Summary: The complete gene complement contained in a set of chromosomes in a fungus.
Publications251 found, 100 shown here
- Genomic expression programs in the response of yeast cells to environmental changesA P Gasch
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5428, USA
Mol Biol Cell 11:4241-57. 2000..Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell...
- Functional profiling of the Saccharomyces cerevisiae genomeGuri Giaever
Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
Nature 418:387-91. 2002..Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics...
- Global analysis of protein expression in yeastSina Ghaemmaghami
Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94143 2240, USA
Nature 425:737-41. 2003..Many of these molecules, including essential proteins and most transcription factors, are present at levels that are not readily detectable by other proteomic techniques nor predictable by mRNA levels or codon bias measurements...
- Global analysis of protein localization in budding yeastWon Ki Huh
Howard Hughes Medical Institute, University of California San Francisco, Department of Biochemistry and Biophysics, 600 16th Street, San Francisco, California 94143 2240, USA
Nature 425:686-91. 2003....
- Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydisJörg Kämper
Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse, D 35043 Marburg, Germany
Nature 444:97-101. 2006..Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens...
- Population genomics of domestic and wild yeastsGianni Liti
Institute of Genetics, Queen s Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
Nature 458:337-41. 2009....
- The transcriptional landscape of the yeast genome defined by RNA sequencingUgrappa Nagalakshmi
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
Science 320:1344-9. 2008..We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated...
- The genome sequence of the rice blast fungus Magnaporthe griseaRalph A Dean
Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA
Nature 434:980-6. 2005..The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation...
- Evolution of pathogenicity and sexual reproduction in eight Candida genomesGeraldine Butler
UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
Nature 459:657-62. 2009..Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes...
- The genome sequence of the filamentous fungus Neurospora crassaJames E Galagan
Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA
Nature 422:859-68. 2003..Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes...
- The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specializationChristina A Cuomo
Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
Science 317:1400-2. 2007..These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts...
- Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzaeJames E Galagan
The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
Nature 438:1105-15. 2005..These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation...
- Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatusWilliam C Nierman
The Institute for Genomic Research, Rockville, Maryland 20850, USA
Nature 438:1151-6. 2005..The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus...
- The genome sequence of Schizosaccharomyces pombeV Wood
The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nature 415:871-80. 2002....
- The genome of Laccaria bicolor provides insights into mycorrhizal symbiosisF Martin
UMR 1136, INRA Nancy Université, Interactions Arbres Microorganismes, INRA Nancy, 54280 Champenoux, France
Nature 452:88-92. 2008....
- Systematic genetic analysis with ordered arrays of yeast deletion mutantsA H Tong
Banting and Best Department of Medical Research, University of Toronto, Toronto ON, Canada M5G 1L6
Science 294:2364-8. 2001..Systematic application of this approach should produce a global map of gene function...
- Dynamics of replication-independent histone turnover in budding yeastMichael F Dion
Faculty of Arts and Sciences, Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
Science 315:1405-8. 2007..In addition, rapid histone turnover is found at known chromatin boundary elements. These results suggest that rapid histone turnover serves to functionally separate chromatin domains and prevent spread of histone states...
- Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)Diego Martinez
Los Alamos National Laboratory Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico 87545, USA
Nat Biotechnol 26:553-60. 2008..Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production...
- Intragenic tandem repeats generate functional variabilityKevin J Verstrepen
Whitehead Institute for Biomedical Research Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
Nat Genet 37:986-90. 2005..We propose that variation in intragenic repeat number provides the functional diversity of cell surface antigens that, in fungi and other pathogens, allows rapid adaptation to the environment and elusion of the host immune system...
- Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78Diego Martinez
US DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Nat Biotechnol 22:695-700. 2004..This genome provides a high quality draft sequence of a basidiomycete, a major fungal phylum that includes important plant and animal pathogens...
- Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organismKatherine A Borkovich
Department of Plant Pathology, University of California, Riverside, California 92521, USA
Microbiol Mol Biol Rev 68:1-108. 2004..The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease...
- Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatusNatalie D Fedorova
The J Craig Venter Institute, Rockville, Maryland, United States of America
PLoS Genet 4:e1000046. 2008..The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories"...
- Genetic interactions between polymorphisms that affect gene expression in yeastRachel B Brem
Program in Computational Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, M2 B876, Seattle, Washington 98109, USA
Nature 436:701-3. 2005..Our results indicate that genetic interactions are widespread in the genetics of transcript levels, and that many QTLs will be missed by single-locus tests but can be detected by two-stage tests that allow for interactions...
- The chemical genomic portrait of yeast: uncovering a phenotype for all genesMaureen E Hillenmeyer
Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
Science 320:362-5. 2008..We found that 97% of gene deletions exhibited a measurable growth phenotype, suggesting that nearly all genes are essential for optimal growth in at least one condition...
- Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organizationJason M Casolari
Department of Systems Biology, Harvard Medical School and Department of Cancer Biology, The Dana Farber Cancer Institute, Boston, MA 02115, USA
Cell 117:427-39. 2004..Taken together, these results indicate that the organization of the genome is coupled via transcriptional state to the nuclear transport machinery...
- Genetic dissection of transcriptional regulation in budding yeastRachel B Brem
Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, D4 100, Seattle, WA 98109, USA and Howard Hughes Medical Institute
Science 296:752-5. 2002..We found eight such trans-acting loci, each affecting the expression of a group of 7 to 94 genes of related function...
- The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansionJeffrey J Coleman
Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
PLoS Genet 5:e1000618. 2009..Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches...
- Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogensJun Xu
Procter and Gamble Co, Miami Valley Innovation Center, Cincinnati, OH 45253 8707, USA
Proc Natl Acad Sci U S A 104:18730-5. 2007..The M. globosa genome sequence also revealed the presence of mating-type genes, providing an indication that Malassezia may be capable of sex...
- High-resolution mapping of meiotic crossovers and non-crossovers in yeastEugenio Mancera
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nature 454:479-85. 2008..In addition, because non-crossover hotspots create holes of reduced linkage within haplotype blocks, our results stress the need to incorporate non-crossovers into genetic linkage analysis...
- Genome sequencing and analysis of Aspergillus oryzaeMasayuki Machida
Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, Higashi 1 1 1, Tsukuba, Ibaraki 305 8566, Japan
Nature 438:1157-61. 2005..Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation...
- Genomics of the fungal kingdom: insights into eukaryotic biologyJames E Galagan
The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02141, USA
Genome Res 15:1620-31. 2005..Since the sequencing of the first fungus in 1996, the number of available fungal genome sequences has increased by an order of magnitude...
- Genome-scale approaches to resolving incongruence in molecular phylogeniesAntonis Rokas
Howard Hughes Medical Institute, Laboratory of Molecular Biology, R M Bock Laboratories, University of Wisconsin Madison, 1525 Linden Drive, Madison, Wisconsin 53706, USA
Nature 425:798-804. 2003..These results have important implications for resolving branches of the tree of life...
- The genome sequence of the model ascomycete fungus Podospora anserinaEric Espagne
Univ Paris Sud, Institut de Genetique et Microbiologie, UMR8621, 91405 Orsay Cedex, France
Genome Biol 9:R77. 2008..The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development...
- Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey beesR Scott Cornman
USDA ARS Bee Research Lab, Beltsville, Maryland, United States of America
PLoS Pathog 5:e1000466. 2009..cuniculi. These comparisons provide insight into the architecture, regulation, and evolution of microsporidian genomes, and will drive investigations into honey bee-Nosema interactions...
- GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomesDavid M A Martin
Post Genomics and Molecular Interactions Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
BMC Bioinformatics 5:178. 2004..GOtcha predicts GO term associations with term-specific probability (P-score) measures of confidence. Term-specific probabilities are a novel feature of GOtcha and allow the identification of conflicts or uncertainty in annotation...
- Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56Robert Driscoll
Wellcome Trust and Cancer Research U K Gurdon Institute and the Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
Science 315:649-52. 2007..These data establish Rtt109p as a member of a new class of histone acetyltransferases and show that its actions are critical for cell survival in the presence of DNA damage during S phase...
- Large-scale essential gene identification in Candida albicans and applications to antifungal drug discoveryTerry Roemer
Elitra Canada, Montreal, Quebec, Canada, H2X 3Y8
Mol Microbiol 50:167-81. 2003..albicans essential gene set, and their respective conditional mutant strains may be directly used as sensitive whole-cell assays for drug screening...
- Genome evolution in yeastsBernard Dujon
Unité de Génétique Moléculaire des Levures, URA 2171 CNRS and UFR 927 Université Pierre et Marie Curie
Nature 430:35-44. 2004....
- Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplicationLi Jun Ma
The Broad Institute of MIT and Harvard, Cambridge, MA, USA
PLoS Genet 5:e1000549. 2009..Expanded families of cell-wall synthesis enzymes, essential for fungal cell integrity but absent in mammalian hosts, reveal potential targets for novel and R. oryzae-specific diagnostic and therapeutic treatments...
- Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylationAntonis Kirmizis
Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge CB2 1QN, UK
Nature 449:928-32. 2007..Thus, the inability of Spp1 to recognize H3 methylated at R2 prevents Set1 from trimethylating H3K4. These results provide the first mechanistic insight into the function of arginine methylation on chromatin...
- Specificity and stability in topology of protein networksSergei Maslov
Department of Physics, Brookhaven National Laboratory, Upton, NY 11973, USA
Science 296:910-3. 2002..This effect decreases the likelihood of cross talk between different functional modules of the cell and increases the overall robustness of a network by localizing effects of deleterious perturbations...
