Publications rDNAome - GANLEY Laboratory

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Publications

To see my publications in Google Scholar, please visit http://goo.gl/3CsWiy

Journal Articles:

Campbell, M.A., Ganley, A.R.D., Gabaldón, T. and Cox, M.P. 2016. The American Naturalist 188: 602-614. “The case of the missing ancient fungal polyploids” Link to article

Khalifa, M.E., Varsani, A., Ganley, A.R.D. and Pearson, M.N. 2016. Virus Research 219: 51-57. “Comparison of Illumina de novo assembled and Sanger sequenced viral genomes: A case study for RNA viruses recovered from the plant pathogenic fungus Sclerotinia sclerotiorumLink to article

Gregory, S.J., Anderson, C.W., Camps-Arbestain, M., Biggs, P.J., Ganley, A.R.D., O’Sullivan, J.M. and McManus, M.T. 2015. PLoS One 10: e0125393. “Biochar in co-contaminated soil manipulates arsenic solubility and microbiological community structure, and promotes organochlorine degradation” Link to article

Cahyani, I., Cridge, A.G., Engelke, D.R., Ganley, A.R.D. and O’Sullivan, J.M. 2015. Molecular and Cellular Biology 35: 544-554. “A sequence-specific interaction between the Saccharomyces cerevisiae rRNA gene repeats and a locus encoding an RNA polymerase I subunit affects ribosomal DNA stability” Link to article

Duchemin, W., Dupont, P.Y., Campbell, M.A., Ganley, A.R.D. and Cox, M.P. 2015. BMC Bioinformatics 16: 8. “HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species” Link to article

Cox, M.P., Dong, T., Shen, G., Dalvi, Y., Scott, D.B. and Ganley, A.R.D. 2014. PLoS Genetics 10: e1004180. “An interspecific fungal hybrid reveals cross-Kingdom rules for allopolyploid gene expression patterns” Link to article

Ganley, A.R.D., and Kobayashi, T. 2014 FEMS Yeast Research 14: 49-59. “Ribosomal DNA and cellular senescence: new evidence supporting the connection between rDNA and aging” Link to article

Floutsakou*, I., Agrawal*, S., Nyugen*, T., Seoighe, C., Ganley, A.R.D., and McStay, B. 2013. Genome Research 23: 2003-2012. “The shared genomic architecture of human nucleolar organizer regions” Link to article (* = authors contributed equally)

Saka, K., Ide, S., Ganley, A.R.D., and Kobayashi, T. 2013. Current Biology 23: 1794-1798. “Cellular senescence in yeast is regulated by rDNA noncoding transcription” Link to article

O’Sullivan, J.M., Pai, D.A., Cridge, A.G., Engelke, D.R., and Ganley, A.R.D. 2013. BioMolecular Concepts 4: 277–286. “The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?” Link to article

Bradshaw, R.E., Slot, J.C., Moore, G.G., Chettri, P., de Wit, Pierre J. G. M., Ehrlich, K.C., Ganley, A.R., Olson, M.A., Rokas, A., Carbone, I., and Cox, M.P. 2013. New Phytologist 198: 525-535. “Fragmentation of an aflatoxin-like gene cluster in a forest pathogen” Link to article

de Wit, Pierre J. G. M., van der Burgt, A., Ökmen, B., Stergiopoulos, I., Abd-Elsalam, K.A., Aerts, A.L., Bahkali, A.H., Beenen, H.G., Chettri, P., Cox, M.P., Datema, E., de Vries, R.P., Dhillon, B., Ganley, A.R., Griffiths, S.A., Guo, Y., Hamelin, R.C., Henrissat, B., Kabir, M.S., Jashni, M.K., Kema, G., Klaubauf, S., Lapidus, A., Levasseur, A., Lindquist, E., Mehrabi, R., Ohm, R.A., Owen, T.J., Salamov, A., Schwelm, A., Schijlen, E., Sun, H., van den Burg, H.A., van Ham, R.C.H.J., Zhang, S., Goodwin, S.B., Grigoriev, I.V., Collemare, J., and Bradshaw, R.E. 2012. PLoS Genetics 8: e1003088. “The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry” Link to article

