The evolution of combinatorial gene regulation in fungi

Cited by (228)

Items 101–200 of 228

1. Regulation of filamentation in the human fungal pathogen C andida tropicalis
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2. Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans
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3. How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes
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4. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering
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5. Biophysical Fitness Landscapes for Transcription Factor Binding Sites
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7. Recent advances on Candida albicans biology and virulence
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8. The Glucocorticoid Receptor and the Coregulator Brm Selectively Modulate Each Other's Occupancy and Activity in a Gene-Specific Manner
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9. A Functional Portrait of Med7 and the Mediator Complex in Candida albicans
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10. Variable Transcription Factor Binding: A Mechanism of Evolutionary Change
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11. Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks
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12. Taking apart Rap1
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13. Cell Cycle Regulated Gene Expression in Yeasts
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14. Evolution of gene regulatory network architectures: Examples of subcircuit conservation and plasticity between classes of echinoderms
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15. Conservation of transcription factor binding events predicts gene expression across species
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16. Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects
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17. The two‐component response regulator Skn7 belongs to a network of transcription factors regulating morphogenesis in Candida albicans and independently limits morphogenesis‐induced ROS accumulation
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18. Inherited adaptation of genome‐rewired cells in response to a challenging environment
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19. A New System for Comparative Functional Genomics of Saccharomyces Yeasts
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20. How Transcription Networks Evolve and Produce Biological Novelty
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21. Metabolic regulation in model ascomycetes – adjusting similar genomes to different lifestyles
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22. Generalizing and learning protein-DNA binding sequence representations by an evolutionary algorithm
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23. Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies
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24. Identification and Characterization of Lineage-Specific Highly Conserved Noncoding Sequences in Mammalian Genomes
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25. Asymmetric positive feedback loops reliably control biological responses
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26. How transcription circuits explore alternative architectures while maintaining overall circuit output
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27. Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway
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28. Structure, evolution and dynamics of transcriptional regulatory networks
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29. Fungal regulatory evolution: cis and trans in the balance
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30. Role of a Candida albicans Nrm1/Whi5 homologue in cell cycle gene expression and DNA replication stress response
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31. Rewiring of the Ppr1 Zinc Cluster Transcription Factor from Purine Catabolism to Pyrimidine Biogenesis in the Saccharomycetaceae
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32. Pervasive Variation of Transcription Factor Orthologs Contributes to Regulatory Network Evolution
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33. Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes
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34. Induction of Candida albicans Drug Resistance Genes by Hybrid Zinc Cluster Transcription Factors
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35. Protein evolution in yeast transcription factor subnetworks
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36. Is Transcription Factor Binding Site Turnover a Sufficient Explanation for Cis-Regulatory Sequence Divergence?
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37. Patterns of Conservation and Diversification in the Fungal Polarization Network
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38. Decoupling of divergent gene regulation by sequence-specific DNA binding factors
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39. Multiple Genomic Changes Associated with Reorganization of Gene Regulation and Adaptation in Yeast
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40. Coupling Phosphate Homeostasis to Cell Cycle-Specific Transcription: Mitotic Activation of Saccharomyces cerevisiae PHO5 by Mcm1 and Forkhead Proteins
    Santhi Pondugula, Daniel W. Neef, Warren P. Voth, Russell P. Darst, Archana Dhasarathy, Melissa Reynolds, Shinya Takahata, David J. Stillman, Michael P. Kladde · 2009 · Molecular and Cellular Biology
41. The Reconstruction of Condition-Specific Transcriptional Modules Provides New Insights in the Evolution of Yeast AP-1 Proteins
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42. CCAT: Combinatorial Code Analysis Tool for transcriptional regulation
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43. Chimeric Sex-Determining Chromosomal Regions and Dysregulation of Cell-Type Identity in a Sterile Zygosaccharomyces Allodiploid Yeast
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44. Transcriptional Control of Hypoxic Hyphal Growth in the Fungal Pathogen Candida albicans
    Manon Henry, Anaïs Burgain, Faïza Tebbji, Adnane Sellam · 2022 · Frontiers in Cellular and Infection Microbiology
45. Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis
    Michalis Barkoulas, Amhed Missael Vargas Velazquez, Alexandre E. Peluffo, Marie‐Anne Félix · 2016 · PLoS Genetics
