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CBBP publications 2010-2019

2019

Variational auto-encoders with Student's t-prior
N. Abiri and M. Ohlsson
ESANN Proceedings, 27th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, 415-420 (2019)
PDF ] [ PDF at journal ]

Deep learning‐based quantification of PET/CT prostate gland uptake: association with overall survival
E. Polymeri, M. Sadik, R. Kaboteh, P. Borrelli, O. Enqvist, J. Ulén, M. Ohlsson, E. Trägårdh, M.H. Poulsen, J.A. Simonsen, P.F. Hoilund‐Carlsen, Å.A. Johnsson and L. Edenbrandt
Clinical Physiology and Functional Imaging 40, 106-113 (2019)
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Establishing strong imputation performance of a denoising autoencoder in a wide range of missing data problems
N. Abiri, B. Linse, P. Edén and M. Ohlsson
Neurocomputing 365, 137-146 (2019
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Quantitative analysis of auxin sensing in leaf primordia argues against proposed role in regulating leaf dorsoventrality
N. Bhatia, H. Åhl, H. Jönsson and M.G. Heisler
eLife 8, e39298 (2019)
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Multi-scale dynamical modelling of T-cell development from an early thymic progenitor state to lineage commitment
V. Olariu, M.A. Yui, P. Krupinski, W. Zhou, J. Deichmann, E.V. Rothenberg and C. Peterson
bioRxiv doi 10.1101/667709 (2019)
BioRxiv ]

Optical DNA mapping combined with Cas9-targeted resistance gene identification for rapid tracking of resistance plasmids in a neonatal intensive care unit outbreak
S.K. Bikkarolla, V. Nordberg, F. Rajer, V. Müller, M.H. Kabir, S. KK, A. Dvirnas, T. Ambjörnsson, C.G. Giske, L. Naver, L. Sandegren and F. Westerlund
mBio 10, e00347 (2019)
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Enzyme-free optical DNA mapping of the human genome using competitive binding
V. Müller, A. Dvirnas, J. Andersson, V. Singh, S. KK, P. Johansson, Y. Ebenstein, T. Ambjörnsson and F. Westerlund
Nucleic Acids Research 47, e89 (2019)
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Human leukocyte antigen-based risk stratification in heart transplant recipients - implications for targeted surveillance
J. Nilsson, D. Ansari, M. Ohlsson, P. Höglund, A.‐S. Liedberg, J.G. Smith, P. Nugues and B. Andersson
Journal of the American Heart Association 8:15, e011124 (2019)
Abstract ] [ HTML at journal ]

Artificial neural network models to predict nodal status in clinically node-negative breast cancer
L. Dihge, M. Ohlsson, P. Edén, P.-O. Bendahl and L. Rydén
BMC Cancer 19:1, 610 (2019)
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Automated bone scan index as an imaging biomarker to predict overall survival in the Zometa European Study/SPCG11
M. Reza, M. Wirth, T. Tammela, V. Cicalese, F. Gomez Veiga, P. Mulders, K. Miller, A. Tubaro, F. Debruyne, A. Patel, C. Caris, W. Witjes, O. Thorsson, P. Wollmer, L. Edenbrandt, M. Ohlsson, E. Trägårdh and A. Bjartell
European Urology Oncology (2019)
Abstract ] [ HTML at journal ]

Stability and local unfolding of SOD1 in the presence of protein crowders
A. Bille, K.S. Jensen, S. Mohanty, M. Akke and A. Irbäck
Journal of Physical Chemistry B 123, 1920-1930 (2019)
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Peptide folding in cellular environments: a Monte Carlo and Markov modeling approach
D. Nilsson, S. Mohanty and A. Irbäck
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, ed. A. Liwo, pp. 453-466 (Springer, Second Edition, 2019)
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Homology and linkage in crossover for linear genomes of variable length
A. Merlevede, H. Åhl and C. Troein
PLOS ONE 14, e0209712 (2019)
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2018

