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Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome
2006
Nucleic Acids Research
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ACKNOWLEDGEMENT The SGD project is supported by the NHGRI grant Conflict of interest statement. None declared. ...
To provide a composite overview of the genes and proteins of S.cerevisiae, the Saccharomyces Genome Database (SGD; 50 http://www.yeastgenome.org/) has created the Genome Snapshot (http://db.yeastgenome.org ...
overview summarizes the status of GO annotation at SGD (Figure 2A). ...
doi:10.1093/nar/gkj117
pmid:16381907
pmcid:PMC1347479
fatcat:bjdo3nfvxrf4jhvybrsnubnpp4
Re-Annotation of Protein-Coding Genes in the Genome of Saccharomyces cerevisiae Based on Support Vector Machines
2013
PLoS ONE
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Based on the annotation data in Saccharomyces Genome Database (SGD), we studied the coding capacity of all 1744 ORFs which lack experimental results and suggested that the overall number of chromosomal ...
The importance of the present work lies in at least two aspects. ...
Hao Tong for critical examining of our methodology and Xue-Lian Wan for initial data selection.
Author Contributions ...
doi:10.1371/journal.pone.0064477
pmid:23874379
pmcid:PMC3707884
fatcat:pgjdhacwfbh5nccqgc56f3nzrm
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources
2011
Nucleic Acids Research
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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 of clinical, agricultural ...
AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. ...
S. cerevisiae at SGD. ...
doi:10.1093/nar/gkr875
pmid:22080559
pmcid:PMC3245136
fatcat:hrjdhiblonfntjitnlnxqwl4ni
The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata
2011
Nucleic Acids Research
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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 ...
As the scope of Candida research, and the number of sequenced strains and related species, has grown in recent years, the need for expanded genomic resources has also grown. ...
SGD for their help. ...
doi:10.1093/nar/gkr945
pmid:22064862
pmcid:PMC3245171
fatcat:qfogwktijnbufkeevqgqiey5ka
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community
2009
Nucleic Acids Research
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The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. ...
All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at aspergillus-curator@genome.stanford.edu. ...
ACKNOWLEDGEMENTS We would like to thank CADRE for data exchange and support, SGD for providing their code base and the Aspergillus research community for giving us their support and the opportunity to ...
doi:10.1093/nar/gkp751
pmid:19773420
pmcid:PMC2808984
fatcat:nfra65frajdqnmywomhkshr7kq
Using the Candida Genome Database
[chapter]
2018
Msphere
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The Candida Genome Database (CGD) curates the Candida literature, and integrates functional information about Candida genes and their products with a set of analysis tools that facilitate searching for ...
of large-scale data, and how to access the microarray data archived at CGD, as well as visualize high-throughput sequencing data through the use of JBrowse. ...
Acknowledgements This work was supported by National Institute of Dental and Craniofacial Research at the US National Institutes of Health (grant no. R01 DE015873).
References ...
doi:10.1007/978-1-4939-7737-6_3
pmid:29761455
pmcid:PMC6005354
fatcat:xhlbkdoipra6jjs4vn6yxok6gu
The Yeast Deletion Collection: A Decade of Functional Genomics
2014
Genetics
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Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. ...
This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. ...
The funding for the yeast deletion project was provided by the National Human Genome Research Institute of the National Institutes of Health.
Literature Cited ...
doi:10.1534/genetics.114.161620
pmid:24939991
pmcid:PMC4063906
fatcat:arxcqlwo2vdh7bdi4cvvint4ly
Systems metabolic engineering: Genome-scale models and beyond
2010
Biotechnology Journal
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The advent of high throughput genome-scale bioinformatics has led to an exponential increase in available cellular system data. ...
This review will highlight advances of the systems metabolic engineering approach with a focus on de novo development and use of genome-scale metabolic reconstructions for metabolic engineering applications ...
