Publications

Publications

2018

Donovan PD, Gonzalez G, Higgins DG, Butler G, Ito K.  Identification of fungi in shotgun metagenomics datasets.  PLoS One. 2018;13(2):e0192898.

Salazar SB, Wang C, Münsterkötter M, Okamoto M, Takahashi-Nakaguchi A, Chibana H, Lopes MM, Güldener U, Butler G, Mira NP. Comparative genomic and transcriptomic analyses unveil novel features of azole resistance and adaptation to the human host in Candida glabrata. FEMS Yeast Res. 2018 Feb 1;18(1). doi: 10.1093/femsyr/fox079.

2017

Lyden A, Lombardi L, Sire W, Li P, Simpson JC, Butler G, Lee GU. Characterization of carboxylate nanoparticle adhesion with the fungal pathogen Candida albicans. Nanoscale. 2017 Oct 11. doi: 10.1039/c7nr04724j

Lombardi L, Turner SA, Zhao F, Butler G. Gene editing in clinical isolates of Candida parapsilosis using CRISPR/Cas9.  Sci Rep. 2017 Aug 14;7(1):8051. doi: 10.1038/s41598-017-08500-1.

Wolfe KH, Butler G. Evolution of Mating in the Saccharomycotina. Annu Rev Microbiol. 2017 Jun 28. doi: 10.1146/annurev-micro-090816-093403.

Branco J, Ola M, Silva RM, Fonseca E, Gomes NC, Martins-Cruz C, Silva AP, Silva-Dias A, Pina-Vaz C, Erraught C, Brennan L, Rodrigues AG, Butler G, Miranda IM. Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance. Clin Microbiol Infect. 2017 Feb 11. pii: S1198-743X(17)30090-3. doi: 10.1016/j.cmi.2017.02.002.

2016

Bernardo RT, Cunha DV, Wang C, Pereira L, Silva S, Salazar SB, Schröder MS, Okamoto M, Takahashi-Nakaguchi A, Chibana H, Aoyama T, Sá-Correia I, Azeredo J, Butler G, Mira NP. The CgHaa1-regulon mediates response and tolerance to acetic acid stress in the human pathogen Candida glabrata. G3 (Bethesda). 2016 Nov 4. pii: g3.116.034660. doi: 10.1534/g3.116.034660.

Schröder MS, Martinez de San Vicente K, Prandini TH, Hammel S, Higgins DG, Bagagli E, Wolfe KH, Butler G.  Multiple origins of the pathogenic yeast Candida orthopsilosis by separate hybridizations between two parental species. PLoS Genet. 2016 Nov 2;12(11):e1006404.

Donovan PD, Schröder MS, Higgins DG, Butler G (2016) ‘Identification of Non-Coding RNAs in the Candida parapsilosis Species Group’. PLoS ONE 11(9):e0163235

Wang C, Schröder MS, Hammel S, Butler G. (2016) ‘Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species’. Methods in Molecular Biology, 1361 :1-40.

2015

Wu G, Zhao H, Li C, Rajapakse MP, Wong WC, Xu J, Saunders CW, Reeder NL, Reilman RA, Scheynius A, Sun S, Billmyre BR, Li W, Averette AF, Mieczkowski P, Heitman J, Theelen B, Schröder MS, De Sessions PF, Butler G, Maurer-Stroh S, Boekhout T, Nagarajan N, Dawson TL Jr. (2015) ‘Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin’. PLoS Genetics, 11(11):e1005614.

Branco J, Silva AP, Silva RM, Silva-Dias A, Pina-Vaz C, Butler G, Rodrigues AG, Miranda IM. (2015) ‘Fluconazole and Voriconazole Resistance in Candida parapsilosis Is Conferred by Gain-of-Function Mutations in MRR1 Transcription Factor Gene’. Antimicrobial Agents and Chemotherapy, 59 :6629-6633.

2014

Turner SA, Butler G (2014) ‘The Candida Pathogenic Species Complex’. Cold Spring Harbor Perspectives in Medicine, 4 .

Holland LM, Schröder MS, Turner SA, Taff H, Andes D, Grózer Z, Gácser A, Ames L, Haynes K, Higgins DG, Butler G. (2014) ‘Comparative Phenotypic Analysis of the Major Fungal Pathogens Candida parapsilosis and Candida albicans’. PLoS Pathogens, 10(9):e1004365.  YouTube

Sarah L. Maguire, Can Wang, Linda M. Holland, François Brunel, Cécile Neuvéglise, Jean-Marc Nicaud, Martin Zavrel, Theodore C. White, Kenneth H. Wolfe, and Geraldine Butler (2014) ‘Zinc finger transcription factors displaced SREBP proteins as the major sterol regulators during Saccharomycotina evolution’. PLoS Genetics, 10(1):e1004076.

