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Items: 40

1.

Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea.

Muraguchi H, Umezawa K, Niikura M, Yoshida M, Kozaki T, Ishii K, Sakai K, Shimizu M, Nakahori K, Sakamoto Y, Choi C, Ngan CY, Lindquist E, Lipzen A, Tritt A, Haridas S, Barry K, Grigoriev IV, Pukkila PJ.

PLoS One. 2015 Oct 28;10(10):e0141586. doi: 10.1371/journal.pone.0141586. eCollection 2015.

2.

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea.

Chavez L, Huang Y, Luong K, Agarwal S, Iyer LM, Pastor WA, Hench VK, Frazier-Bowers SA, Korol E, Liu S, Tahiliani M, Wang Y, Clark TA, Korlach J, Pukkila PJ, Aravind L, Rao A.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):E5149-58. doi: 10.1073/pnas.1419513111. Epub 2014 Nov 18.

3.

Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes.

Iyer LM, Zhang D, de Souza RF, Pukkila PJ, Rao A, Aravind L.

Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1676-83. doi: 10.1073/pnas.1321818111. Epub 2014 Jan 7.

4.

5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea.

Cheng CK, Au CH, Wilke SK, Stajich JE, Zolan ME, Pukkila PJ, Kwan HS.

BMC Genomics. 2013 Mar 20;14:195. doi: 10.1186/1471-2164-14-195.

5.

Novel proteins required for meiotic silencing by unpaired DNA and siRNA generation in Neurospora crassa.

Hammond TM, Xiao H, Boone EC, Decker LM, Lee SA, Perdue TD, Pukkila PJ, Shiu PK.

Genetics. 2013 May;194(1):91-100. doi: 10.1534/genetics.112.148999. Epub 2013 Mar 15.

6.

SAD-3, a Putative Helicase Required for Meiotic Silencing by Unpaired DNA, Interacts with Other Components of the Silencing Machinery.

Hammond TM, Xiao H, Boone EC, Perdue TD, Pukkila PJ, Shiu PK.

G3 (Bethesda). 2011 Oct;1(5):369-76. doi: 10.1534/g3.111.000570. Epub 2011 Oct 1.

7.

Coprinopsis cinerea.

Pukkila PJ.

Curr Biol. 2011 Aug 23;21(16):R616-7. doi: 10.1016/j.cub.2011.05.042. No abstract available.

8.

Fluorescent and bimolecular-fluorescent protein tagging of genes at their native loci in Neurospora crassa using specialized double-joint PCR plasmids.

Hammond TM, Xiao H, Rehard DG, Boone EC, Perdue TD, Pukkila PJ, Shiu PK.

Fungal Genet Biol. 2011 Sep;48(9):866-73. doi: 10.1016/j.fgb.2011.05.002. Epub 2011 May 31.

PMID:
21664475
9.

Analysis of the Basidiomycete Coprinopsis cinerea reveals conservation of the core meiotic expression program over half a billion years of evolution.

Burns C, Stajich JE, Rechtsteiner A, Casselton L, Hanlon SE, Wilke SK, Savytskyy OP, Gathman AC, Lilly WW, Lieb JD, Zolan ME, Pukkila PJ.

PLoS Genet. 2010 Sep 23;6(9):e1001135. doi: 10.1371/journal.pgen.1001135.

10.

QIP, a protein that converts duplex siRNA into single strands, is required for meiotic silencing by unpaired DNA.

Xiao H, Alexander WG, Hammond TM, Boone EC, Perdue TD, Pukkila PJ, Shiu PK.

Genetics. 2010 Sep;186(1):119-26. doi: 10.1534/genetics.110.118273. Epub 2010 Jun 15.

11.

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).

Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, Canbäck B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigó R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kües U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ.

Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11889-94. doi: 10.1073/pnas.1003391107. Epub 2010 Jun 14.

12.

Meiotic cytogenetics in Coprinus cinereus.

Zolan ME, Pukkila PJ.

Methods Mol Biol. 2009;558:115-27. doi: 10.1007/978-1-60761-103-5_8. Review.

PMID:
19685322
13.

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis.

Martin F, Aerts A, Ahrén D, Brun A, Danchin EG, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V, Salamov A, Shapiro HJ, Wuyts J, Blaudez D, Buée M, Brokstein P, Canbäck B, Cohen D, Courty PE, Coutinho PM, Delaruelle C, Detter JC, Deveau A, DiFazio S, Duplessis S, Fraissinet-Tachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Grimwood J, Hoegger PJ, Jain P, Kilaru S, Labbé J, Lin YC, Legué V, Le Tacon F, Marmeisse R, Melayah D, Montanini B, Muratet M, Nehls U, Niculita-Hirzel H, Oudot-Le Secq MP, Peter M, Quesneville H, Rajashekar B, Reich M, Rouhier N, Schmutz J, Yin T, Chalot M, Henrissat B, Kües U, Lucas S, Van de Peer Y, Podila GK, Polle A, Pukkila PJ, Richardson PM, Rouzé P, Sanders IR, Stajich JE, Tunlid A, Tuskan G, Grigoriev IV.

Nature. 2008 Mar 6;452(7183):88-92. doi: 10.1038/nature06556.

PMID:
18322534
14.

An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinerea.