- The parasexual cycle in Candida albicans provides an alternative pathway to meiosis for the formation of recombinant strainsAnja Forche
Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
PLoS Biol 6:e110. 2008..albicans. We discuss, in light of the long association of C. albicans with warm-blooded animals, the potential advantages of a parasexual cycle over a conventional sexual cycle...
- The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid speciesKevin P Byrne
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Genome Res 15:1456-61. 2005..cerevisiae (551, including 22 previously unidentified), Saccharomyces castellii (599), and Candida glabrata (404)...
- Comparative genomics of protoploid SaccharomycetaceaeJean Luc Souciet
Universite de Strasbourg, CNRS UMR, France
Genome Res 19:1696-709. 2009..Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified...
- Exploring the metabolic and genetic control of gene expression on a genomic scaleJ L DeRisi
Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA 94305 5428, USA
Science 278:680-6. 1997..These results demonstrate the feasibility and utility of this approach to genomewide exploration of gene expression patterns...
- Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenumMarco A van den Berg
DSM Anti Infectives, PO Box 425, 2600 AK Delft, The Netherlands
Nat Biotechnol 26:1161-8. 2008....
- Patterns of intron gain and loss in fungiCydney B Nielsen
Department of Biology, Massachusetts Institute of Technology Cambridge, Massachusetts, USA
PLoS Biol 2:e422. 2004..Contrary to standard models, we find no increased frequency of intron loss toward the 3' ends of genes. Thus, recent intron dynamics do not support a model whereby 5' intron positional bias is generated solely by 3'-biased intron loss...
- The origins of multicellularity: a multi-taxon genome initiativeInaki Ruiz-Trillo
Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
Trends Genet 23:113-8. 2007..Here, we introduce this initiative and the biological questions that underpin it, summarize the rationale guiding the choice of organisms and discuss the anticipated benefits to the broader scientific community...
- Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeastFeng He
Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
Mol Cell 12:1439-52. 2003....
- Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activityHuck Hui Ng
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
Mol Cell 11:709-19. 2003....
- Molecular evidence for an ancient duplication of the entire yeast genomeK H Wolfe
Department of Genetics, University of Dublin, Trinity College, Ireland
Nature 387:708-13. 1997..Tetraploidy may have facilitated the evolution of anaerobic fermentation in Saccharomyces...
- The complete sequence of the mitochondrial genome of Saccharomyces cerevisiaeF Foury
Unite de Biochimie Physiologique, Louvain la Neuve, Belgium
FEBS Lett 440:325-31. 1998..Our data suggest that shuffling of mobile elements plays an important role in the remodelling of the yeast mitochondrial genome...
- Cell-to-cell stochastic variation in gene expression is a complex genetic traitJuliet Ansel
Universite de Lyon, Lyon, France
PLoS Genet 4:e1000049. 2008..The complex genetic architecture of noise buffering couples genetic to non-genetic robustness and provides a molecular basis to the probabilistic nature of complex traits...
- Dissecting the regulatory circuitry of a eukaryotic genomeF C Holstege
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
Cell 95:717-28. 1998....
- Role of the Hog1 stress-activated protein kinase in the global transcriptional response to stress in the fungal pathogen Candida albicansBrice Enjalbert
Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
Mol Biol Cell 17:1018-32. 2006..albicans has diverged from corresponding networks in model yeasts and that the C. albicans SAPK pathway functions in parallel with other pathways to regulate the core transcriptional response to stress...
- Proteome survey reveals modularity of the yeast cell machineryAnne Claude Gavin
Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nature 440:631-6. 2006..This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling...
- Genome-wide patterns of histone modifications in yeastCatherine B Millar
Department of Biological Chemistry, Geffen School of Medicine and the Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
Nat Rev Mol Cell Biol 7:657-66. 2006..Such patterns might be important for the regulation of heterochromatin-mediated silencing, chromosome segregation, DNA replication and gene expression...
- ORC and Cdc6p interact and determine the frequency of initiation of DNA replication in the genomeC Liang
Cold Spring Harbor Laboratory, New York 11724, USA
Cell 81:667-76. 1995..We suggest that ORC and Cdc6p form a prereplication complex at individual replicators and therefore cooperate to determine the frequency of initiation of DNA replication in the genome...
- Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88Herman J Pel
DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands
Nat Biotechnol 25:221-31. 2007..niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis...
- A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genomeTravis N Mavrich
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 18:1073-83. 2008..3' NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3' NFRs in gene looping...
- Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiaeManolis Kellis
The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02138, USA
Nature 428:617-24. 2004..Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions...
- Mechanistic plasticity of sexual reproduction and meiosis in the Candida pathogenic species complexJennifer L Reedy
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
Curr Biol 19:891-9. 2009....
- The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformansBrendan J Loftus
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 307:1321-4. 2005..neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes...