2013

Mohan Pammi, Linda Holland, Geraldine Butler, Attila Gacser, Joseph M. Bliss (2013) ‘Candida parapsilosis is a Significant Neonatal Pathogen: A Systematic Review and Meta-analysis’. Pediatric Infectious Disease Journal, 32 (5):206-216.

Gioti, A,Nystedt, B,Li, WJ,Xu, J,Andersson, A,Averette, AF,Munch, K,Wang, XY,Kappauf, C,Kingsbury, JM,Kraak, B,Walker, LA,Johansson, HJ,Holm, T,Lehtio, J,Stajich, JE,Mieczkowski, P,Kahmann, R,Kennell, JC,Cardenas, ME,Lundeberg, J,Saunders, CW,Boekhout, T,Dawson, TL,Munro, CA,de Groot, PWJ,Butler, G,Heitman, J,Scheynius, A (2013) ‘Genomic Insights into the Atopic Eczema-Associated Skin Commensal Yeast Malassezia sympodialis’. mBio, 4(1):e00572-12

Connolly LA, Riccombeni A, Grózer Z, Holland LM, Lynch DB, Andes DR, Gácser A, Butler G. (2013) ‘The APSES transcription factor Efg1 is a global regulator that controls morphogenesis and biofilm formation in Candida parapsilosis’. Molecular Microbiology, 90 (1):36-53.

Butler, G. (2013) ‘Hypoxia and Gene Expression in Eukaryotic Microbes’. Annual Review of Microbiology, 67 :291-312.

Maguire SL, Ohéigeartaigh SS, Byrne KP, Schröder MS, O’Gaora P, Wolfe KH, Butler G (2013) ‘Comparative Genome Analysis and Gene Finding in Candida Species Using CGOB’. Molecular Biology and Evolution, 30 (6):1281-1291.

2012

Riccombeni1 A, Vidanes1 G, Proux-Wera E, Wolfe KH, Butler G (2012) ‘Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis’. PLoS ONE, 7(4):e35750.

Alessandro Riccombeni and Geraldine Butler (2012) ‘Role of Genomics and RNA-seq in Studies of Fungal Virulence’. Current Fungal Infection Reports, 6 :274-297.

2011

Sai S, Holland LM, McGee CF, Lynch DB, Butler G; (2011) ‘Evolution of Mating within the Candida parapsilosis Species Group’. Eukaryotic Cell, 10 (4):578-587.

Guida, A,Lindstadt, C,Maguire, SL,Ding, C,Higgins, DG,Corton, NJ,Berriman, M,Butler, G (2011) ‘Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis’. BMC Genomics, 12:628

Ding, C,Vidanes, GM,Maguire, SL,Guida, A,Synnott, JM,Andes, DR,Butler, G (2011) ‘Conserved and Divergent Roles of Bcr1 and CFEM Proteins in Candida parapsilosis and Candida albicans’. PLoS ONE, 6(12):e28151

Silva, AP,Miranda, IM,Guida, A,Synnott, J,Rocha, R,Silva, R,Amorim, A,Pina-Vaz, C,Butler, G,Rodrigues, AG; (2011) ‘Transcriptional Profiling of Azole-Resistant Candida parapsilosis Strains’. Antimicrobial Agents and Chemotherapy, 55 :3546-3556.

Sai, SX,Holland, LM,McGee, CF,Lynch, DB,Butler, G; (2011) ‘Evolution of Mating within the Candida parapsilosis Species Group’. Eukaryotic Cell, 10 :578-587.

2006-2011

Haynes K, Stead DA, Walker J, Holcombe L, Gibbs SR, Yin Z, Selway L, Butler G, Brown AJ, ; (2010) ‘Impact of the transcriptional regulator, Ace2, on the Candida glabrata secretome’. Proteomics, 10 :212-223. [DOI]

Lynch, DB,Logue, ME,Butler, G,Wolfe, KH; (2010) ‘Chromosomal G+C Content Evolution in Yeasts: Systematic Interspecies Differences, and GC-Poor Troughs at Centromeres’. Genome Biology and Evolution, 2 :572-583. [DOI]

Synnott, JM,Guida, A,Mulhern-Haughey, S,Higgins, DG,Butler, G; (2010) ‘Regulation of the Hypoxic Response in Candida albicans’. Eukaryotic Cell, 9 :1734-1746. [DOI]

Fitzpatrick, DA,O’Gaora, P,Byrne, KP,Butler, G; (2010) ‘Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser’. Genomics, 11 . [DOI]

Holcombe, LJ,McAlester, G,Munro, CA,Enjalbert, B,Brown, AJP,Gow, NAR,Ding, C,Butler, G,O’Gara, F,Morrissey, JP; (2010) ‘Pseudomonas aeruginosa secreted factors impair biofilm development in Candida albicans’. MICROBIOL-SGM, 156 :1476-1486. [DOI]

Fitzpatrick, D. A. and O’Gaora, P. and Byrne, K. P. and Butler, G. (2010) ‘Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser’. BMC Genomics, 11 .