A multicenter study investigating the molecular fingerprint of psychological resilience in breast cancer patients: study protocol of the SCAN-B resilience study
U. Axelsson, L. Rydén, P. Johnsson, P. Edén, J. Månsson, I. Rahm Hallberg and C.A.K. Borrebaeck
BMC Cancer 18, 789 (2018)
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Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins
B. Landrein, P. Formosa-Jordan, A.l. Malivert, C. Schuster, C.W. Melnyk, W. Yang, C. Turnbull, E.M. Meyerowitz, J.C.W. Locke and H. Jönsson
Proceedings of the National Academy of Sciences 115, 1382-1387 (2018)
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Kinetic models of hematopoietic differentiation
V. Olariu and C. Peterson
WIREs System Biology and Medicine, e1424 (2018)
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The self-organization of plant microtubules inside the cell volume yields their cortical localization, stable alignment, and sensitivity to external cues
V. Mirabet, P. Krupinski, O. Hamant, E.M. Meyerowitz, H. Jönsson and A. Boudaoud
PLOS Computational Biology 14, e1006011 (2018)
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Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis
J. Krog, M. Alizadehheidari, E. Werner, S. Kumar Bikkarolla, J.O. Tegenfeldt, B. Mehlig, M.A. Lomholt, F. Westerlund and T. Ambjörnsson
Journal of Chemical Physics 149, 215101 (2018)
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The interaction of transcription factors controls the spatial layout of plant aerial stem cell niches
J. Gruel, J. Deichmann, B. Landrein, T. Hitchcock and H. Jönsson
npj Systems Biology and Applications 4, 36 (2018)
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Haematopoietic stem cells: entropic landscapes of differentiation
K. Wiesner, J. Teles, M. Hartnor and C. Peterson
The Royal Society Interface Focus 8, 20180040 (2018)
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Zero-crossing statistics for non-Markovian time series
M. Nyberg, L. Lizana and T. Ambjörnsson
Physical Review E 97, 032114 (2018)
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Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach
A. Dvirnas, C. Pichler, C.L. Stewart, S. Quaderi, L.K. Nyberg, V. Müller, S. Kumar Bikkarolla, E. Kristiansson, L. Sandegren, F. Westerlund and T. Ambjörnsson
PLOS One 13, e0193900 (2018)
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MoonFit, a minimal interface for fitting ODE dynamical models, bridging simulation by experimentalists and customization by C++ programmers
P.A. Robert, H. Jönsson and M.M. Hermann
bioRxivdoi 10.1101/281188 (2018)
BioRxiv ]

Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry
F.B. Daher, Y. Chen, B. Bozorg, J. Clough, H. Jönsson and S.A. Braybrook
eLife 7, e38161 (2018)
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Single-cell approaches for understanding morphogenesis using computational morphodynamics
P. Formosa-Jordan, J. Teles and H. Jönsson
In Mathematical Modelling in Plant Biology, ed. R. Morris, pp. 87-106 (2018)
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Fitting a function to time-dependent ensemble averaged data
K. Fogelmark, M.A. Lomholt, A. Irbäck and T. Ambjörnsson
Scientific Reports 8, 6984 (2018)
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The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis
A. Johnning, N. Karami, E. Tång Hallbäck, V. Müller, L. Nyberg, M. Boungermino Pereira, C. Stewart, T. Ambjörnsson, F. Westerlund, I. Adlerberth and E. Kristiansson
Microbial Genomics 4, 11 (2018)
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Fenton reaction facilitates organic nitrogen acquisition by an ectomycorrhizal fungus
M. Op De Beeck, C. Troein, C. Peterson, P. Persson and A. Tunlid
The New Phytologist 218, 335-343 (2018)
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Improving prediction of heart transplantation outcome using deep learning techniques
D. Medved, M. Ohlsson, P. Höglund, B. Andersson, P. Nugues and J. Nilsson
Scientific Reports 8, 3613 (2018)
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The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen
C. Nicolás, T. Martin-Bertelsen, D. Floudas, J. Bentzer, M. Smits, T. Johansson, C. Troein, P. Persson and A. Tunlid
The ISME Journal (2018)
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Markov modeling of peptide folding in the presence of protein crowders
D. Nilsson, S. Mohanty and A. Irbäck
Journal of Chemical Physics 148, 055101 (2018)
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2017