Poole, A.M., Kobayashi, T. and Ganley, A.R.D. 2012. BioEssays 34: 725-729. “A positive role for yeast extrachromosomal rDNA circles?” Link to article

Ganley, A.R.D. and T. Kobayashi. 2011. Molecular Biology and Evolution 28: 2883-2891. “Monitoring the rate and dynamics of concerted evolution of the ribosomal DNA repeats of Saccharomyces cerevisiae using experimental evolution.” Link to article

Ganley, A.R.D., S. Ide, K. Saka, and T. Kobayashi. 2009. Molecular Cell 35: 683-693. “The effect of replication initiation on gene amplification in the rDNA and its relationship to aging.” Link to article

Regier, J.C., J.W. Shultz, A.R.D. Ganley, A. Hussey, D. Shi, B. Ball, A. Zwick, J.E. Stajich, M.P. Cummings, J.W. Martin, and C.W. Cunningham. 2008. Systematic Biology 57: 920-938. “Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence.” Link to article

Ganley, A.R.D. and T. Kobayashi. 2007. Genome Research. 17: 184-191. “Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole genome shotgun sequence data.” Link to article

Kobayashi, T. and A.R.D. Ganley. 2005 Science 309: 1581-1584. “Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats.” Link to article

Ganley, A.R.D., K. Hayashi, T. Horiuchi, and T. Kobayashi. 2005. Proceedings of the National Academy of Sciences (USA) 102: 11787-11792. “Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting.” Link to article

Morehouse, E., T.Y. James, A.R.D. Ganley, R. Vilgalys, L. Berger, P.J. Murphy, and J.E. Longcore. 2003. Molecular Ecology 12: 395-403. “Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone.” Link to article

Ganley, A.R.D., and B. Scott. 2002. Fungal Genetics and Biology 35: 39-51. “Concerted evolution in the ribosomal RNA genes of an Epichloë endophyte hybrid: Comparison between tandemly-arranged rDNA and dispersed 5S rrn genes.” Link to article

Ganley, A.R.D. and B. Scott. 1998. Genetics 150: 1625-1637. “Extraordinary ribosomal spacer length heterogeneity in a Neotyphodium endophyte hybrid: Implications for concerted evolution.” Link to article

Editorials:

Petranovic, D. and Ganley, A.R.D. 2014. FEMS Yeast Research 14: 1. “Yeast cell aging and death” Link to article

Book Chapters:

Agrawal, S. and Ganley, A.R.D. 2016 “Complete sequence construction of the highly repetitive ribosomal RNA gene repeats in eukaryotes using whole genome sequence data” in Methods in Molecular Biology 1455: 161-181. Link to article

Ganley, A.R.D. 2013 “Concerted Evolution” in Brenner’s Encyclopedia of Genetics, 2nd Edition (eds. S. Maloy & K. Hughes), Academic Press. Link to article

Hein, N., Sanij, E., Quin, J., Hannan, K.M., Ganley, A.R.D. and R. Hannan. 2012 “The Nucleolus and Ribosomal Genes in Aging and Senescence” in Senescence (ed. T. Nagata), InTech. Link to article

Ganley, A.R.D. and T. Kobayashi. 2007 “Phylogenetic footprinting to find functional DNA elements” in Comparative Genomics (ed. N.H. Bergman), pp. 367-380, Methods in Molecular Biology Series. Humana Press, Totowa, NJ. Link to article

Letters to the Editor:

Ganley, A.R.D., Breitenbach, M., Kennedy, B.K. and T. Kobayashi. 2012. FEMS Yeast Research 12: 267-268. “Yeast hypertrophy: cause or consequence of aging? Reply to Bilinski et al.” Link to letter

Bidartondo et al. 2008. Science 319: 1616. “Preserving accuracy in GenBank.” Link to letter

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