- The yeast genome project: what did we learn?B Dujon
Unité de Génétique Moléculaire des Levures URA 1149 CNRS, Paris, France
Trends Genet 12:263-70. 1996..Offering the possibility of large-scale reverse genetics, yeast will be a powerful model for post-sequencing studies. But geneticists are now faced with the difficulty of asking novel questions...
- Singular value decomposition for genome-wide expression data processing and modelingO Alter
Departments of Genetics and Biochemistry, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 97:10101-6. 2000....
- A genomewide screen in Saccharomyces cerevisiae for genes that suppress the accumulation of mutationsMeng Er Huang
Ludwig Institute for Cancer Research, Department of Medicine and Cancer Center, University of California at San Diego, School of Medicine, La Jolla, CA 92093, USA
Proc Natl Acad Sci U S A 100:11529-34. 2003..Study of such genes should provide useful clues in identification of human genes potentially involved in cancer predisposition and in understanding their mechanisms of action...
- A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiaeL Ni
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
Mol Biol Cell 12:2147-70. 2001..Genome-wide screens of defined collections of mutants hold significant promise for dissecting many biological processes in yeast...
- Candida Albicans: a molecular revolution built on lessons from budding yeastJudith Berman
Department of Genetics, Cell Biology and Development, 6 160 Jackson Hall, 321 Church Street SE, Minneapolis, Minnesota 55455, USA
Nat Rev Genet 3:918-30. 2002..They also reveal the extent of similarities and differences between C. albicans and its benign relative, Saccharomyces cerevisiae...
- Molecular characterization of a chromosomal rearrangement involved in the adaptive evolution of yeast strainsJosé E Pérez-Ortín
Departament de Bioquimica i Biologia Molecular, Universitat de Valencia, Spain
Genome Res 12:1533-9. 2002..This is the first time that a gross chromosomal rearrangement is shown to be involved in the adaptive evolution of Saccharomyces cerevisiae...
- Natural history and evolutionary principles of gene duplication in fungiIlan Wapinski
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 449:54-61. 2007..Surprisingly, paralogous modules of genes rarely arise, even after whole-genome duplication. Rather, gene duplication may drive the modularization of functional networks through specialization, thereby disentangling cellular systems...
- A high-resolution atlas of nucleosome occupancy in yeastWilliam Lee
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
Nat Genet 39:1235-44. 2007..A quantitative model of nucleosome occupancy indicates that DNA structural features may account for much of the global nucleosome occupancy...
- Population genomic analysis of outcrossing and recombination in yeastDouglas M Ruderfer
Lewis Sigler Institute for Integrative Genomics and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
Nat Genet 38:1077-81. 2006..Our results provide the initial foundation for population studies of association between genotype and phenotype in S. cerevisiae...
- Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatusMathieu Paoletti
School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
Curr Biol 15:1242-8. 2005..The possible presence of a sexual cycle is highly significant for the population biology and disease management of the species...
- Global transcriptome and deletome profiles of yeast exposed to transition metalsYong Hwan Jin
Nicholas School of the Environment and Earth Sciences, Duke University, Durham, North Carolina, United States of America
PLoS Genet 4:e1000053. 2008....
- Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiaeSeong Ho Kim
School of Biology, Georgia Institute of Technology, USA
Mol Biol Evol 23:1068-75. 2006..In particular, we detect signs of purifying selection on the more slowly evolving duplicate...
- Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiaeYoav Arava
Department of Biochemistry, Stanford University, Stanford, CA 94305 5307, USA
Proc Natl Acad Sci U S A 100:3889-94. 2003..Global analysis revealed an unexpected correlation: Ribosome density decreases with increasing ORF length. Models to account for this surprising observation are discussed...
- Bidirectional promoters generate pervasive transcription in yeastZhenyu Xu
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nature 457:1033-7. 2009....
- Getting started with yeastFred Sherman
Department of Biochemistry and Biophysics, University of Rochester Medical School, Rochester, New York 14642, USA
Methods Enzymol 350:3-41. 2002
- A genome-wide view of the spectrum of spontaneous mutations in yeastMichael Lynch
Department of Biology, Indiana University, Bloomington, IN 47405, USA
Proc Natl Acad Sci U S A 105:9272-7. 2008....
- High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicingKara Juneau
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 104:1522-7. 2007..This robust methodology can be used to explore environmentally distinct splicing responses and should be readily adaptable to the study of other organisms, including humans...
- The COG database: a tool for genome-scale analysis of protein functions and evolutionR L Tatusov
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 28:33-6. 2000..The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes...
- Phylogenomics: the beginning of incongruence?Olivier Jeffroy
Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec, Canada, H3C3J7
Trends Genet 22:225-31. 2006..We propose that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence...
- Genome-wide analysis of Rad52 foci reveals diverse mechanisms impacting recombinationDavid Alvaro
Department of Genetics and Development, Columbia University Medical Center, New York, New York, USA
PLoS Genet 3:e228. 2007..Our cell biological approach demonstrates the diversity of processes that converge on homologous recombination, protect against spontaneous DNA damage, and facilitate efficient repair...
