas Vasuki, Nagarajan Natarajan, Zhengdong Lu, Berkant Savas and Inderjit S. Dhillon
  Scalable Affiliation Recommendation using Auxiliary Networks
  ACM Transactions on Intelligent Systems and Technology, 2011, 3(1), 3:1-3:20.

 

Lars Eldén and Berkant Savas
  Perturbation Theory and Optimality Conditions for the Best Multilinear Rank Approximation of a Tensor
  SIAM Journal on Matrix Analysis and Applications, 2011, 32(4), 1422-1450.
   Fulltext  PDF  
 Web of Science® Times Cited: 3

 

Michael Hörnquist and Mika Gustafsson
  Stability and Flexibility from a System Analysis of Gene RegulatoryNetworks Based on Ordinary Differential Equations
  The Open Bioinformatics Journal, 2011, 5, 26-33.
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Berkant Savas and Lek-Heng Lim
  Quasi-Newton Methods on Grassmannians and Multilinear Approximations of Tensors
  SIAM Journal on Scientific Computing, 2010, 32(6), 3352-3393.
 Web of Science® Times Cited: 15

 

Krzysztof Marciniak and Maciej Blaszak
  Construction of coupled Harry Dym hierarchy and its solutions from Stackel systems
  NONLINEAR ANALYSIS-THEORY METHODS and APPLICATIONS, 2010, 73(9), 3004-3017.
   Fulltext  PDF  
 Web of Science® Times Cited: 2

 

Mika Gustafsson and Michael Hörnquist
  Gene Expression Prediction by Soft Integration and the Elastic Net: Best Performance of the DREAM3 Gene Expression Challenge
  PLoS ONE, 2010, 5(2), e9134.
   Fulltext  PDF  
 Web of Science® Times Cited: 10

 

Mika Gustafsson, Michael Hörnquist, J Bjorkegren and Jesper Tegnér
  Genome-wide system analysis reveals stable yet flexible network dynamics in yeast
  IET SYSTEMS BIOLOGY, 2009, 3(4), 219-228.
   Fulltext  PDF  
 Web of Science® Times Cited: 5

 

Mika Gustafsson, Michael Hörnquist, Jesper Tegnér and et al. 155 external authors
  The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
 
Altmetric usage: 2

  Nature Genetics, 2009, 41, 553-562.
 Web of Science® Times Cited: 190

 

Mika Gustafsson, Michael Hörnquist, Jesper Lundstrom, Johan Bjorkegren and Jesper Tegnér
  Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions
  CHALLENGES OF SYSTEMS BIOLOGY: COMMUNITY EFFORTS TO HARNESS BIOLOGICAL COMPLEXITY, 2009, 1158, 265-275.
   Fulltext  PDF  
 Web of Science® Times Cited: 9

 

Lars Eldén and Berkant Savas
  A Newton-Grassmann method for computing the best multilinear rank-(r1,r2,r3) approximation of a tensor
  SIAM Journal on Matrix Analysis and Applications, 2009, 32(2), 248-271.
 Web of Science® Times Cited: 26

 

Maciej Blaszak and Krzysztof Marciniak
  Stackel systems generating coupled KdV hierarchies and their finite-gap and rational solutions
  JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, 2008, 41(48), .
 Web of Science® Times Cited: 3

 

Krzysztof Marciniak and Maciej Blaszak
  Non-Hamiltonian systems separable by Hamilton-Jacobi method
  Journal of Geometry and Physics, 2008, 58(5), 557-575.
 Web of Science® Times Cited: 2

 

Krzysztof Marciniak and Stefan Rauch
  Separable systems of coordinates for triangular Newton equations q¨i = Mi(q1,..., qi)
  Studies in applied mathematics (Cambridge), 2007, 118(1), 45-84.
 Web of Science® Times Cited: 2

 

Fredrik Karlsson and Michael Hörnquist
  Order or chaos in Boolean gene networks depends on the mean fraction of canalizing functions
  Physica A: Statistical Mechanics and its Applications, 2007, 384(2), 747-757.
 Web of Science® Times Cited: 8

 

Anna Lombardi and Michael Hörnquist
  Controllability analysis of networks
  Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2007, 75(056110), .
 Web of Science® Times Cited: 17

 

Berkant Savas and Lars Eldén
  Handwritten digit classification using higher order singular value decomposition
  Pattern Recognition, 2007, 40(3), 993-1003.
 Web of Science® Times Cited: 50

 

