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Items: 23

1.

Corrigendum to "Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens" [J. Biotechnol. 380 (2020) 35-39].

Daly P, Peng M, Casado López S, Lipzen A, Ng V, Singan VR, Wang M, Grigoriev IV, de Vries RP, Mäkelä MR.

J Biotechnol. 2020 Jan 13. pii: S0168-1656(20)30007-9. doi: 10.1016/j.jbiotec.2020.01.006. [Epub ahead of print] No abstract available.

PMID:
31948745
2.

Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect.

Xie M, Zhang J, Singan VR, McGranahan MJ, LaFayette PR, Jawdy SS, Engle N, Doeppke C, Tschaplinski TJ, Davis MF, Lindquist E, Barry K, Schmutz J, Parrott WA, Chen F, Tuskan GA, Chen JG, Muchero W.

Plant Direct. 2020 Jan 3;4(1):e00178. doi: 10.1002/pld3.178. eCollection 2020 Jan.

3.

Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses.

Varoquaux N, Cole B, Gao C, Pierroz G, Baker CR, Patel D, Madera M, Jeffers T, Hollingsworth J, Sievert J, Yoshinaga Y, Owiti JA, Singan VR, DeGraaf S, Xu L, Blow MJ, Harrison MJ, Visel A, Jansson C, Niyogi KK, Hutmacher R, Coleman-Derr D, O'Malley RC, Taylor JW, Dahlberg J, Vogel JP, Lemaux PG, Purdom E.

Proc Natl Acad Sci U S A. 2019 Dec 5. pii: 201907500. doi: 10.1073/pnas.1907500116. [Epub ahead of print]

4.

Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens.

Daly P, Peng M, Casado López S, Lipzen A, Ng V, Singan VR, Wang M, Grigoriev IV, de Vries RP, Mäkelä MR.

J Biotechnol. 2020 Jan 20;308:35-39. doi: 10.1016/j.jbiotec.2019.11.014. Epub 2019 Nov 25. Erratum in: J Biotechnol. 2020 Jan 13;:.

PMID:
31778732
5.

Inorganic nitrogen availability alters Eucalyptus grandis receptivity to the ectomycorrhizal fungus Pisolithus albus but not symbiotic nitrogen transfer.

Plett KL, Singan VR, Wang M, Ng V, Grigoriev IV, Martin F, Plett JM, Anderson IC.

New Phytol. 2019 Nov 15. doi: 10.1111/nph.16322. [Epub ahead of print]

PMID:
31729063
6.

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood.

Daly P, López SC, Peng M, Lancefield CS, Purvine SO, Kim YM, Zink EM, Dohnalkova A, Singan VR, Lipzen A, Dilworth D, Wang M, Ng V, Robinson E, Orr G, Baker SE, Bruijnincx PCA, Hildén KS, Grigoriev IV, Mäkelä MR, de Vries RP.

Environ Microbiol. 2018 Nov;20(11):4141-4156. doi: 10.1111/1462-2920.14416. Epub 2018 Oct 18.

PMID:
30246402
7.

Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus.

Zhang J, Yang Y, Zheng K, Xie M, Feng K, Jawdy SS, Gunter LE, Ranjan P, Singan VR, Engle N, Lindquist E, Barry K, Schmutz J, Zhao N, Tschaplinski TJ, LeBoldus J, Tuskan GA, Chen JG, Muchero W.

New Phytol. 2018 Oct;220(2):502-516. doi: 10.1111/nph.15297. Epub 2018 Jul 11.

8.

A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus.

Xie M, Muchero W, Bryan AC, Yee K, Guo HB, Zhang J, Tschaplinski TJ, Singan VR, Lindquist E, Payyavula RS, Barros-Rios J, Dixon R, Engle N, Sykes RW, Davis M, Jawdy SS, Gunter LE, Thompson O, DiFazio SP, Evans LM, Winkeler K, Collins C, Schmutz J, Guo H, Kalluri U, Rodriguez M, Feng K, Chen JG, Tuskan GA.

Plant Cell. 2018 Jul;30(7):1645-1660. doi: 10.1105/tpc.18.00168. Epub 2018 Jun 11.

9.

Fungal Epigenomics: Detection and Analysis.

Mondo SJ, Kuo RC, Singan VR.

Methods Mol Biol. 2018;1775:155-170. doi: 10.1007/978-1-4939-7804-5_14.

PMID:
29876817
10.

Fungal Transcriptomics.

Singan VR, Kuo RC, Chen C.

Methods Mol Biol. 2018;1775:83-92. doi: 10.1007/978-1-4939-7804-5_8.

