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Items: 1 to 50 of 51

1.

Image-based modeling of kidney branching morphogenesis reveals GDNF-RET based Turing-type mechanism and pattern-modulating WNT11 feedback.

Menshykau D, Michos O, Lang C, Conrad L, McMahon AP, Iber D.

Nat Commun. 2019 Jan 16;10(1):239. doi: 10.1038/s41467-018-08212-8.

PMID:
30651543
2.

Global optimization using Gaussian processes to estimate biological parameters from image data.

Barac D, Multerer MD, Iber D.

J Theor Biol. 2018 Dec 7. pii: S0022-5193(18)30592-7. doi: 10.1016/j.jtbi.2018.12.002. [Epub ahead of print]

PMID:
30529487
3.

Simulation of Morphogen and Tissue Dynamics.

Multerer MD, Wittwer LD, Stopka A, Barac D, Lang C, Iber D.

Methods Mol Biol. 2018;1863:223-250. doi: 10.1007/978-1-4939-8772-6_13.

PMID:
30324601
4.

Travelling waves in somitogenesis: Collective cellular properties emerge from time-delayed juxtacrine oscillation coupling.

Tomka T, Iber D, Boareto M.

Prog Biophys Mol Biol. 2018 Sep;137:76-87. doi: 10.1016/j.pbiomolbio.2018.04.004. Epub 2018 Apr 24. Review.

PMID:
29702125
5.

Growth and size control during development.

Vollmer J, Casares F, Iber D.

Open Biol. 2017 Nov;7(11). pii: 170190. doi: 10.1098/rsob.170190. Review.

6.

Differential interactions between Notch and ID factors control neurogenesis by modulating Hes factor autoregulation.

Boareto M, Iber D, Taylor V.

Development. 2017 Oct 1;144(19):3465-3474. doi: 10.1242/dev.152520.

7.

Growth control in the Drosophila eye disc by the cytokine Unpaired.

Vollmer J, Fried P, Aguilar-Hidalgo D, Sánchez-Aragón M, Iannini A, Casares F, Iber D.

Development. 2017 Mar 1;144(5):837-843. doi: 10.1242/dev.141309.

8.

An Unbiased Analysis of Candidate Mechanisms for the Regulation of Drosophila Wing Disc Growth.

Vollmer J, Iber D.

Sci Rep. 2016 Dec 20;6:39228. doi: 10.1038/srep39228.

9.

A Model of the Spatio-temporal Dynamics of Drosophila Eye Disc Development.

Fried P, Sánchez-Aragón M, Aguilar-Hidalgo D, Lehtinen B, Casares F, Iber D.

PLoS Comput Biol. 2016 Sep 14;12(9):e1005052. doi: 10.1371/journal.pcbi.1005052. eCollection 2016 Sep.

10.

A quantitative analysis of growth control in the Drosophila eye disc.

Vollmer J, Fried P, Sánchez-Aragón M, Lopes CS, Casares F, Iber D.

Development. 2016 May 1;143(9):1482-90. doi: 10.1242/dev.129775. Epub 2016 Mar 10.

11.

MOCCASIN: converting MATLAB ODE models to SBML.

Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC.

Bioinformatics. 2016 Jun 15;32(12):1905-6. doi: 10.1093/bioinformatics/btw056. Epub 2016 Feb 9.

12.

Read-Out of Dynamic Morphogen Gradients on Growing Domains.

Fried P, Iber D.

PLoS One. 2015 Nov 24;10(11):e0143226. doi: 10.1371/journal.pone.0143226. eCollection 2015.

13.

Image-based modelling of organogenesis.

Iber D, Karimaddini Z, Ünal E.

Brief Bioinform. 2016 Jul;17(4):616-27. doi: 10.1093/bib/bbv093. Epub 2015 Oct 27.

PMID:
26510443
14.

Axis Patterning by BMPs: Cnidarian Network Reveals Evolutionary Constraints.

