Sort by
Items per page

Send to

Choose Destination

Search results

Items: 39


Model annotation and discovery with the Physiome Model Repository.

Sarwar DM, Kalbasi R, Gennari JH, Carlson BE, Neal ML, Bono B, Atalag K, Hunter PJ, Nickerson DP.

BMC Bioinformatics. 2019 Sep 6;20(1):457. doi: 10.1186/s12859-019-2987-y.


Computational Modeling of Glucose Uptake in the Enterocyte.

Afshar N, Safaei S, Nickerson DP, Hunter PJ, Suresh V.

Front Physiol. 2019 Apr 12;10:380. doi: 10.3389/fphys.2019.00380. eCollection 2019.


Sec17 (α-SNAP) and an SM-tethering complex regulate the outcome of SNARE zippering in vitro and in vivo.

Schwartz ML, Nickerson DP, Lobingier BT, Plemel RL, Duan M, Angers CG, Zick M, Merz AJ.

Elife. 2017 Sep 19;6. pii: e27396. doi: 10.7554/eLife.27396.


eSolv, a CellML-based simulation front-end for online teaching.

de Boer TP, van der Werf S, Hennekam B, Nickerson DP, Garny A, Gerbrands M, Bouwmeester RAM, Rozendal AP, Torfs E, van Rijen HVM.

Adv Physiol Educ. 2017 Sep 1;41(3):425-427. doi: 10.1152/advan.00127.2016. No abstract available.


Modular modelling with Physiome standards.

Cooling MT, Nickerson DP, Nielsen PM, Hunter PJ.

J Physiol. 2016 Dec 1;594(23):6817-6831. doi: 10.1113/JP272633. Epub 2016 Aug 29.


Aneuploidy shortens replicative lifespan in Saccharomyces cerevisiae.

Sunshine AB, Ong GT, Nickerson DP, Carr D, Murakami CJ, Wasko BM, Shemorry A, Merz AJ, Kaeberlein M, Dunham MJ.

Aging Cell. 2016 Apr;15(2):317-24. doi: 10.1111/acel.12443. Epub 2016 Jan 13.


LUCID: A Quantitative Assay of ESCRT-Mediated Cargo Sorting into Multivesicular Bodies.

Nickerson DP, Merz AJ.

Traffic. 2015 Dec;16(12):1318-29. doi: 10.1111/tra.12331. Epub 2015 Nov 16.


Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.

Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N.

Front Bioeng Biotechnol. 2015 Feb 24;3:19. doi: 10.3389/fbioe.2015.00019. eCollection 2015. Review.


The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units.

de Bono B, Safaei S, Grenon P, Nickerson DP, Alexander S, Helvensteijn M, Kok JN, Kokash N, Wu A, Yu T, Hunter P, Baldock RA.

Front Physiol. 2015 Feb 24;6:24. doi: 10.3389/fphys.2015.00024. eCollection 2015.


Ubiquitin binding by the CUE domain promotes endosomal localization of the Rab5 GEF Vps9.

Shideler T, Nickerson DP, Merz AJ, Odorizzi G.

Mol Biol Cell. 2015 Apr 1;26(7):1345-56. doi: 10.1091/mbc.E14-06-1156. Epub 2015 Feb 11.


Using CellML with OpenCMISS to Simulate Multi-Scale Physiology.

Nickerson DP, Ladd D, Hussan JR, Safaei S, Suresh V, Hunter PJ, Bradley CP.

Front Bioeng Biotechnol. 2015 Jan 5;2:79. doi: 10.3389/fbioe.2014.00079. eCollection 2014.


COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N.

BMC Bioinformatics. 2014 Dec 14;15:369. doi: 10.1186/s12859-014-0369-z.


SM proteins Sly1 and Vps33 co-assemble with Sec17 and SNARE complexes to oppose SNARE disassembly by Sec18.

Lobingier BT, Nickerson DP, Lo SY, Merz AJ.

Elife. 2014 May 16;3:e02272. doi: 10.7554/eLife.02272.