Tracer particle diffusion in a system with hardcore interacting particles
S. Pigeon, K. Fogelmark, B. Söderberg, G. Mukhopadhyay and T. Ambjörnsson
Journal of Statistical Physics 12, 123209 (2017)
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Noise reduction in single time frame optical DNA maps
P.C. Torche, V. Müller, F. Westerlund and T. Ambjörnsson
PLOS One 12, e0179041 (2017)
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Tumor tissue protein signatures reflect histological grade of breast cancer
P. Skoog, M. Ohlsson, M. Fernö, L. Rydén, C.A.K. Borrebaeck and C. Wingren
PLoS ONE 12:6, e0179775 (2017)
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Mechanochemical polarization of contiguous cell walls shapes plant pavement cells
M. Majda, P. Grones, I.-M. Sintorn, T. Vain, P. Milani, P. Krupinski, B. Zagórska-Marek, C. Viotti, H. Jönsson, E.J. Mellerowicz, O. Hamant and S. Robert
Developmental Cell 43, 290-304 (2017)
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Revisiting the erythroid-myeloid lineage decision - a data-driven dynamical model analysis
J. Teles, V. Olariu and C. Peterson
bioRxiv doi: https://doi.org/10.1101/197822 (2017)
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Cell type boundaries organize plant development
M. P. Caggiano, X. Yu, N. Bhatia, A. Larsson, H. Ram, C.K. Ohno, P. Sappl, E.M. Meyerowitz, H. Jönsson and M.G. Heisler
eLife 6, e27421 (2017)
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Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal
H.M. Meyer, J. Teles, P. Formosa-Jordan, Y. Refahi, R. San-Bento, G. Ingram, H. Jönsson, J.C Locke and A.H. Roeder
eLife 6, e19131 (2017)
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A deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths
V. Olariu, E. Manesso and C. Peterson
Royal Society Open Science 4, 160765 (2017)
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Different reprogramming propensities in plants and mammals: Are small variations in the core network wirings responsible?
V. Olariu, J. Nilsson, H. Jönsson and C. Peterson
PLoS ONE 12, e0175251 (2017)
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Protein folding/unfolding in the presence of interacting macromolecular crowders
A. Irbäck and S. Mohanty
The European Physical Journal Special Topics 226, 627-638 (2017)
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3D skeletal uptake of 18F sodium fluoride in PET/CT images is associated with overall survival in patients with prostate cancer
S. Lindgren Belal, M. Sadik, R. Kaboteh, N. Hasani, O. Enqvist, L. Svärm, F. Kahl, J. Simonsen, M.H. Poulsen, M. Ohlsson, P.F. Høilund-Carlsen, L. Edenbrandt and E. Trägårdh
EJNMMI Research 7, 15 (2017)
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2016

