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Publications

PhD Theses    Master Theses    Bachelor Theses

2016

Shifting foundations: the mechanical cell wall and development
S. A Braybrook and H. Jönsson
Current Opinion in Plant Biology 29, 115-120 (2016)
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Nanog, Oct4 and Tet1 interplay in establishing pluripotency
V. Olariu, C. Lövkvist and K. Sneppen
Scientific Reports 6, 25438 (2016)
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Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits
B. Il Je, J. Gruel, Y.K. Lee, P. Bommert, E.D. Arevalo, A. L Eveland, Q. Wu, A. Goldshmidt, R. Meeley, M. Bartlett, M. Komatsu, H. Sakai, H. Jönsson and D. Jackson
Nature Genetics 48, 785-791 (2016)
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An epidermis-driven mechanism positions and scales stem cell niches in plants
J. Gruel, B. Landrein, P. Tarr, C. Schuster, Y. Refahi, A. Sampathkumar, O. Hamant, E.M. Meyerowitz and H. Jönsson
Science Advances 2, e1500989 (2016)
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Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping
V. Müller, N. Karami, L.K. Nyberg, C. Pichler, P.C. Torche Pedreschi, S. Quaderi, J. Fritzsche, T. Ambjörnsson, C. Åhrén, and F. Westerlund
ACS Infectious Diseases 2, 322 (2016)
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A simple method to calculate first-passage time densities with arbitrary initial conditions
M. Nyberg, T. Ambjörnsson and L. Lizana
New Journal of Physics 18, 063019 (2016)
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Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules
L.K. Nyberg, S. Quaderi, G. Emilsson, N. Karami, E. Lagerstedt, V. Müller, C. Noble, S. Hammarberg, A.N. Nilsson, F. Sjöberg, J. Fritzsche, E. Kristiansson, L. Sandegren, T. Ambjörnsson, and F. Westerlund
Scientific Reports 6, 30410 (2016)
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A somatic mutation of GFI1B identified in leukemia alters cell fate via a SPI1 (PU.1) centered genetic regulatory network
E. Anguita, R. Gupta, V. Olariu, P.J. Valk, C. Peterson, R. Delwel and T. Enver
Developmental Biology 411, 277-86 (2016)
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Irreversibility of T-Cell Specification: Insights from Computational Modelling of a Minimal Network Architecture
E. Manesso, H.Y. Kueh, G. Freedman, E.V. Rothenberg and C. Peterson
PLoS ONE 11, e0161260 (2016)
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Technical Advances of the Recombinant Antibody Microarray Technology Platform for Clinical Immunoproteomics
P. Delfani, L. Dexlin Mellby, M. Nordström, A. Holmér, M. Ohlsson, C. A. K. Borrebaeck and C. Wingren
PLoS ONE 11, e0159138 (2016)
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Peptide folding in the presence of interacting protein crowders
A. Bille, S. Mohanty and A. Irbäck
Journal of Chemical Physics 144, 175105 (2016)
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Selection shapes transcriptional logic and regulatory specialization in genetic networks
K. Fogelmark, C. Peterson and C. Troein
PLoS ONE 11, e0150340 (2016)
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2015

Extension of nanoconfined DNA: Quantitative comparison between experiment and theory
V. Iarko, E. Werner, L. K. Nyberg, V. Müller, J. Fritzsche, T. Ambjörnsson, J. P. Beech, J. O. Tegenfeldt, K. Mehlig, F. Westerlund, B. Mehlig
Phys. Rev. E 92, 062701 (2015)
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Analysis of the influence of HLA-A matching relative to HLA-B and -DR matching on heart transplant outcomes
D. Ansari, D. Bucin, P. Höglund, M. Ohlsson, B. Andersson and J. Nilsson
Transplantation Direct 1, e38 (2015)
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Equilibrium simulation of trp-cage in the presence of protein crowders
A. Bille, B. Linse, S. Mohanty and A. Irbäck
Journal of Chemical Physics 143, 175102 (2015)
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Detailed comparison of amyloid PET and CSF biomarkers for identifying early Alzheimer disease
S. Palmqvist, H. Zetterberg, N. Mattsson, P. Johansson, L. Minthon, K. Blennow, M. Ohlsson and O. Hansson
Neurology 14, 1240-1249 (2015)
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How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model
M. Reiter-Schad, E. Werner, J.O. Tegenfeldt, B. Mehlig and T. Ambjörnsson
Journal of Chemical Physics 143, 115101 (2015)
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Thermodynamics of amyloid formation and the role of intersheet interactions
A. Irbäck and J. Wessén
Journal of Chemical Physics 143, 105104 (2015)
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Finding risk groups by optimizing artificial neural networks on the area under the survival curve using genetic algorithms
J. Kalderstam, P. Edén and M. Ohlsson
PLoS ONE 10, e0137597 (2015)
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Visualizing the entire DNA from a chromosome in a single frame
C. Freitag, C. Noble, J. Fritzsche, F. Persson, A. N. Nilsson, M. Reiter-Schad, A.Graneli, T. Ambjörnsson, K. U. Mir and J. O. Tegenfeldt
Biomicrofluidics 9, 044114 (2015)
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Bacteriophage strain typing by rapid single molecule analysis
A. Grunwald, M. Dahan, A. Giesbertz, A.N. Nilsson, L.K. Nyberg, E. Weinhold, T. Ambjörnsson, F. Westerlund and Y. Ebenstein
Nucleic Acids Research (2015)
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A model for melting of confined DNA
E. Werner, M. Reiter-Schad, T. Ambjörnsson and B. Mehlig
Physical Review E 91, 060702 (2015)
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Single-cell network analysis identifies DDIT3 as a nodal lineage regulator in hematopoiesis
C. Pina, J. Teles, C. Fugazza, G. May, D. Wang, Y. Guo, S. Soneji, J. Brown, P. Edén, M. Ohlsson, C. Peterson and T. Enver
Cell Reports 11, 1-8 (2015)
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Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA
S. Ahlberg, T. Ambjörnsson and L. Lizana
New Journal of Physics 17, 043036 (2015)
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A fast and scalable algorithm for alignment of optical DNA mappings
C. Noble, A.N. Nilsson, C. Freitag, J.P. Beech, J.O. Tegenfeldt and T. Ambjörnsson
PLoS ONE 10, e0121905 (2015)
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Nanoconfined circular and linear DNA: equilibrium conformations and unfolding kinetics
M. Alizadehheidari, E. Werner, C. Noble, M. Reiter-Schad, L. K. Nyberg, J. Fritzsche, B. Mehlig, J.O. Tegenfeldt, T. Ambjörnsson, F. Persson and F. Westerlund
Macromolecules 78, 871-878 (2015)
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ABO-identical blood group matching has no survival benefit for AB heart transplant recipients
H. Bergenfeldt, P. Höglund, B. Andersson, G. Rådegran, M. Ohlsson and J. Nilsson
The Annals of Thoracic Surgery 99:3, 762-768 (2015)
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The international heart transplant survival algorithm (IHTSA): a new model to improve organ sharing and survival
J. Nilsson, M. Ohlsson, P. Höglund, B. Ekmehag, B. Koul and B. Andersson
PLoS ONE 10, e29868 (2015)
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2014

Ageing single file motion
R. Metzler, L.P. Sanders, M.A. Lomholt, L. Lizana, K. Fogelmark and T. Ambjörnsson
European Physical Journal 223, 3287-3293 (2014)
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Severe slowing-down and universality of the dynamics in disordered interacting many-body systems: ageing and ultraslow diffusion
L.P. Sanders, M.A. Lomholt, L. Lizana, K. Fogelmark, R. Metzler and T. Ambjörnsson
New Journal of Physics 16, 113050 (2014)
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Bone scan index as a prognostic imaging biomarker during androgen deprivation therapy
M. Reza, A. Bjartell, M. Ohlsson, R. Kaboteh, P. Wollmer, L. Edenbrandt and E. Trägårdh
EJNMMI Research 4:58, (2014)
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Smooth functional transition across a mutational pathway with an abrupt protein fold switch
C. Holzgräfe and S. Wallin
Biophysical Journal 107, 1217-1225 (2014)
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Conformational and aggregation properties of the 1‒93 fragment of apolipoprotein A-I
J. Petrlova, A. Bhattacherjee, W. Boomsma, S. Wallin, J.O. Lagerstedt and A. Irbäck
Protein Science 23, 1559-1571 (2014)
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Single-file diffusion with non-thermal initial conditions
L. Lizana, M.A. Lomholt and T. Ambjörnsson
Physica A 395, 148-153 (2014)
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Universality and non-universality for mobility in heterogeneous single-file systems and Rouse chains
M.A. Lomholt and T. Ambjörnsson
Physical Review E 89, 032101 (2014)
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Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli
A. N. Nilsson, G. Emilsson, L. Nyberg, C. Noble, L. Svensson Stadler, J. Fritzsche, E. R. B. Moore, J. O. Tegenfeldt, T. Ambjörnsson and F. Westerlund
Nucleic Acids Research 42, e118 (2014)
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Non-Markovian effects in the first-passage dynamics of obstructed tracer particle diffusion in one-dimensional systems
R. Forslind, L.P. Sanders, T. Ambjörnsson and L. Lizana
Journal of Chemical Physics 141, 094902 (2014)
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Single-cell PCR profiling of gene expression in hematopoiesis
J. Teles, T. Enver and C. Pina
Methods in Molecular Biology 1185, 21-42 (2014)
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Analysis of regional bone scan index measurements for the survival of patients with prostate cancer
J. Kalderstam, M. Sadik, L. Edenbrandt and M. Ohlsson
BMC Medical Imaging 14, 24 (2014)
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Rethinking transcriptional activation in the Arabidopsis circadian clock
K. Fogelmark and C. Troein
PLoS Computational Biology 10, e1003705 (2014)
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Subcellular and supracellular mechanical stress prescribes cytoskeleton behavior in Arabidopsis cotyledon pavement cells
A. Sampathkumar, P. Krupinski, R. Wightman, P. Milani, A. Berquand, A. Boudaoud, O. Hamant, H. Jönsson and E. Meyerowitz
eLife 3, e01967 (2014)
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Physical forces regulate plant development and morphogenesis
A. Sampathkumar, A. Yan, P. Krupinski and E. Meyerowitz
Current Biology 10, R475-R483 (2014)
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Light and circadian regulation of clock components aids flexible responses to environmental signals
L. E. Dixon, S. K. Hodge, G. van Ooijen, C. Troein, O. E. Akman and A. J. Millar
New Phytologist 203, 543-577 (2014)
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Robust estimation of diffusion-optimized ensembles for enhanced sampling
P. Tian, S.Æ. Jónsson, J. Ferkinghoff-Borg, S.V. Krivov, K. Lindorff-Larsen, A. Irbäck and W. Boomsma
Journal of Chemical Theory and Computation 10, 543-553 (2014)
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Hybrid Monte Carlo with non-uniform step size
C. Holzgräfe, A. Bhattacherjee and A. Irbäck
Journal of Chemical Physics 140, 044105 (2014)
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Stress and strain provide positional and directional cues in development
B. Bozorg, P. Krupinski and H. Jönsson
PLoS Computational Biology 10, e1003410 (2014)
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2013

Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus
F. Rineau, F. Shah, M. M. Smits, P. Persson, T. Johansson, R. Carleer, C. Troein and A. Tunlid
The ISME Journal 7, 2010-2022 (2013)
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SBSI: An extensible distributed software infrastructure for parameter estimation in systems biology
R. Adams, A. Clark, A. Yamaguchi, N. Hanlon, N. Tsorman, S. Ali, G. Lebedeva, A. Goltsov, A. Sorokin, O. E. Akman, C. Troein, A.J. Millar, I. Goryanin and S. Gilmore
Bioinformatics 29, 664-665 (2013)
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The moss Physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain
K. Landberg, E.R.A. Pederson, T. Viaene, B. Bozorg, J. Friml, H. Jönsson, M. Thelander and E. Sundberg
Plant Physiology 162 1406-1419 (2013)
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Dynamic analysis of gene expression and genome-wide transcription factor binding during lineage specification of multipotent progenitors
G. May, S. Soneji, A.J. Tipping, J. Teles, S.J. McGowan, M. Wu, Y. Guo, C. Fugazza, J. Brown, G. Karlsson, C. Pina, V. Olariu, S. Taylor, D.G. Tenen, C. Peterson and T. Enver
Cell Stem Cell 6, 754-768 (2013)
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Exploring protein-peptide binding specificity through computational peptide screening
A. Bhattacherjee and S. Wallin
PLoS Computational Biology 9, e1003277 (2013)
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Perturbative solution to susceptible-infected-susceptible epidemics on networks
L.P. Sanders, B. Söderberg, D. Brockmann and T. Ambjörnsson
Physical Review E 88, 032713 (2013)
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Local unfolding and aggregation mechanisms of SOD1: a Monte Carlo exploration
A. Bille, S.Æ. Jónsson, M. Akke and A. Irbäck
Journal of Physical Chemistry B 117, 9194-9202 (2013)
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Transcriptional regulation of lineage commitment - a stochastic model of cell fate decisions
J. Teles, C. Pina, P. Edén, M. Ohlsson, T. Enver and C. Peterson
PLoS Computational Biology 9, e1003197 (2013)
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Progression of bone metastases in patients with prostate cancer - automated detection of new lesions and calculation of bone scan index
R. Kaboteh, P. Gjertsson, H. Leek, M. Lomsky, M. Ohlsson, K. Sjöstrand and L. Edenbrandt
EJNMMI Research 3, 64 (2013)
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Prognosis of patients without perfusion defects with and without rest study in myocardial perfusion scintigraphy
L. Edenbrandt, M. Ohlsson and E. Trägårdh
EJNMMI Research 3, 58 (2013)
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All-atom Monte Carlo simulations of protein folding and aggregation
A. Irbäck and S. Mohanty
In Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, ed. A. Liwo, pp. 433-444 (Springer, 2013)
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Microscopic origin of the logarithmic time evolution of aging processes in complex systems
M.A. Lomholt, L. Lizana, R. Metzler and T. Ambjörnsson
Physical Review Letters 110, 208301 (2013)
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Mechanical resistance in unstructured proteins
S.Æ. Jónsson, S. Mitternacht and A. Irbäck
Biophysical Journal 104, 2725-2732 (2013)
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CODUSA - customize optimal donor using simulated annealing in heart transplantation
D. Ansari, B. Andersson, M. Ohlsson, P. Höglund, R. Andersson and J. Nilsson
Scientific Reports 3, (2013)
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Training neural networks directly on the concordance index for censored data using genetic algorithms
J. Kalderstam, P. Edén, P.-O. Bendahl, C. Strand, M. Fernö and M. Ohlsson
Artificial Intelligence in Medicine 52, 125-132 (2013)
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In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function
E. Follin, M. Karlsson, C. Lundegaard, M. Nielsen, S. Wallin, K. Paulsson and H. Westerdahl
Immunogenetics 65, 299-311 (2013)
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Plant stem cell maintenance involves direct transcriptional repression of differentiation program
R.K. Yadav, M. Perales, J. Gruel, C. Ohno, M. Heisler, T. Girke, H. Jönsson and G.V. Reddy
Molecular Systems Biology 9, 654 (2013)
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Bone scan index: a prognostic imaging biomarker for high-risk prostate cancer patients receiving primary hormonal therapy
R. Kaboteh, J.-E. Damber, P. Gjertsson, P. Höglund, M. Lomsky, M. Ohlsson and L. Edenbrandt
EJNMMI Research 3, 9 (2013)
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Cerebrospinal fluid levels of heart-type fatty acid binding protein are elevated prodromally in Alzheimer's disease and vascular dementia
B. Olsson, J. Hertze, M. Ohlsson, K. Nägga, K. Höglund, H. Basun, P. Annas, L. Lannfelt, N. Andreasen, L. Minthon, H. Zetterberg, K. Blennow and O. Hansson
Journal of Alzheimer's Disease 34, 673-679 (2013)
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Aggregate geometry in amyloid fibril nucleation
A. Irbäck, S.Æ. Jónsson, N. Linnemann, B. Linse and S. Wallin
Physical Review Letters 110, 058101 (2013)
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Dynamical modelling of haematopoiesis: an integrated view over the system in homeostasis and under perturbation
E. Manesso, J. Teles, D. Bryder and C. Peterson
Journal of the Royal Society Interface 10, 20120817 (2013)
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Computational modeling of T-cell formation kinetics: output regulated by initial proliferation-linked deferral of developmental competence
E. Manesso, V. Chickarmane, H.Y. Kueh, E.V. Rothenberg and C. Peterson
Journal of the Royal Society Interface 10, 20120774 (2013)
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2012

First passage times for a tracer particle in single file diffusion and fractional Brownian motion
L.P. Sanders and T. Ambjörnsson
Journal of Chemical Physics 136, 175103 (2012)
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Computational multiscale modelling of embryo development
P. Krupinski, V. Chickarmane and C. Peterson
Current Opinion in Genetics & Development 22, 613-618 (2012)
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A novel automated platform to quantify the extent of skeletal tumor involvement in prostate cancer patients with bone scan index
D. Ulmert, R. Kaboteh, J. J. Fox, C. Savage, M. J. Evans, H. Lilja, P-E. Abrahamsson, T. Björk, A. Gerdtsson, A. Bjartell, P. Gjertsson, P. Höglund, M. Lomsky, M. Ohlsson, J. Richter, M. Sadik, M. J. Morris, H. I. Scher, K. Sjöstrand, A. Yu, M. Suurkula, A. J. Vickers, L. Edenbrandt and S. M. Larson
European Urology 62:1, 78-84 (2012)
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Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties
N. Olsson, S. Wallin, P. James, C. A. K. Borrebaeck and C. Wingren
Protein Science 21, 1897-1910 (2012)
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Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study
I. Staneva, Y. Huang, Z. Liu and S. Wallin
PLoS Computational Biology 8, e1002682 (2012)
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Optical advantages and function of multifocal spherical fish lenses
Y.L. Gagnon, B. Söderberg and R.H.H. Kröger
Journal of the Optical Society of America A 29, 1786-1793 (2012)
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Probing the role of stochasticity in a model of the embryonic stem cell — heterogeneous gene expression and reprogramming efficiency
V. Chickarmane, V. Olariu and C. Peterson
BMC Systems Biology 6, 98 (2012)
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Likelihood of acute coronary syndrome in emergency department chest pain patients varies with time of presentation
U. Ekelund, M. Akbarzadeh, A. Khoshnood, J. Björk and M. Ohlsson
BMC Research Notes 5:420, (2012)
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Monte Carlo simulations of protein aggregation
S. Æ. Jónsson, I. Staneva, S. Mohanty and A. Irbäck
Physics Procedia 34, 49-54 (2012)
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Distinct phases of free α-synuclein — a Monte Carlo study
S. Æ. Jónsson, S. Mohanty and A. Irbäck
Proteins: Structure, Function, and Bioinformatics 80, 2169-2177 (2012)
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Inferring rules of lineage commitment in haematopoiesis
C. Pina, C. Fugazza, A.J. Tipping, J.Brown, S. Soneji, J. Teles, C. Peterson and T. Enver
Nature Cell Biology 14, 287-294 (2012)
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Evaluation of a previously suggested plasma biomarker panel to identify Alzheimer's disease
M. Björkqvist, M. Ohlsson, L. Minthon and O. Hansson
PLoS ONE 7, e29868 (2012)
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Subtle Monte Carlo updates in dense molecular systems
S. Bottaro, W. Boomsma, K. E. Johansson, C. Andreetta, T. Hamelryck and J. Ferkinghoff-Borg
Journal of Chemical Theory and Computation 8, 695-702 (2012)
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An artificial neural network to safely reduce the number of ambulance ECGs transmitted for physician assessment in a system with prehospital detection of ST elevation myocardial infarction
J.L. Forberg, A. Khoshnood, M. Green, M. Ohlsson, J. Björk, S. Jovinge, L. Edenbrandt and U. Ekelund
Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine 20, (2012)
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On evaluating models in computational morphodynamics
H. Jönsson, J. Gruel, P. Krupinski and C. Troein
Current Opinion in Plant Biology 15, 103-110 (2012)
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Risk predictions for individual patients from logistic regression can be visualized with bar-line charts
J. Björk, U. Ekelund and M. Ohlsson
Journal of Clinical Epidemiology 65, 335-342 (2012)
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Coupled folding-binding in a hydrophobic/polar protein model: Impact of synergistic folding and disordered flanks
A. Bhattacherjee and S. Wallin
Biophysical Journal 102, 569-578 (2012)
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2011

Diagnostic evaluation of three cardiac software packages using a consecutive group of patients
L. Johansson, M. Lomsky, J. Marving, M. Ohlsson, S.-E. Svensson and L. Edenbrandt
EJNMMI Research 1, 1-7 (2011)
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Mutation-induced fold switching among lattice proteins
C. Holzgräfe, A. Irbäck and C. Troein
Journal of Chemical Physics 135, 195101 (2011)
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WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex
R. K. Yadav, M. Perales, J. Gruel, T. Girke, H. Jönsson and G. V. Reddy
Genes & Development 25, 2025-2030 (2011)
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Prediction of severe acute pancreatitis at admission to hospital using artificial neural networks
B. Andersson, R. Andersson, M. Ohlsson and J. Nilsson
Pancreatology 11, 328-335 (2011)
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Clinical data do not improve artificial neural network interpretation of myocardial perfusion scintigraphy
P. Gjertsson, L. Johansson, M. Lomsky, M. Ohlsson, S. R. Underwood and L. Edenbrandt
Clinical Physiology and Functional Imaging 31, 240-245 (2011)
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Accelerating atomic-level protein simulations by flat-histogram techniques
S. Æ. Jónsson, S. Mohanty and A. Irbäck
Journal of Chemical Physics 135, 125102 (2011)
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Molecular serum portraits in patients with primary breast cancer predict the development of distant metastases
A. Carlsson, C. Wingren, M. Kristensson, C. Rose, M. Fernö, H. Olsson, H. Jernström, S. Ek, E. Gustavsson, C. Ingvar, M. Ohlsson, C. Peterson and C. A. K. Borrebaeck
Proceedings of the National Academy of Sciences USA 108, 14252-14257 (2011)
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Binding free energy landscape of domain-peptide interactions
I. Staneva and S. Wallin
PLoS Computational Biology 7, e1002131 (2011)
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Generic workflow for quality assessment of quantitative label-free LC-MS analysis
M. Sandin, M. Krogh, K. M. Hansson and F. Levander
Proteomics 11, 1114-1124 (2011)
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Hunting for protein markers of hypoxia by combining plasma membrane enrichment with a new approach to membrane protein analysis
P. Cifani, M. Bendz, K. Wårell, K. Hansson, F. Levander, M. Sandin, M. Krogh, M. Ovenberger, E.  Fredlund, M. Vaapil, A. Pietras, S. Påhlman and P. James
Journal of Proteome Research 10, 1645-1656 (2011)
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Monte Carlo study of the formation and conformational properties of dimers of Aβ42 variants
S. Mitternacht, I. Staneva, T. Härd and A. Irbäck
Journal of Molecular Biology 410, 357-367 (2011)
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Simulating the mammalian blastocyst - molecular and mechanical interactions pattern the embryo
P. Krupinski, V. Chickarmane and C. Peterson
PLoS Computational Biology 7, e1001128 (2011)
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Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models
H. S. Chan, Z. Zhang, S. Wallin and Z. Liu
Annual Review of Physical Chemistry 62, 301-326 (2011)
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Dissimilar bouncy walkers
M. A. Lomholt, L. Lizana and T. Ambjörnsson
Journal of Chemical Physics 134, 045101 (2011)
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Models of sequestration and receptor cross-talk for explaining multiple mutants in plant stem cell regulation
P. Sahlin, P. Melke and H. Jönsson
BMC Systems Biology 5, 2 (2011)
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Effective all-atom potentials for proteins
A. Irbäck and S. Mohanty
In Multiscale Approaches to Protein Modeling, ed. A. Kolinski, pp. 111-126 (Springer, 2011)
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2010

Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array-comparative genomic hybridization
A. Isinger-Ekstrand, J. Johansson, M. Ohlsson, P. Francis, J. Staaf, M. Jönsson, Å. Borg and M. Nilbert
Cancer Genetics and Cytogenetics 200, 120-126 (2010)
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Using Gaussian process with test rejection to detect T-cell epitopes in pathogen genomes
L. You, V. Brusic, M. Gallagher and M. Bodén
IEEE/ACM transactions on computational biology and bioinformatics 7, 741-751 (2010)
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Gene expression signatures in childhood acute leukemias are largely unique and distinct from those of normal tissues and other malignancies
A. Andersson, P. Edén, T. Olofsson and T. Fioretos
BMC Medical Genomics 3, 6 (2010)
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Foundation of fractional Langevin equation: Harmonization of a many-body problem
L. Lizana, T. Ambjörnsson, A. Taloni, E. Barkai and M.A. Lomholt
Physical Review E 81, 051118 (2010)
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Alignment between PIN1 polarity and microtubule orientation in the shoot apical meristem reveals a tight coupling between morphogenesis and auxin transport
M. Heisler, O. Hamant, P. Krupinski, M. Uyttewaal, C. Ohno, H. Jönsson, J. Traas and E. Meyerowitz
PLoS Biology 8, e1000516 (2010)
[ HTML at journal ]

A modeling study on how cell division affects properties of epithelial tissues under isotropic growth
P. Sahlin and H. Jönsson
PLoS ONE 5, e11750 (2010)
[ HTML at journal ]

A cell-based model for quorum sensing in heterogeneous bacterial colonies
P. Melke, P. Sahlin, A. Levchenko and H. Jönsson
PLoS Computational Biology 6, e1000819 (2010)
[ HTML at journal ]

Identification of uniquely expressed transcription factors in highly purified B-cell lymphoma samples
U. Andréasson, P. Edén, C. Peterson, C-M Högerkorp, M. Jerkeman, N. Andersen, M. Berglund, C. Sundström, R. Rosenquist, C. A. K. Borrebaeck and S. Ek
American Journal of Hematology 85, 418-425 (2010)
[ HTML at journal ]

Comparing the folding free-energy landscapes of Aβ42 variants with different aggregation properties
S. Mitternacht, I. Staneva, T. Härd and A. Irbäck
Proteins: Structure, Function, and Bioinformatics 78, 2600-2608 (2010)
[ HTML at journal ]

Microscopic mechanism of specific peptide adhesion to semiconductor substrates
M. Bachmann, K. Goede, A. G. Beck-Sickinger, M. Grundmann, A. Irbäck and W. Janke
Angewandte Chemie International Edition 49, 9530-9533 (2010))
[ HTML at journal ]

Observing plasmonic-molecular resonance coupling on single gold nanorods
W. Ni, T. Ambjörnsson, S. P. Apell, H. Chen and J. Wang
Nano Letters 10, 77-84 (2010)
[ HTML at journal ]

Modeling auxin-regulated development
P. Krupinski and H. Jönsson
Cold Spring Harbor Perspectives in Biology 2, a001560 (2010)
[ HTML at journal ]

Adjusting a light dispersion model to fit measurements from vertebrate ocular media as well as ray-tracing in fish lenses
Y. L. Gagnon, R. H. H. Kröger and B. Söderberg
Vision Research 50, 850-853 (2010)
[ HTML at journal ]

Unfolding times for proteins in a force clamp
S. Luccioli, A. Imparato, S. Mitternacht, A. Irbäck and A. Torcini
Physical Review E 81, 010902(R) (2010)
[ HTML at journal ]