PMID:
29876811
11.

The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa.

Thieme N, Wu VW, Dietschmann A, Salamov AA, Wang M, Johnson J, Singan VR, Grigoriev IV, Glass NL, Somerville CR, Benz JP.

Biotechnol Biofuels. 2017 Jun 12;10:149. doi: 10.1186/s13068-017-0807-z. eCollection 2017.

12.

A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism.

Xiong Y, Wu VW, Lubbe A, Qin L, Deng S, Kennedy M, Bauer D, Singan VR, Barry K, Northen TR, Grigoriev IV, Glass NL.

PLoS Genet. 2017 May 3;13(5):e1006737. doi: 10.1371/journal.pgen.1006737. eCollection 2017 May.

13.

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments.

Daly P, van Munster JM, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Pullan ST, Delmas S, Waldron PR, Grigoriev IV, Tucker GA, Simmons BA, Archer DB.

Biotechnol Biofuels. 2017 Feb 7;10:35. doi: 10.1186/s13068-017-0700-9. eCollection 2017.

14.

Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas.

Fochi V, Chitarra W, Kohler A, Voyron S, Singan VR, Lindquist EA, Barry KW, Girlanda M, Grigoriev IV, Martin F, Balestrini R, Perotto S.

New Phytol. 2017 Jan;213(1):365-379. doi: 10.1111/nph.14279. Epub 2016 Nov 11.

15.

Implementation of the Rank-Weighted Co-localization (RWC) algorithm in multiple image analysis platforms for quantitative analysis of microscopy images.

Singan VR, Simpson JC.

Source Code Biol Med. 2016 Feb 16;11:2. doi: 10.1186/s13029-016-0048-8. eCollection 2016.

16.

Correction: Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses.

Schwessinger B, Bahar O, Thomas N, Holton N, Nekrasov V, Ruan D, Canlas PE, Daudi A, Petzold CJ, Singan VR, Kuo R, Chovatia M, Daum C, Heazlewood JL, Zipfel C, Ronald PC.

PLoS Pathog. 2015 Apr 23;11(4):e1004872. doi: 10.1371/journal.ppat.1004872. eCollection 2015 Apr.

17.

Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses.

Schwessinger B, Bahar O, Thomas N, Holton N, Nekrasov V, Ruan D, Canlas PE, Daudi A, Petzold CJ, Singan VR, Kuo R, Chovatia M, Daum C, Heazlewood JL, Zipfel C, Ronald PC.

PLoS Pathog. 2015 Mar 30;11(3):e1004809. doi: 10.1371/journal.ppat.1004809. eCollection 2015 Mar. Erratum in: PLoS Pathog. 2015 Apr;11(4):e1004872. Thomas, Nicolas [corrected to Thomas, Nicholas].

18.

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.

Stadler C, Rexhepaj E, Singan VR, Murphy RF, Pepperkok R, Uhlén M, Simpson JC, Lundberg E.

Nat Methods. 2013 Apr;10(4):315-23. doi: 10.1038/nmeth.2377. Epub 2013 Feb 24.

PMID:
23435261
19.

Quantitative image analysis approaches for probing Rab GTPase localization and function in mammalian cells.

Singan VR, Handzic K, Simpson JC.

Biochem Soc Trans. 2012 Dec 1;40(6):1389-93. doi: 10.1042/BST20120145. Review.

PMID:
23176486
20.

A method for improved clustering and classification of microscopy images using quantitative co-localization coefficients.

Singan VR, Handzic K, Curran KM, Simpson JC.

BMC Res Notes. 2012 Jun 8;5:281. doi: 10.1186/1756-0500-5-281.

21.

Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway.

Simpson JC, Joggerst B, Laketa V, Verissimo F, Cetin C, Erfle H, Bexiga MG, Singan VR, Hériché JK, Neumann B, Mateos A, Blake J, Bechtel S, Benes V, Wiemann S, Ellenberg J, Pepperkok R.

Nat Cell Biol. 2012 Jun 3;14(7):764-74. doi: 10.1038/ncb2510.

PMID:
22660414
22.

Dual channel rank-based intensity weighting for quantitative co-localization of microscopy images.

Singan VR, Jones TR, Curran KM, Simpson JC.

BMC Bioinformatics. 2011 Oct 21;12:407. doi: 10.1186/1471-2105-12-407.

23.

wFleaBase: the Daphnia genome database.

Colbourne JK, Singan VR, Gilbert DG.

BMC Bioinformatics. 2005 Mar 7;6:45.

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