Super-resolution genome mapping in silicon nanochannels
J.Jeffet, A. Kobo, T. Su, A. Grunwald, O. Green, A.N. Nilsson, E. Eisenberg, T. Ambjörnsson, F. Westerlund, E. Weinhold, D. Shabat, P.K. Purohit and Y. Ebenstein
ACS Nano 10, 9823 (2016)
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Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping
V. Müller, F. Rajer, K. Frykholm, L.K. Nyberg, S. Quaderi, J. Fritzsche, E. Kristiansson, T. Ambjörnsson, L. Sandegren and F. Westerlund
Scientific Reports 6, 37938 (2016)
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Tracer particles in two-dimensional elastic networks diffuse logarithmically slow
L. Lizana, T. Ambjörnsson and M.A. Lomholt
Journal of Physics A: Mathematical and Theoretical 50, 034001 (2016)
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Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche
L. Willis, Y. Refahi, R. Wightman, B. Landrein, J. Teles, K.C. Huang, E.M. Meyerowitz and H. Jönsson
Proceedings of the National Academy of Sciences 113, 8238-8246 (2016)
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Spatio-temporal registration of 3D microscopy image sequences of Arabidopsis floral meristems
G. Michelin, Y. Refahi, R. Wightman, H. Jönsson, J. Traas, C. Godin and G. Malandain
Biomedical Imaging 13, 1127-1130 (2016)
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Bone scan index as an imaging biomarker in metastatic castration-resistant prostate cancer: A multicentre study based on patients treated with Abiraterone Acetate (Zytiga) in clinical practice
M. Reza, M. Ohlsson, R. Kaboteh, A. Anand, I. Franck-Lissbrant, J.E. Damber, A. Widmark, C. Thellenberg-Karlsson, L. Budäus, T. Steuber, T. Eichenauer, P. Wollmer, L. Edenbrandt, E. Trägårdh and A. Bjartell
European Urology Focus 2, 540-546 (2016)
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Auxin acts through MONOPTEROS to regulate plant cell polarity and pattern phyllotaxis
N. Bhatia, B. Bozorg, A. Larsson, C. Ohno, H. Jönsson and M.G. Heisler
Current Biology 26, R1233-R1235 (2016)
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Statistical power considerations in genotype-based recall randomized controlled trials
N. Atabaki-Pasdar, M. Ohlsson, D. Shungin, A. Kurbasic, E. Ingelsson, E. Pearson, A. Ali and P.W. Franks
Scientific Reports 6, 37307 (2016)
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A Model analysis of mechanisms for radial microtubular patterns at root hair initiation sites
P. Krupinski, B. Bozorg, A. Larsson, S. Pietra, M. Grebe and H. Jönsson
Front. Plant Sci. 7, 1560 (2016)
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A continuous growth model for plant tissue
B. Bozorg, P. Krupinski and H. Jönsson
Physical Biology 13, 065002 (2016)
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Shifting foundations: the mechanical cell wall and development
S.A. Braybrook and H. Jönsson
Current Opinion in Plant Biology 29, 115-120 (2016)
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Nanog, Oct4 and Tet1 interplay in establishing pluripotency
V. Olariu, C. Lövkvist and K. Sneppen
Scientific Reports 6, 25438 (2016)
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Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits
B. Il Je, J. Gruel, Y.K. Lee, P. Bommert, E.D. Arevalo, A. L Eveland, Q. Wu, A. Goldshmidt, R. Meeley, M. Bartlett, M. Komatsu, H. Sakai, H. Jönsson and D. Jackson
Nature Genetics 48, 785-791 (2016)
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An epidermis-driven mechanism positions and scales stem cell niches in plants
J. Gruel, B. Landrein, P. Tarr, C. Schuster, Y. Refahi, A. Sampathkumar, O. Hamant, E.M. Meyerowitz and H. Jönsson
Science Advances 2, e1500989 (2016)
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Rapid tracing of resistance plasmids in a nosocomial outbreak using optical DNA mapping
V. Müller, N. Karami, L.K. Nyberg, C. Pichler, P.C. Torche Pedreschi, S. Quaderi, J. Fritzsche, T. Ambjörnsson, C. Åhrén and F. Westerlund
ACS Infectious Diseases 2, 322 (2016)
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A simple method to calculate first-passage time densities with arbitrary initial conditions
M. Nyberg, T. Ambjörnsson and L. Lizana
New Journal of Physics 18, 063019 (2016)
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Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules
L.K. Nyberg, S. Quaderi, G. Emilsson, N. Karami, E. Lagerstedt, V. Müller, C. Noble, S. Hammarberg, A.N. Nilsson, F. Sjöberg, J. Fritzsche, E. Kristiansson, L. Sandegren, T. Ambjörnsson and F. Westerlund
Scientific Reports 6, 30410 (2016)
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A somatic mutation of GFI1B identified in leukemia alters cell fate via a SPI1 (PU.1) centered genetic regulatory network
E. Anguita, R. Gupta, V. Olariu, P.J. Valk, C. Peterson, R. Delwel and T. Enver
Developmental Biology 411, 277-86 (2016)
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Irreversibility of T-Cell specification: Insights from computational modelling of a minimal network architecture
E. Manesso, H.Y. Kueh, G. Freedman, E.V. Rothenberg and C. Peterson
PLoS ONE 11, e0161260 (2016)
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Technical advances of the recombinant antibody microarray technology platform for clinical immunoproteomics
P. Delfani, L. Dexlin Mellby, M. Nordström, A. Holmér, M. Ohlsson, C.A.K. Borrebaeck and C. Wingren
PLoS ONE 11, e0159138 (2016)
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Peptide folding in the presence of interacting protein crowders
A. Bille, S. Mohanty and A. Irbäck
Journal of Chemical Physics 144, 175105 (2016)
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Selection shapes transcriptional logic and regulatory specialization in genetic networks
K. Fogelmark, C. Peterson and C. Troein
PLoS ONE 11, e0150340 (2016)
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2015

