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Items: 45

1.

The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018).

Harris NL, Wiencko H, Chapman B, Cock PJA, Hokamp K, Lapp H, Fields C, Greshake Tzovaras B.

F1000Res. 2018 Aug 17;7. pii: ISCB Comm J-1309. doi: 10.12688/f1000research.15936.1. eCollection 2018.

2.

Shared Transcriptional Control and Disparate Gain and Loss of Aphid Parasitism Genes.

Thorpe P, Escudero-Martinez CM, Cock PJA, Eves-van den Akker S, Bos JIB.

Genome Biol Evol. 2018 Oct 1;10(10):2716-2733. doi: 10.1093/gbe/evy183.

3.

The 2017 Bioinformatics Open Source Conference (BOSC).

Harris NL, Cock PJA, Chapman B, Fields CJ, Hokamp K, Lapp H, Munoz-Torres M, Tzovaras BG, Wiencko H.

F1000Res. 2017 Oct 19;6. pii: ISCB Comm J-1858. doi: 10.12688/f1000research.12929.1. eCollection 2017.

4.

The 2016 Bioinformatics Open Source Conference (BOSC).

Harris NL, Cock PJ, Chapman B, Fields CJ, Hokamp K, Lapp H, Muñoz-Torres M, Wiencko H.

F1000Res. 2016 Oct 6;5. pii: ISCB Comm J-2464. eCollection 2016.

5.

Evidence for an Opportunistic and Endophytic Lifestyle of the Bursaphelenchus xylophilus-Associated Bacteria Serratia marcescens PWN146 Isolated from Wilting Pinus pinaster.

Vicente CS, Nascimento FX, Barbosa P, Ke HM, Tsai IJ, Hirao T, Cock PJ, Kikuchi T, Hasegawa K, Mota M.

Microb Ecol. 2016 Oct;72(3):669-81. doi: 10.1007/s00248-016-0820-y. Epub 2016 Jul 26.

PMID:
27461253
6.

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

Bolleman JT, Mungall CJ, Strozzi F, Baran J, Dumontier M, Bonnal RJ, Buels R, Hoehndorf R, Fujisawa T, Katayama T, Cock PJ.

J Biomed Semantics. 2016 Jun 13;7:39. doi: 10.1186/s13326-016-0067-z.

7.

The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.

Eves-van den Akker S, Laetsch DR, Thorpe P, Lilley CJ, Danchin EG, Da Rocha M, Rancurel C, Holroyd NE, Cotton JA, Szitenberg A, Grenier E, Montarry J, Mimee B, Duceppe MO, Boyes I, Marvin JM, Jones LM, Yusup HB, Lafond-Lapalme J, Esquibet M, Sabeh M, Rott M, Overmars H, Finkers-Tomczak A, Smant G, Koutsovoulos G, Blok V, Mantelin S, Cock PJ, Phillips W, Henrissat B, Urwin PE, Blaxter M, Jones JT.

Genome Biol. 2016 Jun 10;17(1):124. doi: 10.1186/s13059-016-0985-1.

8.

The genome and genetics of a high oxidative stress tolerant Serratia sp. LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus.

Vicente CS, Nascimento FX, Ikuyo Y, Cock PJ, Mota M, Hasegawa K.

BMC Genomics. 2016 Apr 23;17:301. doi: 10.1186/s12864-016-2626-1.

9.

Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets.

Thorpe P, Cock PJ, Bos J.

BMC Genomics. 2016 Mar 2;17:172. doi: 10.1186/s12864-016-2496-6.

10.

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

Harris NL, Cock PJ, Lapp H, Chapman B, Davey R, Fields C, Hokamp K, Munoz-Torres M.

PLoS Comput Biol. 2016 Feb 25;12(2):e1004691. doi: 10.1371/journal.pcbi.1004691. eCollection 2016 Feb.

11.

Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate.

Palomares-Rius JE, Hedley P, Cock PJ, Morris JA, Jones JT, Blok VC.

PeerJ. 2016 Feb 4;4:e1654. doi: 10.7717/peerj.1654. eCollection 2016.

12.

A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual.

Eves-van den Akker S, Lilley CJ, Reid A, Pickup J, Anderson E, Cock PJ, Blaxter M, Urwin PE, Jones JT, Blok VC.

Mol Ecol. 2015 Dec;24(23):5842-51. doi: 10.1111/mec.13434.

13.

Newly identified RNAs of raspberry leaf blotch virus encoding a related group of proteins.

Lu Y, McGavin W, Cock PJ, Schnettler E, Yan F, Chen J, MacFarlane S.

J Gen Virol. 2015 Nov;96(11):3432-9. doi: 10.1099/jgv.0.000277. Epub 2015 Sep 9.

PMID:
26358478
14.

