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Comparative genomic analysis of fungal genomes reveals intron-rich ancestors
Jason E Stajich, Fred S Dietrich, Scott W Roy
Genome Biol. 2007; 8(10): R223. Published online 2007 October 19. doi: 10.1186/gb-2007-8-10-r223
PMCID:
PMC2246297
Abstract Full Text PDF–745K Supplementary Material

Is Cited by the Following 22 Articles in this Archive:

Diverse Forms of RPS9 Splicing Are Part of an Evolving Autoregulatory Circuit
Alex M. Plocik, Christine Guthrie
PLoS Genet. 2012 March; 8(3): e1002620. Published online 2012 March 29. doi: 10.1371/journal.pgen.1002620
PMCID:
PMC3315480
Abstract Full Text PDF–750K Supplementary Material
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis
Alessandro Guida, Claudia Lindstädt, Sarah L Maguire, Chen Ding, Desmond G Higgins, Nicola J Corton, Matthew Berriman, Geraldine Butler
BMC Genomics. 2011; 12: 628. Published online 2011 December 22. doi: 10.1186/1471-2164-12-628
PMCID:
PMC3287387
Abstract Full Text PDF–1.6M Supplementary Material
Causes and Consequences of Genome Expansion in Fungi
Yogeshwar D. Kelkar, Howard Ochman
Genome Biol Evol. 2012; 4(1): 13–23. Published online 2011 November 24. doi: 10.1093/gbe/evr124
PMCID:
PMC3267396
Abstract Full Text PDF–593K
A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes
Miklos Csuros, Igor B. Rogozin, Eugene V. Koonin
PLoS Comput Biol. 2011 September; 7(9): e1002150. Published online 2011 September 15. doi: 10.1371/journal.pcbi.1002150
PMCID:
PMC3174169
Abstract Full Text PDF–1.5M Supplementary Material
Diverse environmental stresses elicit distinct responses at the level of pre-mRNA processing in yeast
Megan Bergkessel, Gregg B. Whitworth, Christine Guthrie
RNA. 2011 August; 17(8): 1461–1478. doi: 10.1261/rna.2754011
PMCID:
PMC3153971
Free in PMC on 2012/08/01
Why eukaryotic cells use introns to enhance gene expression: Splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity
Deng-Ke Niu, Yu-Fei Yang
Biol Direct. 2011; 6: 24. Published online 2011 May 18. doi: 10.1186/1745-6150-6-24
PMCID:
PMC3118952
Abstract Full Text PDF–334K
Distribution of Introns in Fungal Histone Genes
Choong-Soo Yun, Hiromi Nishida
PLoS One. 2011; 6(1): e16548. Published online 2011 January 27. doi: 10.1371/journal.pone.0016548
PMCID:
PMC3029354
Abstract Full Text PDF–313K Supplementary Material
DNA double-strand break repair and the evolution of intron density
Ashley Farlow, Eshwar Meduri, Christian Schlötterer
Trends Genet. 2011 January; 27(1): 1–6. doi: 10.1016/j.tig.2010.10.004
PMCID:
PMC3020277
Abstract Full Text Supplementary Material
The role of exon shuffling in shaping protein-protein interaction networks
Douglas V Cancherini, Gustavo S França, Sandro J de Souza
BMC Genomics. 2010; 11(Suppl 5): S11. Published online 2010 December 22. doi: 10.1186/1471-2164-11-S5-S11
PMCID:
PMC3045794
Abstract Full Text PDF–460K Supplementary Material
Two Origins for the Gene Encoding α-Isopropylmalate Synthase in Fungi
Erica M. Larson, Alexander Idnurm
PLoS One. 2010; 5(7): e11605. Published online 2010 July 15. doi: 10.1371/journal.pone.0011605
PMCID:
PMC2904702
Abstract Full Text PDF–734K Supplementary Material
Using Deep RNA Sequencing for the Structural Annotation of the Laccaria Bicolor Mycorrhizal Transcriptome
Peter E. Larsen, Geetika Trivedi, Avinash Sreedasyam, Vincent Lu, Gopi K. Podila, Frank R. Collart
PLoS One. 2010; 5(7): e9780. Published online 2010 July 6. doi: 10.1371/journal.pone.0009780
PMCID:
PMC2897884
Abstract Full Text PDF–472K Supplementary Material
Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts
Meryem Mekouar, Isabelle Blanc-Lenfle, Christophe Ozanne, Corinne Da Silva, Corinne Cruaud, Patrick Wincker, Claude Gaillardin, Cécile Neuvéglise