Modeling plant growth and pattern formation
H. Jönsson and P. Krupinski
Current Opinion in Plant Biology 13, 5-11 (2010)
[ HTML at journal ]

2009

The Proteios Software Environment: an extensible multiuser platform for management and analysis of proteomics data
J. Häkkinen, G. Vincic, O. Månsson, K. Wårell and F. Levander
Journal of Proteome Research 8, 3037-3043 (2009)
[ HTML at journal ]

BASE - 2nd generation software for microarray data management and analysis
J. Vallon-Christersson, N. Nordborg, M. Svensson and J. Häkkinen
BMC Bioinformatics 10, 330 (2009)
[ HTML at journal ]

Omics analyses reveal a potential link between hormone-sensitive lipase and polyamine metabolism
C. Fernandez, M. Krogh, K. Wårell, K. Alm, S. Oredsson, L. Persson, P. James and C. Holm
Journal of Proteome Research 8, 5008-5019 (2009)
[ HTML at journal ]

All-atom Monte Carlo approach to protein-peptide binding
I. Staneva and S. Wallin
Journal of Molecular Biology 393, 1118-1128 (2009)
[ HTML at journal ]

Diffusion of finite-sized hard-core interacting particles in a one-dimensional box: Tagged particle dynamics
L. Lizana and T. Ambjörnsson
Physical Review E 80, 051103 (2009)
[ HTML at journal ]

Expression of P190 and P210 BCR/ABL1 in normal human CD34+ cells induces similar gene expression profiles and results in a STAT5-dependent expansion of the erythroid lineage
M. Järås, P. Johnels, H. Ågerstam, C. Lassen, M. Rissler, P. Edén, J. Cammenga, T. Olofsson, O. W. Bjerrum, J. Richter, X. Fan and T. Fioretos
Experimental Hematology 37, 367-375 (2009)
[ HTML at journal ]

Single DNA denaturation and bubble dynamics
R. Metzler, T. Ambjörnsson, A. Hanke and H. C. Fogedby
Journal of Physics: Condensed Matter 21, 034111 (2009)
[ HTML at journal ]

Bubble merging in breathing DNA as a vicious walker problem in opposite potentials
J. N. Pedersen, M. S. Hansen, T. Novotny, T. Ambjörnsson and R. Metzler
Journal of Chemical Physics 130, 164117 (2009)
[ HTML at journal ]

NMDA receptor stimulation induces reversible fission of the neuronal endoplasmic reticulum
K. Kucharz, M. Krogh, A. N. Ng and H. Toresson
PLoS ONE 4, e5250 (2009)
[ HTML at journal ]

Proteomic expression analysis and comparison of protein and mRNA expression profiles in human malignant gliomas
O. Persson, U. Brynnel, F. Levander, B. Widegren, L. Salford and M. Krogh
Proteomics - Clinical Applications 3, 83-94 (2009)
[ HTML at journal ]

How to find simple and accurate rules for viral protease cleavage specifities
T. Rögnvaldsson, T. A. Etchells, L. You, D. Garwicz, I. H. Jarman and P. J. G. Lisboa
BMC Bioinformatics 10, 149 (2009)
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Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks
F. Colecchia, D. Kottwitz, M. Wagner, C. Pfenninger, G. Thiel, I. Tamm, C. Peterson and U. Nuber
Nucleic Acids Research 37, e82 (2009)
[ HTML at journal ]

Stem cell states, fates and the rules of attraction
T. Enver, M. Pera, C. Peterson and P. W. Andrews
Cell Stem Cell 4, 387-397 (2009)
[ HTML at journal ]

An effective all-atom potential for proteins
A. Irbäck, S. Mitternacht and S. Mohanty
PMC Biophysics 2, 2 (2009)
[ HTML at journal ]

Regulated transport as a mechanism for pattern generation: Capabilities for phyllotaxis and beyond
P. Sahlin, B. Söderberg and H. Jönsson
Journal of Theoretical Biology 258, 60-70 (2009)
[ HTML at journal ]

Exploring new possibilities for case based explanation of artificial neural network ensembles
M. Green, U. Ekelund, L. Edenbrandt, J. Björk, J. L. Forberg and M. Ohlsson
Neural Networks 22, 75-81 (2009)
[ HTML at journal ]

In search of the best method to predict acute coronary syndrome using only the electrocardiogram from the emergency department
J. L. Forberg, M. Green, J. Björk, M. Ohlsson, L. Edenbrandt, H. Öhlin and U. Ekelund
Journal of Electrocardiology 42, 58-63 (2009)
[ HTML at journal ]

Changing the mechanical unfolding pathway of FnIII10 by tuning the pulling strength
S. Mitternacht, S. Luccioli, A. Torcini, A. Imparato and A. Irbäck
Biophysical Journal 96, 429-441 (2009)
[ HTML at journal ]

Computational modeling of the hematopoietic erythroid-myeloid switch reveals insights into co-operativity, priming and irreversibility
V. Chickarmane, T. Enver and C. Peterson
PLoS Computational Biology 5, e1000268 (2009)
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2008

Computer-assisted interpretation of planar whole-body bone scans
M. Sadik, I. Hamadeh, P. Nordblom, M. Suurkula, P. Höglund, M. Ohlsson and L. Edenbrandt
The Journal of Nuclear Medicine 49, 1958-1965 (2008)
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Developmental patterning by mechanical signals in Arabidopsis
O. Hamant, M. Heisler, H. Jönsson, P. Krupinski, M. Uyttewaal, P. Bokov, F. Corson, P. Sahlin, A. Boudaoud, E. M. Meyerowitz, Y. Couder and J. Traas
Science 322, 1650-1655 (2008)
[ HTML at journal ]

Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment
D.-W. Li, S. Mohanty, A. Irbäck and S. Huo
PLoS Computational Biology 4, e1000238 (2008)
[ HTML at journal ]

A computational model for understanding stem cell, trophectoderm and endoderm lineage determination
V. Chickarmane and C. Peterson
PLoS ONE 3, e3478 (2008)
[ HTML at journal ]

Effects of the peripheral layers on the optical properties of spherical fish lenses
Y. L. Gagnon, B. Söderberg and R. H. Kröger
Journal of the Optical Society of America A 25, 2468-2475 (2008)
[ Abstract ] [ HTML at journal ]

Disturbed cholesterol homeostasis in hormone-sensitive lipase null mice
C. Fernandez, M. Lindholm, M. Krogh, S. Lucas, S. Larsson, P. Osmark, K. Berger, J. Boren, B. A. Fielding, K. N. Frayn and C. Holm
American Journal of Physiology. Endocrinology and Metabolism (2008)
[ HTML at journal ]

Explaining artificial neural network ensembles: A case study with electrocardiograms from chest pain patients
M. Green, U. Ekelund, L. Edenbrandt, J. Björk, J. L. Foreberg and M. Ohlsson
Proceedings of the 25th International Conference on Machine Learning, ed. M. Hauskrecht (2008)
[ Abstract ] [ PDF ]

Evaluation of a decision support system for interpretation of myocardial perfusion gated SPECT
M. Lomsky, P. Gjertsson, L. Johansson, J. Richter, M. Ohlsson, D. Tout, R. S. Underwood and L. Edenbrandt
European Journal of Nuclear Medicine and Molecular Imaging 35, 1523-1529 (2008)
[ Abstract ] [ HTML at journal ]

Detection of pancreatic cancer using antibody microarray-based serum protein profiling
J. Ingvarsson, C. Wingren, A. Carlsson, P. Ellmark, B. Wahren, G. Engström, U. Harmenberg, M. Krogh, C. Peterson and C. Borrebaeck
Proteomics 8, 2211-2219 (2008)
[ HTML at journal ]

Gene expression profiling in primary breast cancer distinguishes patients developing local recurrence after breast conservation surgery with or without postoperative radiotherapy
E. Niméus, M. Krogh, P. Malmström, C. Strand, I. Fredriksson, P. Karlsson, B. Nordenskjöld, O. Stål, G. Östberg, C. Peterson and M. Fernö
Breast Cancer Research 10, R34 (2008)
[ HTML at journal ]

Comments on Practical experiences on the necessity of external validation by I. R. König, J. D. Malley, C. Weimar, H.-C. Diener and A. Ziegler, Statistics in Medicine, DOI: 10.1002/sim.3069
J. Björk, M. Green and U. Ekelund
Statistics in Medicine 27, 2737-2738 (2008)
[ HTML at journal ]

Genes associatied with the tumor microenvironment are differentially expressed in cured versus primary chemotherapy-refractory diffuse large B-cell lymphoma
J. Linderoth, P. Edén, M. Ehinger, J. Valcich, M. Jerkeman, P.-O. Bendahl, M. Berglund, G. Enblad, M. Erlanson, G. Roos and E. Cavallin-Ståhl
British Journal of Haematology 141, 423-432 (2008)
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Metabolomic and proteomic analysis of a clonal producing β-cell line (INS-1 832/13)
C. Fernandez, U. Fransson, E. Hallgard, P. Spégel, C. Holm, M. Krogh, K. Wårell, P. James and H. Mulder
Journal of Proteome Research 1, 400-411 (2008)
[ HTML at journal ]

Spontaneous β-barrel formation: an all-atom Monte Carlo study of Aβ(16-22) oligomerization
A. Irbäck and S. Mitternacht
Proteins: Structure, Function, and Bioinformatics 71 207-214 (2008)
[ HTML at journal ]

Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data
C. Ritz and P. Edén
BMC Genomics 19:25 (2008)
[ HTML at journal ]

Recurrent gross mutations of the PTEN tumor suppressor gene in breast cancers with deficient DSB repair
L. H. Saal, S. K. Gruvberger-Saal, C. Persson, K. Lövgren, M. Jumpannen, J. Staaf, G. Jönsson, M. Pires, M. Maurer, K. Holm, S. Koujak, S. Subramaniyam, J. Vallon-Christersson, H. Olsson, T. Su, L. Memeo, T. Ludwig, S. P. Ethier, M. Krogh, M. Szabolcs, V. V. V. S. Murty, J. Isola, H. Hibshoosh, R. Parsons and Å. Borg
Nature Genetics 40, 102-107 (2008)
[ HTML at journal ]

Protein folding, unfolding and aggregation studied using an all-atom model with a simplified interaction potential
A. Irbäck
Lecture Notes in Physics 736, 269-291 (2008)
[ PDF ]

2007

Improved modeling of the substrate specificities of HIV-1 protease
T. Rögnvaldsson, T. A. Etchells, L. You, D. Garwicz, P. J. G. Lisboa and I. Jarman
LU TP 07-31

SPECLUST: a web tool for clustering of mass spectra
P. Johansson, R. Alm, C. Emanuelsson, J. Häkkinen and M. Ringnér
LU TP 07-14
[ Abstract ]

Bioinformatic approaches for modeling the substrate specificity of HIV-1 protease: An overview
T. Rögnvaldsson, L. You and D. Garwicz
Expert Review of Molecular Diagnostics 7, 435-451 (2007)
[ HTML at journal ]

Confirmation of a BRAF mutation-associated gene expression signature in melanoma
P. Johansson, S. Pavey and N. Hayward
Pigment Cell Research 20, 216-221 (2007)
[ HTML at journal ]

Understanding prediction systems for HLA-binding peptides and T-cell epitope identification
L. You, P. Zhang, M. Bodén and V. Brusic
Lecture Notes in Bioinformatics 4774, 337-348 (2007)
[ HTML at journal ]

Large-scale proteomics analysis of human ovarian cancer for biomarkers
S. Bengtsson, M. Krogh, C. A. Szigyarto, M. Uhlen, K. Schedvins, C. Silfverswärd, S. Linder, G. Auer, A. Alaiya and P. James
Journal of Proteome Research 6, 1440 -1450 (2007)
[ HTML at journal ]

Hypothermia affects translocation of numerous cytoplasmic proteins following global cerebral ischemia
M. Teilum, M. Krogh, T. Wieloch and G. Mattiasson
Journal of Proteome Research 6, 2822 -2832 (2007)
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Microarray analysis of gliomas reveals chromosomal position-associated gene expression patterns and identifies potential immunotherapy targets
O. Persson, M. Krogh, L. H. Saal, E. Englund, J. Liu, R. Parsons, N. Mandahl, Å. Borg, B. Widegren and L. G. Salford
Journal of Neuro-Oncology 85, 11-24 (2007)
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Proteomic analysis of striatal proteins in a rat model of L-DOPA-induced dyskinesia
B. Valastro, A. Dekundy, M. Krogh, M. Lundblad, P. James, W. Danysz, G. Quack and M. A. Cenci
Journal of Neurochemistry 102, 1395-409 (2007)
[ HTML at journal ]

Proteomic variation is larger within than between strawberry varieties
R. Alm, A. Ekefjärd, M. Krogh, J. Häkkinen and C. Emanuelsson
Journal of Proteome Research 6, 3011-3020 (2007)
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Self-Organization in High-Density Bacterial Colonies: Efficient Crowd Control
H. Cho, H. Jönsson, K. Campbell, P. Melke, J. W. Williams, B. Jedynak, A. M. Stevens, A. Groisman and A. Levchenko
PLoS Biology 5, e302 (2007)
[ HTML at journal ]

A probabilistic treatment of the missing spot problem in 2D gel electrophoresis experiments
M. Krogh, C. Fernandez, M. Teilum, S. Bengtsson and P. James
Journal of Proteome Research 6, 3335-3343 (2007)
[ HTML at journal ]