- Transcriptional response of Candida albicans to nitric oxide and the role of the YHB1 gene in nitrosative stress and virulenceBethann S Hromatka
Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
Mol Biol Cell 16:4814-26. 2005....
- Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genomeJonathan L Gordon
Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
PLoS Genet 5:e1000485. 2009..Many of the gained genes in S. cerevisiae have functions associated with ethanol production, growth in hypoxic environments, or the uptake of alternative nutrient sources...
- Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genomeIstvan Albert
Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Nature 446:572-6. 2007..Transcriptional start sites tended to reside about one helical turn inside the nucleosome border. These findings reveal an intimate relationship between chromatin architecture and the underlying DNA sequence it regulates...
- Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1Anne Rufiange
Centre de recherche en cancérologie de l Université Laval, L Hôtel Dieu de Québec CHUQ, Quebec, Canada
Mol Cell 27:393-405. 2007..Taken together, our data underline the dynamic nature of replication-independent nucleosome assembly/disassembly, specify a link to transcription, and implicate Asf1 and H3 K56 acetylation...
- Fungal secondary metabolism - from biochemistry to genomicsNancy P Keller
University of Wisconsin Madison, Department of Plant Pathology, 882 Russell Labs, 1630 Linden Drive, Madison, Wisconsin 53706, USA
Nat Rev Microbiol 3:937-47. 2005....
- Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeastP James
Department of Biomolecular Chemistry, University of Wisconsin, Madison 53706, USA
Genetics 144:1425-36. 1996..Our analysis indicates that the libraries and host strain provide significant improvements in both the number of interacting clones identified and the efficiency of two-hybrid selections...
- Nep1-like proteins from plant pathogens: recruitment and diversification of the NPP1 domain across taxaMark Gijzen
Agriculture and Agri Food Canada, 1391 Sandford Street, London, Ont, Canada N5V 4T3
Phytochemistry 67:1800-7. 2006..Interest in NLPs is gaining momentum as more members of this protein family are discovered in more species of plant pathogens...
- Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolatesDaniel J Kvitek
Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
PLoS Genet 4:e1000223. 2008..These results highlight the value of understanding the genetic basis of phenotypic variation and raise caution about using laboratory strains for comparative genomics...
- A yeast hybrid provides insight into the evolution of gene expression regulationItay Tirosh
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
Science 324:659-62. 2009..These results provide insights on the regulatory changes in cis and trans during the divergence of species and upon hybridization...
- Exploring genetic interactions and networks with yeastCharles Boone
Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
Nat Rev Genet 8:437-49. 2007..A comparative understanding of genetic-interaction networks promises insights into some long-standing genetic problems, such as the nature of quantitative traits and the basis of complex inherited disease...
- Evolutionary programming as a platform for in silico metabolic engineeringKiran Raosaheb Patil
Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
BMC Bioinformatics 6:308. 2005....
- A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinasesVerena Seidl
Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Austria
FEBS J 272:5923-39. 2005..jecorina chitinases, and those from other filamentous fungi, including hypothetical proteins of annotated fungal genome databases, showed that the fungal chitinases can be divided into three groups: groups A and B (corresponding ..
- A catalog of neutral and deleterious polymorphism in yeastScott W Doniger
Computational Biology Program, Washington University, St Louis, Missouri, United States of America
PLoS Genet 4:e1000183. 2008..Our results show that the genome sequences of both closely and distantly related species provide a means of identifying deleterious polymorphisms that disrupt functionally conserved coding and noncoding sequences...
- Widespread bidirectional promoters are the major source of cryptic transcripts in yeastHelen Neil
Institut Pasteur, Unité de Génétique des Interactions Macromoléculaires, CNRS, URA2171, 75015 Paris, France
Nature 457:1038-42. 2009....
- Transposable elements in filamentous fungiMarie Josée Daboussi
Institut de Genetique et Microbiologie, Universite Paris Sud, F 91405 Orsay cedex, France
Annu Rev Microbiol 57:275-99. 2003..the evolutionary dynamics of TEs should provide important insights into the interactions between TEs and the fungal genome. Another issue of major significance is the practical applications of TEs in gene tagging and population ..
- SGD: Saccharomyces Genome DatabaseJ M Cherry
Department of Genetics, Stanford University, Stanford, CA 94305 5120, USA
Nucleic Acids Res 26:73-9. 1998..SGD can be accessed via the World Wide Web at http://genome-www.stanford.edu/Saccharomyces/..
- GC content and recombination: reassessing the causal effects for the Saccharomyces cerevisiae genomeMarie Claude Marsolier-Kergoat
Institut de Biologie et de Technologies de Saclay, Commissariat àl Energie Atomique Saclay, 91191 Gif sur Yvette, France
Genetics 183:31-8. 2009..These results pave the way for further analyses aimed at the detailed untangling of drives involved in the evolutionary shaping of the yeast genome...
