Publications rDNAome - GANLEY Laboratory
Publications
To see my publications in Google Scholar, please visit http://goo.gl/3CsWiy
Journal Articles:
Macdonald, E., Whibley, A., Waters, P.D., Patel, H., Edwards, R.J. and Ganley, A.R.D. 2024 Genetics in press “Origin and maintenance of large ribosomal RNA gene repeat size in mammals” Link to article
Devlin, D., Ganley, A.R.D. and Takeuchi, N. 2023 Current Opinion in Systems Biology 36: 100486 “A pan-metazoan view of germline-soma distinction challenges our understanding of how the metazoan germline evolves” Link to article
Jain, K., Vickers, M.H., Jacob, B., Middleditch, M.J., Chudakova, D.A., Ganley, A.R.D., O’Sullivan, J.M. and J.K. Perry. 2023 Journal of Cell Communication and Signaling 17: 925–937 “The growth hormone receptor interacts with transcriptional regulator HMGN1 upon GH‐induced nuclear translocation” Link to article
Benitez, R., Harris, A., Mansfield, E., Silcock, P., Eyres, G., Villas-Bôas, S.G., Jeffs, A. & Ganley, A.R.D. 2023 PLoS One 18: e0281762 “Direct liquid transmission of sound has little impact on fermentation performance in Saccharomyces cerevisiae” Link to article
Cox, M.P., Guo, Y., Winter, D.J., Sen, D., Cauldron, N.C., Shiller, J., Bradley, E.L., Ganley, A.R.D., Gerth, M.L., Lacey, R.F., McDougal, R.L., Panda, P., Williams, N.M., Grunwald, N.J., Mesarich, C.H. and R.E. Bradshaw. 2022 Frontiers in Microbiology 13: 1038444 “Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families” Link to article
Antony, C., George, S.S., Blum, J., Somers, P., Thorsheim, C.L., Wu-Corts, D.J., Ai, Y., Gao, L., Lv, K., Tremblay, M.G., Moss, T., Tan, K., Wilusz, J.E., Ganley, A.R.D., Pimkin, M. and V.R. Paralkar. 2022 Molecular Cell 82: 3826-3839 “Control of ribosomal RNA synthesis by hematopoietic transcription factors” Link to article
Sharma, D., Hermann-Le Denmat, S., Matzke, N.J., Hannan, K., Hannan, R.D., O’Sullivan, J.M. and Ganley, A.R.D.. 2022 Genomics 114: 110430 “A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations” Link to article
Behling, A.H., Winter, D.J., Ganley, A.R.D. and M.P. Cox. 2022 Journal of Evolutionary Biology 35: 1126-1137 “Cross-kingdom transcriptomic trends in the evolution of hybrid gene expression” Link to article
Quenu, M., Treindl, A., Lee, K., Takemoto, D., Thuenen, T., Ashrafi, S., Winter, D., Ganley, A.R.D., Leuchtmann, A.,Young, C. and M.P. Cox. 2022 Journal of Fungi 8: 670 “Telomere-to-telomere genome sequences along a fungal genus transect reveals highly variable chromosome rearrangement rates but absolute stasis of chromosome number” Link to article
Arras, S.D.M., Hibbard, T.R., Mitsugi-McHattie, L., Woods, M.A., Johnson, C.E., Munkacsi, A., Hermann-Le Denmat, S. and Ganley, A.R.D. 2022 FEMS Yeast Research 22: foac017 “A simple, cheap, and robust protocol for the identification of mating type in Saccharomyces cerevisiae” Link to article
Sibbin, K., Yap, P., Nyaga, D., Heller, R., Evans, S., Strachan, K., Alburaiky, S., Nguyen, H.M., Hermann-Le Denmat, S., Ganley, A.R.D., O’Sullivan, J.M. and F.H. Bloomfield. 2022 American Journal of Medical Genetics: Part A 188: 1299-1306 “A de novo ACTB gene pathogenic variant in identical twins with phenotypic variation for hydrops and jejunal atresia” Link to article
Olivier, F.A.B., Bang, K.W., Zarate, E., Kinzurik, M., Chudakova, D., Ganley, A.R.D. and S.G. Villas-Boas. 2022 Fungal Genetics and Biology 158: 103646 “Aerial warfare: An inducible production of volatile bioactive metabolites in a novel species of Scytinostroma sp.” Link to article
Adadi, P., Harris, A., Bremer, P., Silcock, P., Ganley, A.R.D., Jeffs, A.G. and G.T. Eyres. 2021 Molecules 26: 7239 “The effect of sound frequency and intensity on yeast growth, fermentation performance and volatile composition of beer” Link to article
Harris, A., Lindsay, M.A., Ganley, A.R.D., Jeffs, A. and S.G. Villas-Boas. 2021 Metabolites 11: 605 “Sound stimulation can affect Saccharomyces cerevisiae growth and production of volatile metabolites in liquid medium” Link to article
Son, J., Hannan, K.M., Poortinga, G., Hein, N., Cameron, D.P., Ganley, A.R.D., Sheppard, K.E., Pearson, R.B., Hannan, R.D. and E. Sanij. 2020. Frontiers in Cell and Developmental Biology 8: 568 “rDNA chromatin activity status as a biomarker of sensitivity to the RNA polymerase I transcription inhibitor CX-5461” Link to article
Zhou, H., Visnovska, T., Gong, H., Schmeier, S., Hickford, J. and Ganley, A.R.D.. 2019. Molecular Phylogenetics and Evolution 133: 352-361 “Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes” Link to article
Woolley, S., E.C. Parke, D. Kelley, A.M. Poole, and Ganley, A.R.D.. 2019. Biology and Philosophy 34: 11 “Striving for clarity about the “Lamarckian” nature of CRISPR-Cas systems” Link to article
Diesch, J., Bywater, M.J., Sanij, E., Cameron, D.P., Schierding, W., Brajanovski, N., Son, J., Sornkom, J., Hein, N., Evers, M., Pearson, R.B., McArthur, G.A., Ganley, A.R.D. O’Sullivan, J.M., Hannan, R.D. & G. Poortinga. 2019. Communications Biology 2: 39 “Changes in long-range rDNA-genomic interactions associate with altered RNA polymerase II gene programs during malignant transformation” Link to article
Agrawal, S. and Ganley, A.R.D. 2018. PLoS One 13: e0207531 “The conservation landscape of the human ribosomal RNA gene repeats” Link to article
Winter, D.J., Ganley, A.R.D., C. Young, I. Liachko, C. Schardl, P.-Y. Dupont, D. Berry, A. Ram, B. Scott, and M. Cox. 2018. PLoS Genetics 14: e1007467 “Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae” Link to article
Campbell, M.A., B.A. Tapper, W.R. Simpson, R.D. Johnson, W. Mace, A. Ram, Y. Lukito, P.-Y. Dupont, L.J. Johnson, D.B. Scott, Ganley, A.R.D., and M.P. Cox. 2017 Mycologia 109: 715-729 “Epichloë hybrida sp. nov., an emerging model system for investigating fungal allopolyploidy” Link to article
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 sclerotiorum” Link 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.D., 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.D., 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