Fitzpatrick DA, O’Gaora P, Byrne KP, Butler G.; (2010) ‘Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser’. BMC Genomics, 11 :290-303. [DOI]

Fitzpatrick DA, O’Gaora P, Byrne KP, Butler G; (2010) ‘Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser’. Genomics, 11 . [DOI]

Synnott JM, Guida A, Mulhern-Haughey S, Higgins DG, Butler G.; (2010) ‘Regulation of the hypoxic response in Candida albicans’. Eukaryotic Cell, .

Lynch DB, Logue ME, Butler G, Wolfe KH.; (2010) ‘Chromosomal G + C Content Evolution in Yeasts: Systematic Interspecies Differences, and GC-Poor Troughs at Centromeres’. Genome Biology and Evolution, 2 :572-583.

Fitzpatrick DA, O’Gaora P, Byrne KP, Butler G; (2010) ‘Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser’. BMC Genomics, 11 . [DOI]

Butler G, ; (2010) ‘Fungal sex and pathogenesis’. Clinical Microbiology Reviews, 23 (1):140-159. [DOI]

Morrissey JP, Holcombe LJ, McAlester G, Munro CA, Enjalbert B, Brown AJ, Gow NA, Ding C, Butler G, O’Gara F, ; (2010) ‘Pseudomonas aeruginosa secreted factors impair biofilm development in Candida albicans’. Microbiology, 156 :1476-1486. [DOI]

Rossignol, T,Ding, C,Guida, A,d’Enfert, C,Higgins, DG,Butler, G; (2009) ‘Correlation between Biofilm Formation and the Hypoxic Response in Candida parapsilosis’. Eukaryotic Cell, 8 :550-559. [DOI]

Butler, G,Rasmussen, MD,Lin, MF,Santos, MAS,Sakthikumar, S,Munro, CA,Rheinbay, E,Grabherr, M,Forche, A,Reedy, JL,Agrafioti, I,Arnaud, MB,Bates, S,Brown, AJP,Brunke, S,Costanzo, MC,Fitzpatrick, DA,de Groot, PWJ,Harris, D,Hoyer, LL,Hube, B,Klis, FM,Kodira, C,Lennard, N,Logue, ME,Martin, R,Neiman, AM,Nikolaou, E,Quail, MA,Quinn, J,Santos, MC,Schmitzberger, FF,Sherlock, G,Shah, P,Silverstein, KAT,Skrzypek, MS,Soll, D,Staggs, R,Stansfield, I,Stumpf, MPH,Sudbery, PE,Srikantha, T,Zeng, QD,Berman, J,Berriman, M,Heitman, J,Gow, NAR,Lorenz, MC,Birren, BW,Kellis, M,Cuomo, CA; (2009) ‘Evolution of pathogenicity and sexual reproduction in eight Candida genomes’. Nature, 459 :657-662. [DOI]

Berriman M, Jackson AP, Gamble JA, Yeomans T, Moran GP, Saunders D, Harris D, Aslett M, Barrell JF, Butler G, Citiulo F, Coleman DC, de Groot PW, Goodwin TJ, Barrell B, Quail MA, McQuillan J, Munro CA, Pain A, Poulter RT, Rajandream MA, Renauld H, Spiering MJ, Tivey A, Gow NA, Sullivan DJ, ; (2009) ‘Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans’. Genome Research, 19 (12):2231-2244. [DOI]

Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M,Cuomo CA. ; (2009) ‘Evolution of pathogenicity and sexual reproduction in eight Candida genomes’. Nature, 459 :657-662. [DOI]

Roetzer A, Gregori C, Jennings AM, Quintin J, Ferrandon D, Butler G, Kuchler K, Ammerer G, Schüller C.; (2008) ‘Candida glabrata environmental stress response involves Saccharomyces cerevisiae Msn2/4 orthologous transcription factors’. Molecular Microbiology, 69 :603-620.