Genikhovich G, Fried P, Prünster MM, Schinko JB, Gilles AF, Fredman D, Meier K, Iber D, Technau U.

Cell Rep. 2015 Mar 17;10(10):1646-1654. doi: 10.1016/j.celrep.2015.02.035. Epub 2015 Mar 12.

15.

LBIBCell: a cell-based simulation environment for morphogenetic problems.

Tanaka S, Sichau D, Iber D.

Bioinformatics. 2015 Jul 15;31(14):2340-7. doi: 10.1093/bioinformatics/btv147. Epub 2015 Mar 13.

PMID:
25770313
16.

An interplay of geometry and signaling enables robust lung branching morphogenesis.

Menshykau D, Blanc P, Unal E, Sapin V, Iber D.

Development. 2014 Dec;141(23):4526-36. doi: 10.1242/dev.116202. Epub 2014 Oct 30.

17.

Dynamic scaling of morphogen gradients on growing domains.

Fried P, Iber D.

Nat Commun. 2014 Oct 8;5:5077. doi: 10.1038/ncomms6077.

PMID:
25295831
18.

Simulating tissue morphogenesis and signaling.

Iber D, Tanaka S, Fried P, Germann P, Menshykau D.

Methods Mol Biol. 2015;1189:323-38. doi: 10.1007/978-1-4939-1164-6_21.

PMID:
25245703
19.

Feedback, receptor clustering, and receptor restriction to single cells yield large Turing spaces for ligand-receptor-based Turing models.

Kurics T, Menshykau D, Iber D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Aug;90(2):022716. Epub 2014 Aug 22.

PMID:
25215767
20.

Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs.

Lopez-Rios J, Duchesne A, Speziale D, Andrey G, Peterson KA, Germann P, Unal 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, Zeller R.

Nature. 2014 Jul 3;511(7507):46-51. doi: 10.1038/nature13289. Epub 2014 Jun 18.

PMID:
24990743
21.

Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes.

Fengos G, Schmidt A, Martin K, Fluri E, Aebersold R, Iber D, Pertz O.

Proteome Sci. 2014 May 1;12:23. doi: 10.1186/1477-5956-12-23. eCollection 2014.

22.

How do digits emerge? - mathematical models of limb development.

Iber D, Germann P.

Birth Defects Res C Embryo Today. 2014 Mar;102(1):1-12. doi: 10.1002/bdrc.21057. Review.

PMID:
24677720
23.

Species-specific differences in follicular antral sizes result from diffusion-based limitations on the thickness of the granulosa cell layer.

Bächler M, Menshykau D, De Geyter Ch, Iber D.

Mol Hum Reprod. 2014 Mar;20(3):208-21. doi: 10.1093/molehr/gat078. Epub 2013 Nov 11.

PMID:
24217389
24.

Inter-dependent tissue growth and Turing patterning in a model for long bone development.

Tanaka S, Iber D.

Phys Biol. 2013 Oct;10(5):056009. doi: 10.1088/1478-3975/10/5/056009. Epub 2013 Oct 8.

PMID:
24104059
25.

Studies of morphogens: keep calm and carry on.

Stathopoulos A, Iber D.

Development. 2013 Oct;140(20):4119-24. doi: 10.1242/dev.095141.

26.
27.

The control of branching morphogenesis.

Iber D, Menshykau D.

Open Biol. 2013 Sep 4;3(9):130088. doi: 10.1098/rsob.130088. Review.

28.

Computational modelling of bovine ovarian follicle development.

Iber D, Geyter CD.

BMC Syst Biol. 2013 Jul 15;7:60. doi: 10.1186/1752-0509-7-60.

29.

Kidney branching morphogenesis under the control of a ligand-receptor-based Turing mechanism.

Menshykau D, Iber D.

Phys Biol. 2013 Aug;10(4):046003. doi: 10.1088/1478-3975/10/4/046003. Epub 2013 Jun 17.

PMID:
23770927
30.

Enhanced cellular sensitivity from partitioning the integrin receptors into multiple clusters.

