2023
Fowler KR, Leon F, Johnson A.D. Ancient transcriptional regulators can easily evolve new pair-wise cooperativity. Proc Natl Acad Sci USA. 2023 July 11; 120(28): e2302445120.
Lee CD, Ziv N, Johnson A.D. Cell-type memory in single-cell eukaryote requires the continuous presence of a specific transcription regulator. Proc Natl Acad Sci USA. 2023 May 23;120(21):e2220568120.
2022
Ziv N, Brenes LR, Johnson A.D. Multiple molecular events underlie stochastic switching between 2 heritable cell states in fungi. Plos Biol. 2022;20(5):e3001657. PDF
2021
Singh-Babak S.D., Babak T., Fraser H.B., Johnson A.D. (2021). Lineage-specific selection and the evolution of virulence in the Candida clade. Proc. Natl. Acad. Sci. USA. March 2021:118(12): e2016818118. PDF
Mancera E., Nocedal I., Hammel S., Gulati M., Mitchell K.F., Andes D.R., Nobile C.J., Butler G., Johnson A.D. Evolution of the complex transcription network controlling biofilm formation in Candida species. ELife.2021Apr7;10:e64682. PDF
West P.T., Peters S.L., Olm M.R., Yu F.B., Gause H., Lou Y.C., Firek B.A., Baker R., Johnson A.D., Morowitz M.J., Hettich R.L., Banfield J.F. Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics. Microbiome. 2021;9(1):142. PDF
2020
Lohse M.B., Ennis C.L., Hartooni N., Johnson A.D., Nobile C.J. A screen for small molecules to target Candida albicans biofilms. Journal Fungi. 2020 Dec. PDF
Nobile C.J., Ennis C.L., Hartooni N., Johnson A.D., Lohse M.B. A selective serotonin reuptake inhibitor, a proton pump inhibitor, and two calcium channel blockers inhibit Candida albicans biofilms. Microorganisms. 2020 May; 8(5):microorganisms8050756. PDF
Lohse M.B., Gulati M., Craik C.S., Johnson A.D., Nobile C.J. Combination of antifungal drugs and protease inhibitors prevent Candida albicans biofilm formation and disrupt mature biofilms. Frontiers in Microbiology 2020 May 25. PDF
Brenes L.R., Lohse M.B., Hartooni N., Johnson A.D. A set of diverse genes influence the frequency of white-opaque switching in Candida albicans. G3 (Bethesda). 2020 Aug; 10(8):g3.120.401249. PDF
Lohse M.B., Brenes L.R., Ziv N., Winter M.B., Craik C.S., Johnson A.D. An opaque cell-specific expression program of secreted proteases and transporters allows cell-type cooperation in Candida albicans. Genetics. 2020 Aug; genetics.303613.2020. PDF
Britton C.S., Sorrells T.R., Johnson A.D. Protein-coding changes preceded cis-regulatory gains in newly evolved transcription circuit. Science. 2020 Jan; 367(6473):96-100. PDF
2019
Dalal C.K., Zuleta I.A., Lohse M.B., Zordan R.E., El-Samad H., Johnson A.D. A population shift between two heritable cell types of the pathogen Candida albicans is based both on switching and selective proliferation. Proc. Natl. Acad. Sci. USA. 2019 Dec; 116(52):26918-26924 PDF
Takagi J., Singh-Babak S.D., Lohse, M.B., Dalal C.K., Johnson A.D. Candida albicans white and opaque cells exhibit distinct spectra of organ colonization in mouse models of infection. PLoS ONE, 2019 June; 14(6): e0218037. PDF
2018
Sorrells T.R., Johnson A.N., Howard C.J., Britton C.S., Fowler K.R., Feigerle J.T., Weil P.A., Johnson A.D. Intrinsic cooperativity potentiates parallel cis-regulatory evolution. eLife. 2018 Sep 10; pii: e37563. PDF
Lohse M.B., Gulati M., Johnson A.D., Nobile C.J. Development and regulation of single- and multi-species Candida albicans biofilms. Nature Reviews Microbiology. 2018 Jan. PDF
2017
Dalal C.K. and Johnson, A.D. How transcription circuits explore alternative architectures while maintaining overall circuit output. Genes and Development. 2017 Jul 15. PDF
Craik V.B., Johnson, A.D., Lohse M.B. Sensitivity of White and Opaque Candida albicans to Antifungal Drugs. Antimicrobial Agents and Chemotherapy. 2017 May 15; pii. AAC.00166-17
Nocedal I., Mancera E., Johnson, A.D. Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator. eLife 2017 Mar 22; pii. e23250. PDF
Lohse M.B., Gulati M., Arevalo A.V., Fishburn A., Johnson A.D., Nobile C.J. Assessment and optimizations of Candida albicans in vitro biofilm assays. Antimicrobial Agents and Chemotherapy. 2017 Mar 13; pii: AAC.02749-16.
