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CBBP publications 2000-2009

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)
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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)
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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)
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All-atom Monte Carlo approach to protein-peptide binding
I. Staneva and S. Wallin
Journal of Molecular Biology 393, 1118-1128 (2009)
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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)
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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)
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Single DNA denaturation and bubble dynamics
R. Metzler, T. Ambjörnsson, A. Hanke and H.C. Fogedby
Journal of Physics: Condensed Matter 21, 034111 (2009)
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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)
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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)
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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)
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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)
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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)
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An effective all-atom potential for proteins
A. Irbäck, S. Mitternacht and S. Mohanty
PMC Biophysics 2, 2 (2009)
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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)
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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)
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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)
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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)
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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)
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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)
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A computational model for understanding stem cell, trophectoderm and endoderm lineage determination
V. Chickarmane and C. Peterson
PLoS ONE 3, e3478 (2008)
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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)
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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.A.K. Borrebaeck
Proteomics 8, 2211-2219 (2008)
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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)
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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)
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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)
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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)
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Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data
C. Ritz and P. Edén
BMC Genomics 19:25 (2008)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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Modelling meristem development in plants
M. Heisler and H. Jönsson
Current Opinion in Plant Biology 10, 92-97 (2007)
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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)
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2006

Computer modeling of plant development
M. Heisler and H. Jönsson
Journal of Plant Growth Regulation 25, 267-269 (2006)
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Modeling auxin transport and plant development
M. Heisler and H. Jönsson
Journal of Plant Growth Regulation 25, 302-312 (2006)
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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. 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)
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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, pp. 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)
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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, pp. 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)
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)
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.A.K. Borrebaeck
Blood 101, 2307-2313 (2003)
Abstract ] [ PDF ] [ HTML at journal ]

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 ] [ PDF at journal ]

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 ]

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 ]

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 ]

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 ]

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