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Items: 36

1.

Building a mechanistic mathematical model of hepatitis C virus entry.

Kalemera M, Mincheva D, Grove J, Illingworth CJR.

PLoS Comput Biol. 2019 Mar 18;15(3):e1006905. doi: 10.1371/journal.pcbi.1006905. [Epub ahead of print]

2.

Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus.

Doyle SR, Illingworth CJR, Laing R, Bartley DJ, Redman E, Martinelli A, Holroyd N, Morrison AA, Rezansoff A, Tracey A, Devaney E, Berriman M, Sargison N, Cotton JA, Gilleard JS.

BMC Genomics. 2019 Mar 15;20(1):218. doi: 10.1186/s12864-019-5592-6.

3.

Measurements of intrahost viral diversity require an unbiased diversity metric.

Zhao L, Illingworth CJR.

Virus Evol. 2019 Jan 30;5(1):vey041. doi: 10.1093/ve/vey041. eCollection 2019 Jan.

4.

A novel framework for inferring parameters of transmission from viral sequence data.

Lumby CK, Nene NR, Illingworth CJR.

PLoS Genet. 2018 Oct 16;14(10):e1007718. doi: 10.1371/journal.pgen.1007718. eCollection 2018 Oct.

5.

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites.

Reid AJ, Talman AM, Bennett HM, Gomes AR, Sanders MJ, Illingworth CJR, Billker O, Berriman M, Lawniczak MK.

Elife. 2018 Mar 27;7. pii: e33105. doi: 10.7554/eLife.33105.

6.

Inferring Fitness Effects from Time-Resolved Sequence Data with a Delay-Deterministic Model.

Nené NR, Dunham AS, Illingworth CJR.

Genetics. 2018 May;209(1):255-264. doi: 10.1534/genetics.118.300790. Epub 2018 Mar 2.

7.

On the effective depth of viral sequence data.

Illingworth CJR, Roy S, Beale MA, Tutill H, Williams R, Breuer J.

Virus Evol. 2017 Nov 14;3(2):vex030. doi: 10.1093/ve/vex030. eCollection 2017 Jul.

8.

Rapid identification of genes controlling virulence and immunity in malaria parasites.

Abkallo HM, Martinelli A, Inoue M, Ramaprasad A, Xangsayarath P, Gitaka J, Tang J, Yahata K, Zoungrana A, Mitaka H, Acharjee A, Datta PP, Hunt P, Carter R, Kaneko O, Mustonen V, Illingworth CJR, Pain A, Culleton R.

PLoS Pathog. 2017 Jul 12;13(7):e1006447. doi: 10.1371/journal.ppat.1006447. eCollection 2017 Jul.

9.

The effective rate of influenza reassortment is limited during human infection.

Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA, Lin X, Ransier A, Stockwell TB, Das SR, Gilbert AS, Lambkin-Williams R, Ginsburg GS, Woods CW, Koelle K, Illingworth CJ.

PLoS Pathog. 2017 Feb 7;13(2):e1006203. doi: 10.1371/journal.ppat.1006203. eCollection 2017 Feb.

10.

Addicted? Reduced host resistance in populations with defensive symbionts.

Martinez J, Cogni R, Cao C, Smith S, Illingworth CJ, Jiggins FM.

Proc Biol Sci. 2016 Jun 29;283(1833). pii: 20160778. doi: 10.1098/rspb.2016.0778.

11.

SAMFIRE: multi-locus variant calling for time-resolved sequence data.

Illingworth CJ.

Bioinformatics. 2016 Jul 15;32(14):2208-9. doi: 10.1093/bioinformatics/btw205. Epub 2016 Apr 22.

12.

In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization.

Shaw CD, Lonchamp J, Downing T, Imamura H, Freeman TM, Cotton JA, Sanders M, Blackburn G, Dujardin JC, Rijal S, Khanal B, Illingworth CJ, Coombs GH, Carter KC.

Mol Microbiol. 2016 Mar;99(6):1134-48. doi: 10.1111/mmi.13291. Epub 2016 Feb 9.

13.

Fitness Inference from Short-Read Data: Within-Host Evolution of a Reassortant H5N1 Influenza Virus.

Illingworth CJ.

Mol Biol Evol. 2015 Nov;32(11):3012-26. doi: 10.1093/molbev/msv171. Epub 2015 Aug 4.

14.

Identifying selection in the within-host evolution of influenza using viral sequence data.

Illingworth CJ, Fischer A, Mustonen V.

PLoS Comput Biol. 2014 Jul 31;10(7):e1003755. doi: 10.1371/journal.pcbi.1003755. eCollection 2014 Jul.

15.

High-definition reconstruction of clonal composition in cancer.

Fischer A, Vázquez-García I, Illingworth CJR, Mustonen V.

Cell Rep. 2014 Jun 12;7(5):1740-1752. doi: 10.1016/j.celrep.2014.04.055. Epub 2014 May 29.

16.

Assessing the effect of dynamics on the closed-loop protein-folding hypothesis.

Chintapalli SV, Illingworth CJ, Upton GJ, Sacquin-Mora S, Reeves PJ, Mohammedali HS, Reynolds CA.

J R Soc Interface. 2013 Nov 20;11(91):20130935. doi: 10.1098/rsif.2013.0935. Print 2014 Feb 6.

17.

High-resolution mapping of complex traits with a four-parent advanced intercross yeast population.

Cubillos FA, Parts L, Salinas F, Bergström A, Scovacricchi E, Zia A, Illingworth CJ, Mustonen V, Ibstedt S, Warringer J, Louis EJ, Durbin R, Liti G.

Genetics. 2013 Nov;195(3):1141-55. doi: 10.1534/genetics.113.155515. Epub 2013 Sep 13.

