Genetic and physical maps of Saccharomyces cerevisiae

Cherry, J. Michael; Ball, Catherine A.; Weng, Shuai; Juvik, Gail; Schmidt, Rita; Adler, Caroline; Dunn, Barbara; Dwight, Selina S.; Riles, Linda; Mortimer, Robert; Botstein, David

doi:10.1038/387s067

Cited by 274 publications

(257 citation statements)

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“…To our knowledge, it is only the homobasidiomycete fungi that show a linkage between MIP and mating-type. For example, in S. cerevisiae, S. pombe, and C. neoformans, the mating-type locus is on a different chromosome than MIP in each of these fungi (Cherry et al, 1997;Wood et al, 2002;A. Forche and T.Y.…”

Section: Discussionmentioning

confidence: 98%

Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi

James¹,

Kües²,

Rehner³

et al. 2004

Fungal Genetics and Biology

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Section: Discussionmentioning

confidence: 98%

Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi

James¹,

Kües²,

Rehner³

et al. 2004

Fungal Genetics and Biology

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“…We compared DARN! with tRNAscan-SE on the genomic sequences of the yeast [4] provided by RFAM [8], which is the reference database for ncRNAs. This database has collected all the tRNAs that are located on chromosome 3 (containing 316,613 nucleotides) and on the first 165,534 nucleotides of chromosome 16 of the yeast genome.…”

Section: Resultsmentioning

confidence: 99%

DARN! A Weighted Constraint Solver for RNA Motif Localization

Zytnicki¹,

Gaspin²,

Schiex³

2008

Constraints

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Following recent discoveries about the important roles of non-coding RNAs (ncRNAs) in the cellular machinery, there is now great interest in identifying new occurrences of ncRNAs in available genomic sequences. In this paper, we show how the problem of finding new occurrences of characterized ncRNAs can be modeled as the problem of finding all locally-optimal solutions of a weighted constraint network using dedicated weighted global constraints, encapsulating patternmatching algorithms and data structures. This is embodied in DARN!, a software tool for ncRNA localization, which, compared to existing pattern-matching based tools, offers additional expressivity (such as enabling RNA-RNA interactions to be described) and improved specificity (through the exploitation of scores and local optimality) without compromises in CPU efficiency. This is demonstrated on the actual search for tRNAs and H/ACA sRNA on different genomes.

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“…AraCyc contains the metabolic information of Arabidopsis thaliana ( [91], http://www.arabidopsis.org/biocyc/index.jsp). Several detailed databases of yeast gene function, regulation and metabolism are available, including the Saccharomyces Genome Database (SGD, [92], http://www.yeastgenome. org/), a proprietary Yeast Proteome Database (YPD, https:// www.proteome.com/proteome/), and the Munich Information Center for Protein Sequences (MIPS, [93], http://mips.…”

Section: Integrated Databasesmentioning

confidence: 99%

Integration of Metabolic Reactions and Gene Regulation

Yeang

2010

Mol Biotechnol

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Metabolic reactions and gene regulation are two primary processes of cells. In response to environmental changes cells often adjust the regulatory programs and shift the metabolic states. An integrative investigation and modeling of these two processes would improve our understanding about the cellular systems and may generate substantial impacts in medicine, agriculture, environmental protection, and energy production. We review the studies of the various aspects of the crosstalk between metabolic reactions and gene regulation, including models, empirical evidence, and available databases.

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Genetic and physical maps of Saccharomyces cerevisiae

Cited by 274 publications

References 0 publications

Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi

Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi

DARN! A Weighted Constraint Solver for RNA Motif Localization

Integration of Metabolic Reactions and Gene Regulation

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