Tomas Johansson
  An iterative method for a Cauchy problem for the heat equation
  IMA Journal of Applied Mathematics, 2006, 71(2), 262-286.
 Web of Science® Times Cited: 6

 

Vladimir Kozlov, George Baravdish, Tomas Johansson and Daniel Lesnic
  An alternating method for the stationary Stokes system
  Zeitschrift für angewandte Mathematik und Mechanik, 2006, 86(4), 268-280.
 Web of Science® Times Cited: 16

 

Krzysztof Marciniak and Maciej Blaszak
  From Stäckel systems to integrable hierarchies of PDE's: Beneti class of separation relations.
  Journal of mathematical physics : a publication of the American institute of physics, 2006, 47, 0329041-03290426.
 Web of Science® Times Cited: 5

 

Olof Svensson, Fausto Di Biase, Alexander Stokolos and Tomasz Weiss
  On the sharpness of the Stolz approach
  Annales Academiae Scientiarum Fennicae Mathematica, 2006, 31(1), 47-59.
 Web of Science® Times Cited: 2

 

Mika Gustafsson, Michael Hörnquist and Anna Lombardi
  Comparison and validation of community structures in complex networks
  Physica A: Statistical Mechanics and its Applications, 2006, 367, 559-576.
 Web of Science® Times Cited: 28

 

Berkant Savas
  Dimensionality reduction and volume minimization - generalization of the determinant minimization criterion for reduced rank regression problems
  Linear Algebra and its Applications, 2006, 418(1), 201-214.

 

David Lindgren and Berkant Savas
  Rank Reduction and Volume Minimization Approach to State-Space Subspace System Identification
  Signal Processing, 2006, 86(11), 3275-3285.
 Web of Science® Times Cited: 1

 

Lars Elden and Berkant Savas
  The maximum likelihood estimate in reduced-rank regression
  Numerical Linear Algebra with Applications, 2005, 12(8), 731-741.
 Web of Science® Times Cited: 2

 

Krzysztof Marciniak and M. Blaszak
  Geometric reduction of Hamiltonian systems
  Reports on mathematical physics, 2005, 55(3), 325-339.
 Web of Science® Times Cited: 2

 

M Blaszak and Krzysztof Marciniak
  From separation relations to soliton hierarchies
  Czechoslovak Journal of Physics, 2005, 55(11), 1343-1350.

 

Vesteinn Thorsson, Vesteinn Thorsson, Michael Hörnquist, Michael Hörnquist, Andrew F. Siegel, Andrew F. Siegel, Leroy Hood and Leroy Hood
  Reverse engineering galactose regulation in yeast through model selection
  Statistical Applications in Genetics and Molecular Biology, 2005, 4(1), .
 Web of Science® Times Cited: 7

 

Mika Gustafsson, Michael Hörnquist and Anna Lombardi
  Constructing and analyzing a large-scale gene-to-gene regulatory network Lasso-constrained inference and biological validation
  IEEE/ACM Transactions on Computational Biology & Bioinformatics, 2005, 2(3), 254-261.
 Web of Science® Times Cited: 39

 

Javier Soria and Olof Svensson
  A counterexample to a weak-type estimate for potential spaces and tangential approach regions
  , 2005, , .

 

Tomas Johansson
  An iterative procedure for solving a Cauchy problem for second order elliptic equations
  Mathematische Nachrichten, 2004, 272, 46-54.
 Web of Science® Times Cited: 11

 

Maciej Blaszak and Krzysztof Marciniak
  Dirac reduction of dual poisson-presymplectic pairs
  Journal of Physics A: Mathematical and General, 2004, 37(19), 5173-5187.
 Web of Science® Times Cited: 5

 

K. A. Eriksen, Michael Hörnquist and K. Sneppen
  Visualization of large-scale correlations in gene expressions
  Functional & Integrative Genomics, 2004, 4(4), 241-245.

