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Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome

J. E. Hirschman
2006 Nucleic Acids Research  
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

Dan Lin, Xin Yin, Xianlong Wang, Peng Zhou, Feng-Biao Guo, Mukund Thattai
2013 PLoS ONE  
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

M. B. Arnaud, G. C. Cerqueira, D. O. Inglis, M. S. Skrzypek, J. Binkley, M. C. Chibucos, J. Crabtree, C. Howarth, J. Orvis, P. Shah, F. Wymore, G. Binkley (+4 others)
2011 Nucleic Acids Research  
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

D. O. Inglis, M. B. Arnaud, J. Binkley, P. Shah, M. S. Skrzypek, F. Wymore, G. Binkley, S. R. Miyasato, M. Simison, G. Sherlock
2011 Nucleic Acids Research  
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

Martha B. Arnaud, Marcus C. Chibucos, Maria C. Costanzo, Jonathan Crabtree, Diane O. Inglis, Adil Lotia, Joshua Orvis, Prachi Shah, Marek S. Skrzypek, Gail Binkley, Stuart R. Miyasato, Jennifer R. Wortman (+1 others)
2009 Nucleic Acids Research  
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]

Marek S. Skrzypek, Jonathan Binkley, Gavin Sherlock
2018 Msphere  
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

Guri Giaever, Corey Nislow
2014 Genetics  
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

John Blazeck, Hal Alper
2010 Biotechnology Journal  
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

L. Fernandez-Ricaud, J. Warringer, E. Ericson, K. Glaab, P. Davidsson, F. Nilsson, G. J. L. Kemp, O. Nerman, A. Blomberg
2007 Nucleic Acids Research  
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

Muhammad Aamer Mehmood
2014 Journal of Data Mining in Genomics & Proteomics  
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

Theo A Knijnenburg, Jean-Marc G Daran, Marcel A van den Broek, Pascale AS Daran-Lapujade, Johannes H de Winde, Jack T Pronk, Marcel JT Reinders, Lodewyk FA Wessels
2009 BMC Genomics  
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

Michael Riffle, Jimmy K. Eng
2009 Proteomics  
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

Irena Spasić, Warwick B Dunn, Giles Velarde, Andy Tseng, Helen Jenkins, Nigel Hardy, Stephen G Oliver, Douglas B Kell
2006 BMC Bioinformatics  
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

Elisabetta Sauta, Andrea Demartini, Francesca Vitali, Alberto Riva, Riccardo Bellazzi
2020 BMC Bioinformatics  
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

Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Rose Oughtred, Lorrie Boucher, Sven Heinicke, Daici Chen, Chris Stark, Ashton Breitkreutz, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Julie Nixon (+10 others)
2014 Nucleic Acids Research  
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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