2016
Ene I.V., Lohse M.B., Vladu A.V., Morschhäuser J., Johnson A.D., Bennet R.J. Phenotypic Profiling Reveals that Candida albicans Opaque Cells Represent a Metabolically Specialized Cell State Compared to Default White Cells. mBio 2016 Nov 22; pii. e01269-16 PDF
Winter M.B., Salcedo E.C., Lohse M.B., Hartooni N., Gulati M., Sanchez H., Takagi J., Hube B., Andes D.R., Johnson A.D., Craik C.S., Nobile C.J. Global Identification of Biofilm-Specific Proteolysis in Candida albicans. MBio 2016 Sep 13; pii. e01514-16. PDF
Dalal C.K., Zuleta I.A., Mitchell K.F., Andes D.R., El-Samad H., Johnson A.D. Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression. eLife. 2016 Sep 10; pii. e18981. PDF
Hanson-Smith V., Johnson A.D. PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories. PLoS Computational Biology. 2016 Jul 29. PDF
Lohse M.B., Ene I.V., Craik V.B., Hernday A.D., Mancera E., Morschhäuser J., Bennett R.J., Johnson A.D. Systematic Genetic Screen for Transcriptional Regulators of the Candida albicans White-Opaque Switch. Genetics. 2016 Jun 8; pii. genetics.116.190645. PDF
Lohse M.B., Kongsomboovech P., Madrigal M., Hernday A.D., Nobile, C.J. Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts. Yeast Functional Genomics: Methods and Protocols. 2016. PDF
Hernday A.D., Lohse M.B., Nobile C.J., Noiman L., Laksana C.N., Johnson A.D. Ssn6 Defines a New Level of Regulation of White-Opaque Switching in Candida albicans and Is Required For the Stochasticity of the Switch. MBio. 2016 Jan 26;7(1). pii: e01565-15. PDF
Lohse M.B., Johnson A.D. Identification and Characterization of Wor4, a New Transcriptional Regulator of White-Opaque Switching. G3 (Bethesda). 2016 Jan 15. pii: g3.115.024885. PDF
2015
Nocedal I., Johnson A.D. How Transcription Networks Evolve and Produce Biological Novelty. Cold Spring Harb Symp Quant Biol. 2015 Dec 9. pii: 027557 PDF
Nobile C.J., Johnson A.D. Candida albicans Biofilms and Human Disease. Annu Rev Microbiol. 69:71-92. PDF
Sorrells T.R., Booth L.N., Tuch B.B., Johnson A.D. (2015) Intersecting transcription networks constrain gene regulatory evolution. Nature. 2015 Jul 16;523(7560):361-5. PDF
Sorrells T.R., Johnson A.D. (2015) Making Sense of Transcription Networks. Cell 161(4):714-723 PDF
Fox E.P., Bui C.K., Nett J.E., Hartooni N., Mui M.C., Andes D.R., Nobile C.J., Johnson A.D. (2015) An expanded regulatory network temporally controls Candida albicans biofilm formation. Mol Microbiol PDF
Mancera E., Porman A.M., Cuomo C.A., Bennett R.J., Johnson A.D. (2015) Finding a Missing Gene: EFG1 Regulates Morphogenesis in Candida tropicalis. G3 5(5):849-56. PDF
2014
Howard, C.J., Hanson-Smith, V., Kennedy, K.J., Miller, C.J., Lou, H.J., Johnson, A.D., Turk, B.E., Holt, L.J. (2014) Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity. eLife 3 PDF
Fox, E.P., Cowley, E.S., Nobile, C.J., Hartooni, N., Newman, D.K., Johnson, A.D. (2014) Anaerobic bacteria grow within Candida albicans biofilms and induce biofilm formation in suspension cultures. Curr Biol 24(20):2411-6 PDF
