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Items: 40

1.

Modeling Uniaxial Nonuniform Cell Proliferation.

Lai De Oliveira A, Binder BJ.

Bull Math Biol. 2019 Apr 3. doi: 10.1007/s11538-019-00601-4. [Epub ahead of print]

PMID:
30945102
2.

TAMMiCol: Tool for analysis of the morphology of microbial colonies.

Tronnolone H, Gardner JM, Sundstrom JF, Jiranek V, Oliver SG, Binder BJ.

PLoS Comput Biol. 2018 Dec 3;14(12):e1006629. doi: 10.1371/journal.pcbi.1006629. eCollection 2018 Dec.

3.

Characterizing the shape patterns of dimorphic yeast pseudohyphae.

Gontar A, Bottema MJ, Binder BJ, Tronnolone H.

R Soc Open Sci. 2018 Oct 17;5(10):180820. doi: 10.1098/rsos.180820. eCollection 2018 Oct.

4.

Diffusion-Limited Growth of Microbial Colonies.

Tronnolone H, Tam A, Szenczi Z, Green JEF, Balasuriya S, Tek EL, Gardner JM, Sundstrom JF, Jiranek V, Oliver SG, Binder BJ.

Sci Rep. 2018 Apr 16;8(1):5992. doi: 10.1038/s41598-018-23649-z.

5.

Nutrient-limited growth with non-linear cell diffusion as a mechanism for floral pattern formation in yeast biofilms.

Tam A, Green JEF, Balasuriya S, Tek EL, Gardner JM, Sundstrom JF, Jiranek V, Binder BJ.

J Theor Biol. 2018 Jul 7;448:122-141. doi: 10.1016/j.jtbi.2018.04.004. Epub 2018 Apr 7.

PMID:
29630992
6.

Understanding interactions between populations: Individual based modelling and quantification using pair correlation functions.

Dini S, Binder BJ, Green JEF.

J Theor Biol. 2018 Feb 14;439:50-64. doi: 10.1016/j.jtbi.2017.11.014. Epub 2017 Dec 7.

PMID:
29197512
7.

Quantifying the dominant growth mechanisms of dimorphic yeast using a lattice-based model.

Tronnolone H, Gardner JM, Sundstrom JF, Jiranek V, Oliver SG, Binder BJ.

J R Soc Interface. 2017 Sep;14(134). pii: 20170314. doi: 10.1098/rsif.2017.0314.

8.

Differential Clonal Expansion in an Invading Cell Population: Clonal Advantage or Dumb Luck?

Newgreen DF, Zhang D, Cheeseman BL, Binder BJ, Landman KA.

Cells Tissues Organs. 2017;203(2):105-113. doi: 10.1159/000452793. Epub 2017 Feb 20. Review.

PMID:
28214862
9.

Identifying the necrotic zone boundary in tumour spheroids with pair-correlation functions.

Dini S, Binder BJ, Fischer SC, Mattheyer C, Schmitz A, Stelzer EH, Bean NG, Green JE.

J R Soc Interface. 2016 Oct;13(123). pii: 20160649.

10.

Quantifying the effect of experimental design choices for in vitro scratch assays.

Johnston ST, Ross JV, Binder BJ, Sean McElwain DL, Haridas P, Simpson MJ.

J Theor Biol. 2016 Jul 7;400:19-31. doi: 10.1016/j.jtbi.2016.04.012. Epub 2016 Apr 13.

PMID:
27086040
11.

Spectral analysis of pair-correlation bandwidth: application to cell biology images.

Binder BJ, Simpson MJ.

R Soc Open Sci. 2015 Feb 11;2(2):140494. doi: 10.1098/rsos.140494. eCollection 2015 Feb.

12.

Incomplete penetrance: The role of stochasticity in developmental cell colonization.

Binder BJ, Landman KA, Newgreen DF, Ross JV.

J Theor Biol. 2015 Sep 7;380:309-14. doi: 10.1016/j.jtbi.2015.05.028. Epub 2015 Jun 3.

PMID:
26047851
13.

Quantifying two-dimensional filamentous and invasive growth spatial patterns in yeast colonies.

Binder BJ, Sundstrom JF, Gardner JM, Jiranek V, Oliver SG.

PLoS Comput Biol. 2015 Feb 26;11(2):e1004070. doi: 10.1371/journal.pcbi.1004070. eCollection 2015 Feb.

14.

Approximating spatially exclusive invasion processes.

Ross JV, Binder BJ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 May;89(5):052709. Epub 2014 May 15.

PMID:
25353831
15.

The minimal CO2-concentrating mechanism of Prochlorococcus spp. MED4 is effective and efficient.

Hopkinson BM, Young JN, Tansik AL, Binder BJ.

Plant Physiol. 2014 Dec;166(4):2205-17. doi: 10.1104/pp.114.247049. Epub 2014 Oct 14.

16.

Interpreting scratch assays using pair density dynamics and approximate Bayesian computation.

Johnston ST, Simpson MJ, McElwain DL, Binder BJ, Ross JV.

Open Biol. 2014 Sep;4(9):140097. doi: 10.1098/rsob.140097.

17.

Assessing the role of spatial correlations during collective cell spreading.

Treloar KK, Simpson MJ, Binder BJ, McElwain DL, Baker RE.

Sci Rep. 2014 Jul 16;4:5713. doi: 10.1038/srep05713.

18.

On the derivation of approximations to cellular automata models and the assumption of independence.

Davies KJ, Green JE, Bean NG, Binder BJ, Ross JV.

Math Biosci. 2014 Jul;253:63-71. doi: 10.1016/j.mbs.2014.04.004. Epub 2014 Apr 24.

