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Items: 27

1.

An RNAi supplemented diet as a reverse genetics tool to control bluegreen aphid, a major pest of legumes.

Jacques S, Reidy-Crofts J, Sperschneider J, Kamphuis LG, Gao LL, Edwards OR, Singh KB.

Sci Rep. 2020 Jan 31;10(1):1604. doi: 10.1038/s41598-020-58442-4.

2.

Flax rust infection transcriptomics reveals a transcriptional profile that may be indicative for rust Avr genes.

Wu W, Nemri A, Blackman LM, Catanzariti AM, Sperschneider J, Lawrence GJ, Dodds PN, Jones DA, Hardham AR.

PLoS One. 2019 Dec 12;14(12):e0226106. doi: 10.1371/journal.pone.0226106. eCollection 2019.

3.

Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation.

Li F, Upadhyaya NM, Sperschneider J, Matny O, Nguyen-Phuc H, Mago R, Raley C, Miller ME, Silverstein KAT, Henningsen E, Hirsch CD, Visser B, Pretorius ZA, Steffenson BJ, Schwessinger B, Dodds PN, Figueroa M.

Nat Commun. 2019 Nov 7;10(1):5068. doi: 10.1038/s41467-019-12927-7.

4.

Machine learning in plant-pathogen interactions: empowering biological predictions from field scale to genome scale.

Sperschneider J.

New Phytol. 2019 Mar 4. doi: 10.1111/nph.15771. [Epub ahead of print] Review.

5.

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development.

DeBoer K, Melser S, Sperschneider J, Kamphuis LG, Garg G, Gao LL, Frick K, Singh KB.

BMC Genomics. 2019 Feb 14;20(1):135. doi: 10.1186/s12864-019-5521-8.

6.

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0.

Sperschneider J, Dodds PN, Gardiner DM, Singh KB, Taylor JM.

Mol Plant Pathol. 2018 Sep;19(9):2094-2110. doi: 10.1111/mpp.12682. Epub 2018 May 11.

7.

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity.

Schwessinger B, Sperschneider J, Cuddy WS, Garnica DP, Miller ME, Taylor JM, Dodds PN, Figueroa M, Park RF, Rathjen JP.

mBio. 2018 Feb 20;9(1). pii: e02275-17. doi: 10.1128/mBio.02275-17.

8.

De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust.

Miller ME, Zhang Y, Omidvar V, Sperschneider J, Schwessinger B, Raley C, Palmer JM, Garnica D, Upadhyaya N, Rathjen J, Taylor JM, Park RF, Dodds PN, Hirsch CD, Kianian SF, Figueroa M.

mBio. 2018 Feb 20;9(1). pii: e01650-17. doi: 10.1128/mBio.01650-17.

9.

Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat.

Chen J, Upadhyaya NM, Ortiz D, Sperschneider J, Li F, Bouton C, Breen S, Dong C, Xu B, Zhang X, Mago R, Newell K, Xia X, Bernoux M, Taylor JM, Steffenson B, Jin Y, Zhang P, Kanyuka K, Figueroa M, Ellis JG, Park RF, Dodds PN.

Science. 2017 Dec 22;358(6370):1607-1610. doi: 10.1126/science.aao4810.

PMID:
29269475
10.

ApoplastP: prediction of effectors and plant proteins in the apoplast using machine learning.

Sperschneider J, Dodds PN, Singh KB, Taylor JM.

New Phytol. 2018 Mar;217(4):1764-1778. doi: 10.1111/nph.14946. Epub 2017 Dec 15.

11.

Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors.

Anderson JP, Sperschneider J, Win J, Kidd B, Yoshida K, Hane J, Saunders DGO, Singh KB.

Sci Rep. 2017 Sep 5;7(1):10410. doi: 10.1038/s41598-017-10405-y.

12.

Computational Methods for Predicting Effectors in Rust Pathogens.

Sperschneider J, Dodds PN, Taylor JM, Duplessis S.

Methods Mol Biol. 2017;1659:73-83. doi: 10.1007/978-1-4939-7249-4_7.

PMID:
28856642
13.

LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell.

Sperschneider J, Catanzariti AM, DeBoer K, Petre B, Gardiner DM, Singh KB, Dodds PN, Taylor JM.