The molecular signature of MDS stem cells supports a stem cell origin of 5q- myelodysplastic syndromes
L. Nilsson, P. Edén, E. Olsson, R. Månsson, I. Åstrand-Grundström, B. Strömbeck, K. Theilgaard-Moench, K. Anderson, R. Hast, E. Hellström-Lindberg, J. Samuelsson, G. Bergh, C. Nerlov, B. Johansson, M. Sigvardsson, Å. Borg and S. E. Jacobsen
Blood 110, 3005-3014 (2007)
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Is transcriptional regulation of metabolic pathways an optimal strategy for fitness?
C. Troein, D. Ahrén, M. Krogh and C. Peterson
PLoS ONE 9, e855 (2007)
[ Abstract ] [ PDF ] [ HTML at journal ]

Genomic profiling of malignant melanoma using tiling-resolution arrayCGH
G. Jönsson, C. Dahl, J. Staaf, T. Sandberg, P.-O. Bendahl, M. Ringnér, P. Guldberg and Å. Borg
Oncogene 26, 4738-4748 (2007)
[ Abstract ] [ HTML at journal ]

Comparison of standard resampling methods for performance estimation of artificial neural network ensembles
M. Green and M. Ohlsson
In Proceedings of Third International Conference on Computational Intelligence in Medicine and Healthcare, Plymouth, England, ed. E. Ifeachor (2007)
[ Abstract ] [ PDF ]

The mass distance fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy MS
F. Potthast, B. Gerrits, J. Häkkinen, D. Rutishauser, C. H. Ahrens, B. Roschitzki, K. Baerenfaller, R. Munton, P. Walther, S. N. Lövenich, P. Gehrig, P. Seif, P. H. Seeberger and R. Schlapbach
Journal of Chromatography B854, 173-182 (2007)
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Microarray-based classification of a consecutive series of 121 childhood acute leukemias: prediction of leukemic and genetic subtype as well as of minimal residual disease status
A. Andersson, C. Ritz, D. Lindgren, P. Edén, C. Lassen, J. Heldrup, T. Olofsson, J. Råde, M. Fontes, A. Porwit-McDonald, M. Behrendtz, M. Höglund, B. Johansson and T. Fioretos
Leukemia 21, 1198-1203 (2007)
[ Abstract ]

Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis
Y. Liu and M. Ringnér
Genome Biology 8, R77 (2007)
[ Abstract ] [ PDF ] [ HTML at journal ]

Best leads in the standard electrocardiogram for the emergency detection of acute coronary syndrome
M. Green, M. Ohlsson, J. L. Forberg, J. Björk, L. Edenbrandt and U. Ekelund
Journal of Electrocardiology 40, 251-256 (2007)
[ HTML at journal ]

Differences in solution behavior among four semiconductor-binding peptides
S. Mitternacht, S. Schnabel, M. Bachmann, W. Janke and A. Irbäck
Journal of Physical Chemistry B111, 4355-4360 (2007)
[ HTML at journal ]

Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity
L. H. Saal, P. Johansson, K. Holm, S. K. Gruvberger-Saal, Q. B. She, M. Maurer, S. Koujak, A. A. Ferrando, P. Malmström, L. Memeo, J. Isola, P. O. Bendahl, N. Rosen, H. Hibshoosh, M. Ringnér, Å. Borg and R. Parsons
Proceedings of the National Academy of Sciences USA 104, 7564-7569 (2007)
[ Abstract ] [ PDF ] [ HTML at journal ]

Estrogen receptor β expression is associated with tamoxifen response in ERα-negative breast carcinoma
S. K. Gruvberger-Saal, P. O. Bendahl, L. H. Saal, M. Laakso, P. Edén, C. Peterson, P. Malmström, J. Isola, Å. Borg and M. Fernö
Clinical Cancer Research 13, 1987-1994 (2007)
[ Abstract ] [ PDF ] [ HTML at journal ]

High-resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization
G. Jönsson, J. Staaf, E. Olsson, M. Heidenblad, J. Vallon-Christersson, K. Osoegawa, P. de Jong, S. Oredsson, M. Ringnér, M. Höglund and Å. Borg
Genes, Chromosomes and Cancer 46, 543-558 (2007)
[ Abstract ] [ PDF ] [ HTML at journal ]

Proteomic data exchange and storage: using proteios
P. Gärdén and R. Alm
Methods in Molecular Biology 367, 241-60 (2007)
[ Abstract ]

Automated reporting from gel-based proteomics experiments using the open source Proteios database application
F. Levander, M. Krogh, K. Wårell, P. Gärdén, P. James and J. Häkkinen
Proteomics 7, 668-674 (2007)
[ Abstract ] [ HTML at journal ]

Somatostatin effects on the proteome of the LNCaP cell-line
Z. Liu, S. Bengtsson, M. Krogh, M. Marquez, S. Nilsson, P. James, A. Aliaya and A. R. Holmberg
International Journal of Oncology 30, 1173-1179 (2007)

Diagnostic and prognostic gene expression signatures in 177 soft tissue sarcomas: hypoxia-induced transcription profile signifies metastatic potential
P. Francis, H. M. Namløs, C. Müller, P. Edén, J. Fernebro, J.-M. Berner, B. Bjerkehagen, M. Åkerman, P.-O. Bendahl, A. Isinger, A. Rydholm, O.Myklebost and M. Nilbert
BMC Genomics 8, 73 (2007)
[ HTML at journal ]

Basal-like phenotype is not associated with patient survival in estrogen-receptor-negative breast cancers
M. Jumppanen, S. Gruvberger-Saal, P. Kauraniemi, M. Tanner, P. O. Bendahl, M. Lundin, M. Krogh, P. Kataja, Å. Borg, M. Fernö and J. Isola
Breast Cancer Research 9, R16 (2007)
[ HTML at journal ]

Modelling meristem development in plants
M. Heisler and H. Jönsson
Current Opinion in Plant Biology 10, 92-97 (2007)
[ HTML at journal ]

Classification of genomic and proteomic data using support vector machines
P. Johansson and M. Ringnér
In Fundamentals of Data Mining in Genomics and Proteomics, eds. D. P. Berrar, W. Dubitzky and M. Granzow, Springer Verlag, pp. 187-202 (2007)
[ PDF ]

Automated interpretation of PET/CT images in patients with lung cancer
H. Gutte, D. Jakobsson, F. Olofsson, M. Ohlsson, S. Valind, A. Loft, L. Edenbrandt and A. Kjær
Nuclear Medicine Communications 28, 79-84 (2007)
[ Abstract ]

Analysis of DIGE data using a linear mixed model allowing for protein-specific dye effects
M. Krogh, Y. Liu, S. Waldemarson, B. Valastro and P. James
Proteomics 7, 4235-4244 (2007)
[ HTML at journal ]

2006

Computer modeling of plant development
M. Heisler and H. Jönsson
Journal of Plant Growth Regulation 25, 267-269 (2006)
[ HTML at journal ]

Modeling auxin transport and plant development
M. Heisler and H. Jönsson
Journal of Plant Growth Regulation 25, 302-312 (2006)
[ HTML at journal ]

Detection of cleavage sites for HIV-1 protease in native proteins
L. You
Proceeding of LSS Computational Systems Bioinformatics Conference, Stanford, CA, August 14-18 (2006)

A rate equation approach to elucidate the kinetics and robustness of the TGF-β pathway
P. Melke, H. Jönsson, P. ten Dijke, E. Pardali and C. Peterson
Biophysical Journal 91, 4368-4380 (2006)
[ Abstract ] [ PDF ]

Comparison between neural networks and multiple logistic regression to predict acute coronary syndrome in the emergency room
M. Green, J. Björk, J. Forberg, U. Ekelund, L. Edenbrandt and M. Ohlsson
Artificial Intelligence in Medicine 38, 305-318 (2006)
[ Abstract ] [ HTML at journal ]

Protein aggregation and unfolding studied using an all-atom model with a simplified energy function
A. Irbäck and S. Mitternacht
In Proceedings of the Workshop From Computational Biophysics to Systems Biology 2006, Jülich, eds. U. H. E. Hansmann et al., pp. 15-20 (2006)
[ PDF ]

Gene expression profilers and conventional clinical markers to predict distant recurrences for premenopausal breast cancer patients after adjuvant chemotherapy
E. Niméus-Malmström, C. Ritz, P. Edén, A. Johnsson, C. Strand, G. Östberg, M. Fernö and C. Peterson
European Journal of Cancer 42, 2729-2737 (2006)
[ Abstract ] [ PDF ] [ HTML at journal ]

Thermal versus mechanical unfolding of ubiquitin
A. Irbäck and S. Mitternacht
Proteins: Structure, Function, and Bioinformatics 65, 759-766 (2006)
[ HTML at journal ]

Transcriptional dynamics of the embryonic stem cell switch
V. Chickarmane, C. Troein, U. Nuber, H. M. Sauro and C. Peterson
PLoS Computational Biology 2, e123 (2006)
[ Abstract ] [ PDF ] [ Supplement ] [ HTML at journal ]

An introduction to BASE
C. Troein, J. Vallon-Christersson and L. H. Saal
In Methods in Enzymology 441, DNA Microarrays, Part B: Databases and Statistics, eds. A. Kimmel and B. Oliver, 99-119, Elsevier (2006)
[ Abstract ] [ HTML at journal ]

Pulsatile blood flow, shear force, energy dissipation and Murray´s Law
P. R. Painter, P. Edén and H.-U. Bengtsson
Theoretical Biology and Medical Modelling 3 (2006)
[ Abstract ] [ HTML at journal ]

The added value of ECG-gating for the diagnosis of myocardial infarction using myocardial perfusion scintigraphy and artificial neural networks
P. Gjertsson, M. Lomsky, J. Richter, M. Ohlsson, D. Tout, A. van Aswegen, R. Underwood and L. Edenbrandt
Clinical Physiology and Functional Imaging 26, 301-304 (2006)
[ Abstract ]

Osteopontin is a downstream effector of the PI3-kinase pathway in melanomas that is inversely correlated with functional PTEN
L. Packer, S. Pavey, A. Parker, M. Stark, P. Johansson, B. Clarke, P. Pollock, M. Ringnér and N. Hayward
Carcinogenesis 27, 1778-1786 (2006)
[ Abstract ] [ HTML at journal ]

A simple statistical model for prediction of acute coronary syndrome in chest pain patients in the emergency department
J. Björk, J. L. Forberg, M. Ohlsson, L. Edenbrandt, H. Öhlin and U. Ekelund
BMC Medical Informatics and Decision Making 6 (2006)
[ Abstract ] [ HTML at journal ]

Risk factor identification and mortality prediction in cardiac surgery using artificial neural networks
J. Nilsson, M. Ohlsson, L. Thulin, P. Höglund, S. A. Nashef and J. Brandt
The Journal of Thoracic and Cardiovascular Surgery 132, 12-19 (2006)
[ Abstract ] [ HTML at journal ]

PROFASI: a Monte Carlo simulation package for protein folding and aggregation
A. Irbäck and S. Mohanty
Journal of Computational Chemistry 27, 1548-1555 (2006)
[ HTML at journal ]

Improving missing value imputation of microarray data by using spot quality weights
P. Johansson and J. Häkkinen
BMC Bioinformatics 7, 306 (2006)
[ Abstract ] [ PDF ] [ HTML at journal ]

Patient gender and radiopharmaceutical tracer is of minor importance for the interpretation of myocardial perfusion images using an artificial neural network
K. Tägil, R. S. Underwood, G. Davies, K. A. Latus, M. Ohlsson, C. Wallin and L. Edenbrandt
Clinical Physiology and Functional Imaging 26, 146-150 (2006)
[ Abstract ] [ HTML at journal ]

A new computer-based decision-support system for the interpretation of bone scans
M. Sadik, D. Jakobsson, F. Olofsson, M. Ohlsson, M. Suurkula and L. Edenbrandt
Nuclear Medicine Communications 27, 417-423 (2006)
[ Abstract ]

Decision support for the initial triage of patients with acute myocardial infarction
S.-E. Olsson, M. Ohlsson, H. Öhlin, S. Dzaferagic, M.-L. Nilsson, P. Sandkull and L. Edenbrandt
Clinical Physiology and Functional Imaging 26, 151-156 (2006)
[ Abstract ] [ HTML at journal ]

Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra
R. Alm, P. Johansson, K. Hjernø, C. Emanuelsson, M. Ringnér and J. Häkkinen
Journal of Proteome Research 5, 785-792 (2006)
[ Abstract ] [ PDF ]

Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays
A. Le Quéré, K. A. Eriksen, B. Rajashekar, A. Schützendübel, B. Canbäck, T. Johansson and A. Tunlid
Molecular Ecology 15, 535 (2006)
[ Abstract ] [ PDF at journal ]

An auxin-driven polarized transport model for phyllotaxis
H. Jönsson, M. Heisler, B. E. Shapiro, E. M. Meyerowitz and E. Mjolsness
Proceedings of the National Academy of Sciences USA 103, 1633-1638 (2006)
[ Abstract ] [ PDF at journal ]

A software architecture for developmental modeling in plants: the computable plant project
V. Gor, B. E. Shapiro, H. Jönsson, M. Heisler, G. V. Reddy, E. M. Meyerowitz and E. Mjolsness
in Bioinformatics of Genome Regulation and Structure II, eds. N. Kolchanov, R. Hoffestaedt, L. Milanesi, pp 345-354, Kluwer Academic Publishers (2006)
[ Abstract ]

Gene expression profiles relate to SS18/SSX fusion type and development of metastasis in synovial sarcoma
J. Fernebro, P. Francis, P. Edén, Å. Borg, I. Panagopoulos, F. Mertens, J. Vallon-Christersson, M. Åkerman, N. Mandahl and M. Nilbert
International Journal of Cancer 118, 1165-1172 (2006)
[ Abstract ] [ PDF at journal ]