NCBI BLAST+ integrated into Galaxy.

Cock PJ, Chilton JM, Grüning B, Johnson JE, Soranzo N.

Gigascience. 2015 Aug 25;4:39. doi: 10.1186/s13742-015-0080-7. eCollection 2015.

15.

Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy.

Espada M, Silva AC, Eves van den Akker S, Cock PJ, Mota M, Jones JT.

Mol Plant Pathol. 2016 Feb;17(2):286-95. doi: 10.1111/mpp.12280. Epub 2015 Jun 16.

PMID:
25981957
16.

Distinct circular single-stranded DNA viruses exist in different soil types.

Reavy B, Swanson MM, Cock PJ, Dawson L, Freitag TE, Singh BK, Torrance L, Mushegian AR, Taliansky M.

Appl Environ Microbiol. 2015 Jun 15;81(12):3934-45. doi: 10.1128/AEM.03878-14. Epub 2015 Apr 3.

17.

Community-driven development for computational biology at Sprints, Hackathons and Codefests.

Möller S, Afgan E, Banck M, Bonnal RJ, Booth T, Chilton J, Cock PJ, Gumbel M, Harris N, Holland R, Kalaš M, Kaján L, Kibukawa E, Powel DR, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis AJ, Guimera R, Katayama T, Chapman BA.

BMC Bioinformatics. 2014;15 Suppl 14:S7. doi: 10.1186/1471-2105-15-S14-S7. Epub 2014 Nov 27.

18.

Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida.

Thorpe P, Mantelin S, Cock PJ, Blok VC, Coke MC, Eves-van den Akker S, Guzeeva E, Lilley CJ, Smant G, Reid AJ, Wright KM, Urwin PE, Jones JT.

BMC Genomics. 2014 Oct 23;15:923. doi: 10.1186/1471-2164-15-923.

19.

The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes.

Eves-van den Akker S, Lilley CJ, Danchin EG, Rancurel C, Cock PJ, Urwin PE, Jones JT.

Genome Biol Evol. 2014 Aug 13;6(9):2181-94. doi: 10.1093/gbe/evu171.

20.

The Bioinformatics Open Source Conference (BOSC) 2013.

Harris NL, Cock PJ, Chapman BA, Goecks J, Hotz HR, Lapp H.

Bioinformatics. 2015 Jan 15;31(2):299-300. doi: 10.1093/bioinformatics/btu413. Epub 2014 Jul 14. No abstract available.

21.

Galaxy as a platform for identifying candidate pathogen effectors.

Cock PJ, Pritchard L.

Methods Mol Biol. 2014;1127:3-15. doi: 10.1007/978-1-62703-986-4_1.

PMID:
24643548
22.

The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode.

Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJ, Eves-van den Akker S, Holroyd N, Hunt M, Mantelin S, Naghra H, Pain A, Palomares-Rius JE, Zarowiecki M, Berriman M, Jones JT, Urwin PE.

Genome Biol. 2014 Mar 3;15(3):R43. doi: 10.1186/gb-2014-15-3-r43.

23.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T.

J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5.

24.

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology.

Cock PJ, Grüning BA, Paszkiewicz K, Pritchard L.

PeerJ. 2013 Sep 17;1:e167. doi: 10.7717/peerj.167. eCollection 2013.

25.

Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations.

Jupe F, Witek K, Verweij W, Sliwka J, Pritchard L, Etherington GJ, Maclean D, Cock PJ, Leggett RM, Bryan GJ, Cardle L, Hein I, Jones JD.

Plant J. 2013 Nov;76(3):530-44. doi: 10.1111/tpj.12307. Epub 2013 Oct 8.

26.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T.

J Biomed Semantics. 2013 Feb 11;4(1):6. doi: 10.1186/2041-1480-4-6.

27.

Activation of hatching in diapaused and quiescent Globodera pallida.

Palomares-Rius JE, Jones JT, Cock PJ, Castillo P, Blok VC.

Parasitology. 2013 Apr;140(4):445-54. doi: 10.1017/S0031182012001874. Epub 2012 Dec 20.

PMID:
23253858
28.

Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython.

Talevich E, Invergo BM, Cock PJ, Chapman BA.

BMC Bioinformatics. 2012 Aug 21;13:209. doi: 10.1186/1471-2105-13-209.

29.

Comparison of transcript profiles in different life stages of the nematode Globodera pallida under different host potato genotypes.

Palomares-Rius JE, Hedley PE, Cock PJ, Morris JA, Jones JT, Vovlas N, Blok V.

Mol Plant Pathol. 2012 Dec;13(9):1120-34. doi: 10.1111/j.1364-3703.2012.00821.x. Epub 2012 Aug 1.

PMID:
22863280
30.

Novel bacteriophages containing a genome of another bacteriophage within their genomes.