 

Krzysztof Marciniak and M Blaszak
  Dirac reduction revisited
  Journal of Nonlinear Mathematical Physics, 2003, 10(4), 451-463.
 Web of Science® Times Cited: 4

 

M. Blaszak and Krzysztof Marciniak
  Separability preserving Dirac reductions of Poisson pencils on Riemannian manifolds
  Journal of Physics A: Mathematical and General, 2003, 36(5), 1337-1356.
 Web of Science® Times Cited: 2

 

Erik Lennholm and Michael Hörnquist
  Revisiting Salerno's sine-Gordon model of DNA: Active regions and robustness
  Physica D: Non-linear phenomena, 2003, 177(1-4), 233-241.
 Web of Science® Times Cited: 18

 

Michael Hörnquist, J. Hertz and M. Wahde
  Effective dimensionality for principal component analysis of time series expression data
  Biosystems (Amsterdam. Print), 2003, 71(3), 311-317.
 Web of Science® Times Cited: 8

 

K.A. Eriksen and Michael Hörnquist
  Scale-free growing networks imply linear preferential attachment
  Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 2002, 65(1), .
 Web of Science® Times Cited: 5

 

Krzysztof Marciniak and M. Blaszak
  Separation of variables in quasi-potential systems of bi-cofactor form
  Journal of Physics A: Mathematical and General, 2002, 35(12), 2947-2964.
 Web of Science® Times Cited: 12

 

Michael Hörnquist, J. Hertz and M. Wahde
  Effective dimensionality of large-scale expression data using principal component analysis
  Biosystems (Amsterdam. Print), 2002, 65(2-3), 147-156.
 Web of Science® Times Cited: 10

 

Krzysztof Marciniak and Stefan Rauch-Wojciechowski
  On integrable perturbations of harmonic oscillator
  Reports on mathematical physics, 2001, 48, 139-147.
 Web of Science® Times Cited: 1

 

Krzysztof Marciniak and S. Rauch-Wojciechowski
  Integrable perturbations of the harmonic oscillator and Poisson pencils
  Inverse Problems, 2001, 17(2), 191-209.
 Web of Science® Times Cited: 2

 

Michael Hörnquist, Erik Lennholm and C Basu
  Discrete breathers in aperiodic diatomic FPU lattices with long range order
  Physica D: Non-linear phenomena, 2000, 136(1-2), 93-124.
 Web of Science® Times Cited: 5

 

Chapters in Books

Mika Gustafsson and Michael Hörnquist
  Integrating various data sources for improved quality in reverse engineering of gene regulatory networks
  Handbook of Research on Computational Methodologies in Gene Regulatory Networks, IGI Global, 2009, 476-496.

 

Karljohan Lundin Palmerius and George Baravdish
  Higher precision in volume haptics through subdivision of proxy movements
  Haptics: Perception, Devices and Scenarios: 6th International Conference, EuroHaptics 2008 Madrid, Spain, June 10-13, 2008 Proceedings, Springer Berlin/Heidelberg, 2008, 694-699.

 

Stefan Rauch and Krzysztof Marciniak
  Separation of variables for differential equations
  Encyclopedia of Mathematical Physics, Elsevier, 2006, 526-535.

 

Peer Reviewed Conference Articles

Christian Heinemann, Freddie Åström, George Baravdish, Kai Krajsek, Michael Felsberg and Hanno Scharr
  Using Channel Representations in Regularization Terms: A Case Study on Image Diffusion
  In Proceedings of the 9th International Conference on Computer Vision Theory and Applications, 2014.

 

Freddie Åström, Michael Felsberg, George Baravdish and Claes Lundström
  Targeted Iterative Filtering
  Fourth International Conference on Scale Space and Variational Methods in Computer Vision (SSVM 2013), 2-6 June 2013, Schloss Seggau, Graz region, Austria, 2013.


  Fulltext PDF

Xin Sui, Tsung-Hsien Lee, Joyce Jiyoung Whang, Berkant Savas, Saral Jain, Keshav Pingali and Inderjit S. Dhillon
  Parallel clustered low-rank approximation of graphs and its application to link prediction
  Proceedings of the International Workshop on Languages and Compilers for Parallel Computing, 2012.

 

Han Hee Song, Berkant Savas, Tae Won Cho, Vacha Dave, Zhengdong Lu, Inderjit S. Dhillon, Yin Zhang and Lili Qiu
  Clustered Embedding of Massive Social Networks
  Proceedings of the 12th ACM SIGMETRICS/PERFORMANCE joint international conference on Measurement and Modeling of Computer Systems, 2012.

 

Freddie Åström, George Baravdish and Michael Felsberg
  On Tensor-Based PDEs and their Corresponding Variational Formulations with Application to Color Image Denoising
  ECCV 2012: 12th European Conference on Computer Vision, 7-12 October, Firenze, Italy, 2012.


  Fulltext PDF

George Baravdish, Gianpaolo Evangelista, Olof Svensson and Faten Sofya
  PDE-SVD Based Audio Denoising
  Proceedings of the 5th International Symposium on Communications Control and Signal Processing (ISCCSP), 2012, 2012.


