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Items: 27

1.

The White-Rot Basidiomycete Dichomitus squalens Shows Highly Specific Transcriptional Response to Lignocellulose-Related Aromatic Compounds.

Kowalczyk JE, Peng M, Pawlowski M, Lipzen A, Ng V, Singan V, Wang M, Grigoriev IV, Mäkelä MR.

Front Bioeng Biotechnol. 2019 Sep 20;7:229. doi: 10.3389/fbioe.2019.00229. eCollection 2019.

2.

Overexpression of a Prefoldin β subunit gene reduces biomass recalcitrance in the bioenergy crop Populus.

Zhang J, Xie M, Li M, Ding J, Pu Y, Bryan AC, Rottmann W, Winkeler KA, Collins CM, Singan V, Lindquist EA, Jawdy SS, Gunter LE, Engle NL, Yang X, Barry K, Tschaplinski TJ, Schmutz J, Tuskan GA, Muchero W, Chen JG.

Plant Biotechnol J. 2019 Sep 9. doi: 10.1111/pbi.13254. [Epub ahead of print]

3.

Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a tree.

Muchero W, Sondreli KL, Chen JG, Urbanowicz BR, Zhang J, Singan V, Yang Y, Brueggeman RS, Franco-Coronado J, Abraham N, Yang JY, Moremen KW, Weisberg AJ, Chang JH, Lindquist E, Barry K, Ranjan P, Jawdy S, Schmutz J, Tuskan GA, LeBoldus JM.

Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):11573-11578. doi: 10.1073/pnas.1804428115. Epub 2018 Oct 18.

4.

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
5.

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.

6.

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.

7.

A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein.

Bryan AC, Zhang J, Guo J, Ranjan P, Singan V, Barry K, Schmutz J, Weighill D, Jacobson D, Jawdy S, Tuskan GA, Chen JG, Muchero W.

G3 (Bethesda). 2018 Jul 31;8(8):2631-2641. doi: 10.1534/g3.118.200188.

8.

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
9.

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
10.

Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum.

de Freitas Pereira M, Veneault-Fourrey C, Vion P, Guinet F, Morin E, Barry KW, Lipzen A, Singan V, Pfister S, Na H, Kennedy M, Egli S, Grigoriev I, Martin F, Kohler A, Peter M.

Front Microbiol. 2018 Feb 13;9:141. doi: 10.3389/fmicb.2018.00141. eCollection 2018.

11.

Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales.

Castanera R, Pérez G, López-Varas L, Amselem J, LaButti K, Singan V, Lipzen A, Haridas S, Barry K, Grigoriev IV, Pisabarro AG, Ramírez L.

BMC Genomics. 2017 Nov 16;18(1):883. doi: 10.1186/s12864-017-4243-z.

12.

Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant-cyanobacteria symbiosis.

Warshan D, Espinoza JL, Stuart RK, Richter RA, Kim SY, Shapiro N, Woyke T, C Kyrpides N, Barry K, Singan V, Lindquist E, Ansong C, Purvine SO, M Brewer H, Weyman PD, Dupont CL, Rasmussen U.

ISME J. 2017 Dec;11(12):2821-2833. doi: 10.1038/ismej.2017.134. Epub 2017 Aug 11.

13.

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.

14.

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.

15.

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.

16.

The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation.

Doré J, Kohler A, Dubost A, Hundley H, Singan V, Peng Y, Kuo A, Grigoriev IV, Martin F, Marmeisse R, Gay G.

Environ Microbiol. 2017 Mar;19(3):1338-1354. doi: 10.1111/1462-2920.13670. Epub 2017 Feb 6.

PMID:
28076886
17.

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.

18.

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.

19.

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.

20.

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].

21.

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
22.

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
23.

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.

24.

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
25.

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.

26.

Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica.

Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS.

Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10376-81. Epub 2007 Jun 11.

27.

wFleaBase: the Daphnia genome database.

Colbourne JK, Singan VR, Gilbert DG.

BMC Bioinformatics. 2005 Mar 7;6:45.

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