Lilly WW, Stajich JE, Pukkila PJ, Wilke SK, Inoguchi N, Gathman AC.

Mycol Res. 2008 Mar;112(Pt 3):389-98. doi: 10.1016/j.mycres.2007.11.013. Epub 2007 Dec 14.

PMID:
18313909
15.

Characterization of interactions between and among components of the meiotic silencing by unpaired DNA machinery in Neurospora crassa using bimolecular fluorescence complementation.

Bardiya N, Alexander WG, Perdue TD, Barry EG, Metzenberg RL, Pukkila PJ, Shiu PK.

Genetics. 2008 Jan;178(1):593-6. doi: 10.1534/genetics.107.079384.

16.

DCL-1 colocalizes with other components of the MSUD machinery and is required for silencing.

Alexander WG, Raju NB, Xiao H, Hammond TM, Perdue TD, Metzenberg RL, Pukkila PJ, Shiu PK.

Fungal Genet Biol. 2008 May;45(5):719-27. Epub 2007 Oct 22.

PMID:
18036854
17.
18.

A temperature-sensitive mutation of Coprinus cinereus, hyt1-1, that causes swelling of hyphal tips.

Maida S, Fujii M, Skrzynia C, Pukkila PJ, Kamada T.

Curr Genet. 1997 Sep;32(3):231-6.

PMID:
9339349
19.

A physical assay for meiotic recombination in Coprinus cinereus.

Freedman T, Pukkila PJ.

Mol Gen Genet. 1997 Apr 28;254(4):372-8.

PMID:
9180690
20.

Meiotic sister chromatid recombination.

Petes TD, Pukkila PJ.

Adv Genet. 1995;33:41-62. Review. No abstract available.

PMID:
7484457
21.

De novo methylation of repeated sequences in Coprinus cinereus.

Freedman T, Pukkila PJ.

Genetics. 1993 Oct;135(2):357-66.

23.
24.

Targeted transformation in Coprinus cinereus.

Binninger DM, Le Chevanton L, Skrzynia C, Shubkin CD, Pukkila PJ.

Mol Gen Genet. 1991 Jun;227(2):245-51.

PMID:
2062305
25.

VARIATION IN RIBOSOMAL DNA AMONG BIOLOGICAL SPECIES OF ARMILLARIA, A GENUS OF ROOT-INFECTING FUNGI.

Anderson JB, Bailey SS, Pukkila PJ.

Evolution. 1989 Dec;43(8):1652-1662. doi: 10.1111/j.1558-5646.1989.tb02615.x.

PMID:
28564337
26.

Molecular characterization of TRP1, a gene coding for tryptophan synthetase in the basidiomycete Coprinus cinereus.

Skrzynia C, Binninger DM, Alspaugh JA 2nd, Pukkila PJ.

Gene. 1989 Sep 1;81(1):73-82.

PMID:
2806911
27.
28.

DNA-mediated transformation of the basidiomycete Coprinus cinereus.

Binninger DM, Skrzynia C, Pukkila PJ, Casselton LA.

EMBO J. 1987 Apr;6(4):835-40.

29.

Inversion of 5S ribosomal RNA genes within the genus Coprinus.

Cassidy JR, Pukkila PJ.

Curr Genet. 1987;12(1):33-6.

PMID:
2835172
30.
31.

Inheritance of DNA methylation in Coprinus cinereus.

Zolan ME, Pukkila PJ.

Mol Cell Biol. 1986 Jan;6(1):195-200.

32.

Silver staining of meiotic chromosomes in the fungus, Coprinus cinereus.

Pukkila PJ, Lu BC.

Chromosoma. 1985;91(2):108-12.

PMID:
2580673
33.

Unusual organization and lack of recombination in the ribosomal RNA genes of Coprinus cinereus.

Rhodes Cassidy J, Moore D, Lu BC, Pukkila PJ.

Curr Genet. 1984 Oct;8(8):607-13. doi: 10.1007/BF00395706.

PMID:
24178000
34.

Analysis of meiotic development in Coprinus cinereus.

Pukkila PJ, Yashar BM, Binninger DM.

Symp Soc Exp Biol. 1984;38:177-94.

PMID:
6549591
35.

Polymorphisms in DNA of Coprinus cinereus.

Wu MM, Cassidy JR, Pukkila PJ.

Curr Genet. 1983 Sep;7(5):385-92. doi: 10.1007/BF00445879.

PMID:
24173420
36.

Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli.

Pukkila PJ, Peterson J, Herman G, Modrich P, Meselson M.

Genetics. 1983 Aug;104(4):571-82.

37.

Relationships between the correction of mismatched bases in DNA and mutability.

Holliday R, Pukkila PJ, Dickson JM, Spanos A, Murray V.

Cold Spring Harb Symp Quant Biol. 1979;43 Pt 2:1317-23. No abstract available.

PMID:
290445
38.

The recognition of mismatched base pairs in DNA by DNase I from Ustilago maydis.

Pukkila PJ.

Mol Gen Genet. 1978 May 31;161(3):245-50.

PMID:
353513
39.

Biochemical analysis of genetic recombination in eukaryotes.

Pukkila PJ.

Heredity (Edinb). 1977 Oct;39(2):193-217. Review.

PMID:
199560

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