Genome, Fungal

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  Subject Areas on Research

  • A High-Resolution Map of Meiotic Recombination in Cryptococcus deneoformans Demonstrates Decreased Recombination in Unisexual Reproduction. 
  • A PCR-based strategy to generate integrative targeting alleles with large regions of homology. 
  • A Rac homolog functions downstream of Ras1 to control hyphal differentiation and high-temperature growth in the pathogenic fungus Cryptococcus neoformans. 
  • A eukaryote-like cardiolipin synthase is present in Streptomyces coelicolor and in most actinobacteria. 
  • A fluorogenic C. neoformans reporter strain with a robust expression of m-cherry expressed from a safe haven site in the genome. 
  • A multispecies-based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae. 
  • A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. 
  • A unique chromosomal rearrangement in the Cryptococcus neoformans var. grubii type strain enhances key phenotypes associated with virulence. 
  • Advances in understanding the evolution of fungal genome architecture. 
  • Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt. 
  • Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. 
  • Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss. 
  • Aquaporins in Saccharomyces: Characterization of a second functional water channel protein. 
  • Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists. 
  • Assessing transcription factor motif drift from noisy decoy sequences. 
  • Centromere scission drives chromosome shuffling and reproductive isolation. 
  • Chromosomal translocation and segmental duplication in Cryptococcus neoformans. 
  • Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites. 
  • Circadian clock-controlled genes isolated from Neurospora crassa are late night- to early morning-specific. 
  • Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. 
  • Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. 
  • Comparative genome-wide screening identifies a conserved doxorubicin repair network that is diploid specific in Saccharomyces cerevisiae. 
  • Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. 
  • Comparative genomics applied to Mucor species with different lifestyles. 
  • Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens. 
  • Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. 
  • Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi. 
  • Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans. 
  • Components of a new gene family of ferroxidases involved in virulence are functionally specialized in fungal dimorphism. 
  • Conservation, duplication, and loss of the Tor signaling pathway in the fungal kingdom. 
  • Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon. 
  • Conserved nucleosome positioning defines replication origins. 
  • Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes. 
  • Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. 
  • Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms. 
  • Deciphering the model pathogenic fungus Cryptococcus neoformans. 
  • Delineating the requirements for spontaneous DNA damage resistance pathways in genome maintenance and viability in Saccharomyces cerevisiae. 
  • Development and characterization of a genetic linkage map of Cryptococcus neoformans var. neoformans using amplified fragment length polymorphisms and other markers. 
  • Direct allelic variation scanning of the yeast genome. 
  • Disruption of a nonribosomal peptide synthetase in Aspergillus fumigatus eliminates gliotoxin production. 
  • Distribution and abundance of microsatellites in the yeast genome can Be explained by a balance between slippage events and point mutations. 
  • Double-strand breaks associated with repetitive DNA can reshape the genome. 
  • E Pluribus Unum: The Fungal Kingdom as a Rosetta Stone for Biology and Medicine. 
  • Enfumafungin synthase represents a novel lineage of fungal triterpene cyclases. 
  • Estimating genomic coexpression networks using first-order conditional independence. 
  • Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus. 
  • Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans. 
  • Evolution of pathogenicity and sexual reproduction in eight Candida genomes. 
  • Evolution of the sex-related locus and genomic features shared in microsporidia and fungi. 
  • Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication. 
  • Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans. 
  • Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. 
  • Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination. 
  • Fungal horizons: the Asilomar Fungal Genetics Conference 2007. 
  • Fungal mating: Candida albicans flips a switch to get in the mood. 
  • Fungal pathogenesis: gene clusters unveiled as secrets within the Ustilago maydis code. 
  • Gene Network Polymorphism Illuminates Loss and Retention of Novel RNAi Silencing Components in the Cryptococcus Pathogenic Species Complex. 
  • Gene prediction and verification in a compact genome with numerous small introns. 
  • Genetic Control of Genomic Alterations Induced in Yeast by Interstitial Telomeric Sequences. 
  • Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete. 
  • Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to Cryptococcus Pathogens. 
  • Genetic isolation between two recently diverged populations of a symbiotic fungus. 
  • Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii. 
  • Genome sequencing and analysis of Aspergillus oryzae. 
  • Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. 
  • Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. 
  • Genome-destabilizing effects associated with top1 loss or accumulation of top1 cleavage complexes in yeast. 
  • Genome-wide analysis of genomic alterations induced by oxidative DNA damage in yeast. 
  • Genome-wide analysis of re-replication reveals inhibitory controls that target multiple stages of replication initiation. 
  • Genome-wide association analysis of clinical vs. nonclinical origin provides insights into Saccharomyces cerevisiae pathogenesis. 
  • Genome-wide functional analysis of phosphatases in the pathogenic fungus Cryptococcus neoformans. 
  • Genome-wide high-resolution mapping of UV-induced mitotic recombination events in Saccharomyces cerevisiae. 
  • Genome-wide high-resolution mapping of chromosome fragile sites in Saccharomyces cerevisiae. 
  • Genomes of Ashbya fungi isolated from insects reveal four mating-type loci, numerous translocations, lack of transposons, and distinct gene duplications. 
  • Genomic deletions and point mutations induced in Saccharomyces cerevisiae by the trinucleotide repeats (GAA·TTC) associated with Friedreich's ataxia. 
  • Genomic evidences for the existence of a phenylpropanoid metabolic pathway in Aspergillus oryzae. 
  • Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis. 
  • Genomic mismatch scanning: a new approach to genetic linkage mapping. 
  • Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. 
  • Genomic structure of and genome-wide recombination in the Saccharomyces cerevisiae S288C progenitor isolate EM93. 
  • Genomics of Aspergillus oryzae. 
  • Genomics reveals traces of fungal phenylpropanoid-flavonoid metabolic pathway in the f ilamentous fungus Aspergillus oryzae. 
  • Global analysis of the evolution and mechanism of echinocandin resistance in Candida glabrata. 
  • Going green in Cryptococcus neoformans: the recycling of a selectable drug marker. 
  • HDAC genes play distinct and redundant roles in Cryptococcus neoformans virulence. 
  • Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. 
  • High-Resolution Mapping of Homologous Recombination Events in rad3 Hyper-Recombination Mutants in Yeast. 
  • High-resolution genome-wide analysis of irradiated (UV and γ-rays) diploid yeast cells reveals a high frequency of genomic loss of heterozygosity (LOH) events. 
  • Identification and characterization of rns4/vps32 mutation in the RNase T1 expression-sensitive strain of Saccharomyces cerevisiae: Evidence for altered ambient response resulting in transportation of the secretory protein to vacuoles. 
  • Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarray. 
  • Identification of clinical strains of Candida albicans by DNA fingerprinting with the polymerase chain reaction. 
  • Identification of csypyrone B1 as the novel product of Aspergillus oryzae type III polyketide synthase CsyB. 
  • Identification of the mating-type (MAT) locus that controls sexual reproduction of Blastomyces dermatitidis. 
  • Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). 
  • Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. 
  • Light controls growth and development via a conserved pathway in the fungal kingdom. 
  • Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae. 
  • Mapping nucleosome positions using DNase-seq. 
  • Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. 
  • Mechanistic plasticity of sexual reproduction and meiosis in the Candida pathogenic species complex. 
  • Metal Chelation as a Powerful Strategy to Probe Cellular Circuitry Governing Fungal Drug Resistance and Morphogenesis. 
  • Microbe Profile: Cryptococcus neoformans species complex. 
  • Microsatellite analysis of genetic diversity among clinical and nonclinical Saccharomyces cerevisiae isolates suggests heterozygote advantage in clinical environments. 
  • Microsporidia evolved from ancestral sexual fungi. 
  • Modeling the function of bacterial virulence factors in Saccharomyces cerevisiae. 