Lohse, M.B., Rosenberg, O.S., Cox, J.S., Stroud, R.M., Finer-Moore, J.S., Johnson, A.D. (2014) Structure of a new DNA-binding domain which regulates pathogenesis in a wide variety of fungi. Proc Natl Acad Sci 111(29):10404-10 PDF
Nobile, C.J., Fox, E.P., Hartooni, N., Mitchell, K.F., Hnisz, D., Andes, D.R., Kuchler, K., Johnson, A.D. (2014) A histone deacetylase complex mediates biofilm dispersal and drug resistance in Candida albicans. MBio 5(3):e01201-14 PDF
Pérez, J.C., Fordyce, P.M., Lohse, M.B., Hanson-Smith, V., DeRisi, J.L., Johnson, A.D. (2014) How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes. Genes Dev 28(12):1272-7 PDF
2013
Pérez, J.C., Johnson, A.D. (2013) Regulatory circuits that enable proliferation of the fungus Candida albicans in a Mammalian Host. PLoS Pathogens vol. 9 (12) pp. e1003780 PDF
Baker, C.B., Hanson-Smith, V., Johnson, A.D. (2013) Following gene duplication, paralog interference constrains transcriptional circuit evolution. Science vol. 342 (6154) pp. 104-108 PDF
Hernday, A.D., Lohse, M.B., Fordyce, P.M., Nobile, C.J., DeRisi, J.L., Johnson, A.D. (2013) Structure of the transcriptional network controlling white-opaque switching in Candida albicans. Molecular Microbiology 90(1) 22 PDF
Lohse, M.B., Hernday, A.D., Fordyce, P.M., Noiman, L., Sorrells, T.R., Hanson-Smith V., Nobile, C.J., DeRisi, J.L., Johnson, A.D. (2013) Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains. Proc. Natl. Acad. Sci. USA 110:7660-7665. PDF
Pérez, J.C., Kumamoto, C.A., Johnson, A.D. (2013) Candida albicans Commensalism and Pathogenicity Are Intertwined Traits Directed by a Tightly Knit Transcriptional Regulatory Circuit. PLoS Biology 11(3): e1001510. PDF
2012
Fox, E.P., Nobile, C.J. (2012) Untangling the transcriptional network controlling biofilm development in Candida albicans. Transcription. 3(6): 315–322 PDF
Baker, C.R., Booth, L.N., Sorrells, T.R., Johnson, A.D. (2012) Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification. Cell. 151:80-95 PDF
Nobile, C.J., Fox, E.P., Nett, J.E., Sorrells, T.R., Mitrovich, Q.M., Hernday, A.D., Tuch, B.B., Andes, D.R., Johnson, A.D. (2012) A recently evolved transcriptional network controls biofilm development in Candida albicans. Cell. 148:126-38 PDF
Cain, C.W., Lohse, M.B., Homann, O.R., Sil, A., Johnson, A.D. (2012). A conserved transcriptional regulator governs fungal morphology in widely diverged species. Genetics. 190:511-21. PDF
2011
Baker, C.R., Tuch, B.B., Johnson, A.D. (2011) Extensive DNA-binding specificity divergence of a conserved transcription regulator. Proc. Natl. Acad. Sci. USA 108:7493-7498. PDF
2010
Booth, L.N., Tuch, B., Johnson, A.D. (2010). Intercalation of a new tier of transcription regulation into an ancient circuit. Nature 468:959-963. PDF
Mitrovich, Q.M., Tuch, B.B., De La Vega, F.M., Guthrie, C., Johnson, A.D. (2010). Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss. Science 303: 838-841. PDF
Hernday, A.D., Noble, S.M., Mitrovich, Q.M., Johnson, A.D. (2010). Genetics and molecular biology in Candida albicans. Methods Enzymol. 470:737-758. PDF