18.

Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses.

Illingworth CJ, Parts L, Bergström A, Liti G, Mustonen V.

PLoS One. 2013 May 2;8(5):e62266. doi: 10.1371/journal.pone.0062266. Print 2013.

19.

EMu: probabilistic inference of mutational processes and their localization in the cancer genome.

Fischer A, Illingworth CJ, Campbell PJ, Mustonen V.

Genome Biol. 2013 Apr 29;14(4):R39. doi: 10.1186/gb-2013-14-4-r39.

20.

Identifying subset errors in multiple sequence alignments.

Roy A, Taddese B, Vohra S, Thimmaraju PK, Illingworth CJ, Simpson LM, Mukherjee K, Reynolds CA, Chintapalli SV.

J Biomol Struct Dyn. 2014;32(3):364-71. doi: 10.1080/07391102.2013.770371. Epub 2013 Mar 25.

PMID:
23527867
21.

Components of selection in the evolution of the influenza virus: linkage effects beat inherent selection.

Illingworth CJ, Mustonen V.

PLoS Pathog. 2012 Dec;8(12):e1003091. doi: 10.1371/journal.ppat.1003091. Epub 2012 Dec 27.

22.

The statistical significance of selected sense-antisense peptide interactions.

Illingworth CJ, Chintipalli SV, Serapian SA, Miller AD, Veverka V, Carr MD, Reynolds CA.

J Comput Chem. 2012 Jun 15;33(16):1440-7. doi: 10.1002/jcc.22977. Epub 2012 Apr 4.

PMID:
22488506
23.

A method to infer positive selection from marker dynamics in an asexual population.

Illingworth CJ, Mustonen V.

Bioinformatics. 2012 Mar 15;28(6):831-7. doi: 10.1093/bioinformatics/btr722. Epub 2012 Jan 5.

24.

Quantifying selection acting on a complex trait using allele frequency time series data.

Illingworth CJ, Parts L, Schiffels S, Liti G, Mustonen V.

Mol Biol Evol. 2012 Apr;29(4):1187-97. doi: 10.1093/molbev/msr289. Epub 2011 Nov 23.

25.

Effects of point mutations in pVHL on the binding of HIF-1α.

Domene C, Illingworth CJ.

Proteins. 2012 Mar;80(3):733-46. doi: 10.1002/prot.23230. Epub 2011 Nov 22.

PMID:
22105711
26.

Binding of more than one Tva800 molecule is required for ASLV-A entry.

Gray ER, Illingworth CJ, Coffin JM, Stoye JP.

Retrovirology. 2011 Nov 18;8:96. doi: 10.1186/1742-4690-8-96.

27.

Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.

Illingworth CJ, Mustonen V.

Genetics. 2011 Nov;189(3):989-1000. doi: 10.1534/genetics.111.133975. Epub 2011 Sep 6.

28.

Closed loop folding units from structural alignments: experimental foldons revisited.

Chintapalli SV, Yew BK, Illingworth CJ, Upton GJ, Reeves PJ, Parkes KE, Snell CR, Reynolds CA.

J Comput Chem. 2010 Nov 30;31(15):2689-701. doi: 10.1002/jcc.21562.

PMID:
20839296
29.

Connectivity and binding-site recognition: applications relevant to drug design.

Illingworth CJ, Scott PD, Parkes KE, Snell CR, Campbell MP, Reynolds CA.

J Comput Chem. 2010 Nov 30;31(15):2677-88. doi: 10.1002/jcc.21561.

PMID:
20839295
30.

Chemical basis for the selectivity of the von Hippel Lindau tumor suppressor pVHL for prolyl-hydroxylated HIF-1alpha.

Illingworth CJ, Loenarz C, Schofield CJ, Domene C.

Biochemistry. 2010 Aug 17;49(32):6936-44. doi: 10.1021/bi100358t.

PMID:
20695530
31.

Toward a consistent treatment of polarization in model QM/MM calculations.

Illingworth CJ, Parkes KE, Snell CR, Ferenczy GG, Reynolds CA.

J Phys Chem A. 2008 Nov 27;112(47):12151-6. doi: 10.1021/jp710168q.

PMID:
18986123
32.

Assessing the role of polarization in docking.

Illingworth CJ, Morris GM, Parkes KE, Snell CR, Reynolds CA.

J Phys Chem A. 2008 Nov 27;112(47):12157-63. doi: 10.1021/jp710169m.

PMID:
18986122
33.

Quantitative measurement of protease ligand conformation.

Illingworth CJ, Parkes KE, Snell CR, Reynolds CA.

J Comput Aided Mol Des. 2008 Feb;22(2):105-9. doi: 10.1007/s10822-008-9173-z. Epub 2008 Jan 19.

PMID:
18204905
34.

Criteria for confirming sequence periodicity identified by Fourier transform analysis: application to GCR2, a candidate plant GPCR?

Illingworth CJ, Parkes KE, Snell CR, Mullineaux PM, Reynolds CA.

Biophys Chem. 2008 Mar;133(1-3):28-35. Epub 2007 Nov 22.

PMID:
18086512
35.

Computational studies of Family A and Family B GPCRs.

Vohra S, Chintapalli SV, Illingworth CJ, Reeves PJ, Mullineaux PM, Clark HS, Dean MK, Upton GJ, Reynolds CA.

Biochem Soc Trans. 2007 Aug;35(Pt 4):749-54. Review.

PMID:
17635140
36.

Classical polarization in hybrid QM/MM methods.

Illingworth CJ, Gooding SR, Winn PJ, Jones GA, Ferenczy GG, Reynolds CA.

J Phys Chem A. 2006 May 25;110(20):6487-97.

PMID:
16706406

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