Comprehensive regional and temporal gene expression profiling of the rat brain during the first 24 h after experimental stroke identifies dynamic ischemia-induced gene expression patterns, and reveals a biphasic activation of genes in surviving tissue
M. Rickhag, T. Wieloch, G. Gidö, E. Elmér, M. Krogh, J. Murray, S. Lohr, H. Bitter, D. J. Chin, D. von Schack, M. Shamloo and K. Nikolich
Journal of Neurochemistry 96, 14-29 (2006)
[ Abstract ] [ PDF at journal ]

2005

A comparison of ten statistical methods for finding genes in microarray gene expression data based on five criteria
M. Krogh
LU TP 05-47

On the universality of capillary properties
H.-U. Bengtsson and P. Edén
LU TP 05-41

An experimental screen for genes that have undergone a period of accelerated evolution
A. Le Quere, K. A. Eriksen, B. Rajashekar A. Schutzendubel, B. Canbäck, T. Johansson and A. Tunlid
Journal of Biotechnology 118, S12-S12 (2005)

Comprehensive bioinformatic analysis of the specificity of human immunodeficiency virus type 1 protease
L. You, D. Garwicz and T. Rögnvaldsson
Journal of Virology 79, 12477-12486 (2005)
[ Abstract ]

Molecular signatures in childhood acute leukemia and their correlations to expression patterns in normal hematopoietic subpopulations
A. Andersson, T. Olofsson, D. Lindgren, B. Nilsson, C. Ritz, P. Edén, C. Lassen, J. Råde, M. Fontes, H. Mörse, J. Heldrup, M. Behrendtz, F. Mitelman, M. Höglund, B. Johansson and T. Fioretos
Proceedings of the National Academy of Sciences USA 102, 19069-19074 (2005)
[ Abstract ]

Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast
M. Ringnér and M. Krogh
PLoS Computational Biology 1, e72 (2005)
[ Abstract ] [ PDF ] [ Supplement ]

Toward personal eHealth in cardiology. Results from the EPI-MEDICS telemedicine project.
P. Rubel, J. Fayn, G. Nollo, D. Assanelli, B. Li, L. Restier, S. Adami, S. Arod, H. Atoui, M. Ohlsson, L. Simon-Chautemps, D. Telisson, C. Malossi, G.-L. Ziliani, A. Galassi, L. Edenbrandt and P. Chevalier
Journal of Electrocardiology 38, 100-106 (2005)
[ Abstract ] [ PDF ]

Interpretation of captopril renography using artificial neural networks
M. Nielsen, G. Granerus, M. Ohlsson, H. Holst, O. Thorsson and L. Edenbrandt
Clinical Physiology and Functional Imaging 25, 293-296 (2005)
[ Abstract ] [ PDF at journal ]

Random maps and attractors in random Boolean networks
B. Samuelsson and C. Troein
Physical Review E 72, 046112 (2005)
[ Abstract ] [ PDF ] [ HTML at journal ]

Dissecting the mechanical unfolding of ubiquitin
A. Irbäck, S. Mitternacht and S. Mohanty
Proceedings of the National Academy of Sciences USA 102, 13427-13432 (2005)
[ PDF at journal ]

Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization
G. Jönsson, T. L. Naylor, J. Vallon-Christersson, J. Staaf, J. Huang, M. R. Ward, J. D. Greshock, L. Luts, H. Olsson, N. Rahman, M. Stratton, M. Ringnér, Å. Borg and B. L. Weber
Cancer Research 65, 7612-7621 (2005)
[ Abstract ] [ PDF ]

Signal transduction pathway profiling of individual tumor samples
T. Breslin, M. Krogh, C. Peterson and C. Troein
BMC Bioinformatics 6:163 (2005)
[ Abstract ] [ PDF ] [ PDF at journal ]

Detection of acute coronary syndromes in chest pain patients using neural network ensembles
M. Green, J. Björk, J. Hansen, U. Ekelund, L. Edenbrandt and M. Ohlsson
In Proceedings of Second International Conference on Computational Intelligence in Medicine and Healthcare, Lisbon, Portugal, ed. J. Fonseca (2005)
[ Abstract ] [ PDF ]

Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem
H. Jönsson, M. Heisler, G. V. Reddy, V. Agrawal, V. Gor, B. E. Shapiro, E. Mjolsness and E. M. Meyerowitz
Bioinformatics 21, i232-i240 (2005)
[ Abstract ] [ Supplement ] [ PDF at journal ]

An improved algorithm for simulations of divergent-light halos
L. Gislén, J. O. Mattsson and B. Söderberg
Applied Optics 44:18, 3638-3645 (2005)
[ Abstract ] [ PDF ]

Random Feynman graphs
B. Söderberg
Proceedings of CNET 2004, SCIENCE OF COMPLEX NETWORKS: From Biology to the Internet and WWW, eds. J. F. F. Mendes et al.,
AIP conf. proc. 776, 118-132 (Melville, N.Y., 2005)
[ Abstract ] [ PDF ]

Gene expression profiling of leukemic cell lines reveals conserved molecular signatures among subtypes with specific genetic aberrations
A. Andersson, P. Edén, D. Lindgren, J. Nilsson, C. Lassen, J. Heldrup, M. Fontes, Å. Borg, F. Mittelman, B. Johansson, M. Höglund and T. Fioretos
Leukemia 19, 1042-1050 (2005)
[ Abstract ] [ PDF at journal ]

Intratumor versus intertumor heterogeneity in gene expression profiles from soft tissue sarcoma
P. Francis, J. Fernebro, P. Edén, A. Laurell, A. Rydholm, H.A. Domanski, T. Breslin, C. Hegardt, Å. Borg and M. Nilbert
Genes Chromosomes Cancer 3, 302-308 (2005)
[ Abstract ] [ PDF ] [ PDF at journal ]

Advanced optics in a jellyfish eye
D.-E. Nilsson, L. Gislén, M. M. Coates, C. Skogh and A. Garm
Nature 435, 201-205 (2005)
[ Abstract ] [ PDF ]

Localization of DNA damage by current exchanging repair enzymes: effects of cooperativity on detection time
K. Astrup Eriksen
Theoretical Biology and Medical Modelling 2, 15 (2005)
[ Abstract ] [ PDF ]

Proteios: an open source proteomics initiative
P. Gärdén, R. Alm and J. Häkkinen
Bioinformatics 21, 2085-2087 (2005)
[ Abstract ] [ PDF ]

Gene expression profiling demonstrates that TGF-β1 signals exclusively through receptor complexes involving Alk5 and identifies targets of TGF-β signaling
G. Karlsson, Y. Liu, J. Larsson, M.-J. Goumans, J.-S. Lee, S. S. Thorgeirsson, M. Ringnér and S. Karlsson
Physiological Genomics 21, 396-403 (2005)
[ Abstract ] [ PDF ]

Peptide folding and aggregation studied using a simplified atomic model
A. Irbäck
Journal of Physics: Condensed Matter 17, S1553-S1564 (2005)
[ PDF ]

Folding thermodynamics of peptides
A. Irbäck and S. Mohanty
Biophysical Journal 88, 1560-1569 (2005)
[ PDF ]

Microarray-based analyses of hypoxia-induced transcriptional changes in breast cancer cell lines
I. Hedenfalk, N. Glarner, Å. Kronblad, S. Veerla, M. Ringnér and G. Landberg
Cancer Genomics and Proteomics 2, 83-96 (2005)
[ Abstract ] [ PDF ]

An explicit spatial model of yeast microcolony growth
H. Jönsson and A. Levchenko
Multiscale Modeling and Simulation 3, 346-361 (2005)
[ Abstract ] [ PDF ]

2004

Robustness in filter designs. Implications for receptor internalization
K. Astrup Eriksen
LU TP 04-14
[ Abstract ] [ PDF ]

Structures in molecular networks
K. Sneppen, S. Maslov and K. Astrup Eriksen
In Forces, growth and form in soft condensed matter: at the interface between physics and biology, eds. A. T. Skjeltorp and A. V. Belushkin, 181-193, Kluwer Academic (2004)

Analyzing molecular networks
K. Sneppen, S. Maslov and K. Astrup Eriksen
Proceedings of the Idea-Finding Symposium for the Frankfurt Institute for Advanced Studies 2003, EP Systema Bt, Debrecen (2004)
[ Abstract ] [ PDF ]

Comparing functional annotation analyses with Catmap
T. Breslin, P. Edén and M. Krogh
BMC Bioinformatics 5, 193 (2004)
[ Abstract ] [ PDF ]

On the optical theory of underwater vision in humans
A. Gislén and L. Gislén
Journal of the Optical Society of America A 21, 2061-2064 (2004)
[ PDF at journal ] [ HTML at journal ]

Oligomerization of amyloid Aβ(16-22) peptides using hydrogen bonds and hydrophobicity forces
G. Favrin, A. Irbäck and S. Mohanty
Biophysical Journal 87, 3657-3664 (2004); erratum 89, 754 (2005)
[ PDF ] [ Supplement ]

Genetic networks with canalyzing Boolean rules are always stable
S. Kauffman, C. Peterson, B. Samuelsson and C. Troein
Proceedings of the National Academy of Sciences USA 101, 17102-17107 (2004)
[ Abstract ] [ PDF ] [ Supplement ]

Detecting acute myocardial infarction in the 12-lead ECG using Hermite expansions and neural networks
H. Haraldsson, L. Edenbrandt and M. Ohlsson
Artificial Intelligence in Medicine 32, 127-136 (2004)
[ Abstract ] [ PDF ]

ACID: a database for microarray clone information
M. Ringnér, S. Veerla, S. Andersson, J. Staaf and J. Häkkinen
Bioinformatics 20, 2305-2306 (2004)
[ Abstract ] [ PDF ]

Upstream plasticity and downstream robustness in evolution of molecular networks
S. Maslov, K. Sneppen, K. Astrup Eriksen and K. K. Yan
BMC Evolutionary Biology 4, 9 (2004)
[ Abstract ] [ PDF at journal ]

Improving automatic peptide mass fingerprint protein identification by combining multiple peak sets
T. Rögnvaldsson, J. Häkkinen, C. Lindberg, G. Marko-Varga, F. Potthast and J. Samuelsson
Journal of Chromatography B807, 209-15 (2004)
[ Abstract ] [ PDF ]

''Good old'' clinical markers have similar power in breast cancer prognosis as microarray gene expression profilers
P. Edén, C. Ritz, C. Rose, M. Fernö and C. Peterson
European Journal of Cancer 40, 1837-1841 (2004)
[ Abstract ] [ PDF ]

Multiclass discovery in array data
Y. Liu and M. Ringnér
BMC Bioinformatics 5, 70 (2004)
[ Abstract ] [ PDF ]

Microarray expression profiling in melanoma reveals a BRAF mutation signature
S. Pavey,  P. Johansson, L. Packer, J. Taylor, M. Stark, P. M. Pollock, G. J. Walker, G. M. Boyle, U. Harper, S. J. Cozzi, K. Hansen, L. Yudt, C. Schmidt, P. Hersey, K. A. O. Ellem, M. G. E. O'Rourke, P. G. Parsons, P. Meltzer, M. Ringnér and N. K. Hayward
Oncogene 23, 4060-4067 (2004)
[ Abstract ] [ PDF ] [ Supplement ]

Folding thermodynamics of three β-sheet peptides: a model study
A. Irbäck and F. Sjunnesson
Proteins: Structure, Function, and Bioinformatics 56, 110-116 (2004)
[ PDF ]

PHOREST: a web-based tool for comparative analyses of expressed sequence tag data
D. Ahrén, C. Troein, T. Johansson and A. Tunlid
Molecular Ecology Notes 4, 311-314 (2004)
[ Abstract ] [ PDF at journal ]

Diffusion on complex networks: a way to probe their large-scale topological structures
I. Simonsen, K. Astrup Eriksen, S. Maslov and K. Sneppen
Physica A 336, 163-173 (2004)
[ Abstract ] [ PDF ]

A strategy for identifying putative causes of gene expression variation in human cancers
S. Hautaniemi, M. Ringnér, P. Kauraniemi, R. Autio, H. Edgren, O. Yli-Harja, J. Astola, A. Kallioniemi and O. Kallioniemi
Journal of the Franklin Institute 341, 77-88 (2004)
[ Abstract ] [ PDF ]

Predicting continuous values of prognostic markers in breast cancer from microarray gene expression profiles
S. K. Gruvberger-Saal, P. Edén, M. Ringnér, B. Baldetorp, G. Chebil, Å. Borg, M. Fernö, C. Peterson and P. S. Meltzer
Molecular Cancer Therapeutics 3, 161-168 (2004)
[ Abstract ] [ PDF ]

Coupled folding-binding versus docking: a lattice model study
N. Gupta and A. Irbäck
Journal of Chemical Physics 120, 3983-3989 (2004)
[ PDF ]

Genomic signal processing
X. Wang, Y. Chen, E. R. Dougherty and C. Peterson (eds.)
Journal of Applied Signal Processing 2004:1, 3-4 (2004)
[ PDF ]

Regional cerebral blood flow in Alzheimer's disease: classification and analysis of heterogeneity
S. Warkentin, M. Ohlsson, P. Wollmer, L. Edenbrandt and L. Minthon
Dementia and Geriatric Cognitive Disorders 17, 207-214 (2004)
[ Abstract ] [ PDF at journal ]

Sequence-based study of two related proteins with different folding behaviors
G. Favrin, A. Irbäck and S. Wallin
Proteins: Structure, Function, and Bioinformatics 54, 8-12 (2004)
[ PDF ]

WeAidU - a decision support system using artificial neural networks
M. Ohlsson
Artificial Intelligence in Medicine 30, 49-60 (2004)
[ Abstract ] [ PDF ] [ Postscript ]

Modeling plant development with gene regulation networks including signaling and cell division
H. Jönsson and B. E. Shapiro, E. M. Meyerowitz and E. Mjolsness
Bioinformatics of Genome Regulation and Structure, eds. N. Kolchanov and R. Hofestaedt, Kluwer Academic Publishers, Boston, (2004). (ISBN 1-4020-7735-1)
[ Abstract ]

