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Items: 1 to 50 of 54

1.

Publisher Correction: Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis.

Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FH.

Nat Methods. 2019 Sep;16(9):932. doi: 10.1038/s41592-019-0546-0.

PMID:
31406386
2.

Id4 Downstream of Notch2 Maintains Neural Stem Cell Quiescence in the Adult Hippocampus.

Zhang R, Boareto M, Engler A, Louvi A, Giachino C, Iber D, Taylor V.

Cell Rep. 2019 Aug 6;28(6):1485-1498.e6. doi: 10.1016/j.celrep.2019.07.014.

3.

Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis.

Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FH.

Nat Methods. 2019 Aug;16(8):743-749. doi: 10.1038/s41592-019-0495-7. Epub 2019 Jul 29. Erratum in: Nat Methods. 2019 Sep;16(9):932.

PMID:
31363225
4.

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.

5.

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

Barac D, Multerer MD, Iber D.

J Theor Biol. 2019 Nov 21;481:233-248. doi: 10.1016/j.jtbi.2018.12.002. Epub 2018 Dec 7.

PMID:
30529487
6.

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
7.

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
8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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
17.

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.

18.

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
19.

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.

20.

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
21.

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
22.

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
23.

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
24.

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.

25.

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
26.

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
27.

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
28.

Studies of morphogens: keep calm and carry on.

Stathopoulos A, Iber D.

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

29.
30.

The control of branching morphogenesis.

Iber D, Menshykau D.

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

31.

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.

32.

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
33.

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
34.

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
35.

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
36.

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
37.

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.

38.
39.

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

Schwede T, Iber D.

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

40.

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.

42.

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.

43.

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.

44.

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.

45.

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
46.

Organisation of B-cell receptors on the cell membrane.

Iber D, Gruhn T.

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

PMID:
16986327
47.
48.

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
50.

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

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