- The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research communityMartha B Arnaud
Department of Genetics, Stanford University Medical School, Stanford, CA 94305 5120, USA
Nucleic Acids Res 38:D420-7. 2010..All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at email@example.com...
- A genetic engineering strategy for the improved production of the anti-helminthicJEFFREY DAVID KITTENDORF; Fiscal Year: 2012..Specifically, Alluvium's approach is guided by the DNA sequence of the fungal genome in which key regulatory and/or biosynthetic genes responsible for paraherquamide production have been ..
- Desaturases and Acetylenases from Basidiomycete FungiROBERT MINTO; Fiscal Year: 2004..A delta-12 desaturase sequence mined from the White Rot Fungal Genome project will be isolated and characterized...
- ANTISENSE REPRESSION IN CRYPTOCOCCUS NEOFORMANSGary Cox; Fiscal Year: 2000..What is needed is a rapid means to evaluate the function of multiple genes in the fungal genome to identify new antifungal targets...
- Twenty Third Fungal Genetics ConferenceMarc Orbach; Fiscal Year: 2005..nematodes, insects and fungi, Fungal Circadian Rhythms and photobiology, Applications resulting from fungal genome projects, Teaching fungal biology and genetics, Proteomics of filamentous fungi, Basidiomycete genomics, ..
- Gene Duplication and Genome EvolutionAustin Hughes; Fiscal Year: 2004..5) Examining the role of transposable elements in duplication of genomic segments by testing for nonrandom association between these elements and putatively duplicated blocks in the yeast genome. ..
- Characterization of a large protein interaction networkAndreas Wagner; Fiscal Year: 2005..The proposed work will put this speculation to an end for a key genetic network, some of whose conserved components are also involved in the etiology of human disease. ..
- EVOLUTION OF IMMUNE RECOGNITION AND EVASIONAustin L Hughes; Fiscal Year: 2010..In addition, by increasing our understanding of the population diversity and evolutionary history of human immune system genes, this research will enhance our knowledge of human immune function in health and disease. ..
- Genetic analysis of Cryptococcus neoformans virulenceJoseph Heitman; Fiscal Year: 2009..These studies will enable a genome-wide definition of the gene set contributing to virulence of this common human fungal pathogen. ..
- Genetics of mating and fruiting in Cryptococcus neoformansJoseph Heitman; Fiscal Year: 2010..neoformans and C. gattii applicable to development of treatment approaches, diagnostics, or environmental interventions to reduce exposure to infectious spores. ..
- Role of Calcineurin in Fungal VirulenceJoseph Heitman; Fiscal Year: 2009..Importantly, this pathway can be targeted for therapeutic intervention using non-immunosuppressive calcineurin inhibitors that retain antifungal activity and synergistic drug combinations that we have discovered. ..
- GPCR signaling cascades in Cryptococcus neoformansJoseph Heitman; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..
- Microarray Expression Analysis of Burkholderia MalleiWilliam Nierman; Fiscal Year: 2003..Function and virulence validation of the identified virulence genes will be explored by construction and phenotype analysis of targeted knockout strains. ..
- Regulation of Burkholderia mallei virulence genesWilliam Nierman; Fiscal Year: 2005..It will provide critical information on virulence control and virulence mechanisms of B. mallei and will be crucial to the development of effective therapeutic interventions and vaccine strategies. ..
- Host-Pathogen Interactions in Invasive AspergillosisWILLIAM CHARLES NIERMAN; Fiscal Year: 2010..necessary to maintain protective immunity against the invading fungus. This hithertn inaccessible ... in order to >.E =.m m'- N'3 ..' 'C3 _.n '-' a.. m._ o'< m- ..
- Transcriptional Integration of MetabolismELTON YOUNG; Fiscal Year: 2007..abstract_text> ..
- The Transcriptome of Pathogenic Aspergillus FumigatusWilliam Nierman; Fiscal Year: 2003..abstract_text> ..
- Sequence Determinants of Meiotic Recombination HotspotsWalter Steiner; Fiscal Year: 2007..pombe are also active in the distantly related budding yeast Saccharomyces cerevisiae. Sequences that are active in both organisms may be widely conserved among eukaryotes, including man. [unreadable] [unreadable] [unreadable]..
- Genome Instability in Cells and Tissues of the ZebrafishForrest Spencer; Fiscal Year: 2006..abstract_text> ..
- REGULATION OF MEIOTIC DEVELOPMENT BY MTS1-MTS2 PROTEINWAYNE WAHLS; Fiscal Year: 2004..4) To test alternative hypotheses that the Mts1-Mts2-M26 complex either enhances the use of a pre-existing recombinational initiation site or creates a new initiation site. The PI request four years of support to carry out this study. ..