Standards and tools supporting collaborative development of the virtual physiological human.

Nickerson DP, Garny A, Nielsen PM, Hunter PJ.

Conf Proc IEEE Eng Med Biol Soc. 2013;2013:5541-4. doi: 10.1109/EMBC.2013.6610805.


Vps9 family protein Muk1 is the second Rab5 guanosine nucleotide exchange factor in budding yeast.

Paulsel AL, Merz AJ, Nickerson DP.

J Biol Chem. 2013 Jun 21;288(25):18162-71. doi: 10.1074/jbc.M113.457069. Epub 2013 Apr 23.


Class E compartments form in response to ESCRT dysfunction in yeast due to hyperactivity of the Vps21 Rab GTPase.

Russell MR, Shideler T, Nickerson DP, West M, Odorizzi G.

J Cell Sci. 2012 Nov 1;125(Pt 21):5208-20. doi: 10.1242/jcs.111310. Epub 2012 Aug 16.


Comparison of the Gibbs and Suga formulations of cardiac energetics: the demise of "isoefficiency".

Han JC, Taberner AJ, Tran K, Goo S, Nickerson DP, Nash MP, Nielsen PM, Crampin EJ, Loiselle DS.

J Appl Physiol (1985). 2012 Oct;113(7):996-1003. doi: 10.1152/japplphysiol.00693.2011. Epub 2012 Aug 9. Review.


Relating components of pressure-volume area in Suga's formulation of cardiac energetics to components of the stress-time integral.

Han JC, Taberner AJ, Tran K, Nickerson DP, Nash MP, Nielsen PM, Crampin EJ, Loiselle DS.

J Appl Physiol (1985). 2012 Oct;113(7):988-95. doi: 10.1152/japplphysiol.00438.2012. Epub 2012 Jul 26. Review.


Termination of isoform-selective Vps21/Rab5 signaling at endolysosomal organelles by Msb3/Gyp3.

Nickerson DP, Russell MRG, Lo SY, Chapin HC, Milnes J, Merz AJ.

Traffic. 2012 Oct;13(10):1411-1428. doi: 10.1111/j.1600-0854.2012.01390.x. Epub 2012 Aug 5.


A tool for multi-scale modelling of the renal nephron.

Nickerson DP, Terkildsen JR, Hamilton KL, Hunter PJ.

Interface Focus. 2011 Jun 6;1(3):417-25. doi: 10.1098/rsfs.2010.0032. Epub 2011 Mar 30.


Myocardial twitch duration and the dependence of oxygen consumption on pressure-volume area: experiments and modelling.

Han JC, Tran K, Taberner AJ, Nickerson DP, Kirton RS, Nielsen PM, Ward ML, Nash MP, Crampin EJ, Loiselle DS.

J Physiol. 2012 Sep 15;590(18):4603-22. doi: 10.1113/jphysiol.2012.228965. Epub 2012 May 8.


Subunit organization and Rab interactions of Vps-C protein complexes that control endolysosomal membrane traffic.

Plemel RL, Lobingier BT, Brett CL, Angers CG, Nickerson DP, Paulsel A, Sprague D, Merz AJ.

Mol Biol Cell. 2011 Apr 15;22(8):1353-63. doi: 10.1091/mbc.E10-03-0260. Epub 2011 Feb 16.


Revision history aware repositories of computational models of biological systems.

Miller AK, Yu T, Britten R, Cooling MT, Lawson J, Cowan D, Garny A, Halstead MD, Hunter PJ, Nickerson DP, Nunns G, Wimalaratne SM, Nielsen PM.

BMC Bioinformatics. 2011 Jan 14;12:22. doi: 10.1186/1471-2105-12-22.


The Physiome Model Repository 2.

Yu T, Lloyd CM, Nickerson DP, Cooling MT, Miller AK, Garny A, Terkildsen JR, Lawson J, Britten RD, Hunter PJ, Nielsen PM.

Bioinformatics. 2011 Mar 1;27(5):743-4. doi: 10.1093/bioinformatics/btq723. Epub 2011 Jan 6.