Extension of nanoconfined DNA: Quantitative comparison between experiment and theory
V. Iarko, E. Werner, L.K. Nyberg, V. Müller, J. Fritzsche, T. Ambjörnsson, J.P. Beech, J.O. Tegenfeldt, K. Mehlig, F. Westerlund and B. Mehlig
Physical Review E 92, 062701 (2015)
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Analysis of the influence of HLA-A matching relative to HLA-B and -DR matching on heart transplant outcomes
D. Ansari, D. Bucin, P. Höglund, M. Ohlsson, B. Andersson and J. Nilsson
Transplantation Direct 1, e38 (2015)
Abstract ] [ HTML at journal ]

Equilibrium simulation of trp-cage in the presence of protein crowders
A. Bille, B. Linse, S. Mohanty and A. Irbäck
Journal of Chemical Physics 143, 175102 (2015)
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Detailed comparison of amyloid PET and CSF biomarkers for identifying early Alzheimer disease
S. Palmqvist, H. Zetterberg, N. Mattsson, P. Johansson, L. Minthon, K. Blennow, M. Ohlsson and O. Hansson
Neurology 14, 1240-1249 (2015)
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How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model
M. Reiter-Schad, E. Werner, J.O. Tegenfeldt, B. Mehlig and T. Ambjörnsson
Journal of Chemical Physics 143, 115101 (2015)
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Thermodynamics of amyloid formation and the role of intersheet interactions
A. Irbäck and J. Wessén
Journal of Chemical Physics 143, 105104 (2015)
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Finding risk groups by optimizing artificial neural networks on the area under the survival curve using genetic algorithms
J. Kalderstam, P. Edén and M. Ohlsson
PLoS ONE 10, e0137597 (2015)
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Visualizing the entire DNA from a chromosome in a single frame
C. Freitag, C. Noble, J. Fritzsche, F. Persson, A.N. Nilsson, M. Reiter-Schad, A. Graneli, T. Ambjörnsson, K.U. Mir and J.O. Tegenfeldt
Biomicrofluidics 9, 044114 (2015)
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Bacteriophage strain typing by rapid single molecule analysis
A. Grunwald, M. Dahan, A. Giesbertz, A.N. Nilsson, L.K. Nyberg, E. Weinhold, T. Ambjörnsson, F. Westerlund and Y. Ebenstein
Nucleic Acids Research 43, e117 (2015)
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A model for melting of confined DNA
E. Werner, M. Reiter-Schad, T. Ambjörnsson and B. Mehlig
Physical Review E 91, 060702 (2015)
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Single-cell network analysis identifies DDIT3 as a nodal lineage regulator in hematopoiesis
C. Pina, J. Teles, C. Fugazza, G. May, D. Wang, Y. Guo, S. Soneji, J. Brown, P. Edén, M. Ohlsson, C. Peterson and T. Enver
Cell Reports 11, 1-8 (2015)
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Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA
S. Ahlberg, T. Ambjörnsson and L. Lizana
New Journal of Physics 17, 043036 (2015)
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A fast and scalable algorithm for alignment of optical DNA mappings
C. Noble, A.N. Nilsson, C. Freitag, J.P. Beech, J.O. Tegenfeldt and T. Ambjörnsson
PLoS ONE 10, e0121905 (2015)
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Nanoconfined circular and linear DNA: Equilibrium conformations and unfolding kinetics
M. Alizadehheidari, E. Werner, C. Noble, M. Reiter-Schad, L.K. Nyberg, J. Fritzsche, B. Mehlig, J.O. Tegenfeldt, T. Ambjörnsson, F. Persson and F. Westerlund
Macromolecules 78, 871-878 (2015)
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ABO-identical blood group matching has no survival benefit for AB heart transplant recipients
H. Bergenfeldt, P. Höglund, B. Andersson, G. Rådegran, M. Ohlsson and J. Nilsson
The Annals of Thoracic Surgery 99, 762-768 (2015)
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The international heart transplant survival algorithm (IHTSA): a new model to improve organ sharing and survival
J. Nilsson, M. Ohlsson, P. Höglund, B. Ekmehag, B. Koul and B. Andersson
PLoS ONE 10, e29868 (2015)
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2014