Li, H., Johnson, A.D. (2010). Evolution of transcription networks—lessons from yeasts. Curr. Biol. 20:R746-753. PDF
Tuch, B.B., Mitrovich, Q.M., Homann, O.R., Hernday, A.D., Monighetti, C.K., De La Vega, F.M., Johnson, A.D. (2010). The transcriptomes of two heritable cell types illuminate the circuit governing their differentiation. PLoS Genet. 6(8):e1001070. PDF
Lohse, M.B., Johnson, A.D. (2010). Temporal anatomy of an epigenetic switch in cell programming: the white-opaque transition of C. albicans. Mol. Microbiol. 78:331-343. PDF
Lohse, M.B., Zordan, R.E., Cain, C.W., Johnson, A.D. (2010). Distinct class of DNA-binding domains is exemplified by a master regulator of phenotypic switching in Candida albicans. Proc. Natl. Acad. Sci. USA 107:14105-14110. PDF
Noble, S.M., French, S., Kohn, L.A., Chen, V., Johnson, A.D. (2010). Systematic screens of a Candida albicans homozygous deletion library decouple morphogenetic switching and pathogenicity. Nature Genetics. 42:590-598. PDF
Homann OR, Johnson AD (2010) MochiView: versatile software for genome browsing and DNA motif analysis. BMC Biol. 21;8:49. PDF
2009
Homann, O.R., Dea, J., Noble, S.M., Johnson, A.D. (2009) A phenotypic profile of the Candida albicans regulatory network. PLoS Genet. 5(12):e1000783. PDF
Stroschein-Stevenson, S.L., Foley, E., O'Farrell, P.H., and Johnson, A.D. (2009) Phagocytosis of Candida albicans by RNAi-treated Drosophilia S2 cells. Methods Mol Biol 470:347-58. PDF
Lohse, M.B., Johnson, A.D. (2009) White-opaque switching in Candida albicans. Curr. Opin. Microbiol. 12(6):650-4. PDF
Elson, S.L., Noble, S.M., Solis, N.V., Filler, S.G., Johnson, A.D. (2009) An RNA transport system in Candida albicans regulates hyphal morphology and invasive growth. PLoS Genetics 5(9):e1000664. PDF
Holt, L.J., Tuch, B.B., Villén, J., Johnson, A.D., Gygi, S.P., Morgan, D.O. (2009) Global analysis of Cdk1 substrate Phosphorylation sites provides insights into evolution. Science 325(5948):1682-1686. PDF
Nobile, C.J., Nett J.E., Hernday, A.D., Homann, O.R., Deneault, J., Nantel, A., Andes, D.R., Johnson, A.D., and Mitchell, A.P. (2009) Biofilm matrix regulation by Candida albicans Zap1. PLoS Biology 7(6):e1000133. PDF
2008
Tuch, B.B., Li, H., & Johnson, A.D. (2008). Evolution of eukaryotic transcription circuits. Science 319:1797-1799. PDF
Tuch, B.B., Galgoczy, D.J., Hernday, A.D., Li H., Johnson A.D. (2008). The evolution of combinatorial gene regulation in fungi. PLoS Biology 6(2):e38. PDF
Lohse, M.B., & Johnson, A.D. (2008). Differential phagocytosis of white versus opaque Candida albicans by Drosophila and mouse phagocytes. PLoS One 3(1). PDF
2007
Zordan R.E., Miller M.G., Galgoczy D.J., Tuch B.B., Johnson A.D. (2007). Interlocking transcriptional feedback loops control white-opaque switching in Candida albicans. PLoS Biology 5(10)e256. PDF
Noble, S.M., & Johnson, A.D. (2007). Genetics of Candida albicans, a diploid human fungal pathogen. Annu. Rev. Genet. 41:193-211. PDF