Genome Biol. 2010; 11(6): R65. Published online 2010 June 23. doi: 10.1186/gb-2010-11-6-r65
PMCID:
PMC2911113
Abstract Full Text PDF–1.3M Supplementary Material
Evolution of spliceosomal introns following endosymbiotic gene transfer
Nahal Ahmadinejad, Tal Dagan, Nicole Gruenheit, William Martin, Toni Gabaldón
BMC Evol Biol. 2010; 10: 57. Published online 2010 February 23. doi: 10.1186/1471-2148-10-57
PMCID:
PMC2834692
Abstract Full Text PDF–780K Supplementary Material
Nonsense-Mediated Decay Enables Intron Gain in Drosophila
Ashley Farlow, Eshwar Meduri, Marlies Dolezal, Liushuai Hua, Christian Schlötterer
PLoS Genet. 2010 January; 6(1): e1000819. Published online 2010 January 22. doi: 10.1371/journal.pgen.1000819
PMCID:
PMC2809761
Abstract Full Text PDF–309K Supplementary Material
Population Genomics of Intron Splicing in 38 Saccharomyces cerevisiae Genome Sequences
Daniel A. Skelly, James Ronald, Caitlin F. Connelly, Joshua M. Akey
Genome Biol Evol. 2009; 1: 466–478. Published online 2009 November 17. doi: 10.1093/gbe/evp046
PMCID:
PMC2839277
Abstract Full Text PDF–540K Supplementary Material
Primer -- The Fungi
Jason E. Stajich, Mary L. Berbee, Meredith Blackwell, David S. Hibbett, Timothy Y. James, Joseph W. Spatafora, John W. Taylor
Curr Biol. Author manuscript; available in PMC 2010 August 1.
Published in final edited form as: Curr Biol. 2009 September 29; 19(18): R840–R845. doi: 10.1016/j.cub.2009.07.004
PMCID:
PMC2913116
Full Text PDF–1.9M
The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion
Jeffrey J. Coleman, Steve D. Rounsley, Marianela Rodriguez-Carres, Alan Kuo, Catherine C. Wasmann, Jane Grimwood, Jeremy Schmutz, Masatoki Taga, Gerard J. White, Shiguo Zhou, David C. Schwartz, Michael Freitag, Li-jun Ma, Etienne G. J. Danchin, Bernard Henrissat, Pedro M. Coutinho, David R. Nelson, Dave Straney, Carolyn A. Napoli, Bridget M. Barker, Michael Gribskov, Martijn Rep, Scott Kroken, István Molnár, Christopher Rensing, John C. Kennell, Jorge Zamora, Mark L. Farman, Eric U. Selker, Asaf Salamov, Harris Shapiro, Jasmyn Pangilinan, Erika Lindquist, Casey Lamers, Igor V. Grigoriev, David M. Geiser, Sarah F. Covert, Esteban Temporini, Hans D. VanEtten
PLoS Genet. 2009 August; 5(8): e1000618. Published online 2009 August 28. doi: 10.1371/journal.pgen.1000618
PMCID:
PMC2725324
Abstract Full Text PDF–624K Supplementary Material
Intronization, de-intronization and intron sliding are rare in Cryptococcus
Scott W Roy
BMC Evol Biol. 2009; 9: 192. Published online 2009 August 7. doi: 10.1186/1471-2148-9-192
PMCID:
PMC2740785
Abstract Full Text PDF–282K
Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences
Zhang Zhang, Jeffrey P. Townsend
PLoS Comput Biol. 2009 June; 5(6): e1000421. Published online 2009 June 26. doi: 10.1371/journal.pcbi.1000421
PMCID:
PMC2695770
Abstract Full Text PDF–811K Supplementary Material
SNUGB: a versatile genome browser supporting comparative and functional fungal genomics
Kyongyong Jung, Jongsun Park, Jaeyoung Choi, Bongsoo Park, Seungill Kim, Kyohun Ahn, Jaehyuk Choi, Doil Choi, Seogchan Kang, Yong-Hwan Lee
BMC Genomics. 2008; 9: 586. Published online 2008 December 4. doi: 10.1186/1471-2164-9-586
PMCID:
PMC2649115
Abstract Full Text PDF–1.9M
Exon definition as a potential negative force against intron losses in evolution
Deng-Ke Niu
Biol Direct. 2008; 3: 46. Published online 2008 November 13. doi: 10.1186/1745-6150-3-46
PMCID:
PMC2614967
Abstract Full Text PDF–265K Supplementary Material
Malin: maximum likelihood analysis of intron evolution in eukaryotes
Miklós Csűrös
Bioinformatics. 2008 July 1; 24(13): 1538–1539. Published online 2008 May 12. doi: 10.1093/bioinformatics/btn226
PMCID:
PMC2718671
Abstract Full Text PDF–236K
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