2003

A connection between gene expression and the strength of transcription factor binding
M. Krogh and K. Astrup Eriksen
LU TP 03-30
[ Abstract ]

A fuzzy matching approach to multiple structure alignment of proteins
H. Haraldsson and M. Ohlsson
LU TP 03-17
[ Abstract ] [ PDF ] [ Postscript ]

Pervasive self-care solutions in telecardiology. Typical use cases from the epi-medics project
F. Gouaux, L. S. Chautemps, J. Fayn, S. Adami, M. Arzi, D. Assanelli, M. C. Forlini, C. Malossi, A. Martinez, M. Ohlsson, J. Placide, G. L. Ziliani and P. Rubel
Studies in Health Technology and Informatics 95, 119-124 (2003).
[ Abstract ]

Computational biology -- opportunities and challenges for theoretical physicists
C. Peterson
Proceedings of the Seventh Workshop on Quantum Chromodynamics, eds. H. M. Fried, B. Muller and Y. Gabellini, Singapore, World Scientific (2003)
[ Abstract ]

Random Boolean network models and the yeast transcriptional network
S. Kauffman, C. Peterson, B. Samuelsson and C. Troein
Proceedings of the National Academy of Sciences USA 100, 14796-14799 (2003)
[ Abstract ] [ PDF ] [ Supplement ]

Procedures for simulating divergent-light halos
L. Gislén
Applied Optics 42, 6559-6563 (2003)
[ Abstract ] [ PDF ]

An approximate maximum likelihood approach, applied to phylogenetic trees
H. Jönsson and B. Söderberg
Journal of Computational Biology 10, 737-749 (2003)
[ Abstract ] [ Postscript ] [ PDF ]

The gene expression response of breast cancer to growth regulators: patterns and correlation with tumor expression profiles
H. E. Cunliffe, M. Ringnér, S. Bilke, R. L. Walker, J. M. Cheung, Y. Chen and P. S. Meltzer
Cancer Research 63, 7158-7166 (2003)
[ Abstract ] [ PDF ]

Random graph models with hidden color
B. Söderberg
Acta Physica Polonica B 34, 5085-5102 (2003)
[ Abstract ] [ PDF ]

Protein folding in the absence of a clear free-energy barrier
A. Irbäck
Acta Physica Polonica B 34, 4867-4878 (2003)
[ PDF ]

Superpolynomial growth in the number of attractors in Kauffman networks
B. Samuelsson and C. Troein
Acta Physica Polonica B 34, 5051-5061 (2003)
[ Abstract ] [ PDF ]

Probabilistic estimation of microarray data reliability and underlying gene expression
S. Bilke, T. Breslin and M. Sigvardsson
BMC Bioinformatics 4, 40 (2003)
[ Abstract ] [ PDF ]

Signalling in multicellular models of plant development
H. Jönsson, B. E. Shapiro, E. M.  Meyerowitz and E. Mjolsness
On Growth, Form and Computers, eds. S. Kumar and P. Bentley, Academic Press, London, (2003). (ISBN 0-12-428765-4)
[ Abstract ]

Matching protein structures with fuzzy alignments
R. Blankenbecler, M. Ohlsson, C. Peterson and M. Ringnér
Proceedings of the National Academy of Sciences 100, 11936-11940 (2003)
[ Abstract ] [ PDF ] [ Supplement ]

Role of ventilation scintigraphy in diagnosis of acute pulmonary embolism. an evaluation using artificial neural networks
E. Evander, H. Holst, A. Järund, M. Ohlsson, P. Wollmer, K. Åström and L. Edenbrandt
European Journal of Nuclear Medicine and Molecular Imaging 30, 961-965 (2003)
[ Abstract ]

Gene expression profile in multiple sclerosis patients and healthy controls: identifying pathways relevant to disease
R. Bomprezzi, M. Ringnér, S. Kim, M. L. Bittner, J. Khan, Y. Chen, A. Elkahloun, A. Yu, B. Bielekova, P. S. Meltzer, R. Martin, H. F. McFarland and J. M. Trent
Human Molecular Genetics 12, 2191-2199 (2003)
[ Abstract ] [ PDF ]

Properties of random graphs with hidden color
B. Söderberg
Physical Review E 68, 026107 (2003)
[ Abstract ] [ PDF ]

Thermodynamics of α- and β-structure formation in proteins
A. Irbäck, B. Samuelsson, F. Sjunnesson and S. Wallin
Biophysical Journal 85, 1466-1473 (2003)
[ PDF ] [ Supplement ]

Two-state folding over a weak free-energy barrier
G. Favrin, A. Irbäck, B. Samuelsson and S. Wallin
Biophysical Journal 85, 1457-1465 (2003)
[ PDF ]

Observations and simulations of some divergent-light halos
L. Gislén and J. O. Mattsson
Applied Optics 42, 4269-4279 (2003)
[ Abstract ] [ PDF ]

Random graphs with hidden color
B. Söderberg
Physical Review E 68, 015102(R) (2003)
[ Abstract ] [ PDF ]

Analyzing tumor gene expression profiles
C. Peterson and M. Ringnér
Artificial Intelligence in Medicine 28, 59-74 (2003)
[ Abstract ] [ PDF ]

RNA analysis of B-cell lines arrested at defined stages of differentiation allows for an approximation of gene expression patterns during B-cell development
P. Tsapogas, T. Breslin, S. Bilke, A. Lagergren, R. Månsson, D. Liberg, C. Peterson and M. Sigvardsson
Journal of Leukocyte Biology 74, 102-110 (2003)
[ Abstract ] [ PDF ] [ Supplement ]

A minimalistic all-atom approach to protein folding
A. Irbäck
Journal of Physics: Condensed Matter 15, S1797-S1807 (2003)
[ PDF ]

A simple model for the arterial system
H.-U. Bengtsson and P. Edén
Journal of Theoretical Biology 221, 437-443 (2003)
[ Abstract ] [ PDF ]

CD44 stimulated human B cells express transcripts specifically involved in immunomodulation and inflammation as analyzed by DNA microarrays
C.M. Högerkorp, S. Bilke, T. Breslin, S. Ingvarsson and C. Borrebaeck
Blood 101, 2307-2313 (2003)
[ Abstract ] [ PDF ]

Microarray-based cancer diagnosis with artificial neural networks
M. Ringnér and C. Peterson
Biotechniques 34, S30-S35 (2003)
[ Abstract ] [ PDF ]

Superpolynomial growth in the number of attractors in Kauffman networks
B. Samuelsson and C. Troein
Physical Review Letters 90, 098701 (2003)
[ Abstract ] [ PDF ]

Predicting the future of breast cancer
Å. Borg, M. Fernö and C. Peterson
Nature Medicine 9, 16-18 (2003)
[ PDF ]

Testing similarity measures with continuous and discrete protein models
S. Wallin, J. Farwer and U. Bastolla
Proteins: Structure, Function, and Genetics 50, 144-157 (2003)
[ Abstract ] [ PDF ]

Expression profiling to predict outcome in breast cancer: the influence of sample selection
S. K. Gruvberger, M. Ringnér, P. Edén, Å. Borg, M. Fernö, C. Peterson and P. S. Meltzer
Breast Cancer Research 5, 23-26 (2003)
[ Abstract ] [ PDF ]

2002

A general formalism for inhomogeneous random graphs
B. Söderberg
Physical Review E 66, 066121 (2002)
[ Abstract ] [ PDF ]

Neural optimization [substantially revised new version]
C. Peterson and B. Söderberg
The Handbook of Brain Theory and Neural Networks (2nd edition), ed. M. A. Arbib, Bradford Books/The MIT Press, Cambridge (2002)
[ Abstract ] [ PDF ]

Classification of expression patterns using artificial neural networks
M. Ringnér, P. Edén and P. Johansson
In A Practical Approach to Microarray Data Analysis, eds. D. P. Berrar, W. Dubitzky and M. Granzow, 201-215 (Kluwer Academic Publishers, 2002)
[ Abstract ] [ PDF ]

Early B-cell factor, E2A, and PAX-5 cooperate to activate the early B cell-specific mb-1 promoter
M. Sigvardsson, D. R. Clark, D. Fitzsimmons, M. Doyle, P. Akerblad, T. Breslin, S. Bilke, R. Li, C. Yeamans, G. Zhang and J. Hagman
Molecular and Cellular Biology 22, 8539-51 (2002)
[ Abstract ] [ PDF ]

Effective field theoretical approach to black hole production
S. Bilke, E. Lipartia and M. Maul
LU TP 02-10
[ Abstract ] [ Postscript ]

A new learning scheme for neural network ensembles
H. Haraldsson and M. Ohlsson
LU TP 02-04
[ Abstract ] [ PDF ] [ Postscript ]

Tractable approximations for probabilistic models: the adaptive TAP mean field approach
M. Opper and O. Winther
Physical Review Letters 86, 3695-3999 (2001)
[ Abstract ] [ Postscript ]

An information-based neural approach to generic constraint satisfaction
H. Jönsson and B. Söderberg
Artificial Intelligence 142:1, 1-17 (2002)
[ Abstract ] [ PDF ]

Neural networks - a diagnostic tool in acute myocardial infarction with concomitant left bundle branch block
S.-E. Olsson, H. Öhlin, M. Ohlsson and L. Edenbrandt
Clinical Physiology and Functional Imaging 22, 295-299 (2002)
[ Abstract ] [ Postscript ]

Enumerating designing sequences in the HP model
A. Irbäck and C. Troein
Journal of Biological Physics 28, 1-15 (2002)
[ PDF ] [ Supplement ]

Bioarray software environment: a platform for comprehensive management and analysis of microarray data
L. H. Saal, C. Troein, J. Vallon-Christersson, S. Gruvberger, Å. Borg and C. Peterson
Genome Biology 3, software0003.1-software0003.6 (2002)
[ Abstract ] [ PDF ] [ HTML at journal ]

A novel approach to local reliability of sequence alignments
M. Schlosshauer and M. Ohlsson
Bioinformatics 18, 847-854 (2002)
[ Abstract ] [ Postscript ]

Value of exercise data for the interpretation of myocardial perfusion SPECT
H. Haraldsson, M. Ohlsson and L. Edenbrandt
Journal of Nuclear Cardiology 9, 169-173 (2002)
[ Abstract ] [ Postscript ]

Analysing array data using supervised methods
M. Ringnér, C. Peterson and J. Khan
Pharmacogenomics 3, 403-415 (2002)
[ Abstract ] [ PDF ]

Folding of a small helical protein using hydrogen bonds and hydrophobicity forces
G. Favrin, A. Irbäck and S. Wallin
Proteins: Structure, Function, and Genetics 47, 99-105 (2002)
[ PDF ]

Stability of the Kauffman model
S. Bilke and F. Sjunnesson
Physical Review E 65, 016129 (2002)
[ Abstract ] [ PDF ]

2001

The optimal reference population for cardiac normality in myocardial SPECT in the detection of coronary artery stenoses: patients with normal coronary angiography or subjects with low likelihood of coronary artery disease?
J. C. Toft, D. Lindahl, M. Ohlsson, J. Palmer, A. Lundin, L. Edenbrandt and B. Hesse
European Journal of Nuclear Medicine 28, 831-835 (2001)
[ Abstract ] [ Postscript ]

Usefulness of serial electrocardiograms for diagnosis of acute myocardial infarction
M. Ohlsson, H. Öhlin, S. Wallerstedt and L. Edenbrandt
The American Journal of Cardiology 88, 478-481 (2001)
[ Abstract ] [ Postscript ]

Droplet motion for the conservative 2d Ising lattice gas dynamics below the critical temperature
G. Favrin, E. Marinari and F. Martinelli
Journal of Physics A 34, 5901-5910 (2001)
[ Abstract ] [ PDF ]

Adaptive and self-averaging thouless-anderson-palmer mean-field theory for probabilistic modeling
M. Opper and O. Winther
Physical Review E 64, 056131 (2001)
[ Abstract ] [ PDF ]

Computing with finite and infinite networks
O. Winther
In Advances in Neural Information Processing Systems 13 (NIPS '2000), eds. T.  K. Leen, T. G. Dietterich and V. Tresp, 336-342, MIT Press (2001)
[ Abstract ] [ Postscript ]

Ensemble learning and linear response theory for ICA
P. A.d.F.R. Hojen-Sorensen, O. Winther and L. K. Hansen
In Advances in Neural Information Processing Systems 13 (NIPS '2000), eds. T.  K. Leen, T. G. Dietterich and V. Tresp, 542-548, MIT Press (2001)
[ Abstract ] [ Postscript ]

The probability of exocytosis: the dependence on ca2+ sensing latency times, ca2+ channel kinetic parameters and clustering
J. Galvanovskis and B. Söderberg
LU TP 01-18
[ Abstract ] [ Postscript ]

Deterministic annealing and nonlinear assignment
H. Jönsson and B. Söderberg
LU TP 01-16
[ Abstract ] [ Postscript ]

Topological properties of citation and metabolic networks
S. Bilke and C. Peterson
Physical Review E 64, 036106 (2001)
[ Abstract ] [ Postscript ] [ PDF ]

Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns
S. Gruvberger, M. Ringnér, Y. Chen, S. Panavally, L. H. Saal, Å. Borg, M. Fernö, C. Peterson and P. S. Meltzer
Cancer Research 61, 5979-5984 (2001)
[ Abstract ] [ PDF ] [ Supplement ]

Hydrogen bonds, hydrophobicity forces and the character of the collapse transition
A. Irbäck, F. Sjunnesson and S. Wallin
Proceedings of the ISI Workshop "Protein Folding: Simple Models and Experiments", eds. P. Bruscolini et al.
Journal of Biological Physics 27, 169-179 (2001)
[ PDF ]