Fitzpatrick, DA,Logue, ME,Butler, G; (2008) ‘Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis’. Journal of Immunology, 9 . [DOI]

Roetzer, A,Gregori, C,Jennings, AM,Quintin, J,Ferrandon, D,Butler, G,Kuchler, K,Ammerer, G,Schuller, C; (2008) ‘Candida glabrata environmental stress response involves Saccharomyces cerevisiae Msn2/4 orthologous transcription factors’. Journal of Microbiology, 69 :603-620. [DOI]

Butler G, Fitzpatrick DA, Logue ME, ; (2008) ‘Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis’. BMC Evolutionary Biology, 8 . [DOI]

Butler G, Fitzpatrick DA, Logue ME, ; (2008) ‘Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis’. BMC Evolutionary Biology, 8 (1). [DOI]

Rossignol T, Logue ME, Reynolds K, Grenon M, Lowndes NF, Butler G.; (2007) ‘Analysis of the transcriptional response of Candida parapsilosis following exposure to farnesol’. Antimicrob Agents Chemother, 51 (2304).

Dignard, D,El-Naggar, AL,Logue, ME,Butler, G,Whiteway, M; (2007) ‘Identification and characterization of MFA1, the gene encoding Candida albicans a-factor pheromone’. Cell, 6 :487-494. [DOI]

Rossignol, T,Logue, ME,Reynolds, K,Grenon, M,Lowndes, NF,Butler, G; (2007) ‘Transcriptional response of Candida parapsilosis following exposure to farnesol’. Antimicrobial Agents and Chemotherapy, 51 :2304-2312. [DOI]

Ding, C,Butler, G; (2007) ‘Development of a gene knockout system in Candida parapsilosis reveals a conserved role for BCR1 in biofilm formation’. Cell, 6 :1310-1319. [DOI]

Ding, C, Butler, G, ; (2007) ‘Development of a gene knockout system in Candida parapsilosis reveals a conserved role for BCR1 in biofilm formation’. Eukaryotic Cell, 6 :1310-1319.

Dignard, D, El-Naggar, AL, Logue, ME, Butler, G, Whiteway, M, ; (2007) ‘Identification and characterization of MFA1, the gene encoding Candida albicans a-factor pheromone’. Eukaryotic Cell, 6 :487-494.

Scannell D.R, Butler G. and Wolfe K.H.; (2007) ‘Yeast genome evolution – the origin of the species’. Yeast, 24 :929-942.

Lasker, BA; Butler, G; Lott, TJ; ; (2006) ‘Molecular genotyping of Candida parapsilosis group I clinical isolates by analysis of polymorphic microsatellite markers’. Journal of Clinical Microbiology, 44 (3):750-759.

Lasker, BA,Butler, G,Lott, TJ; (2006) ‘Molecular genotyping of Candida parapsilosis group I clinical isolates by analysis of polymorphic microsatellite markers’. Journal of Clinical Microbiology, 44 :750-759. [DOI]

MacCallum, DM,Findon, H,Kenny, CC,Butler, G,Haynes, K,Odds, FC; (2006) ‘Different consequences of ACE2 and SW15 gene disruptions for virulence of pathogenic and nonpathogenic yeasts’. Infection and Immunity, 74 :5244-5248. [DOI]

Fitzpatrick, DA,Logue, ME,Stajich, JE,Butler, G; (2006) ‘A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis’. BMC Evolutionary Biology, 6 . [DOI]

Mulhern, SM,Logue, ME,Butler, G; (2006) ‘Candida albicans transcription factor Ace2 regulates metabolism and is required for filamentation in hypoxic conditions’. Cell, 5 :2001-2013. [DOI]

Butler G, Logue ME, Stajich JE, Fitzpatrick DA, ; (2006) ‘A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis’. BMC Evolutionary Biology, 6 . [DOI]

Fitzpatrick, DA; Logue, ME; Stajich, JE; Butler, G; ; (2006) ‘A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis’. BMC EVOLUTIONARY BIOLOGY, 6 (NA).

MacCallum, DM; Findon, H; Kenny, CC; Butler, G; Haynes, K; Odds, FC; ; (2006) ‘Different consequences of ACE2 and SW15 gene disruptions for virulence of pathogenic and nonpathogenic yeasts’. Infection and Immunity, 74 (9):5244-5248.

Mulhern, SM; Logue, ME; Butler, G; ; (2006) ‘Candida albicans transcription factor Ace2 regulates metabolism and is required for filamentation in hypoxic conditions’. EUKARYOTIC CELL, 5 (12):2001-2013.

Logue, ME; Wong, S; Wolfe, KH; Butler, G; ; (2005) ‘A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 allele at its mating type locus’. Eukaryotic Cell, 4 (6):1009-1017.

Laffey, SF,Butler, G; (2005) ‘Phenotype switching affects biofilm formation by Candida parapsilosis’. MICROBIOL-SGM, 151 :1073-1081. [DOI]

Logue, ME,Wong, S,Wolfe, KH,Butler, G; (2005) ‘A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 allele at its mating type locus’. Cell, 4 :1009-1017. [DOI]