An overview of the CellML API and its implementation.

Miller AK, Marsh J, Reeve A, Garny A, Britten R, Halstead M, Cooper J, Nickerson DP, Nielsen PF.

BMC Bioinformatics. 2010 Apr 8;11:178. doi: 10.1186/1471-2105-11-178.


Regulators of Vps4 ATPase activity at endosomes differentially influence the size and rate of formation of intralumenal vesicles.

Nickerson DP, West M, Henry R, Odorizzi G.

Mol Biol Cell. 2010 Mar 15;21(6):1023-32. doi: 10.1091/mbc.E09-09-0776. Epub 2010 Jan 20.


Vps-C complexes: gatekeepers of endolysosomal traffic.

Nickerson DP, Brett CL, Merz AJ.

Curr Opin Cell Biol. 2009 Aug;21(4):543-51. doi: 10.1016/ Epub 2009 Jul 3. Review.


CellML metadata standards, associated tools and repositories.

Beard DA, Britten R, Cooling MT, Garny A, Halstead MD, Hunter PJ, Lawson J, Lloyd CM, Marsh J, Miller A, Nickerson DP, Nielsen PM, Nomura T, Subramanium S, Wimalaratne SM, Yu T.

Philos Trans A Math Phys Eng Sci. 2009 May 28;367(1895):1845-67. doi: 10.1098/rsta.2008.0310.


A physiome standards-based model publication paradigm.

Nickerson DP, Buist ML.

Philos Trans A Math Phys Eng Sci. 2009 May 28;367(1895):1823-44. doi: 10.1098/rsta.2008.0296.


CellML and associated tools and techniques.

Garny A, Nickerson DP, Cooper J, Weber dos Santos R, Miller AK, McKeever S, Nielsen PM, Hunter PJ.

Philos Trans A Math Phys Eng Sci. 2008 Sep 13;366(1878):3017-43. doi: 10.1098/rsta.2008.0094. Review.


Reference descriptions of cellular electrophysiology models.

Nickerson DP, Corrias A, Buist ML.

Bioinformatics. 2008 Apr 15;24(8):1112-4. doi: 10.1093/bioinformatics/btn080. Epub 2008 Mar 1.


A concentric circle model of multivesicular body cargo sorting.

Nickerson DP, Russell MR, Odorizzi G.

EMBO Rep. 2007 Jul;8(7):644-50. Review.


Modeling cardiac electrical activity at the cell and tissue levels.

Austin TM, Hooks DA, Hunter PJ, Nickerson DP, Pullan AJ, Sands GB, Smaill BH, Trew ML.

Ann N Y Acad Sci. 2006 Oct;1080:334-47. Review.


Did2 coordinates Vps4-mediated dissociation of ESCRT-III from endosomes.

Nickerson DP, West M, Odorizzi G.

J Cell Biol. 2006 Dec 4;175(5):715-20. Epub 2006 Nov 27. Erratum in: J Cell Biol. 2006 Dec 18;175(6):1043.


Molecular mechanisms of late endosome morphology, identity and sorting.

Russell MR, Nickerson DP, Odorizzi G.

Curr Opin Cell Biol. 2006 Aug;18(4):422-8. Epub 2006 Jun 15. Review.


The Noble cardiac ventricular electrophysiology models in CellML.

Nickerson DP, Hunter PJ.

Prog Biophys Mol Biol. 2006 Jan-Apr;90(1-3):346-59. Epub 2005 Jun 13. Review.


Modelling the passive and nerve activated response of the rectus femoris muscle to a flexion loading: a finite element framework.

Fernandez JW, Buist ML, Nickerson DP, Hunter PJ.

Med Eng Phys. 2005 Dec;27(10):862-70.


The catalytic activity of cytochrome P450cam towards styrene oxidation is increased by site-specific mutagenesis.

Nickerson DP, Harford-Cross CF, Fulcher SR, Wong LL.

FEBS Lett. 1997 Mar 24;405(2):153-6.

Supplemental Content

Loading ...
Support Center