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Items: 19

1.

Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering.

Raitskin O, Schudoma C, West A, Patron NJ.

PLoS One. 2019 Feb 27;14(2):e0211598. doi: 10.1371/journal.pone.0211598. eCollection 2019.

2.

Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family.

Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen S, Feng L, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T.

Nat Commun. 2018 Oct 3;9(1):3735. doi: 10.1038/s41467-018-06138-9.

3.

Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions.

Bailey PC, Schudoma C, Jackson W, Baggs E, Dagdas G, Haerty W, Moscou M, Krasileva KV.

Genome Biol. 2018 Feb 19;19(1):23. doi: 10.1186/s13059-018-1392-6.

4.

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.

5.

Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains.

Bücherl CA, Jarsch IK, Schudoma C, Segonzac C, Mbengue M, Robatzek S, MacLean D, Ott T, Zipfel C.

Elife. 2017 Mar 6;6. pii: e25114. doi: 10.7554/eLife.25114.

6.

Corrigendum: Endogenous Arabidopsis messenger RNAs transported to distant tissues.

Thieme CJ, Rojas-Triana M, Stecyk E, Schudoma C, Zhang W, Yang L, Miñambres M, Walther D, Schulze WX, Paz-Ares J, Scheible WR, Kragler F.

Nat Plants. 2016 Nov 21;2:16195. doi: 10.1038/nplants.2016.195. No abstract available.

PMID:
27869791
7.

blastjs: a BLAST+ wrapper for Node.js.

Page M, MacLean D, Schudoma C.

BMC Res Notes. 2016 Feb 27;9:130. doi: 10.1186/s13104-016-1938-1.

8.

A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads.

Ikeue D, Schudoma C, Zhang W, Ogata Y, Sakamoto T, Kurata T, Furuhashi T, Kragler F, Aoki K.

Plant Methods. 2015 May 3;11:34. doi: 10.1186/s13007-015-0066-6. eCollection 2015.

9.

Endogenous Arabidopsis messenger RNAs transported to distant tissues.

Thieme CJ, Rojas-Triana M, Stecyk E, Schudoma C, Zhang W, Yang L, Miñambres M, Walther D, Schulze WX, Paz-Ares J, Scheible WR, Kragler F.

Nat Plants. 2015 Mar 23;1(4):15025. doi: 10.1038/nplants.2015.25. Erratum in: Nat Plants. 2016 Nov 21;2:16195.

PMID:
27247031
10.

Give It AGO: The Search for miRNA-Argonaute Sorting Signals in Arabidopsis thaliana Indicates a Relevance of Sequence Positions Other than the 5'-Position Alone.

Thieme CJ, Schudoma C, May P, Walther D.

Front Plant Sci. 2012 Dec 7;3:272. doi: 10.3389/fpls.2012.00272. eCollection 2012.

11.

Conducting molecular biomarker discovery studies in plants.

Schudoma C, Steinfath M, Sprenger H, van Dongen JT, Hincha D, Zuther E, Geigenberger P, Kopka J, Köhl K, Walther D.

Methods Mol Biol. 2012;918:127-50. doi: 10.1007/978-1-61779-995-2_10. Review.

PMID:
22893290
12.

Cracking the elusive alignment hypothesis: the microtubule-cellulose synthase nexus unraveled.

Bringmann M, Landrein B, Schudoma C, Hamant O, Hauser MT, Persson S.

Trends Plant Sci. 2012 Nov;17(11):666-74. doi: 10.1016/j.tplants.2012.06.003. Epub 2012 Jul 9. Review.

13.

Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.

Janssen S, Schudoma C, Steger G, Giegerich R.

BMC Bioinformatics. 2011 Nov 3;12:429. doi: 10.1186/1471-2105-12-429.

14.

The influence of the local sequence environment on RNA loop structures.

Schudoma C, Larhlimi A, Walther D.

RNA. 2011 Jul;17(7):1247-57. doi: 10.1261/rna.2550211. Epub 2011 May 31.

15.

It's a loop world - single strands in RNA as structural and functional elements.

Schudoma C.

Biomol Concepts. 2011 Jun 1;2(3):171-81. doi: 10.1515/bmc.2011.016.

PMID:
25962027
16.

Use of TILLING and robotised enzyme assays to generate an allelic series of Arabidopsis thaliana mutants with altered ADP-glucose pyrophosphorylase activity.

Hädrich N, Gibon Y, Schudoma C, Altmann T, Lunn JE, Stitt M.

J Plant Physiol. 2011 Aug 15;168(12):1395-405. doi: 10.1016/j.jplph.2011.01.013. Epub 2011 Feb 22.

PMID:
21345514
17.

Modeling RNA loops using sequence homology and geometric constraints.

Schudoma C, May P, Walther D.

Bioinformatics. 2010 Jul 1;26(13):1671-2. doi: 10.1093/bioinformatics/btq236. Epub 2010 Apr 28.

18.

Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

Schudoma C, May P, Nikiforova V, Walther D.

Nucleic Acids Res. 2010 Jan;38(3):970-80. doi: 10.1093/nar/gkp1010. Epub 2009 Nov 18.

19.

Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins.

Durek P, Schudoma C, Weckwerth W, Selbig J, Walther D.

BMC Bioinformatics. 2009 Apr 21;10:117. doi: 10.1186/1471-2105-10-117.

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