Publications

2013

• Felizzi F and Iber D,
  Enhanced cellular sensitivity from partitioning adhesion receptors into multiple clusters.
  Phys Rev E

 

Book Chapters

• Iber D, Tanaka S, Fried P, Germann G, 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
  

2012

• 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, 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, 1-14

• Menshykau D, Kraemer C and Iber D
  Branch Mode Selection during early Lung Development
  PLoS Comp Biology, 8, e1002377
  

Conference Proceedings

• D. Menshykau and D. Iber,
  Simulating Organogenesis in COMSOL: Deforming and Interacting Domains,
  Proceedings of COMSOL Conference 2012

 

Reviews

• Iber D and Zeller R
  Making sense - data-based simulations of vertebrate limb development,
  Current Opinion in Genetics & Development

Book Chapters

• 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)
  

• 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)
  

2011

• Celliere G, Fengos G, Herve M and Iber D
  The plasticity of TGF-beta  signaling,
  BMC Syst Biol, 5, 184
  

• Geier F, Fengos G and Iber D
  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
  SHH propagates distal limb bud development by enhancing CYP26b1-mediated retinoic acid clearance via AER-FGF signalling.
  Development, 138, 1913-1923
  

Conference Proceedings

• P. Germann, D. Menshykau, S. Tanaka, and D. Iber, Simulating Organogenesis in COMSOL, Proceedings of COMSOL Conference, 2011

• F. Felizzi, J. Galtier, G. Fengos, D. Iber, Spatial organization of proteomes: a low rank approximation, Proceedings of the 8th WCSB, 2011

• J. Liepe, F. Felizzi, A. Pernus, M. Hanulova, Microtubule tracking from stochastic optical reconstruction microscopy images, Proceedings of the 8th WCSB, 2011

Reviews

• Iber D

  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 Work

2010

• Iber D, Reduction of a detailed biological signaling model, Procedia Computer Science Volume 1, Issue 1, May 2010, Pages 987-996

2007

• Iber D and Gaglia G
  The mechanism of sudden stripe formation during dorso-ventral patterning in Drosophila
  J Math Biol, 54, 179-198

2006

• Iber D, Clarkson J, Yudkin MD and Campbell ID
  The mechanism of cell differentiation in Bacillus subtilis
  Nature, 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. 360, 15-20

• Iber D
  A quantitative study of the benefits of co-regulation using the spoIIA operon as an example.
  Mol Syst Biol. 2, 43

• Iber D and Campbell I
  Integrin activation--the importance of a positive feedback.
  Bull Math Biol. 68, 945-56.

• Meyer-Hermann ME, Maini PK, Iber D
  An analysis of B cell selection mechanisms in germinal centers.
  Math Med Biol, 23, 255-77

• Iber D, Gruhn T
  Organisation of B-cell receptors on the cell membrane.
  Syst Biol, 153, 401-4.

Book Chapter

• Beale R and Iber D
  Somatic evolution of antibody genes.
  Chapter 10 in The Implicit Genome, Editor L.H. Caporale, Oxford University Press

2005

• Iber, D
  Formation of the B cell synapse: retention or recruitment?
  Cell Mol Life Sci, 62, 206-13.

• Iber, D
  The mechanistic basis of compartmentalized gene expression in Bacillus subtilis
  Natural Computing, 4, 325-338.

2002

• Iber D, Maini PK
  A mathematical model for germinal centre kinetics and affinity maturation.
  J Theor Biol, 219, 153-75

2001

• Batista FD, Iber D, Neuberger MS
  B cells acquire antigen from target cells after synapse formation.
  Nature, 411, 489-94.