PUBLICATIONS
JOURNAL PUBLICATIONS
Conference Proceedings
Reviews
Book Chapters
Editorials & Meeting Reports
- Schwaninger CA, Menshykau D, Iber D, Simulating Organogenesis: Algorithms for the Image-based Determination of Growth Fields. ACM Transactions on Modeling and Computer Simulation (TOMACS) (2014) accepted
- Menshykau D, Blanc P, Ünal E, Sapin V and Iber D An Interplay of Geometry and Signaling enables Robust Lung Branching Morphogenesis, Development (2014), in press
- Fried P and Iber D Dynamic Scaling of Morphogen Gradients on Growing Domains. Nature Communications (2014) 5, 5077
- Kurics T*, Menshykau D* and Iber D (* shared first authors), Feedbacks, receptor clustering, and receptor restriction to single cells yield large Turing spaces for ligand-receptor based Turing models. Physical Review E (2014) 90, 022716
- Lopez-Rios J*, Duchesne A*, Speziale D, Andrey G, Peterson KA, Germann P, Ünal E, Liu J, Floriot S, Barbey S, Gallard Y, Müller-Gerbl M, Courtney AD, Klopp C, Rodriguez S, Ivanek R, Beisel C, Wicking C, Iber D, Robert B, McMahon AP, Duboule D and Zeller R (* shared first authors), Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. Nature (2014), 511:46-51
- Fengos G, Schmidt A, Martin K, Fluri E, Aebersold A, Iber D*, Pertz O* (* shared corresponding authors), Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome Science (2014) 12: 23
- Felizzi F and Iber D Integrin clustering as a result of local membrane deformations and local signaling feedbacks. Physica A (2014) 408, 198-211
- Bächler M*, Menshykau D*, De Geyter C and Iber D (* shared first authors), Species-specific differences in follicular antral sizes result from diffusion-based limitations on the thickness of the granulosa cell layer. Molecular Human Reproduction (2014) 20, 208-21. The paper was awarded the SGRM (Swiss Society for Reproductive Medicine) Research Prize 2014.
- Tanaka S and Iber D, Inter-dependent tissue growth and Turing patterning in a model for long bone development. Physical Biology (2013) 10:056009
- Fengos G and Iber D, Prediction Stability in a data-based mechanistic model of sigmaF during sporulation in Bacillus subtilis. Sci Rep (2013) 3: 2755
- Tanaka S and Iber D Simulation of a Microfluidic Gradient Generator using Lattice Boltzmann Methods. Current Synthetic and Systems Biology (2013) 1, 102
- Iber D and De Geyter C Computational Modelling of bovine ovarian follicle development. BMC Syst Biol (2013) 7, 60
- Menshykau D and Iber D Kidney Branching Morphogenesis under the control of a ligand-receptor based Turing mechanism. Phys. Biol (2013) 10, 046003. The paper was selected as one of the Physical Biology's Highlights of 2013.
- Fellizi F and Iber D, Enhanced cellular sensitivity from partitioning the integrin receptors into multiple clusters. Physical Review E (2013) 87, 012701
- Badugu A, Kraemer C, Germann P, Menshykau D and Iber D Digit patterning during limb development as a result of the BMP-receptor interaction. Scientific Reports (2012) 2:991
- Celliere G, Menshykau D and Iber D A simple network is sufficient to control branch point selection, smooth muscle and vasculature formation during lung branching morphogenesis. Biology Open (2012) BIO20121339
- F. Felizzi , F. Comoglio A network of queues approach for B-cell receptor affinity discrimination. Physical Review E (2012) 85, 061926
- J. Gomes, J. Costa, C. Melo, F. Felizzi , P. Monteiro, A. Inacio, T. Wieloch, R. Almeida, M. Graos, C. Duarte, Excitotoxicity downregulates TrkB.FL signaling and upregulates the neuroprotective truncated TrkB receptors in cultured hippocampal and striatal neurons. Journal of Neuroscience (2012) 32, 4610-4622
- Menshykau D, Kraemer C and Iber D Branch Mode Selection during early Lung Development. Plos Comp Biol (2012) 8, e1002377
- Celliere G, Fengos G, Herve M and Iber D (2011) The plasticity of TGF-beta signaling. BMC Syst Biol, 5, 184
- Geier F, Fengos G and Iber D (2011) A computational analysis of the dynamic roles of talin, Dok1, and PIPKI for integrin activation. PLoS ONE 6(11): e24808
- Probst S, Kraemer C, Demougin P, Sheth R, Martin GR, Shiratori H, Hamada H, Iber D, Zeller R and Zuniga A (2011) SHH propagates distal limb bud development by enhancing CYP26b1-mediated retinoic acid clearance via AER-FGF signalling. Development, 138, 1913-1923
- Iber D and Gaglia G (2007) The mechanism of sudden stripe formation during dorso-ventral patterning in Drosophila J Math Biol, 54, 179-198
- Iber D, Clarkson J, Yudkin MD and Campbell ID, The mechanism of cell differentiation in Bacillus subtilis Nature (2006) 441, 371-374
- Iber D, A computational analysis of the impact of the transient genetic imbalance on compartmentalized gene expression during sporulation in Bacillus subtilis. J Mol Biol. (2006) 360, 15-20
- Iber D, A quantitative study of the benefits of co-regulation using the spoIIA operon as an example. Mol Syst Biol (2006) 2, 43
- Iber D and Campbell I, Integrin activation--the importance of a positive feedback. Bull Math Biol (2006) 68, 945-56.