46. The Genomic Landscape of the Fungus-Specific SWI/SNF Complex Subunit, Snf6, in Candida albicans
    Faïza Tebbji, Yaolin Chen, Adnane Sellam, Malcolm S. Whiteway · 2017 · mSphere
47. Intrinsic cooperativity potentiates parallel cis-regulatory evolution
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48. Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit
    Candace S Britton, Trevor R. Sorrells, Alexander D. Johnson · 2020 · Science
49. Evolution of a Membrane Protein Regulon in Saccharomyces
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50. A systematic, large-scale comparison of transcription factor binding site models
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51. Transient Genotype-by-Environment Interactions Following Environmental Shock Provide a Source of Expression Variation for Essential Genes
    Kevin Hasegawa Eng, Daniel J. Kvitek, Sündüz Keleş, Audrey P. Gasch · 2009 · Genetics
52. Characterization of α-factor pheromone and pheromone receptor genes of Ashbya gossypii
    Jürgen Wendland, Alexander Dünkler, Andrea Walther · 2011 · FEMS Yeast Research
53. Assessing phylogenetic motif models for predicting transcription factor binding sites
    John Hawkins, Charles E. Grant, William Stafford Noble, Timothy L. Bailey · 2009 · Bioinformatics
54. DYRK-family kinases regulate Candida albicans morphogenesis and virulence through the Ras1/PKA pathway
    Jessie MacAlpine, Zhongle Liu, Saif Hossain, Luke J. Whitesell, Nicole Robbins, Leah E. Cowen · 2023 · mBio
55. Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach
    Emiliano Rodríguez‐Mega, Alma Piñeyro‐Nelson, Crisanto Gutiérrez, Berenice García‐Ponce, María de la Paz Sánchez, Estephania Zluhan‐Martínez, Elena R Alvarez-Buylla, Adriana Garay‐Arroyo · 2015 · Developmental Dynamics
56. Plant ‘evo-devo’ goes genomic: from candidate genes to regulatory networks
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57. Protein-Protein Interactions in Candida albicans
    Floris Schoeters, Patrick Van Dijck · 2019 · Frontiers in Microbiology
58. Evolutionary divergence of the sex-determining gene MID uncoupled from the transition to anisogamy in volvocine algae
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59. Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi
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60. Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes
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61. Serial ChIP as a tool to investigate the co-localization or exclusion of proteins on plant genes
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62. Mutational Robustness of Gene Regulatory Networks
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63. A single aromatic residue in transcriptional repressor protein KorA is critical for cooperativity with its co‐regulator KorB
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64. Comparative Functional Genomics of Stress Responses in Yeasts
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65. Prediction of Phenotype-Associated Genes via a Cellular Network Approach: A Candida albicans Infection Case Study
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66. Towards an Evolutionary Model of Transcription Networks
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67. Evaluation of candidate point mutation of Kisspeptin 1 gene associated with litter size in Indian Goat breeds and its effect on transcription factor binding sites
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68. A comparative evolutionary study of transcription networks. The global role of feedback and hierachical structures
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69. The master regulator MAT1-1-1 of fungal mating binds to its targets via a conserved motif in the human pathogen Aspergillus fumigatus
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70. Analysis of flocculins in Ashbya gossypii reveals FIG2 regulation by TEC1
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71. Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution
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72. Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression
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73. Mechanisms of Drug Resistance in Fungi and Their Significance in Biofilms
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74. Morphogenic and genetic differences between Candida albicans strains are associated with keratomycosis virulence.
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75. Phenotypic Robustness and the Assortativity Signature of Human Transcription Factor Networks
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76. Inference of gene regulation functions from dynamic transcriptome data
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77. The C. elegans regulatory factor X (RFX) DAF-19M module: A shift from general ciliogenesis to cell-specific ciliary and behavioral specialization
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78. Cancer cell line specific co-factors modulate the FOXM1 cistrome
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79. A Fungal Transcription Regulator of Vacuolar Function Modulates Candida albicans Interactions with Host Epithelial Cells
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80. Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum
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81. Con7 is a key transcription regulator for conidiogenesis in the plant pathogenic fungus Fusarium graminearum
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82. ncDNA and drift drive binding site accumulation
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83. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation
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87. The Path towards Predicting Evolution as Illustrated in Yeast Cell Polarity
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93. Reconfiguration of Transcriptional Control of Lysine Biosynthesis in Candida albicans Involves a Central Role for the Gcn4 Transcriptional Activator
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94. Functional Conservation of Divergent p63-Bound cis-Regulatory Elements
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98. A Comparative Study of Network Motifs in the Integrated Transcriptional Regulation and Protein Interaction Networks of Shewanella
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100. Unravelling the regulatory network underlying divergent expression of the key lipid metabolism transcription factor SREBP in two congeneric oyster species
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