  • Molecular Tools for Carotenogenesis Analysis in the Mucoral Mucor circinelloides. 
  • Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair. 
  • Natural variation in CDC28 underlies morphological phenotypes in an environmental yeast isolate. 
  • Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans. 
  • Ninety-six haploid yeast strains with individual disruptions of open reading frames between YOR097C and YOR192C, constructed for the Saccharomyces genome deletion project, have an additional mutation in the mismatch repair gene MSH3. 
  • Non-coding RNA prediction and verification in Saccharomyces cerevisiae. 
  • Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae. 
  • Phycomyces MADB interacts with MADA to form the primary photoreceptor complex for fungal phototropism. 
  • Phylogenetic and Phylogenomic Definition of Rhizopus Species. 
  • Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. 
  • Polymerase chain reaction fingerprinting in fungi using single primers specific to minisatellites and simple repetitive DNA sequences: strain variation in Cryptococcus neoformans. 
  • Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems. 
  • Population perspectives on functional genomic variation in yeast. 
  • Prolyl isomerases in yeast. 
  • Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis. 
  • Rapid mapping of insertional mutations to probe cell wall regulation in Cryptococcus neoformans. 
  • Recent evolution of the human pathogen Cryptococcus neoformans by intervarietal transfer of a 14-gene fragment. 
  • Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. 
  • Regulation of genome stability by TEL1 and MEC1, yeast homologs of the mammalian ATM and ATR genes. 
  • Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. 
  • RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data. 
  • Saccharomyces cerevisiae: population divergence and resistance to oxidative stress in clinical, domesticated and wild isolates. 
  • Sex in the Mucoralean fungi. 
  • Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi. 
  • Showcasing Fungal Genetics & Genomics with the Genetics Society of America. 
  • Spontaneous frameshift mutations in Saccharomyces cerevisiae: accumulation during DNA replication and removal by proofreading and mismatch repair activities. 
  • Ssk2 mitogen-activated protein kinase kinase kinase governs divergent patterns of the stress-activated Hog1 signaling pathway in Cryptococcus neoformans. 
  • Stable isotope analyses reveal previously unknown trophic mode diversity in the Hymenochaetales. 
  • The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. 
  • The 2013 Thomas Hunt Morgan Medal: Thomas Douglas Petes. 
  • The 9-1-1 checkpoint clamp physically interacts with polzeta and is partially required for spontaneous polzeta-dependent mutagenesis in Saccharomyces cerevisiae. 
  • The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. 
  • The Cryptococcus neoformans genome sequencing project. 
  • The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. 
  • The evolution of sex: a perspective from the fungal kingdom. 
  • The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. 
  • The impact of local genome sequence on defining heterochromatin domains. 
  • The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. 
  • The polymerase eta translesion synthesis DNA polymerase acts independently of the mismatch repair system to limit mutagenesis caused by 7,8-dihydro-8-oxoguanine in yeast. 
  • The reference genome sequence of Saccharomyces cerevisiae: then and now. 
  • Theoretical and practical advances in genome halving. 
  • Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans. 
  • Topoisomerase I and Genome Stability: The Good and the Bad. 
  • Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level. 
  • Uncoupling of genomic and epigenetic signals in the maintenance and inheritance of heterochromatin domains in fission yeast. 
  • Unisexual reproduction of Cryptococcus gattii. 
  • Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. 
  • Variation in efficiency of DNA mismatch repair at different sites in the yeast genome. 
  • Verification of a new gene on Saccharomyces cerevisiae chromosome III. 
  • Whole genome genetic-typing in yeast using high-density oligonucleotide arrays. 
  • Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum. 
  • Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. 
  • Yeast microarrays for genome wide parallel genetic and gene expression analysis. 
  • dUTP incorporation into genomic DNA is linked to transcription in yeast. 
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  Keywords of People

  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Magwene, Paul Mitaari, Professor of Biology, Biology
  • Shinohara, Mari L., Associate Professor of Immunology, Immunology