- Meyer-Hermann ME, Maini PK, Iber D, An analysis of B cell selection mechanisms in germinal centers. Math Med Biol (2006) 23, 255-77
- Iber D, Gruhn T, Organisation of B-cell receptors on the cell membrane. IEEE Proc Syst Biol (2006) 153, 401-4.
- Iber D, Formation of the B cell synapse: retention or recruitment? Cell Mol Life Sci (2005) 62, 206-13.
- Iber D, Maini PK A mathematical model for germinal centre kinetics and affinity maturation. J Theor Biol (2002) 219, 153-75
- Batista FD, Iber D, Neuberger MS, B cells acquire antigen from target cells after synapse formation. Nature (2001) 411, 489-94.
Conference Proceedings
- Karimaddini Z, Ünal E, Menshykau D and Iber D, Simulating Organogenesis in COMSOL: Image-based Modeling, Proceedings of COMSOL Conference 2014, Cambridge
- Velten B, Uenal E and Iber D (2014) Image-based Parameter Inference for Spatio-temporal models of Organogenesis.
NOLTA 2014 (Luzern, CH) International Symposium on Nonlinear Theory & its Applications - Menshykau D, Adivarahan S, Germann P, Lemereux L and Iber D (2013) Simulating Organogenesis in COMSOL: Parameter Optimization for PDE-based models. Proceedings of COMSOL Conference 2013, Rotterdam
- Vollmer J, Menshykau D, and Iber D (2013) Simulating Organogenesis in COMSOL: Cell-based Signaling Models. Proceedings of COMSOL Conference 2013, Rotterdam
- Adivarahan S, Menshykau D, Michos O and Iber D (2013) Dynamic Image-Based Modelling of Kidney Branching Morphogenesis. Lecture Notes in Computer Science (Springer), Computational Methods in Systems Biology (CMSB) 2013 IST Austria
- Menshykau D and Iber D (2012) Simulating Organogenesis in Comsol: Deforming and Interacting Domains, Proceedings of COMSOL Conference 2012
- Germann P, Tanaka S, Menshykau D, and Iber D (2011) Simulating Organogenesis in Comsol, Proceedings of COMSOL Conference 2011
- F. Felizzi, J. Galtier, G. Fengos, D. Iber (2011) Spatial organization of proteomes: a low rank approximation, Proceedings of the 8th WCSB, 2011
- J. Liepe, F. Felizzi, A. Pernus, M. Hanulova. (2011) Microtubule tracking from stochastic optical reconstruction microscopy images, Proceedings of the 8th WCSB, 2011
- Iber D Reduction of a detailed biological signaling model (2010) Procedia Computer Science Volume 1, Issue 1, May 2010, Pages 987-99
Reviews
- Iber D and Germann P (2014) How do digits emerge? - Mathematical Models of Limb Development, Birth Defects Research Part C: Embryo Today: Reviews, 102, 1-12
- Iber D and Menshykau D (2013) The Control of Branching Morphogenesis, Open Biology, 3:130088
- Iber D, Zeller R (2012) Making sense - data-based simulations of vertebrate limb development. Current Opinion in Genetics & Development
- Iber D (2011) Inferring biological mechanisms by data-based mathematical modelling: compartment-specific gene activation during sporulation in Bacillus subtilis as a test case. Advances in Bioinformatics, Article ID 124062, Special Issue: Biomedical Applications of Computational Methods: Results of the Successful Interplay between Bioinformatics and Experimental
- Iber D (2005) The mechanistic basis of compartmentalized gene expression in Bacillus subtilis Natural Computing, 4, 325-338.
Book Chapters
- Iber D, Tanaka S, Fried P, Germann G and Menshykau D Simulating Tissue Morphogenesis and Signaling, Springer Book Series: Methods in Molecular Biology. Book Title: Tissue Morphogenesis: Methods and Protocols. Editor: Celeste Nelson, in press
- Iber D and Fengos G Predictive models for cellular signaling networks. Springer Book Series: Methods in Molecular Biology. Book Title: Computational Modeling of Signaling Networks. Editor: Xuedong Liu, (2012) Volume 880, Chapter 1, 1-22
- Geier F, Fengos G, Felizzi F and Iber D Analysing and constraining signaling networks: parameter estimation for the user. Springer Book Series: Methods in Molecular Biology. Book Title: Computational Modeling of Signaling Networks. Editor: Xuedong Liu, (2012) Volume 880, Chapter 2, 23-39
- Beale R and Iber D (2006) Somatic evolution of antibody genes. Chapter 10 in The Implicit Genome, Editor L.H. Caporale, Oxford University Press
Editorials & Meeting Reports
- Stathopoulos A and Iber D, Studies of morphogens: keep calm and carry on. (2013) Development,140, 4119-4124
- Schwede T and Iber D, ECCB 2012: The 11th European Conference on Computational Biology (2012) Bioinformatics, 28, i303-i305