  Fulltext PDF

Berkant Savas, Inderjit and S. Dhillon
  Clustered low rank approximation of graphs in information science applications
  Proceedings of the SIAM International Conference on Data Mining (SDM), 2011.

 

Zhengdong Lu, Berkant Savas, Wei Tang and Inderjit S. Dhillon
  Supervised Link Prediction Using Multiple Sources
  Proceedings of the IEEE International Conference on Data Mining (ICDM), 2010.

 

George Baravdish and Sasan Gooran
  A Variational Method for Image Reconstruction
  International Conference on Inverse Problems in Engineering: Theory and Practice ICIPE 2008,2008, 2008.

 

Mika Gustafsson and Michael Hörnquist
  In-silico network predictions by ODE and lasso
  DREAM,2008, 2008.

 

Mika Gustafsson and Michael Hörnquist
  Gene expression prediction by the elastic net
  DREAM,2008, 2008.

 

Mika Gustafsson, Michael Hörnquist, Johan Björkegren and Jesper Tegnér
  Soft Integration of Data for Reverse Engineering
  International Conference on Systems Biology,2008, 2008.

 

Berkant Savas and Lek-Heng Lim
  Quasi-Newton algorithm for best multi-linear rank approximation of tensors
  6th International Congress on Industrial and Applied Mathematics,2007, 2007.

 

Krzysztof Marciniak
  Geodesically equivalent flat bi-cofactor systems
  Symmetry and Perturbation Theory SPT,2007, 2007.

 

Berkant Savas
  Dimensionality reduction and volume minimization - generalization of the determinant minimization criterion for reduced rank regression problems
  Working Group on Matrix Computations and Statistics,2005, 2005.

 

Berkant Savas
  Tangent distance algorithm on HOSVD reduced data for handwritten digit recognition
  Workshop on Tensor Decompositions and Applications,2005, 2005.

 

Lars Elden and Berkant Savas
  Pattern Recognition using Higher Order SVD
  3rd IASC world conference onComputational Statistics and Data Analysis,2005, 2005.

 

Krzysztof Marciniak and Maciej Blaszak
  Geometric reduction of Poisson operators
  Proceedings of the SPT 2004 Symmetry and Perturbation Theory Conference,2004, 2005.

 

Berkant Savas
  Analyses and Tests of Handwritten Digit Recognition Algorithms
  Workshop i tillämpad matematik,2004, 2004.

 

Mika Gustafsson, Michael Hörnquist and Anna Lombardi
  Community structure in "gene-to-gene" networks
  BioInformatics Conference,2004, 2004.

 

Mika Gustafsson, Michael Hörnquist and Anna Lombardi
  Combination of gene clusterings enhances biological validity
  Reglermöte,2004, 2004.

 

Ph.D. Theses

Mika Gustafsson
  Gene networks from high-throughput data: Reverse engineering and analysis
  2010.


  Fulltext PDF

Berkant Savas
  Algorithms in data mining using matrix and tensor methods
  2008.


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Licentiate Theses

Berkant Savas
  Algorithms in data mining: reduced rank regression and classification by tensor methods
  2005.

 

Reports

Zhengdong Lu, Berkant Savas, Wei Tang and Inderjit S. Dhillon
  Link prediction using multiple sources of information
  Department of Computer Science, The University of Texas at Austin, TR-10-35, 2010.

 

Berkant Savas and Inderjit S. Dhillon
  Fast and accurate low rank approximation of massive graphs
  Department of Computer Science, The University of Texas at Austin, TR-10-18, 2010.

 

Krzysztof Marciniak and S Rauch-Wojciechowski
  Separable systems of coordinates for triangular Newton equations
  2005.

 

Berkant Savas
  Dimensionality Reduction and Volume Minimization: Generalization of the Determinant Minimization Criterion for Reduced Rank Regression Problems
  LiTH-MAT-R, 2005:11, 2005.

 

Krzysztof Marciniak and Maciej Blaszak
  From Stäckel systems to soliton hierarchies: Benenti class of separation relations
  ITN research report, 2, 2005.

 

Krzysztof Marciniak and Maciej Blaszak
  Geometric reduction of Hamiltonian systems
  ITN research report, 2, 2004.

 

Lars Elden and Berkant Savas
  The Maximum likelihood estimate in reduced-rank regression
  LiTH-MAT-R, 31, 2003.

 


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Last updated: Sat Oct 18 17:19:25 CEST 2014