Swanson MM, Reavy B, Makarova KS, Cock PJ, Hopkins DW, Torrance L, Koonin EV, Taliansky M.

PLoS One. 2012;7(7):e40683. doi: 10.1371/journal.pone.0040683. Epub 2012 Jul 17.

31.

Using Tablet for visual exploration of second-generation sequencing data.

Milne I, Stephen G, Bayer M, Cock PJ, Pritchard L, Cardle L, Shaw PD, Marshall D.

Brief Bioinform. 2013 Mar;14(2):193-202. doi: 10.1093/bib/bbs012. Epub 2012 Mar 24.

PMID:
22445902
32.

Identification and localisation of the NB-LRR gene family within the potato genome.

Jupe F, Pritchard L, Etherington GJ, Mackenzie K, Cock PJ, Wright F, Sharma SK, Bolser D, Bryan GJ, Jones JD, Hein I.

BMC Genomics. 2012 Feb 15;13:75. doi: 10.1186/1471-2164-13-75.

33.

Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA.

McGavin WJ, Mitchell C, Cock PJ, Wright KM, MacFarlane SA.

J Gen Virol. 2012 Feb;93(Pt 2):430-7. doi: 10.1099/vir.0.037937-0. Epub 2011 Nov 2.

PMID:
22049090
34.

Genome-wide identification of genes regulated by the Rcs phosphorelay system in Erwinia amylovora.

Wang D, Qi M, Calla B, Korban SS, Clough SJ, Cock PJ, Sundin GW, Toth I, Zhao Y.

Mol Plant Microbe Interact. 2012 Jan;25(1):6-17. doi: 10.1094/MPMI-08-11-0207.

35.

Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.

Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, McVeigh P, Takanashi T, Tsai IJ, Assefa SA, Cock PJ, Otto TD, Hunt M, Reid AJ, Sanchez-Flores A, Tsuchihara K, Yokoi T, Larsson MC, Miwa J, Maule AG, Sahashi N, Jones JT, Berriman M.

PLoS Pathog. 2011 Sep;7(9):e1002219. doi: 10.1371/journal.ppat.1002219. Epub 2011 Sep 1.

36.

Genetic characterization of the HrpL regulon of the fire blight pathogen Erwinia amylovora reveals novel virulence factors.

McNally RR, Toth IK, Cock PJ, Pritchard L, Hedley PE, Morris JA, Zhao Y, Sundin GW.

Mol Plant Pathol. 2012 Feb;13(2):160-73. doi: 10.1111/j.1364-3703.2011.00738.x. Epub 2011 Aug 10.

PMID:
21831138
37.

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.

Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM.

Nucleic Acids Res. 2010 Apr;38(6):1767-71. doi: 10.1093/nar/gkp1137. Epub 2009 Dec 16. Review.

38.

Evolution of relative reading frame bias in unidirectional prokaryotic gene overlaps.

Cock PJ, Whitworth DE.

Mol Biol Evol. 2010 Apr;27(4):753-6. doi: 10.1093/molbev/msp302. Epub 2009 Dec 14. Erratum in: Mol Biol Evol. 2010 Nov;27(11):2665.

PMID:
20008458
39.

Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida.

Jones JT, Kumar A, Pylypenko LA, Thirugnanasambandam A, Castelli L, Chapman S, Cock PJ, Grenier E, Lilley CJ, Phillips MS, Blok VC.

Mol Plant Pathol. 2009 Nov;10(6):815-28. doi: 10.1111/j.1364-3703.2009.00585.x.

PMID:
19849787
40.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.

Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20.

41.

Evolution of prokaryotic two-component systems: insights from comparative genomics.

Whitworth DE, Cock PJ.

Amino Acids. 2009 Sep;37(3):459-66. doi: 10.1007/s00726-009-0259-2. Epub 2009 Feb 25. Review.

PMID:
19241119
42.

Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships.

Whitworth DE, Cock PJ.

Microbiology. 2008 Feb;154(Pt 2):360-72. doi: 10.1099/mic.0.2007/013672-0.

PMID:
18227240
43.

Evolution of prokaryotic two-component system signaling pathways: gene fusions and fissions.

Cock PJ, Whitworth DE.

Mol Biol Evol. 2007 Nov;24(11):2355-7. Epub 2007 Aug 19.

PMID:
17709334
44.

Evolution of gene overlaps: relative reading frame bias in prokaryotic two-component system genes.

Cock PJ, Whitworth DE.

J Mol Evol. 2007 Apr;64(4):457-62. Epub 2007 Mar 19.

PMID:
17479344
45.

Proceedings: Report of the Committee on the Genetic Constitution of Chromosome 1.

Hamerton JL, Cock PJ.

Cytogenet Cell Genet. 1974;13(1):13-20. No abstract available.

PMID:
4827481

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