A5076684723- Bioinformatics and Genomic Networks
- Fungal and yeast genetics research
- Genomics and Phylogenetic Studies
- Antifungal resistance and susceptibility
- Microbial Metabolic Engineering and Bioproduction
- Biomedical Text Mining and Ontologies
- Sphingolipid Metabolism and Signaling
- Probiotics and Fermented Foods
- Microbial Natural Products and Biosynthesis
- Fungal Infections and Studies
- Plant Pathogens and Fungal Diseases
- Fermentation and Sensory Analysis
- Oral microbiology and periodontitis research
- Gene expression and cancer classification
- Endoplasmic Reticulum Stress and Disease
- Mycotoxins in Agriculture and Food
- Cellular transport and secretion
- Polyamine Metabolism and Applications
- Enzyme Structure and Function
- Amino Acid Enzymes and Metabolism
- Genetics, Bioinformatics, and Biomedical Research
- Yeasts and Rust Fungi Studies
- Gut microbiota and health
- RNA and protein synthesis mechanisms
- Biofuel production and bioconversion
Stanford University
2014-2025
University of Padua
2023
University College London
2023
SIB Swiss Institute of Bioinformatics
2023
University at Buffalo, State University of New York
2023
University of Southern California
2023
Phoenix Bioinformatics
2023
Palo Alto University
2019
Great Lakes Bioenergy Research Center
2014
SRI International
2014
The Saccharomyces Genome Database (SGD, http://www.yeastgenome.org) is the community resource for budding yeast cerevisiae. SGD project provides highest-quality manually curated information from peer-reviewed literature. experimental results reported in literature are extracted and integrated within a well-developed database. These data combined with quality high-throughput provided through Locus Summary pages, powerful query engine rich genome browser. acquisition, integration retrieval of...
Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report genome sequences six and compare these related pathogens non-pathogens. There significant expansions cell wall, secreted transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts homozygous three diploid possibly resulting from recent recombination events. Surprisingly, key components mating meiosis pathways missing several...
The genome of the budding yeast Saccharomyces cerevisiae was first completely sequenced from a eukaryote. It released in 1996 as work worldwide effort hundreds researchers. In time since, has been intensively studied by geneticists, molecular biologists, and computational scientists all over world. Maintenance annotation sequence have long provided Genome Database, one original model organism databases. To deepen our understanding eukaryotic genome, S. strain S288C reference updated recently...
The Candida Genome Database (CGD, http://www.candidagenome.org/) is a freely available online resource that provides gene, protein and sequence information for multiple species, along with web-based tools accessing, analyzing exploring these data. mission of CGD to facilitate accelerate research into pathogenesis biology, by curating the scientific literature in real time, connecting literature-derived annotations latest version genomic its annotations. Here, we report incorporation Assembly...
Abstract Background Secondary metabolite production, a hallmark of filamentous fungi, is an expanding area research for the Aspergilli. These compounds are potent chemicals, ranging from deadly toxins to therapeutic antibiotics potential anti-cancer drugs. The genome sequences multiple Aspergilli have been determined, and provide wealth predictive information about secondary production. Sequence analysis gene overexpression strategies enabled discovery novel metabolites genes involved in...
The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available web-based resource that was designed for researchers and also valuable source of information the entire fungal research community. In addition to being repository central point access genome, transcriptome polymorphism data, AspGD hosts comprehensive comparative genomics toolbox facilitates exploration precomputed orthologs among 20 currently genomes. curators perform gene product annotation based on review...
Abstract The Alliance of Genome Resources (Alliance) is a consortium the major model organism databases and Gene Ontology that guided by vision facilitating exploration related genes in human well-studied organisms providing highly integrated comprehensive platform enables researchers to leverage extensive body genetic genomic studies these organisms. Initiated 2016, building central portal (www.alliancegenome.org) for access data primary along with gene ontology data. All types represented...
Abstract As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting scientific research community since 1993. technologies and evolve, so does SGD: from updates in software architecture, to curation novel data types, incorporation from, collaboration with, other knowledgebases. We are continuing make steps toward providing with an S. cerevisiae pan-genome. Here, we describe upgrades, a new nomenclature system for genes not found reference...
The Alliance of Genome Resources (the Alliance) is a combined effort 7 knowledgebase projects: Saccharomyces Database, WormBase, FlyBase, Mouse the Zebrafish Information Network, Rat and Gene Ontology Resource. seeks to provide several benefits: better service various communities served by these projects; harmonized view data for all biomedical researchers, bioinformaticians, clinicians, students; more sustainable infrastructure. has cross-organism useful comparative views gene function,...
