Search PubMed⌕ Search

Biomedical subjects

Marek S Skrzypek

Publications and source records attributed to Marek S Skrzypek.

6 recordsLinked to original sources
PubMed2006

Sequence resources at the Candida Genome Database.

The Candida Genome Database (CGD, http://www.candidagenome.org/) contains a curated collection of genomic information and community resources for researchers who are interested in the molecular biology of the opportunistic pathogen Candida albicans. With the recent release of a new assembly of the C.albicans genome, Assembly 20, C.albicans genomics has entered a new era. Although the C.albicans genome assembly continues to undergo refinement, multiple assemblies and gene nomenclatures will remain in widespread use by the research community. CGD has now taken on the responsibility of maintaining the most up-to-date version of the genome sequence by providing the data from this new assembly alongside the data from the previous assemblies, as well as any future corrections and refinements. In this database update, we describe the sequence information available for C.albicans, the sequence information contained in CGD, and the tools for sequence retrieval, analysis and comparison that CGD provides. CGD is freely accessible at http://www.candidagenome.org/ and CGD curators may be contacted by email at candida-curator@genome.stanford.edu.

Candida albicans↗
PubMed2006

The Candida Genome Database: facilitating research on Candida albicans molecular biology.

The Candida Genome Database (CGD; http://www.candidagenome.org) is a resource for information about the Candida albicans genomic sequence and the molecular biology of its encoded gene products. CGD collects and organizes data from the biological literature concerning C. albicans, and provides tools for viewing, searching, analysing, and downloading these data. CGD also serves as an organizing centre for the C. albicans research community, providing a gene-name registry, contact information, and research community news. This article describes the information contained in CGD and how to access it, either from the perspective of a bench scientist interested in the function of one or a few genes, or from the perspective of a biologist or bioinformatician interpreting large-scale functional genomic datasets.

Alleles↗
PubMed2005

The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.

The Candida Genome Database (CGD) is a new database that contains genomic information about the opportunistic fungal pathogen Candida albicans. CGD is a public resource for the research community that is interested in the molecular biology of this fungus. CGD curators are in the process of combing the scientific literature to collect all C.albicans gene names and aliases; to assign gene ontology terms that describe the molecular function, biological process, and subcellular localization of each gene product; to annotate mutant phenotypes; and to summarize the function and biological context of each gene product in free-text description lines. CGD also provides community resources, including a reservation system for gene names and a colleague registry through which Candida researchers can share contact information and research interests. CGD is publicly funded (by NIH grant R01 DE15873-01 from the NIDCR) and is freely available at http://www.candidagenome.org/.

Candida albicans↗
PubMed2005

Analysis of gene ontology features in microarray data using the Proteome BioKnowledge Library.

Microarray technology has resulted in an explosion of complex, valuable data. Integrating data analysis tools with a comprehensive underlying database would allow efficient identification of common properties among differentially regulated genes. In this study we sought to compare the utility of various databases in microarray analysis. The Proteome BioKnowledge Library (BKL), a manually curated, proteome-wide compilation of the scientific literature, was used to generate a list of Gene Ontology (GO) Biological Process (BP) terms enriched among proteins involved in cardiovascular disease. Analysis of DNA microarray data generated in a study of rat vascular smooth muscle cell responses revealed significant enrichment in a number of GO BPs that were also enriched among cardiovascular disease-related proteins. Using annotation from LocusLink and chip annotation from the Gene Expression Omnibus yielded fewer enriched cardiovascular disease-associated GO BP terms. Data sets of orthologous genes from mouse and human were generated using the BKL Retriever. Analysis of these sets focusing on BKL Disease annotation, revealed a significant association of these genes with cardiovascular disease. These results and the extensive presence of experimental evidence for BKL GO and Disease features, underscore the benefits of using this database for microarray analysis.

Animals↗
PubMed2002

Mutant analysis reveals complex regulation of sphingolipid long chain base phosphates and long chain bases during heat stress in yeast.

Sphingolipid long chain bases (LCBs) in Saccharomyces cerevisiae, dihydrosphingosine (DHS) and phytosphingosine (PHS) and their phosphates (DHS-P and PHS-P) are thought to play roles in heat stress. However, quantitative studies of LCBs and LCBPs have been limited by analytical methods. A new analytical procedure allowed us to measure changes in all known LCBPs and LCBs in wild-type and mutant cells during heat shock and to correlate the changes with heat stress resistance. All five molecular species of LCBPs increased rapidly but transiently when log and stationary phase cells were heat-stressed and when log-phase cells were induced for thermotolerance, suggesting that LCBPs play a role in heat stress. In support of this hypothesis, cells lacking the minor LCB kinase, Lcb5p, but not the major kinase, Lcb4p, were two-fold less resistant to killing when log-phase cells were induced for thermotolerance. Thus, LCBPs seem to play a minor role in heat-stress resistance. However, their role may be masked by LCBs, which are elevated in mutant strains, such as one lacking Lcb4p. This elevation demonstrates that one function of Lcb4p is to regulate LCB levels. Two new compounds, C(16) DHS and C(16) DHS-P, were identified, with the latter being degraded by the Dpl1p lyase. Our data provide a basis for determining how the basal and heat-induced levels of individual species of LCBs and LCBPs are governed by the Lcb4p and Lcb5p kinases, the Dpl1p lyase and the Lcb3p phosphatase.

DNA Mutational Analysis↗