An information-based neural approach to constraint satisfaction
H. Jönsson and B. Söderberg
Neural Computation 13, 1827-1838 (2001)
[ Abstract ] [ Postscript ]

Using hidden markov models to characterize disease trajectories
M. Ohlsson, C. Peterson and M. Dictor
Proceedings of the Neural Networks and Expert Systems in Medicine and Healthcare Conference, ed. G. M. Papadourakis, Milos Island, Greece, 324-326 (2001)
[ Abstract ] [ Postscript ]

Case-based sensitivity analysis for artificial neural networks with applications in medicine
M. Ohlsson and L. Edenbrandt
Proceedings of the Neural Networks and Expert Systems in Medicine and Healthcare Conference, ed. G. M. Papadourakis, Milos Island, Greece, 102-106 (2001)
[ Abstract ] [ Postscript ]

Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks
J. Khan, J. S. Wei, M. Ringnér, L. H. Saal, M. Ladanyi, F. Westermann, F. Berthold, M. Schwab, C. R. Atonescu, C. Peterson and P. S. Meltzer
Nature Medicine 7, 673-679 (2001)
[ Abstract ] [ PDF ] [ Supplement ]

An independent evaluation of a new method for automated interpretation of lung scintigrams using artificial neural networks
H. Holst, K. Måre, K. Åström, A. Järund, E. Evander, K. Tägil, M. Ohlsson and L. Edenbrandt
European Journal of Nuclear Medicine 28, 33-38 (2001)
[ Abstract ]

An efficient mean field approach to the set covering problem
M. Ohlsson, C. Peterson and B. Söderberg
European Journal of Operations Research 133, 583-595 (2001)
[ Abstract ] [ Postscript ]

Monte Carlo update for chain molecules: biased Gaussian steps in torsional space
G. Favrin, A. Irbäck and F. Sjunnesson
Journal of Chemical Physics 114, 8154-8158 (2001)
[ PDF ]

Adaptive TAP equations
M. Opper and O. Winther
in Advanced Mean Field Methods - Theory and Practice, eds. M. Opper and D. Saad, MIT Press, Cambridge (2001)
[ Abstract ] [ Postscript ]

2000

A Monte Carlo approach to sequence assembly
E. Sandelin
LU TP 00-32
[ Abstract ] [ PDF ]

Efficient approaches to Gaussian process classification
L. Csato, E. Fokoue, M. Opper, B. Schottky and O. Winther
In Advances in Neural Information Processing System 12 (NIPS'99), eds. S. A. Solla, T. K. Leen and K.-R. Muller, 251-257, MIT Press (2000)
[ Abstract ] [ Postscript ]

Gaussian process classification and DVM: mean field results and leave-one-out estimator
M. Opper and O. Winther
In Advances in Large Margin Classifiers, eds. A. J. Smola, P. Bartlett, B. Schlkopf, D. Schuurmans, 311-326, MIT Press (2000)
[ Abstract ] [ Postscript ]

Acute myocardial infarction: analysis of the ECG using artificial neural networks
M. Ohlsson, H. Holst and L. Edenbrandt
Proceedings of the Artificial Neural Networks in Medicine and Biology (ANNIMAB-1) Conference, eds. H. Malmgren et al., 209-214 (2000)
[ Abstract ] [ Postscript ]

Sequence design in coarse-grained protein models
A. Irbäck
Proceedings of the Fifth International Conference on Computational Physics, eds. Y. Hiwatari et al.
Progress of Theoretical Physics Supplement 138, 273-281 (2000)
[ PDF ]

Three-helix-bundle protein in a Ramachandran model
A. Irbäck, F. Sjunnesson and S. Wallin
Proceedings of the National Academy of Sciences USA 97, 13614-13618 (2000)
[ PDF ]

Shuffling yeast gene expression data
S. Bilke
LU TP 00-18
[ Abstract ] [ PDF ]

A novel approach to structure alignment
M. Ohlsson, C. Peterson, M. Ringnér and R. Blankenbecler
LU TP 00-07
[ Abstract ] [ Postscript ]

On hydrophobicity correlations in protein chains
A. Irbäck and E. Sandelin
Biophysical Journal 79, 2252-2258 (2000)
[ PDF ]

Folding and design in coarse-grained protein models
C. Peterson
Proceedings of the XVIIth International Symposium on Lattice Field Theory, eds. M. Campostrini et al., Nuclear Physics B (Proc. Suppl) 83-84, 712-714 (2000)
[ Abstract ] [ Postscript ]

Local routing algorithms based on Potts neural networks
J. Häkkinen, M. Lagerholm, C. Peterson and B. Söderberg
IEEE Transactions on Neural Networks 11, 970-977 (2000)
[ Abstract ] [ Postscript ]

Clustering ECG complexes using Hermite functions and self-organizing maps
M. Lagerholm, C. Peterson, G. Braccini, L. Edenbrandt and L. Sörnmo
IEEE Transactions on Biomedical Engineering 47, 838-848 (2000)
[ Abstract ] [ Postscript ]

Airline crew scheduling using Potts mean field techniques
M. Lagerholm, C. Peterson and B. Söderberg
European Journal of Operations Research 120, 81-96 (2000)
[ Abstract ] [ Postscript ]

Gaussian processes for classification: mean field algorithms
M. Opper and O. Winther
Neural Computation 12, 2655-2684 (2000)
[ Abstract ] [ Postscript ]

1999

Optimal online learning: a Bayesian approach
S.A. Solla and O. Winther
Computer Physics Communication 121-122, 94-97 (1999)
[ Abstract ] [ Postscript ]

Optimization with neural networks
B. Söderberg
Scientific Applications of Neural Nets, eds. J. W. Clark, T. Lindenau and M. L. Ristig,
Lecture Notes in Physics 522, 243-256 (Springer, Berlin 1999)
[ Abstract ] [ Postscript ]

A confident decision support system for interpreting electrocardiograms
H. Holst, M. Ohlsson, C. Peterson and L. Edenbrandt
Clinical Physiology 19, 410-418 (1999)
[ Abstract ] [ Postscript ]

High specificity - a necessity for automated detection of lead reversals in the 12-lead ECG
M. Ohlsson, B. Hedén and L. Edenbrandt
LU TP 99-24
[ Abstract ] [ Postscript ]

Mean field methods for classification with Gaussian processes
M. Opper and O. Winther
Neural Information Processing Systems 11 (NIPS'98), eds. M. S. Kearns, S. A. Solla and D. A. Cohn, 309-315, MIT Press, Cambridge (1999)
[ Abstract ] [ Postscript ]

Monte Carlo study of the phase structure of compact polymer chains
A. Irbäck and E. Sandelin
Journal of Chemical Physics 110, 12256-12262 (1999)
[ PDF ]

Design of sequences with good folding properties in coarse-grained protein models
A. Irbäck, C. Peterson, F. Potthast and E. Sandelin
Structure with Folding & Design 7, 347-360 (1999)
[ Postscript ]

WWW based service for automated interpretation of diagnostic images: the AIDI-heart project
M. Ohlsson, A. Järund and L. Edenbrandt
High-Performance Computing and Networking, Proceedings 1593, 941-950 (1999)
[ Abstract ] [ Postscript ]

1998

Optimal perceptron learning: an online Bayesian approach
S. A. Solla and O. Winther
On-line learning in Neural Networks, ed. D. Saad, 379-398, (Cambridge University Press, Cambridge, 1998)
[ Abstract ] [ Postscript ]

A minimal off-lattice model for α-helical proteins
F. Potthast
LU TP 98-13
[ Abstract ] [ Postscript ]

Intelligent computer reporting "lack of experience": a confidence measure for decision support systems
H. Holst, M. Ohlsson, C. Peterson and L. Edenbrandt
Clinical Physiology 18, 139-147 (1998)
[ Abstract ]

Dynamical-parameter algorithms for protein folding
A. Irbäck
In Monte Carlo Approach to Biopolymers and Protein Folding, eds. P. Grassberger, G. T. Barkema and W. Nadler, pp. 98-109 (World Scientific, Singapore, 1998)
[ PDF ]

From naive mean field theory to the TAP equations
M. Opper and O. Winther
in Advanced Mean Field Methods - Theory and Practice, eds. M. Opper and D. Saad (MIT Press, Cambridge, 2001)
[ Abstract ] [ Postscript ]

Monte Carlo procedure for protein design
A. Irbäck, C. Peterson, F. Potthast and E. Sandelin
Physical Review E 58, R5249-R5252 (1998)
[ Postscript ]

Local interactions and protein folding: a model study on the square and triangular lattices
A. Irbäck and E. Sandelin
Journal of Chemical Physics 108, 2245-2250 (1998)
[ PDF ]

A Potts neuron approach to communication routing
J. Häkkinen, M. Lagerholm, C. Peterson and B. Söderberg
Neural Computation 10, 1587-1599 (1998)
[ Abstract ] [ Postscript ]

Polymers, spin models and field theory
B. Söderberg
In Field Theoretical Tools for Polymer and Particle Physics, eds. H. Meyer-Ortmanns and A. Klümper, pp. 68-77 (Springer, Berlin, 1998)
[ Abstract ] [ Postscript ]

Simulations of toy proteins
A. Irbäck
In Field Theoretical Tools for Polymer and Particle Physics, eds. H. Meyer-Ortmanns and A. Klümper, pp. 143-153 (Springer, Berlin, 1998)
[ PDF ]

The hybrid Monte Carlo method for polymer chains
A. Irbäck
In Field Theoretical Tools for Polymer and Particle Physics, eds. H. Meyer-Ortmanns and A. Klümper, pp. 133-142 (Springer, Berlin, 1998)
[ PDF ]

1997

Artificial neural networks
C. Peterson and B. Söderberg
Chpt. 7 in Local Search in Combinatorial Optimization, eds. E. Aarts and J. K. Lenstra, 173-213 (Wiley, New York, 1997; reprint Princeton Univ. Press, Princeton N.J., 2003)

Automated interpretation of myocardial spect perfusion images using artificial neural networks
D. Lindahl, J. Palmer, M. Ohlsson, C. Peterson, A. Lundin and L.Edenbrandt
The Journal of Nuclear Medicine 38, 1870-1875 (1997)
[ Abstract ] [ Postscript ]

Folding properties in off-lattice protein models
F. Potthast and O. Sommelius
Proceedings of the International Conference on Complex Systems, Nashua, Sept. 1997, ed. Y. Bar-Yam, NESCI (1997)
[ Abstract ] [ Postscript ]

Statistical properties of unrestricted crew scheduling problems
M. Lagerholm, C. Peterson and B. Söderberg
LU TP 97-11
[ Abstract ] [ Postscript ]

On the kinetic behavior and folding properties of an off-lattice heteropolymer model
O. Sommelius
LU TP 97-04
[ Abstract ] [ Postscript ]

The electrostatic persistence length calculated from Monte Carlo, variational and perturbation methods
M. Ullner, B. Jönsson, C. Peterson, O. Sommelius and B. Söderberg
Journal of Chemical Physics 107, 1279-1287 (1997)
[ Abstract ] [ Postscript ]

Local interactions and protein folding: a 3d off-lattice approach
A. Irbäck, C. Peterson, F. Potthast and O. Sommelius
Journal of Chemical Physics 107, 273-282 (1997)
[ Postscript ]

Identification of amino acid sequences with good folding properties in an off-lattice model
A. Irbäck, C. Peterson and F. Potthast
Physical Review E 55, 860-867 (1997)
[ Postscript ]

Airline crew scheduling with Potts neurons
M. Lagerholm, C. Peterson and B. Söderberg
Neural Computation 9, 1589-1599 (1997)
[ Abstract ] [ Postscript ]

Binary assignments of amino acids from pattern conservation
A. Irbäck and F. Potthast
Protein Engineering 10, 1013-1017 (1997)
[ PDF ]

A study of the mean field approach to knapsack problems
M. Ohlsson and H. Pi
Neural Networks 10, 263-271 (1997)
[ Abstract ] [ Postscript ]

1996

Relation between a screened polyelectrolyte and a field theory
B. Söderberg
LU TP 96-22
[ Abstract ] [ Postscript ]

Scaling and scale breaking in polyelectrolytes
C. Peterson, O. Sommelius and B. Söderberg
Journal of Chemical Physics 105, 5233-5241 (1996)
[ Abstract ] [ Postscript ]

A blocking technique for emulating very large polyelectrolytes
C. Peterson, O. Sommelius and B. Söderberg
Physical Review Letters 76, 1079-1082 (1996)
[ Abstract ] [ Postscript ]

A Monte Carlo study of titrating polyelectrolytes
M. Ullner, B. Jönsson, B. Söderberg and C. Peterson
Journal of Chemical Physics 104, 3048-3057 (1996)
[ Abstract ] [ Postscript ]

Agreement between artificial neural networks and human expert for the electrocardiographic diagnosis of healed myocardial infarction
B. Hedén, M. Ohlsson, R. Rittner, O. Pahlm, W. K. Haisty Jr., C. Peterson and L. Edenbrandt
Journal of the American College of Cardiology 28, 1012-1016 (1996)
[ Abstract ] [ Postscript ]

Titrating polyelectrolytes - variational calculations and Monte Carlo simulations
B. Jönsson, M. Ullner, C. Peterson, O. Sommelius and B. Söderberg
Journal of Physical Chemistry 100, 409-417 (1996)
[ Abstract ] [ Postscript ]

A variational approach for minimizing Lennard-Jones energies
C. Peterson, O. Sommelius and B. Söderberg
Physical Review E 53, 1725-1731 (1996)
[ Abstract ] [ Postscript ]

Evidence for non-random hydrophobicity structures in protein chains
A. Irbäck, C. Peterson and F. Potthast
Proceedings of the National Academy of Sciences, USA 93, 9533-9538 (1996)
[ Postscript ]