Sci Rep. 2017 Mar 16;7:44598. doi: 10.1038/srep44598.

14.

Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors.

Williams AH, Sharma M, Thatcher LF, Azam S, Hane JK, Sperschneider J, Kidd BN, Anderson JP, Ghosh R, Garg G, Lichtenzveig J, Kistler HC, Shea T, Young S, Buck SA, Kamphuis LG, Saxena R, Pande S, Ma LJ, Varshney RK, Singh KB.

BMC Genomics. 2016 Mar 5;17:191. doi: 10.1186/s12864-016-2486-8.

15.

Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici.

Figueroa M, Upadhyaya NM, Sperschneider J, Park RF, Szabo LJ, Steffenson B, Ellis JG, Dodds PN.

Front Plant Sci. 2016 Feb 24;7:205. doi: 10.3389/fpls.2016.00205. eCollection 2016. Review.

16.

Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors.

Sperschneider J, Williams AH, Hane JK, Singh KB, Taylor JM.

Front Plant Sci. 2015 Dec 23;6:1168. doi: 10.3389/fpls.2015.01168. eCollection 2015.

17.

EffectorP: predicting fungal effector proteins from secretomes using machine learning.

Sperschneider J, Gardiner DM, Dodds PN, Tini F, Covarelli L, Singh KB, Manners JM, Taylor JM.

New Phytol. 2016 Apr;210(2):743-61. doi: 10.1111/nph.13794. Epub 2015 Dec 17.

18.

Advances and challenges in computational prediction of effectors from plant pathogenic fungi.

Sperschneider J, Dodds PN, Gardiner DM, Manners JM, Singh KB, Taylor JM.

PLoS Pathog. 2015 May 28;11(5):e1004806. doi: 10.1371/journal.ppat.1004806. eCollection 2015 May. No abstract available.

19.

Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity.

Sperschneider J, Gardiner DM, Thatcher LF, Lyons R, Singh KB, Manners JM, Taylor JM.

Genome Biol Evol. 2015 May 19;7(6):1613-27. doi: 10.1093/gbe/evv092.

20.

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes.

Upadhyaya NM, Garnica DP, Karaoglu H, Sperschneider J, Nemri A, Xu B, Mago R, Cuomo CA, Rathjen JP, Park RF, Ellis JG, Dodds PN.

Front Plant Sci. 2015 Jan 8;5:759. doi: 10.3389/fpls.2014.00759. eCollection 2014.

21.

Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors.

Sperschneider J, Ying H, Dodds PN, Gardiner DM, Upadhyaya NM, Singh KB, Manners JM, Taylor JM.

Front Plant Sci. 2014 Sep 1;5:372. doi: 10.3389/fpls.2014.00372. eCollection 2014.

22.

Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8.

Hane JK, Anderson JP, Williams AH, Sperschneider J, Singh KB.

PLoS Genet. 2014 May 8;10(5):e1004281. doi: 10.1371/journal.pgen.1004281. eCollection 2014 May.

23.

A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi.

Sperschneider J, Gardiner DM, Taylor JM, Hane JK, Singh KB, Manners JM.

BMC Genomics. 2013 Nov 20;14:807. doi: 10.1186/1471-2164-14-807.

24.

Predicting pseudoknotted structures across two RNA sequences.

Sperschneider J, Datta A, Wise MJ.

Bioinformatics. 2012 Dec 1;28(23):3058-65. doi: 10.1093/bioinformatics/bts575. Epub 2012 Oct 8.

25.

Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins.

Sperschneider J, Datta A, Wise MJ.

RNA. 2011 Jan;17(1):27-38. doi: 10.1261/rna.2394511. Epub 2010 Nov 22.

26.

DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model.

Sperschneider J, Datta A.

Nucleic Acids Res. 2010 Apr;38(7):e103. doi: 10.1093/nar/gkq021. Epub 2010 Jan 31.

27.

KnotSeeker: heuristic pseudoknot detection in long RNA sequences.

Sperschneider J, Datta A.

RNA. 2008 Apr;14(4):630-40. doi: 10.1261/rna.968808. Epub 2008 Feb 26.

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