- ASM Conference on Candida and CandidiasisAaron Mitchell; Fiscal Year: 2008..The conference will help chart the course of future research and facilitate the urgent necessity to understand, treat, and prevent disease. [unreadable] [unreadable] [unreadable]..
- Molecular Targets of Novel Antifungal CompoundsAmeeta Agarwal; Fiscal Year: 2008..This work will provide a starting point in the development of new antifungal therapies. [unreadable] [unreadable] [unreadable]..
- Pheromone Signaling in Pneumocystis CariniiCharles Thomas; Fiscal Year: 2009..Through these investigations we hope to gain insights into P. carinii biology which may provide new information for novel drug development to treat PCP. ..
- Computational Analysis of Retinal Regulatory Interactions: structure and dynamicsJiang Qian; Fiscal Year: 2010..Beyond investigation of retinal disease, the computational programs developed in this proposal should also be generally useful for a broad community. ..
- Genetic Determinants of Genomic Plasticity and Chromosome EvolutionForrest A Spencer; Fiscal Year: 2010..In humans, distinct chromosome nondisjunction signatures that reveal specific dysfunctional pathways could enhance diagnosis and treatment of disease. ..
- Biochemistry of recombination in gametogenesisWayne P Wahls; Fiscal Year: 2010....
- Comparative Genomics of FrancisellaGeorge Weinstock; Fiscal Year: 2006..abstract_text> ..
- Molecular & Cellular Bioenergetics Gordon Conf. 2005Patricia Kane; Fiscal Year: 2005..The format of the Gordon Conference is designed to maximize opportunities for discussion and to encourage presentation of the latest results in the field. ..
- Pharmacogenomics/natural products + antifungal activityJohn Cleary; Fiscal Year: 2004..Probing this array with eukaryotic mRNA from cells exposed to novel antifungals would predict common mechanism of action and likelihood of toxicity, activity and resistance. ..
- OXYGEN SENSING BY THE RESPIRATORY CHAINKURT KWAST; Fiscal Year: 2005....
- RIBOSOMAL FRAMESHIFTING AS A PROBE OF 5S RRNA FUNCTIONJONATHAN DINMAN; Fiscal Year: 2004..The proposed research will serve to further our understanding of this ubiquitous yet little understood rRNA and will place us in the unique position to link functional aspects of 5S rRNA to its structure within the ribosome. ..
- ENTAMOEBA HISTOLYTICA GENOME PROJECTBrendan Loftus; Fiscal Year: 2002..The vast majority of the research needs and applications will be met by obtaining 99 percent of the genomic sequence. ..
- 2004 FASEB Summer Conference on Trace Element MetabolismDavid Eide; Fiscal Year: 2004..These individuals will be encouraged to present posters to be displayed in two poster sessions. We also will obtain funds to provide travel awards for up to 10 postdocs or senior graduate students. ..
- Francisella GenomicsGeorge Weinstock; Fiscal Year: 2004..tularensis contains a high proportion of unique genes compared to other bacterial genomes. Therefore, knowledge of the complete genome sequences of F. tularensis strains is needed for the understanding of the virulence mechanisms. ..
- The Rate and Molecular Spectrum of Spontaneous MutationsMichael Lynch; Fiscal Year: 2009....
- New strategies for identification of C. albicans fluconazole resistance geneAaron Mitchell; Fiscal Year: 2004..These approaches will define the regulators that govern known resistance mechanisms and may reveal the regulators that govern other clinically relevant resistance mechanisms. ..
- Azoles and Candida in AIDS - A Whole Cell ResponseTHEODORE WHITE; Fiscal Year: 2004....
- REGULATION OF DROSOPHILA NEUROMUSCULAR DEVELOPMENTMichael Young; Fiscal Year: 2004..e) Factors regulating Notch transport to and from the cell surface, and controlling nuclear translocation of Notch will be identified and characterized using certain transport deficient Notch proteins. ..
- Chlamydia co-option of Eukaryotic Lipid DropletsRaphael H Valdivia; Fiscal Year: 2010..abstract_text> ..
- Implications of Genomics Research on Racial DefinitionSeymour Garte; Fiscal Year: 2003..A new paradigm of gene-specific variation will be developed for a biomedically useful method of division of the human population into groups based on criteria different from current definitions of race. ..
- Zinc Transporters and Intracellular Zinc TraffickingDavid Eide; Fiscal Year: 2007..unreadable] [unreadable]..
- Molecular Mechanisms of Genome DuplicationZENGJIAN CHEN; Fiscal Year: 2009..abstract_text> ..
- Sterol Sensing and Transport in Model EukaryoteSTEPHEN STURLEY; Fiscal Year: 2008..We will test the ramifications of overexpression or knockdown of human ARVl in various tissue culture cell models. Lipid efflux to extracellular acceptors will be studied in detail. ..
