Literature DB >> 19577472

Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns.

Karen R Christie1, Eurie L Hong, J Michael Cherry.   

Abstract

The quest to characterize each of the genes of the yeast Saccharomyces cerevisiae has propelled the development and application of novel high-throughput (HTP) experimental techniques. To handle the enormous amount of information generated by these techniques, new bioinformatics tools and resources are needed. Gene Ontology (GO) annotations curated by the Saccharomyces Genome Database (SGD) have facilitated the development of algorithms that analyze HTP data and help predict functions for poorly characterized genes in S. cerevisiae and other organisms. Here, we describe how published results are incorporated into GO annotations at SGD and why researchers can benefit from using these resources wisely to analyze their HTP data and predict gene functions.

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Year:  2009        PMID: 19577472      PMCID: PMC3057094          DOI: 10.1016/j.tim.2009.04.005

Source DB:  PubMed          Journal:  Trends Microbiol        ISSN: 0966-842X            Impact factor:   17.079


  73 in total

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Review 2.  The promise of functional genomics: completing the encyclopedia of a cell.

Authors:  Timothy R Hughes; Mark D Robinson; Nicholas Mitsakakis; Mark Johnston
Journal:  Curr Opin Microbiol       Date:  2004-10       Impact factor: 7.934

3.  Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps.

Authors:  Markus Brameier; Carsten Wiuf
Journal:  J Biomed Inform       Date:  2006-05-20       Impact factor: 6.317

4.  Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase.

Authors:  H J Müller-Dieckmann; G E Schulz
Journal:  J Mol Biol       Date:  1995-03-03       Impact factor: 5.469

Review 5.  Changing perspectives in yeast research nearly a decade after the genome sequence.

Authors:  Kara Dolinski; David Botstein
Journal:  Genome Res       Date:  2005-12       Impact factor: 9.043

Review 6.  Why are there still over 1000 uncharacterized yeast genes?

Authors:  Lourdes Peña-Castillo; Timothy R Hughes
Journal:  Genetics       Date:  2007-04-15       Impact factor: 4.562

7.  Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics.

Authors:  John P McCutcheon; Sean R Eddy
Journal:  Nucleic Acids Res       Date:  2003-07-15       Impact factor: 16.971

8.  Binding specificities of the GYF domains from two Saccharomyces cerevisiae paralogs.

Authors:  Alexander Georgiev; Michael Sjöström; Ake Wieslander
Journal:  Protein Eng Des Sel       Date:  2007-09-04       Impact factor: 1.650

9.  A race through the maze of genomic evidence.

Authors:  Timothy R Hughes; Frederick P Roth
Journal:  Genome Biol       Date:  2008-06-27       Impact factor: 13.583

Review 10.  Linking genes to literature: text mining, information extraction, and retrieval applications for biology.

Authors:  Martin Krallinger; Alfonso Valencia; Lynette Hirschman
Journal:  Genome Biol       Date:  2008-09-01       Impact factor: 13.583

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  19 in total

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Authors:  Michael Y Galperin; Eugene V Koonin
Journal:  Trends Biotechnol       Date:  2010-08       Impact factor: 19.536

Review 2.  Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.

Authors:  Rylee K Hackley; Amy K Schmid
Journal:  J Mol Biol       Date:  2019-08-19       Impact factor: 5.469

Review 3.  Systems biology from a yeast omics perspective.

Authors:  Michael Snyder; Jennifer E G Gallagher
Journal:  FEBS Lett       Date:  2009-12-17       Impact factor: 4.124

4.  Networks' Characteristics Matter for Systems Biology.

Authors:  Andrew K Rider; Tijana Milenković; Geoffrey H Siwo; Richard S Pinapati; Scott J Emrich; Michael T Ferdig; Nitesh V Chawla
Journal:  Netw Sci (Camb Univ Press)       Date:  2014-09-03

Review 5.  Modeling Huntington disease in yeast: perspectives and future directions.

Authors:  Robert P Mason; Flaviano Giorgini
Journal:  Prion       Date:  2011-10-01       Impact factor: 3.931

6.  Evolutionary mobility of the ribosomal DNA array in yeasts.

Authors:  Estelle Proux-Wéra; Kevin P Byrne; Kenneth H Wolfe
Journal:  Genome Biol Evol       Date:  2013       Impact factor: 3.416

7.  Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study.

Authors:  Maria C Costanzo; Julie Park; Rama Balakrishnan; J Michael Cherry; Eurie L Hong
Journal:  Database (Oxford)       Date:  2011-03-15       Impact factor: 3.451

8.  Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report.

Authors:  Esther T Chan; J Michael Cherry
Journal:  Database (Oxford)       Date:  2012-03-20       Impact factor: 3.451

9.  Incidence of genome structure, DNA asymmetry, and cell physiology on T-DNA integration in chromosomes of the phytopathogenic fungus Leptosphaeria maculans.

Authors:  Salim Bourras; Michel Meyer; Jonathan Grandaubert; Nicolas Lapalu; Isabelle Fudal; Juliette Linglin; Benedicte Ollivier; Françoise Blaise; Marie-Hélène Balesdent; Thierry Rouxel
Journal:  G3 (Bethesda)       Date:  2012-08-01       Impact factor: 3.154

10.  A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach.

Authors:  Estelle Proux-Wéra; David Armisén; Kevin P Byrne; Kenneth H Wolfe
Journal:  BMC Bioinformatics       Date:  2012-09-17       Impact factor: 3.169

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