PMID:
24769324
19.

Distinguishing between mechanisms of cell aggregation using pair-correlation functions.

Agnew DJ, Green JE, Brown TM, Simpson MJ, Binder BJ.

J Theor Biol. 2014 Jul 7;352:16-23. doi: 10.1016/j.jtbi.2014.02.033. Epub 2014 Mar 5.

PMID:
24607741
20.

Cell lineage tracing in the developing enteric nervous system: superstars revealed by experiment and simulation.

Cheeseman BL, Zhang D, Binder BJ, Newgreen DF, Landman KA.

J R Soc Interface. 2014 Feb 5;11(93):20130815. doi: 10.1098/rsif.2013.0815. Print 2014 Apr 6. Review.

21.

Quantifying spatial structure in experimental observations and agent-based simulations using pair-correlation functions.

Binder BJ, Simpson MJ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Aug;88(2):022705. Epub 2013 Aug 12.

PMID:
24032862
22.

Experimental and modelling investigation of monolayer development with clustering.

Simpson MJ, Binder BJ, Haridas P, Wood BK, Treloar KK, McElwain DL, Baker RE.

Bull Math Biol. 2013 May;75(5):871-89. doi: 10.1007/s11538-013-9839-0. Epub 2013 Apr 13.

PMID:
23584951
23.

Quantifying the roles of cell motility and cell proliferation in a circular barrier assay.

Simpson MJ, Treloar KK, Binder BJ, Haridas P, Manton KJ, Leavesley DI, McElwain DL, Baker RE.

J R Soc Interface. 2013 Feb 20;10(82):20130007. doi: 10.1098/rsif.2013.0007. Print 2013 May 6.

24.

Generalized index for spatial data sets as a measure of complete spatial randomness.

Hackett-Jones EJ, Davies KJ, Binder BJ, Landman KA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jun;85(6 Pt 1):061908. Epub 2012 Jun 8.

PMID:
23005128
25.

Spatial analysis of multi-species exclusion processes: application to neural crest cell migration in the embryonic gut.

Binder BJ, Landman KA, Newgreen DF, Simkin JE, Takahashi Y, Zhang D.

Bull Math Biol. 2012 Feb;74(2):474-90. doi: 10.1007/s11538-011-9703-z. Epub 2011 Nov 24.

PMID:
22108739
26.

Hybrid free-surface flows in a two-dimensional channel.

Binder BJ, Vanden-Broeck JM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jul;84(1 Pt 2):016302. Epub 2011 Jul 11.

PMID:
21867299
27.

Quantifying evenly distributed states in exclusion and nonexclusion processes.

Binder BJ, Landman KA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Apr;83(4 Pt 1):041914. Epub 2011 Apr 20.

PMID:
21599207
28.

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton.

Cuvelier ML, Allen AE, Monier A, McCrow JP, Messié M, Tringe SG, Woyke T, Welsh RM, Ishoey T, Lee JH, Binder BJ, DuPont CL, Latasa M, Guigand C, Buck KR, Hilton J, Thiagarajan M, Caler E, Read B, Lasken RS, Chavez FP, Worden AZ.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14679-84. doi: 10.1073/pnas.1001665107. Epub 2010 Jul 28.

29.

Neural crest regionalisation for enteric nervous system formation: implications for Hirschsprung's disease and stem cell therapy.

Zhang D, Brinas IM, Binder BJ, Landman KA, Newgreen DF.

Dev Biol. 2010 Mar 15;339(2):280-94. doi: 10.1016/j.ydbio.2009.12.014. Epub 2010 Jan 18.

30.

Exclusion processes on a growing domain.

Binder BJ, Landman KA.

J Theor Biol. 2009 Aug 7;259(3):541-51. doi: 10.1016/j.jtbi.2009.04.025. Epub 2009 May 8.

PMID:
19427868
31.

Modeling proliferative tissue growth: a general approach and an avian case study.

Binder BJ, Landman KA, Simpson MJ, Mariani M, Newgreen DF.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep;78(3 Pt 1):031912. Epub 2008 Sep 16.

PMID:
18851070
32.

Ecological genomics of marine Roseobacters.

Moran MA, Belas R, Schell MA, Gonz√°lez JM, Sun F, Sun S, Binder BJ, Edmonds J, Ye W, Orcutt B, Howard EC, Meile C, Palefsky W, Goesmann A, Ren Q, Paulsen I, Ulrich LE, Thompson LS, Saunders E, Buchan A.

Appl Environ Microbiol. 2007 Jul;73(14):4559-69. Epub 2007 May 25.

33.

Forced solitary waves and fronts past submerged obstacles.

Binder BJ, Vanden-Broeck JM, Dias F.

Chaos. 2005 Sep;15(3):37106.

PMID:
16253001
34.

Application of digital image analysis and flow cytometry to enumerate marine viruses stained with SYBR gold.

Chen F, Lu JR, Binder BJ, Liu YC, Hodson RE.

Appl Environ Microbiol. 2001 Feb;67(2):539-45.

35.
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37.

Application of neural networks to flow cytometry data analysis and real-time cell classification.

Frankel DS, Frankel SL, Binder BJ, Vogt RF.

Cytometry. 1996 Apr 1;23(4):290-302.

38.

Cell Cycle Regulation in Marine Synechococcus sp. Strains.

Binder BJ, Chisholm SW.

Appl Environ Microbiol. 1995 Feb;61(2):708-17.

39.

Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations.

Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA.

Appl Environ Microbiol. 1990 Jun;56(6):1919-25.

40.

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