SOX11 and p53 add prognostic information to MIPI in a homogenously treated cohort of mantle cell lymphoma - a Nordic Lymphoma Group study
L. Nordström, S. Sernbo, P. Edén, K. Grønbæk, A. Kolstad, R. Räty, M-L. Karjalainen, C. Geisler, E. Ralfkiær, C. Sundström, A. Laurell, J. Delabie, M. Ehinger, M. Jerkeman and S. Ek
British Journal of Haematology. 166(1), 98-108 (2014)
Abstract ]

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

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

Revisiting the erythroid-myeloid lineage decision - a data-driven dynamical model analysis
J. Teles, V. Olariu and C. Peterson
bioRxiv, 197822 (2012)
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First passage times for a tracer particle in single file diffusion and fractional Brownian motion
L.P. Sanders and T. Ambjörnsson
Journal of Chemical Physics 136, 175103 (2012)
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Computational multiscale modelling of embryo development
P. Krupinski, V. Chickarmane and C. Peterson
Current Opinion in Genetics & Development 22, 613-618 (2012)
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A novel automated platform to quantify the extent of skeletal tumor involvement in prostate cancer patients with bone scan index
D. Ulmert, R. Kaboteh, J.J. Fox, C. Savage, M.J. Evans, H. Lilja, P.-E. Abrahamsson, T. Björk, A. Gerdtsson, A. Bjartell, P. Gjertsson, P. Höglund, M. Lomsky, M. Ohlsson, J. Richter, M. Sadik, M.J. Morris, H.I. Scher, K. Sjöstrand, A. Yu, M. Suurkula, A.J. Vickers, L. Edenbrandt and S.M. Larson
European Urology 62:1, 78-84 (2012)
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Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties
N. Olsson, S. Wallin, P. James, C.A.K. Borrebaeck and C. Wingren
Protein Science 21, 1897-1910 (2012)
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Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study
I. Staneva, Y. Huang, Z. Liu and S. Wallin
PLoS Computational Biology 8, e1002682 (2012)
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Optical advantages and function of multifocal spherical fish lenses
Y.L. Gagnon, B. Söderberg and R.H.H. Kröger
Journal of the Optical Society of America A 29, 1786-1793 (2012)
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Probing the role of stochasticity in a model of the embryonic stem cell — heterogeneous gene expression and reprogramming efficiency
V. Chickarmane, V. Olariu and C. Peterson
BMC Systems Biology 6, 98 (2012)
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Likelihood of acute coronary syndrome in emergency department chest pain patients varies with time of presentation
U. Ekelund, M. Akbarzadeh, A. Khoshnood, J. Björk and M. Ohlsson
BMC Research Notes 5:420, (2012)
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Monte Carlo simulations of protein aggregation
S.Æ. Jónsson, I. Staneva, S. Mohanty and A. Irbäck
Physics Procedia 34, 49-54 (2012)
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Distinct phases of free α-synuclein — a Monte Carlo study
S.Æ. Jónsson, S. Mohanty and A. Irbäck
Proteins: Structure, Function, and Bioinformatics 80, 2169-2177 (2012)
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Inferring rules of lineage commitment in haematopoiesis
C. Pina, C. Fugazza, A.J. Tipping, J.Brown, S. Soneji, J. Teles, C. Peterson and T. Enver
Nature Cell Biology 14, 287-294 (2012)
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Evaluation of a previously suggested plasma biomarker panel to identify Alzheimer's disease
M. Björkqvist, M. Ohlsson, L. Minthon and O. Hansson
PLoS ONE 7, e29868 (2012)
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Subtle Monte Carlo updates in dense molecular systems
S. Bottaro, W. Boomsma, K.E. Johansson, C. Andreetta, T. Hamelryck and J. Ferkinghoff-Borg
Journal of Chemical Theory and Computation 8, 695-702 (2012)
