2017

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. eLife.23250.

2016

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. mBio.01514-16. 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. eLife.18981. 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.  

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

earlier publications