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Items: 15

1.

Aequatus: an open-source homology browser.

Thanki AS, Soranzo N, Herrero J, Haerty W, Davey RP.

Gigascience. 2018 Nov 1;7(11). doi: 10.1093/gigascience/giy128.

2.

GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline.

Thanki AS, Soranzo N, Haerty W, Davey RP.

Gigascience. 2018 Mar 1;7(3):1-10. doi: 10.1093/gigascience/giy005.

3.

Developing data interoperability using standards: A wheat community use case.

Dzale Yeumo E, Alaux M, Arnaud E, Aubin S, Baumann U, Buche P, Cooper L, Ćwiek-Kupczyńska H, Davey RP, Fulss RA, Jonquet C, Laporte MA, Larmande P, Pommier C, Protonotarios V, Reverte C, Shrestha R, Subirats I, Venkatesan A, Whan A, Quesneville H.

Version 2. F1000Res. 2017 Oct 16 [revised 2017 Jan 1];6:1843. doi: 10.12688/f1000research.12234.2. eCollection 2017.

4.

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

Craig T, Holland R, D'Amore R, Johnson JR, McCue HV, West A, Zulkower V, Tekotte H, Cai Y, Swan D, Davey RP, Hertz-Fowler C, Hall A, Caddick M.

ACS Synth Biol. 2017 Dec 15;6(12):2273-2280. doi: 10.1021/acssynbio.7b00212. Epub 2017 Sep 13.

PMID:
28877583
5.

Data management and best practice for plant science.

Leonelli S, Davey RP, Arnaud E, Parry G, Bastow R.

Nat Plants. 2017 Jun 6;3:17086. doi: 10.1038/nplants.2017.86. No abstract available.

PMID:
28585570
6.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD.

Genome Res. 2017 May;27(5):885-896. doi: 10.1101/gr.217117.116.

7.

Prevalence and Dynamics of Ribosomal DNA Micro-heterogeneity Are Linked to Population History in Two Contrasting Yeast Species.

James SA, West C, Davey RP, Dicks J, Roberts IN.

Sci Rep. 2016 Jun 27;6:28555. doi: 10.1038/srep28555.

8.

CerealsDB 3.0: expansion of resources and data integration.

Wilkinson PA, Winfield MO, Barker GL, Tyrrell S, Bian X, Allen AM, Burridge A, Coghill JA, Waterfall C, Caccamo M, Davey RP, Edwards KJ.

BMC Bioinformatics. 2016 Jun 24;17:256. doi: 10.1186/s12859-016-1139-x.

9.

NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.

Leggett RM, Heavens D, Caccamo M, Clark MD, Davey RP.

Bioinformatics. 2016 Jan 1;32(1):142-4. doi: 10.1093/bioinformatics/btv540. Epub 2015 Sep 17.

10.

Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species.

West C, James SA, Davey RP, Dicks J, Roberts IN.

Syst Biol. 2014 Jul;63(4):543-54. doi: 10.1093/sysbio/syu019. Epub 2014 Mar 27.

11.

wigExplorer, a BioJS component to visualise wig data.

Thanki AS, Jimenez RC, Kaithakottil GG, Corpas M, Davey RP.

Version 3. F1000Res. 2014 Feb 13 [revised 2016 Jan 1];3:53. eCollection 2014.

12.

Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics.

Leggett RM, Ramirez-Gonzalez RH, Clavijo BJ, Waite D, Davey RP.

Front Genet. 2013 Dec 17;4:288. doi: 10.3389/fgene.2013.00288. Review.

13.

TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence.

Davey RP, James SA, Dicks J, Roberts IN.

Bioinformatics. 2010 Nov 15;26(22):2908-9. doi: 10.1093/bioinformatics/btq557. Epub 2010 Oct 5.

PMID:
20926422
14.

Population genomics of domestic and wild yeasts.

Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ.

Nature. 2009 Mar 19;458(7236):337-41. doi: 10.1038/nature07743. Epub 2009 Feb 11.

15.

Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing.

James SA, O'Kelly MJ, Carter DM, Davey RP, van Oudenaarden A, Roberts IN.

Genome Res. 2009 Apr;19(4):626-35. doi: 10.1101/gr.084517.108. Epub 2009 Jan 13.

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