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An artificial neural network to safely reduce the number of ambulance ECGs transmitted for physician assessment in a system with prehospital detection of ST elevation myocardial infarction
J.L. Forberg, A. Khoshnood, M. Green, M. Ohlsson, J. Björk, S. Jovinge, L. Edenbrandt and U. Ekelund
Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine 20, (2012)
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On evaluating models in computational morphodynamics
H. Jönsson, J. Gruel, P. Krupinski and C. Troein
Current Opinion in Plant Biology 15, 103-110 (2012)
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Risk predictions for individual patients from logistic regression can be visualized with bar-line charts
J. Björk, U. Ekelund and M. Ohlsson
Journal of Clinical Epidemiology 65, 335-342 (2012)
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Coupled folding-binding in a hydrophobic/polar protein model: Impact of synergistic folding and disordered flanks
A. Bhattacherjee and S. Wallin
Biophysical Journal 102, 569-578 (2012)
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2011

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

Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array-comparative genomic hybridization
A. Isinger-Ekstrand, J. Johansson, M. Ohlsson, P. Francis, J. Staaf, M. Jönsson, Å. Borg and M. Nilbert
Cancer Genetics and Cytogenetics 200, 120-126 (2010)
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Using Gaussian process with test rejection to detect T-cell epitopes in pathogen genomes
L. You, V. Brusic, M. Gallagher and M. Bodén
IEEE/ACM transactions on computational biology and bioinformatics 7, 741-751 (2010)
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Gene expression signatures in childhood acute leukemias are largely unique and distinct from those of normal tissues and other malignancies
A. Andersson, P. Edén, T. Olofsson and T. Fioretos
BMC Medical Genomics 3, 6 (2010)
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Foundation of fractional Langevin equation: Harmonization of a many-body problem
L. Lizana, T. Ambjörnsson, A. Taloni, E. Barkai and M.A. Lomholt
Physical Review E 81, 051118 (2010)
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Alignment between PIN1 polarity and microtubule orientation in the shoot apical meristem reveals a tight coupling between morphogenesis and auxin transport
M. Heisler, O. Hamant, P. Krupinski, M. Uyttewaal, C. Ohno, H. Jönsson, J. Traas and E. Meyerowitz
PLoS Biology 8, e1000516 (2010)
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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)
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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)
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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)
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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)
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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))
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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)
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Modeling auxin-regulated development
P. Krupinski and H. Jönsson
Cold Spring Harbor Perspectives in Biology 2, a001560 (2010)
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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)
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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)
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Modeling plant growth and pattern formation
H. Jönsson and P. Krupinski
Current Opinion in Plant Biology 13, 5-11 (2010)
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