Mitrovich, Q.M., Tuch, B.B., Guthrie, C., Johnson, A.D. (2007). Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans. Genome Res. 17:492-502. PDF
2006
Tsong, A.E., Tuch, B.B., Li, H. Johnson, A.D. (2006). Evolution of alternative transcriptional circuits with identical logic. Nature 443(7110):415-20. PDF
Bennett, R.J., & Johnson, A.D. (2006). The role of nutrient regulation and the Gpa2 protein in the mating pheromone response of C. albicans. Mol. Microbiol. 62:100-19. PDF
Zordan, R.E., Galgoczy, D.J., & Johnson, A.D. (2006). Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop. Proc. Natl. Acad. Sci. USA 103:12807-12812. PDF
Stroschein-Stevenson, S.L., Foley, E., O'Farrell, P.H., Johnson, A.D. (2006). Identification of Drosophila gene products required for phagocytosis of Candida albicans. PLoS Biology 4(1) e4. PDF
2005
Hromatka, B.S., Noble, S.M., Johnson, A.D. (2005). Transcriptional response of C. albicans to nitric oxide and the role of the YHB1 gene in nitrosative stress and virulence. Mol. Biol. Cell 16: 4814-4826. PDF
Bennett, R.J., and Johnson, A.D. (2005). Mating in Candida albicans and the search for a sexual cycle. Annu. Rev. Microbiol. 59:233-255. PDF
Green, S.R., and Johnson, A.D. (2005). Genome-wide analysis of the functions of a conserved surface on the corepressor Tup1. Mol. Biol. Cell 16:2605-2613. PDF
Noble, S. and Johnson, A.D. (2005). Strains and strategies for large-scale gene deletion studies of the diploid human fungal pathogen, Candida albicans. Eukaryot. Cell 4:298-309. PDF
Kadosh, D. and Johnson, A.D. (2005). Induction of the Candida albicans filamentous growth program by relief of transcriptional repression: a genome-wide analysis. Mol. Biol. Cell 16:2903-2912. PDF
Bennett, R.J., Miller, M.G., Chua, P.R., Maxon, M.E., Johnson, A.D. (2005). Nuclear fusion occurs during mating in C. albicans and is dependent on the KAR3 gene. Mol. Micro. 55:1046-1059. PDF
2004
Galgoczy, D.J., Cassidy-Stone, A., Llinás, M., O’Rourke, S.M., Herskowitz, I., DeRisi, J.L., Johnson, A.D. (2004). Genomic dissection of the cell-type-specification circuit in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 101:18069-18074. PDF
Green, S. R., and Johnson, A.D. (2004). Promoter-dependent Roles for the Srb10 Cyclin-dependent kinase and the Hda1 Deacetylase in Tup1-mediated Repression in Saccharomyces cerevisiae. Mol. Biol. Cell 15:4191-4202. PDF
2003
Tsong, A.E., Miller, M.G., Raisner, R.M., and Johnson, A.D. (2003). Evolution of a combinatorial transcriptional circuit: a case study in yeasts. Cell 115:389-399. PDF
Bennett, R.J., Uhl, M.A., Miller, M.G., and Johnson, A.D. (2003). Identification and characterization of a Candida albicans mating pheromone. Mol. Cell. Biol. 23:8189-8201. PDF
Uhl, M.A., Biery, M., Craig, N., and Johnson, A.D. (2003). Haploinsufficiency-based large-scale forward genetic analysis of filamentous growth in the diploid human fungal pathogen C. albicans. EMBO J. 22:2668-2678. PDF
Bennett, R.J., and Johnson, A.D. (2003). Completion of a parasexual cycle in Candida albicans by induced chromosome loss in tetraploid strains. EMBO J. 22:2505-2515. PDF