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Items: 28

1.

Synthesizing and tuning stochastic chemical reaction networks with specified behaviours.

Murphy N, Petersen R, Phillips A, Yordanov B, Dalchau N.

J R Soc Interface. 2018 Aug;15(145). pii: 20180283. doi: 10.1098/rsif.2018.0283.

2.

A Mechanistic Model for Predicting Cell Surface Presentation of Competing Peptides by MHC Class I Molecules.

Boulanger DSM, Eccleston RC, Phillips A, Coveney PV, Elliott T, Dalchau N.

Front Immunol. 2018 Jul 5;9:1538. doi: 10.3389/fimmu.2018.01538. eCollection 2018.

3.

Model reduction enables Turing instability analysis of large reaction-diffusion models.

Smith S, Dalchau N.

J R Soc Interface. 2018 Mar;15(140). pii: 20170805. doi: 10.1098/rsif.2017.0805.

4.

Predicting DNA hybridization kinetics from sequence.

Zhang JX, Fang JZ, Duan W, Wu LR, Zhang AW, Dalchau N, Yordanov B, Petersen R, Phillips A, Zhang DY.

Nat Chem. 2018 Jan;10(1):91-98. doi: 10.1038/nchem.2877. Epub 2017 Nov 6.

5.

Host genotype and time dependent antigen presentation of viral peptides: predictions from theory.

Eccleston RC, Coveney PV, Dalchau N.

Sci Rep. 2017 Oct 30;7(1):14367. doi: 10.1038/s41598-017-14415-8.

6.

The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition.

Eccleston RC, Wan S, Dalchau N, Coveney PV.

Front Immunol. 2017 Jul 10;8:797. doi: 10.3389/fimmu.2017.00797. eCollection 2017.

7.

A spatially localized architecture for fast and modular DNA computing.

Chatterjee G, Dalchau N, Muscat RA, Phillips A, Seelig G.

Nat Nanotechnol. 2017 Sep;12(9):920-927. doi: 10.1038/nnano.2017.127. Epub 2017 Jul 24.

PMID:
28737747
8.

Efficient Switches in Biology and Computer Science.

Cardelli L, Hernansaiz-Ballesteros RD, Dalchau N, Csikász-Nagy A.

PLoS Comput Biol. 2017 Jan 5;13(1):e1005100. doi: 10.1371/journal.pcbi.1005100. eCollection 2017 Jan. No abstract available.

9.

Noise Reduction in Complex Biological Switches.

Cardelli L, Csikász-Nagy A, Dalchau N, Tribastone M, Tschaikowski M.

Sci Rep. 2016 Feb 8;6:20214. doi: 10.1038/srep20214.

10.

Orthogonal intercellular signaling for programmed spatial behavior.

Grant PK, Dalchau N, Brown JR, Federici F, Rudge TJ, Yordanov B, Patange O, Phillips A, Haseloff J.

Mol Syst Biol. 2016 Jan 25;12(1):849. doi: 10.15252/msb.20156590.

11.

Selector function of MHC I molecules is determined by protein plasticity.

Bailey A, Dalchau N, Carter R, Emmott S, Phillips A, Werner JM, Elliott T.

Sci Rep. 2015 Oct 20;5:14928. doi: 10.1038/srep14928.

12.

Characterization of Intrinsic Properties of Promoters.

Rudge TJ, Brown JR, Federici F, Dalchau N, Phillips A, Ajioka JW, Haseloff J.

ACS Synth Biol. 2016 Jan 15;5(1):89-98. doi: 10.1021/acssynbio.5b00116. Epub 2016 Jan 7.

13.

Probabilistic Analysis of Localized DNA Hybridization Circuits.

Dalchau N, Chandran H, Gopalkrishnan N, Phillips A, Reif J.

ACS Synth Biol. 2015 Aug 21;4(8):898-913. doi: 10.1021/acssynbio.5b00044. Epub 2015 Jul 27.

PMID:
26133087
14.

Is 'peak N' key to understanding the timing of flowering in annual plants?

Guilbaud CS, Dalchau N, Purves DW, Turnbull LA.

New Phytol. 2015 Jan;205(2):918-27. doi: 10.1111/nph.13095. Epub 2014 Oct 8.

15.

Ten simple rules for effective computational research.

Osborne JM, Bernabeu MO, Bruna M, Calderhead B, Cooper J, Dalchau N, Dunn SJ, Fletcher AG, Freeman R, Groen D, Knapp B, McInerny GJ, Mirams GR, Pitt-Francis J, Sengupta B, Wright DW, Yates CA, Gavaghan DJ, Emmott S, Deane C.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003506. doi: 10.1371/journal.pcbi.1003506. eCollection 2014 Mar. No abstract available.