Acknowledgments We acknowledge support from NIH (Grant number: 1R01GM090221-01) and the Camille and Henry Dreyfus New Faculty Award. ...
doi:10.1002/biot.200900247
pmid:20151446
pmcid:PMC2911524
fatcat:kcqqwagubfgavpoh65u2xy7g3y
PROPHECY--a yeast phenome database, update 2006
2007
Nucleic Acids Research
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Via phenotyping of 984 heterozygous diploids for all essential genes the genotypes analysed and presented in PROPHECY have been extended and now include all genes in the yeast genome. ...
Our yeast phenomics database PROPHECY is available at http://prophecy.lundberg.gu.se. ...
An improved phenotype summary page The Saccharomyces Genome Database (SGD) is a very important centralized information resource for the yeast community (http://db.yeastgenome.org) (6). ...
doi:10.1093/nar/gkl1029
pmid:17148481
pmcid:PMC1761427
fatcat:rvyucgx76vcolcp7mcbfgampum
Use of Bioinformatics Tools in Different Spheres of Life Sciences
2014
Journal of Data Mining in Genomics & Proteomics
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The Saccharomyces Genome Database (SGD) contains comprehensive information of the yeast (Saccharomyces cerevisiae) and also provides bioinformatics tools to explore and analyse the data available in SGD ...
Since then, it has become an essential part of biological sciences to process biological data at a much faster rate with the databases and informatics working at the backend. ...
doi:10.4172/2153-0602.1000158
fatcat:m5ziueg3ifaobfnovyguaqlixa
Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data
2009
BMC Genomics
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Results: A microarray compendium of 170 steady-state chemostat cultures of the yeast Saccharomyces cerevisiae is presented and analyzed. ...
Chemostat cultivation offers a powerful tool for such an approach. ...
This work was part of the BioRange programme of the Netherlands Bioinformatics Centre (NBIC), which is supported by a BSIK grant through the Netherlands Genomics Initiative (NGI). ...
doi:10.1186/1471-2164-10-53
pmid:19173729
pmcid:PMC2640415
fatcat:6vrzogzgn5emrccgjqqwwazmz4
Proteomics data repositories
2009
Proteomics
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The resources chosen reflect a current "snapshot" of the state of resources available with an emphasis placed on resources that may be of particular interest to yeast researchers. ...
Resources are described in terms of their intended purpose and the features and functionality provided to users. ...
Acknowledgments This work is supported by the University of Washington's Proteomics Resource (UWPR95794) and the National Center for Research Resources of the National Institutes of Health (P41 RR11823 ...
doi:10.1002/pmic.200900216
pmid:19795424
pmcid:PMC2908408
fatcat:w6drphet6rd6nk3uvzu7d2dnj4
MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics
2006
BMC Bioinformatics
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The genome sequencing projects have shown our limited knowledge regarding gene function, e.g. S. cerevisiae has 5-6,000 genes of which nearly 1,000 have an uncertain function. ...
MeMo has been implemented as a relational database using a hybrid approach combining the advantages of the two technologies. ...
Acknowledgements We are most grateful to the UK BBSRC, EPRSC and NERC for supporting our work. ...
doi:10.1186/1471-2105-7-281
pmid:16753052
pmcid:PMC1522028
fatcat:ebvoob2pjbbttp24othvumtqum
A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks
2020
BMC Bioinformatics
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Applying our method to high-throughput data, we verified its ability to deal with the complexity of a genomic TRN, providing a snapshot of the synergistic TFs regulatory activity. ...
Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. ...
Acknowledgements We would like to acknowledge the University of Florida Research Computing (URL: http://researchcomputing.ufl.edu) for providing computational resources and support that have contributed ...
doi:10.1186/s12859-020-3510-1
pmid:32471360
fatcat:3v6orxxiyjaktmui6opbjebrxm
The BioGRID interaction database: 2015 update
2014
Nucleic Acids Research
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BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats. ...
The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein in- teractions curated from the primary biomedical ...
ACKNOWLEDGEMENTS The authors thank Chris Grove and Paul Sternberg at WormBase for ongoing collaborative development of the Genetic Interaction Ontology. We also thank Mike Cherry ...
doi:10.1093/nar/gku1204
pmid:25428363
pmcid:PMC4383984
fatcat:jeok6meldzhmphu3mpxqxpeoiy
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