The ability of organisms to quickly respond stresses requires the activation many intracellular signal transduction pathways. sphingolipid intermediate ceramide is thought be particularly important for activating and coordinating signaling pathways during mammalian stress responses. Here we present first evidence that other intermediates are molecules in Saccharomyces cerevisiae heat response. Our data show a 2-3-fold transient increase concentration C18-dihydrosphingosine...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features gene products of budding yeast cerevisiae. Although published data from traditional experimental methods are primary sources evidence supporting Gene Ontology (GO) annotations for a product, high-throughput experiments computational predictions can also provide valuable insights in absence an extensive body literature. Therefore, GO available at...
The Candida Genome Database (CGD, http://www.candidagenome.org/) is an internet-based resource that provides centralized access to genomic sequence data and manually curated functional information about genes proteins of the fungal pathogen albicans other species. As scope research, number sequenced strains related species, has grown in recent years, need for expanded resources also grown. To answer this need, CGD beyond storing solely C. albicans, now integrating from multiple Herein we...
The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available, web-based resource for researchers studying fungi of the genus Aspergillus, which includes organisms clinical, agricultural and industrial importance. AspGD curators have now completed comprehensive review entire published literature about nidulans fumigatus, this annotation provided with streamlined, ortholog-based navigation multispecies information. facilitates comparative genomics by providing...
Abstract Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over years, SGD maintained genetic nomenclature, chromosome maps, functional annotation, developed various tools methods for analysis curation a variety emerging data types. More recently, six other model organism focused...
Sphingolipid long chain bases (LCBs) and phosphorylated derivatives, particularly sphingosine 1-phosphate, are putative signaling molecules. To help elucidate the physiological roles of LCB phosphates, we identified two Saccharomyces cerevisiae genes, LCB4 (YOR171c) LCB5 (YLR260w), which encode kinase activity. This conclusion is based upon synthesis activity in Escherichia coli expressing either gene. encodes most (97%) activity, with remainder requiring LCB5. Log phase lcb4-deleted yeast...
Sphingolipid long-chain bases and their phosphorylated derivatives, for example, sphingosine-1-phosphate in mammals, have been implicated as signaling molecules. The possibility that Saccharomyces cerevisiae cells also use long-chain-base phosphates to regulate cellular processes has only recently begun be examined. Here we present a simple sensitive procedure analyzing quantifying S. cells. Our data show the first time phytosphingosine-1-phosphate (PHS-1-P) is at low but detectable level...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is a scientific database for the molecular biology and genetics of yeast cerevisiae, which commonly known as baker's or budding yeast. information in SGD includes functional annotations, mapping sequence information, protein domains structure, expression data, mutant phenotypes, physical genetic interactions primary literature from these data are derived. Here we describe how published phenotypes interaction annotated displayed SGD.
The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of Aspergilli. AspGD combines high-quality manual curation experimental scientific literature examining Aspergilli, cutting-edge comparative approaches to iteratively refine improve structural gene annotations across multiple species, web-based research tools accessing exploring data. All these data are freely available at http://www.aspgd.org. We welcome...
The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available information prompted Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) to enhance depth accessibility annotations. In particular, we have ongoing improve integration experimental sequence-based predictions redesigned web pages. A key feature this redesign is development a GBrowse-derived interactive Proteome...
The Candida Genome Database (CGD, Author Webpage) contains a curated collection of genomic information and community resources for researchers who are interested in the molecular biology opportunistic pathogen albicans. With recent release new assembly C.albicans genome, Assembly 20, genomics has entered era. Although genome continues to undergo refinement, multiple assemblies gene nomenclatures will remain widespread use by research community. CGD now taken on responsibility maintaining...
The Candida Genome Database (CGD, http://www.candidagenome.org/) provides online access to genomic sequence data and manually curated functional information about genes proteins of the human pathogen albicans. Herein, we describe two recently added features, Biochemical Pathways Textpresso full-text literature search tool. tool visualization metabolic pathways analysis tools that facilitate interpretation experimental data, including results large-scale experiments, in context metabolism....
Abstract A comprehensive, computable representation of the functional repertoire all macromolecules encoded within human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating structured body information about gene functions, which now includes experimental findings reported in more than 175,000 publications genes experimentally tractable model organisms 1,2 . Here, we describe results large,...
Sphingoid long chain bases have many effects on cells including inhibition or stimulation of growth. The physiological significance these is unknown in most cases. To begin to understand how compounds inhibit growth, we studied Saccharomyces cerevisiae cells. Growth tryptophan (Trp-) auxotrophs was more strongly inhibited by phytosphingosine (PHS) than growth Trp+ strains, suggesting that PHS diminishes uptake and starves for this amino acid. This hypothesis supported data showing relieved...