Publications
PhD Theses Master Theses Bachelor Theses2012
Distinct phases of free α-synuclein — a Monte Carlo study
S. Æ. Jónsson, S. Mohanty and A. Irbäck
LU TP 12-01; to appear in Proteins: Structure, Function, and Bioinformatics
Optical advantages and function of multifocal spherical fish lenses
Y. Gagnon, B. Söderberg and R. Kröger
LU TP 12-06; submitted to Proceedings of the National Academy of Sciences USA
[ Abstract ]
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
To appear in European Urology (2012)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ Abstract ]
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
On evaluating models in computational morphodynamics
H. Jönsson, J. Gruel, P. Krupinski and C. Troein
Current Opinion in Plant Biology 15, 103-110 (2012)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
Mutation-induced fold switching among lattice proteins
C. Holzgräfe, A. Irbäck and C. Troein
Journal of Chemical Physics 135, 195101 (2011)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
Accelerating atomic-level protein simulations by flat-histogram techniques
S. Æ. Jónsson, S. Mohanty and A. Irbäck
Journal of Chemical Physics 135, 125102 (2011)
[ HTML at journal ]
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)
[ HTML at journal ]
Binding free energy landscape of domain-peptide interactions
I. Staneva and S. Wallin
PLoS Computational Biology 7, e1002131 (2011)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
Simulating the mammalian blastocyst - molecular and mechanical
interactions pattern the embryo
P. Krupinski, V. Chickarmane and C. Peterson
PLoS Computational Biology
7, e1001128 (2011)
[ HTML at journal ]
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)
[ HTML at journal ]
Dissimilar bouncy walkers
M. A. Lomholt, L. Lizana and T. Ambjörnsson
Journal of Chemical Physics 134, 045101 (2011)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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
Automated quantitative bone scan analysis
R. Kaboteh, M. Sadik, M. Suurkula, M. Lomsky, P. Gjertsson,
J. Richter, K. Sjöstrand,
M. Ohlsson and L. Edenbrandt
LU TP 09-06
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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)
[ HTML at journal ]
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 ]
Last updated on May 17, 2012 by
©2005-2012