Detection of frequently overlooked electrocardiographic lead reversals using artificial neural networks
B. Hedén, M. Ohlsson, H. Holst, M. Mjöman, R. Rittner, O. Pahlm, C. Peterson and L. Edenbrandt
American Journal of Cardiology 78, 600-604 (1996)
[ Abstract ] [ Postscript ]

1995

Combinatorial optimization with feedback artificial neural networks
C. Peterson
Proceedings of ICANN '95 International Conference on Artificial Neural Networks, October 1995, Paris, France, eds. F. Fogelman-Soulie and P. Gallinari, EC2 \& Cie (Paris 1995)
[ Abstract ] [ Postscript ]

Studies of an off-lattice model for protein folding: sequence dependence and improved sampling at finite temperature
A. Irbäck and F. Potthast
Journal of Chemical Physics 103, 10298-10305 (1995)
[ PDF ]

Determining dependency structures and estimating nonlinear regression errors without doing regression
C. Peterson
Proceedings of the Fourth International Workshop on Software Engineering and Artificial Intelligence for High Energy and Nuclear Physics, eds. B. Denby and D. Perret-Gallix, International Journal of Modern Physics 611, (1995)
[ Abstract ] [ Postscript ]

Learning by on-line gradient descent
M. Biehl and H. Schwarze
Journal of Physics A 28, 643-656 (1995)
[ Abstract ] [ Postscript ]

Sequence dependence of self-interacting random chains
A. Irbäck and H. Schwarze
Journal of Physics A 28, 2121-2132 (1995)
[ PDF ]

Artificial neural networks for recognition of electrocardiographic electrode misplacement
B. Hedén, M. Ohlsson, L. Edenbrandt, R. Rittner, O. Pahlm and C. Peterson
American Journal of Cardiology 75, 929-933 (1995)
[ Abstract ] [ Postscript ]

A variational approach to the structure and thermodynamics of linear polyelectrolytes with coulomb and screened Coulomb interactions
B. Jönsson, C. Peterson and B. Söderberg
Journal of Physical Chemistry 99, 1251-1266 (1995)
[ Abstract ] [ Postscript ]

1994

Estimating nonlinear regression errors without doing regression
H. Pi and C. Peterson
LU TP 94-19
[ Abstract ] [ Postscript ]

JETNET 3.0 - a versatile artificial neural network package
C. Peterson, T. Rögnvaldsson and L. Lönnblad
Computer Physics Communications 81, 185-220 (1994)
[ Postscript ] [ HTML at journal ]

Predicting system loads with artificial neural networks - method and result from "the great energy predictor shootout"
M. Ohlsson, C. Petersson, H. Pi, T. Rögnvaldsson and B. Söderberg
1994 Annual Proceedings of the American Society of Heating, Refrigerating and Air-Conditioning Engineers, Inc., 1063-1074 (1994)
[ Abstract ] [ Postscript ]

Hybrid Monte Carlo simulation of polymer chains
A. Irbäck
Journal of Chemical Physics 101, 1661-1667 (1994)
[ PDF ]

On Langevin updating in multilayer perceptrons
T. Rögnvaldsson
Neural Computation 6, 916-926 (1994)
[ Abstract ] [ Postscript ]

Finding the embedding dimension and variable dependences in time series
H. Pi and C. Peterson
Neural Computation 6, 509-520 (1994)
[ Abstract ] [ Postscript ]

Delta 2.0 -- a program for finding dependencies in tables of data
H. Pi and C. Peterson
Computer Physics Communications 83, 293-306 (1994)
[ Abstract ] [ Postscript ]

Scaling in Steiner random surfaces
C. F. Baillie, A. Irbäck, W. Janke and D. Johnston
Physics Letters B 325, 45-50 (1994)
[ Abstract ]

1993

Clustering noisy data with deterministic annealing
M. Ohlsson
LU TP 93-28
[ Abstract ] [ Postscript ]

Dependency analysis and neural network modeling of currency exchange rates
H. Pi
the Proceedings of the First International Workshop on Neural Networks in the Capital Markets, London, 1993
[ Abstract ] [ Postscript ]

Bethe lattices in hyperbolic space
B. Söderberg
Physical Review E 47, 4582-4584 (1993)
[ Abstract ] [ Postscript ]

Variational approach to correlations in polymers
B. Jönsson, C. Peterson and B. Söderberg
Physical Review Letters 71, 376-379 (1993)
[ Abstract ] [ Postscript ]

Pattern discrimination using feed-forward networks - a benchmark study of scaling behaviour
T. Rögnvaldsson
Neural Computation 5, 483-491 (1993)
[ Abstract ] [ Postscript ]

Neural networks for optimization problems with inequality constrains - the knapsack problem
M. Ohlsson, C. Peterson and B. Söderberg
Neural Computation 5, 331-339 (1993)
[ Abstract ] [ Postscript ]

Extension and explorations of the elastic arms algorithm
M. Ohlsson
Computer Physics Communications 77, 19-32 (1993)
[ Abstract ] [ Postscript ]

The theory of dynamical random surfaces with extrinsic curvature
J. Ambjørn, A. Irbäck, J. Jurkiewicz and B. Petersson
Nuclear Physics B 393, 571-600 (1993)
[ Abstract ]

Finite-size scaling at phase coexistence
S. Gupta, A. Irbäck and M. Ohlsson
Nuclear Physics B 409, 673-683 (1993)
[ Abstract ] [ Postscript ]

Finite-size scaling on the Ising coexistence line
S. Gupta and A. Irbäck
Nuclear Physics B (Proc. Suppl.) 30, 861-864 (1993)
[ Abstract ]

Combinatorial optimization with neural networks
C. Peterson and B. Söderberg
Modern Heuristic Techniques for Combinatorial Problems,
ed. C. R. Reeves, 197--242 (Blackwell, London 1993)
[ Abstract ] [ Postscript ]

1992

Optimization with Potts neural networks
B. Söderberg
in Complexity in Physics and Technology,
eds. M. S. Garrido and R. Vilela Mendes, 181-190 (World Scientific, Singapore, 1992)
[ Abstract ] [ Postscript ]

Apollonian tiling, the Lorentz group, and regular trees
B. Söderberg
Physical Review A 46, 1859-1866 (1992)
[ Abstract ] [ Postscript ]

Track finding with deformable templates - the elastic arms approach
M. Ohlsson, C. Peterson and A. L. Yuille
Computer Physics Communications 71, 77-98 (1992)
[ Abstract ] [ Postscript ]

Rotor neurons - formalism and dynamics
L. Gislén, C. Peterson and B. Söderberg
Neural Computation 4, 737-745 (1992)
[ Abstract ] [ Postscript ]

Complex scheduling with Potts neural networks
L. Gislén, C. Peterson and B. Söderberg
Neural Computation 4, 805-831 (1992)
[ Abstract ] [ Postscript ]

Mass reconstruction with a neural network
L. Lönnblad, C. Peterson and T. Rögnvaldsson
Physics Letters B 278, 181-186 (1992)
[ Abstract ] [ Postscript ]

An introduction to artificial neural networks
C. Peterson and T. Rögnvaldsson
Proc. 1991 CERN Summer School of Computing, CERN Yellow Report 92-02, 113-170 (1992)
[ Abstract ] [ Postscript ] [ PDF ]

Critical properties of the dynamical random surface with extrinsic curvature
J. Ambjørn, J. Jurkiewicz, S. Varsted, A. Irbäck and B. Petersson
Physics Letters B 275, 295-303 (1992)
[ Abstract ]

Measuring the string tension in random surface models with extrinsic curvature
A. Irbäck, J. Jurkiewicz and S. Varsted
Computer Physics Communications 70, 59-67 (1992)
[ Abstract ]

Spectral density analysis of the chiral transition in nf=4 finite temperature qcd
N. A. Alves, B. A. Berg, D. W. Duke, A. Irbäck and S. Sanielevici
Physics Letters B 280, 261-266 (1992)
[ Abstract ]

Physics beyond instantons: measuring the physical correlation length
S. Gupta and A. Irbäck
Physics Letters B 286, 112-117 (1992)
[ Abstract ]

Scaling properties at the crumpling transition
A. Irbäck
Nuclear Physics B (Proc. Suppl.) 26, 572-574 (1992)
[ Abstract ]

Finite-size scaling on the Ising coexistence line
S. Gupta and A. Irbäck
Proceedings of the Workshop on Dynamics of First Order Phase Transitions,
HLRZ, KFA Jülich, Germany, June 1992, eds. H. J Herrmann, W. Janke and F. Karsch
International Journal of Modern Physics C 3, 1119-1124 (1992)
[ Abstract ]

1991

Self-organizing networks for extracting jet features
L. Lönnblad, C. Peterson, H. Pi and T. Rögnvaldsson
Computer Physics Communications 67, 193-209 (1991)
[ Abstract ] [ Postscript ]

Using neural networks to identify jets
L. Lönnblad, C. Peterson and T. Rögnvaldsson
Nuclear Physics B 349, 675-702 (1991)
[ Abstract ] [ Postscript ]

Dynamics near a first order phase transition with the Metropolis and Swendsen-Wang algorithms
A. Billoire, R. Lacaze, A. Morel, S. Gupta, A. Irbäck and B. Petersson
Nuclear Physics B 358, 231-248 (1991)
[ Abstract ]

Hadronic correlation functions in the QCD plasma phase
K.D. Born, S. Gupta, A. Irbäck, F. Karsch, E. Laermann, B. Petersson and H. Satz
Physical Review Letters 67, 302-305 (1991)
[ Abstract ]

The heavy quark potential in SU(2) gauge theory at high temperature
A. Irbäck, P. LaCock, D. Miller, B. Petersson and T. Reisz
Nuclear Physics B 363, 34-64 (1991)
[ Abstract ]

Hadronic correlation functions in the QCD plasma phase
A. Irbäck
Nuclear Physics B (Proc. Suppl.) 20, 280-283 (1991)
[ Abstract ]

1990

Finding gluon jets with a neural trigger
L. Lönnblad, C. Peterson and T. Rögnvaldsson
Physical Review Letters 65, 1321-1324 (1990)
[ Abstract ] [ Postscript ]

Parallel distributed approaches to combinatorial optimization - benchmark studies on traveling salesman problem
Carsten Peterson
Neural Computation 2, 261-269 (1990)
[ Abstract ] [ Postscript ]

The correlation lengths and the order of the phase transition in 3-dimensional z3 symmetric models
R. V. Gavai, S. Gupta, A. Irbäck, F. Karsch and B. Petersson
Nuclear Physics B 329, 263-284 (1990)
[ Abstract ]

Flavour degrees of freedom and the transition temperature in QCD
R. V. Gavai, S. Gupta, A. Irbäck, F. Karsch, S. Meyer, B. Petersson H. Satz and H. W. Wyld
Physics Letters B 241, 567-573 (1990)
[ Abstract ]

The acceptance probability in the hybrid Monte Carlo method
S. Gupta, A. Irbäck, F. Karsch and B. Petersson
Physics Letters B 242, 437-443 (1990)
[ Abstract ]

Comment on ``finite-size effects at temperature-driven phase transitions''
A. Billoire, R. Lacaze, A. Morel, S. Gupta, A. Irbäck and B. Petersson
Physical Review B 42, 6743-6744 (1990)
[ Abstract ]

Hybrid Monte Carlo simulation of four flavour QCD at finite temperature
A. Irbäck
Nuclear Physics B (Proc. Suppl.) 17, 210-213 (1990)
[ Abstract ]

Minimum action solutions for SU(2) gauge theories on the torus with non-orthogonal twist
M. Garcia-Perez, A. Gonzalez-Arroyo and B. Söderberg
Physics Letters B 235, 117-123 (1990)
[ Abstract ]

Random surfaces with Ising spins
B. Söderberg
in Probabilistic methods in quantum field theory and quantum gravity, eds. P. H. Damgaard, H. Hüffel and A. Rosenblum, 325-329 (Plenum Press, N.Y. 1990)
[ Abstract ] [ Postscript ]

An optoelectronic architecture for multilayer learning in a single photorefractive crystal
C. Peterson, S. Redfield, J. D. Keeler and E. Hartman
Neural Computation 2, 25-34 (1990)
[ Abstract ]

Optoelectronic implementations of multi-layer neural networks in a single photorefractive crystal
C. Peterson, S. Redfield, J. D. Keeler and E. Hartman
Optical Engineering 29, 359-368 (1990)
[ Abstract ]

1989

Teachers and classes with neural networks
L. Gislén, B. Söderberg and C. Peterson
International Journal of Neural Systems 1, 167-176 (1989)
[ Abstract ] [ Postscript ]

A new method for mapping optimization problems onto neural networks
C. Peterson and B. Söderberg
International Journal of Neural Systems 1, 3-22 (1989)
[ Abstract ] [ Postscript ]

Track finding with neural networks
C. Peterson
Nuclear Instruments and Methods A279, 537-545 (1989)
[ Abstract ]

Explorations of the mean field theory learning algorithm
E. Hartman and C. Peterson
Neural Networks 2, 475-494 (1989)
[ Abstract ]

Lattice QCD with small number of flavours
A.Irbäck, F. Karsch, B. Petersson and H. W. Wyld
Physics Letters B 216, 177-183 (1989)
[ Abstract ]

The finite temperature phase transition in four flavour QCD on an 8x123 lattice
R. V. Gavai, S. Gupta, A. Irbäck, F. Karsch, S. Meyer, B. Petersson, H. Satz and H. W. Wyld
Physics Letters B 232, 491-497 (1989)
[ Abstract ]

Twist and finite size effects for the source method
B. Söderberg and L. Lönnblad
Zeitschrift für Physik C 42, 289-296 (1989)
[ Abstract ]

Energy spectrum of SU(2) yang-mills fields with space-like symmetric twist
D. Daniel, A. Gonzalez-Arroyo, C. P. Korthals-Altes and B. Söderberg
Physics Letters B 221:2, 136-142 (1989)
[ Abstract ]