16.

A computational method for automated characterization of genetic components.

Yordanov B, Dalchau N, Grant PK, Pedersen M, Emmott S, Haseloff J, Phillips A.

ACS Synth Biol. 2014 Aug 15;3(8):578-88. doi: 10.1021/sb400152n. Epub 2014 Mar 14.

PMID:
24628037
17.

The circadian clock has transient plasticity of period and is required for timing of nocturnal processes in Arabidopsis.

Dodd AN, Dalchau N, Gardner MJ, Baek SJ, Webb AA.

New Phytol. 2014 Jan;201(1):168-79. doi: 10.1111/nph.12489. Epub 2013 Sep 17.

18.

Programmable chemical controllers made from DNA.

Chen YJ, Dalchau N, Srinivas N, Phillips A, Cardelli L, Soloveichik D, Seelig G.

Nat Nanotechnol. 2013 Oct;8(10):755-62. doi: 10.1038/nnano.2013.189. Epub 2013 Sep 29.

19.

Towards the rational design of synthetic cells with prescribed population dynamics.

Dalchau N, Smith MJ, Martin S, Brown JR, Emmott S, Phillips A.

J R Soc Interface. 2012 Nov 7;9(76):2883-98. Epub 2012 Jun 8.

20.

Understanding biological timing using mechanistic and black-box models.

Dalchau N.

New Phytol. 2012 Mar;193(4):852-8. doi: 10.1111/j.1469-8137.2011.04004.x. Review.

21.

A peptide filtering relation quantifies MHC class I peptide optimization.

Dalchau N, Phillips A, Goldstein LD, Howarth M, Cardelli L, Emmott S, Elliott T, Werner JM.

PLoS Comput Biol. 2011 Oct;7(10):e1002144. doi: 10.1371/journal.pcbi.1002144. Epub 2011 Oct 13.

22.

The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose.

Dalchau N, Baek SJ, Briggs HM, Robertson FC, Dodd AN, Gardner MJ, Stancombe MA, Haydon MJ, Stan GB, Gonçalves JM, Webb AA.

Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):5104-9. doi: 10.1073/pnas.1015452108. Epub 2011 Mar 7.

23.

The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding.

Van Hateren A, James E, Bailey A, Phillips A, Dalchau N, Elliott T.

Tissue Antigens. 2010 Oct;76(4):259-75. doi: 10.1111/j.1399-0039.2010.01550.x. Review. Erratum in: Tissue Antigens. 2010 Nov;76(5):428.

PMID:
21050182
24.

Correct biological timing in Arabidopsis requires multiple light-signaling pathways.

Dalchau N, Hubbard KE, Robertson FC, Hotta CT, Briggs HM, Stan GB, Gonçalves JM, Webb AA.

Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):13171-6. doi: 10.1073/pnas.1001429107. Epub 2010 Jul 1.

25.

Disruption of two defensive signaling pathways by a viral RNA silencing suppressor.

Lewsey MG, Murphy AM, Maclean D, Dalchau N, Westwood JH, Macaulay K, Bennett MH, Moulin M, Hanke DE, Powell G, Smith AG, Carr JP.

Mol Plant Microbe Interact. 2010 Jul;23(7):835-45. doi: 10.1094/MPMI-23-7-0835.

26.

Systems analyses of circadian networks.

Hubbard KE, Robertson FC, Dalchau N, Webb AA.

Mol Biosyst. 2009 Dec;5(12):1502-11. doi: 10.1039/B907714f. Epub 2009 Aug 3. Review.

PMID:
19763342
27.

The Arabidopsis circadian clock incorporates a cADPR-based feedback loop.

Dodd AN, Gardner MJ, Hotta CT, Hubbard KE, Dalchau N, Love J, Assie JM, Robertson FC, Jakobsen MK, Gonçalves J, Sanders D, Webb AA.

Science. 2007 Dec 14;318(5857):1789-92. Epub 2007 Nov 15.

28.

Modulation of environmental responses of plants by circadian clocks.

Hotta CT, Gardner MJ, Hubbard KE, Baek SJ, Dalchau N, Suhita D, Dodd AN, Webb AAR.

Plant Cell Environ. 2007 Mar;30(3):333-349. doi: 10.1111/j.1365-3040.2006.01627.x. Review.

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