Felizzi F, Iber D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jan;87(1):012701. Epub 2013 Jan 3.

PMID:
23410353
31.

Analyzing and constraining signaling networks: parameter estimation for the user.

Geier F, Fengos G, Felizzi F, Iber D.

Methods Mol Biol. 2012;880:23-39. doi: 10.1007/978-1-61779-833-7_2. Review.

PMID:
23361979
32.

Predictive models for cellular signaling networks.

Iber D, Fengos G.

Methods Mol Biol. 2012;880:1-22. doi: 10.1007/978-1-61779-833-7_1. Review.

PMID:
23361978
33.

Making sense-data-based simulations of vertebrate limb development.

Iber D, Zeller R.

Curr Opin Genet Dev. 2012 Dec;22(6):570-7. doi: 10.1016/j.gde.2012.11.005. Epub 2012 Dec 19. Review.

PMID:
23266216
34.

Digit patterning during limb development as a result of the BMP-receptor interaction.

Badugu A, Kraemer C, Germann P, Menshykau D, Iber D.

Sci Rep. 2012;2:991. doi: 10.1038/srep00991. Epub 2012 Dec 18.

35.
36.

ECCB 2012: The 11th European Conference on Computational Biology.

Schwede T, Iber D.

Bioinformatics. 2012 Sep 15;28(18):i303-i305. No abstract available.

37.

Branch mode selection during early lung development.

Menshykau D, Kraemer C, Iber D.

PLoS Comput Biol. 2012;8(2):e1002377. doi: 10.1371/journal.pcbi.1002377. Epub 2012 Feb 16.

39.

A computational analysis of the dynamic roles of talin, Dok1, and PIPKI for integrin activation.

Geier F, Fengos G, Iber D.

PLoS One. 2011;6(11):e24808. doi: 10.1371/journal.pone.0024808. Epub 2011 Nov 16.

40.

Plasticity of TGF-β signaling.

Cellière G, Fengos G, Hervé M, Iber D.

BMC Syst Biol. 2011 Nov 3;5:184. doi: 10.1186/1752-0509-5-184.

41.

SHH propagates distal limb bud development by enhancing CYP26B1-mediated retinoic acid clearance via AER-FGF signalling.

Probst S, Kraemer C, Demougin P, Sheth R, Martin GR, Shiratori H, Hamada H, Iber D, Zeller R, Zuniga A.

Development. 2011 May;138(10):1913-23. doi: 10.1242/dev.063966. Epub 2011 Apr 6.

42.

The mechanism of sudden stripe formation during dorso-ventral patterning in Drosophila.

Iber D, Gaglia G.

J Math Biol. 2007 Feb;54(2):179-98. Epub 2006 Nov 15.

PMID:
17106745
43.

Organisation of B-cell receptors on the cell membrane.

Iber D, Gruhn T.

Syst Biol (Stevenage). 2006 Sep;153(5):401-4.

PMID:
16986327
44.
45.

Integrin activation--the importance of a positive feedback.

Iber D, Campbell ID.

Bull Math Biol. 2006 May;68(4):945-56. Epub 2006 May 13.

PMID:
16802090
47.

The mechanism of cell differentiation in Bacillus subtilis.

Iber D, Clarkson J, Yudkin MD, Campbell ID.

Nature. 2006 May 18;441(7091):371-4.

PMID:
16710423
48.

An analysis of B cell selection mechanisms in germinal centers.

Meyer-Hermann ME, Maini PK, Iber D.

Math Med Biol. 2006 Sep;23(3):255-77. Epub 2006 May 17.

PMID:
16707510
49.

Formation of the B cell synapse: retention or recruitment?

Iber D.

Cell Mol Life Sci. 2005 Jan;62(2):206-13.

PMID:
15666092
50.

A mathematical model for germinal centre kinetics and affinity maturation.

Iber D, Maini PK.

J Theor Biol. 2002 Nov 21;219(2):153-75.

PMID:
12413873

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