- A Genomics Approach to Study C. neoformans var. grubiiFred Dietrich; Fiscal Year: 2006..The resulting data and material from this study will expand our knowledge of the nature of pathogenicity in this important human fungal pathogen. [unreadable] [unreadable]..
- Analysis of Somatic Mutations in Cancer of the KidneyWAYNE VEDECKIS; Fiscal Year: 2005..B) Is there a correlation between other suspected risk factors, hypertension and obesity, and p53 gene mutation prevalence and spectrum? (C) Is there a correlation between survival and p53 gene mutation prevalence and spectrum? ..
- A Skpl-containing Complex Regulating V-ATPase ActivityPatricia Kane; Fiscal Year: 2005..abstract_text> ..
- A compendium of gene expression in stationary phaseMargaret Werner Washburne; Fiscal Year: 2005..parent abstract not available ..
- Azoles and Candida in AIDS-Transcriptional RegulationTHEODORE WHITE; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- Vacuole expansion during flamentation in CandidaJoy Sturtevant; Fiscal Year: 2006..The information obtained in this study on the role of the fungal vacuole in pathogenesis may also aid in the design of new anti-fungal treatment strategies. ..
- Yeast Aspartyl Proteases in Cell Wall IntegrityDAMIAN KRYSAN; Fiscal Year: 2007..A team of outstanding collaborators and advisors has been assembled to provide additional mentoring and support as the investigator makes the transition to an independent researcher. [unreadable] [unreadable]..
- MOLECULAR AND CELLULAR STUDIES OF CIRCADIAN RHYTHMSMichael Young; Fiscal Year: 2008..regulate nuclear accumulation of PER? How does PER phosphorylation influence phosphorylation of TIM? (6) Does DBT's physical association with PER put other substrates of the kinase under circadian control? [unreadable] [unreadable]..
- Therapeutic targeting of HSP90-dependent signalingLarry Karnitz; Fiscal Year: 2008..Collectively, these studies will provide information about the ability to alter the response of ovarian cancer cells to chemotherapeutic agents in vitro and in the clinical setting. [unreadable] [unreadable]..
- Identification of Coxiella burnetti Effector ProteinsRAPHAEL VALDIVIA; Fiscal Year: 2008..We predict that these factors will be attractive candidates for the design of new therapeutics and vaccines. [unreadable] [unreadable] [unreadable] [unreadable]..
- A Model Signaling Mucin in YeastPaul Cullen; Fiscal Year: 2008..We use a model genetic system - budding yeast - to investigate mucin function in MAP kinase pathway activation, cell adherence, and biofilm formation. [unreadable] [unreadable] [unreadable]..
- Mitochondria and CarcinogenesisKeshav K Singh; Fiscal Year: 2010..The proposed study will help determine the contribution of mutant mtDNA to the development of human cancer. ..
- S. Cerevisiae Emergence of an Opportunistic PathogenJOHN MCCUSKER; Fiscal Year: 2009..cerevisiae population both phenotypically, for virulence and virulence-associated traits, and genotypically, for virulence-related genes. ..
- ANALYSIS OF GENETICALLY & ENVIRONMENTALLY OVERLAPPING YEAST QUANTITATIVE TRAITSJohn H McCusker; Fiscal Year: 2010..Therefore, an improved understanding of quantitative traits will aid our understanding of how a harmless commensal/saprophytic yeast can become an opportunistic pathogen. ..
- PHASE VARIATION IN SACCHAROMYCES CEREVISIAEJOHN MCCUSKER; Fiscal Year: 2003..The PHI genes will be introduced to the non-phase variable laboratory strain, 288c, in efforts to reconstruct phase variation. ..
- GENETIC DIVERSITY AND COMPLEX TRAITS IN S CEREVISIAEJOHN MCCUSKER; Fiscal Year: 2002..the development of S. cerevisiae as genetically manipulable model for the pathogenic fungi and as a host for the interspecific reconstitution of fungal virulence. ..
- Fungal-specific drug targets: static vs. cidal starvation & toxic intermediatesJOHN MCCUSKER; Fiscal Year: 2008..The identification of fungicidal antifungal drugs, which is a long-term goal, will greatly improve human health. [unreadable] [unreadable] [unreadable]..
- Cleveland Cell Biology Symposium: RegulationALAN TARTAKOFF; Fiscal Year: 2004..The results should be an intense synthesis of knowledge which will be stimulating for both students and established faculty. ..
- Towards a general theory of evolutionary capacitanceJoanna Masel; Fiscal Year: 2009..Since direct experiments on capacitance cannot be performed in humans, the theoretical and predictive approach described here is particularly important for understanding the scope of capacitance in explaining human variation. ..
- A Genome Sequence Survey of Enterocytozoon bieneusiDonna Akiyoshi; Fiscal Year: 2006..c. Establishment of a website to provide access to the sequence data and clones by the scientific community. ..