Literature DB >> 19903479

Systems biology from a yeast omics perspective.

Michael Snyder1, Jennifer E G Gallagher.   

Abstract

Systems biology represents a paradigm shift from the study of individual genes, proteins or other components to that of the analysis of entire pathways, cellular, developmental, or organismal processes. Large scale studies, primarily initiated in Saccharomyces cerevisiae, have allowed the identification and characterization of components on an unprecedented level. Large scale interaction, transcription factor binding and phosphorylation data have enabled the elucidation of global regulatory networks. These studies have helped provide an understanding of cellular pathways and processes at a global and systems level.

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Year:  2009        PMID: 19903479      PMCID: PMC3262145          DOI: 10.1016/j.febslet.2009.11.011

Source DB:  PubMed          Journal:  FEBS Lett        ISSN: 0014-5793            Impact factor:   4.124


  70 in total

1.  Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile.

Authors:  Maya Schuldiner; Sean R Collins; Natalie J Thompson; Vladimir Denic; Arunashree Bhamidipati; Thanuja Punna; Jan Ihmels; Brenda Andrews; Charles Boone; Jack F Greenblatt; Jonathan S Weissman; Nevan J Krogan
Journal:  Cell       Date:  2005-11-04       Impact factor: 41.582

2.  Global analysis of protein phosphorylation in yeast.

Authors:  Jason Ptacek; Geeta Devgan; Gregory Michaud; Heng Zhu; Xiaowei Zhu; Joseph Fasolo; Hong Guo; Ghil Jona; Ashton Breitkreutz; Richelle Sopko; Rhonda R McCartney; Martin C Schmidt; Najma Rachidi; Soo-Jung Lee; Angie S Mah; Lihao Meng; Michael J R Stark; David F Stern; Claudio De Virgilio; Mike Tyers; Brenda Andrews; Mark Gerstein; Barry Schweitzer; Paul F Predki; Michael Snyder
Journal:  Nature       Date:  2005-12-01       Impact factor: 49.962

3.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.

Authors:  E A Winzeler; D D Shoemaker; A Astromoff; H Liang; K Anderson; B Andre; R Bangham; R Benito; J D Boeke; H Bussey; A M Chu; C Connelly; K Davis; F Dietrich; S W Dow; M El Bakkoury; F Foury; S H Friend; E Gentalen; G Giaever; J H Hegemann; T Jones; M Laub; H Liao; N Liebundguth; D J Lockhart; A Lucau-Danila; M Lussier; N M'Rabet; P Menard; M Mittmann; C Pai; C Rebischung; J L Revuelta; L Riles; C J Roberts; P Ross-MacDonald; B Scherens; M Snyder; S Sookhai-Mahadeo; R K Storms; S Véronneau; M Voet; G Volckaert; T R Ward; R Wysocki; G S Yen; K Yu; K Zimmermann; P Philippsen; M Johnston; R W Davis
Journal:  Science       Date:  1999-08-06       Impact factor: 47.728

4.  Global identification of human transcribed sequences with genome tiling arrays.

Authors:  Paul Bertone; Viktor Stolc; Thomas E Royce; Joel S Rozowsky; Alexander E Urban; Xiaowei Zhu; John L Rinn; Waraporn Tongprasit; Manoj Samanta; Sherman Weissman; Mark Gerstein; Michael Snyder
Journal:  Science       Date:  2004-11-11       Impact factor: 47.728

5.  Cyclin specificity in the phosphorylation of cyclin-dependent kinase substrates.

Authors:  Mart Loog; David O Morgan
Journal:  Nature       Date:  2005-03-03       Impact factor: 49.962

6.  An in vivo map of the yeast protein interactome.

Authors:  Kirill Tarassov; Vincent Messier; Christian R Landry; Stevo Radinovic; Mercedes M Serna Molina; Igor Shames; Yelena Malitskaya; Jackie Vogel; Howard Bussey; Stephen W Michnick
Journal:  Science       Date:  2008-05-08       Impact factor: 47.728

7.  High-quality binary protein interaction map of the yeast interactome network.

Authors:  Haiyuan Yu; Pascal Braun; Muhammed A Yildirim; Irma Lemmens; Kavitha Venkatesan; Julie Sahalie; Tomoko Hirozane-Kishikawa; Fana Gebreab; Na Li; Nicolas Simonis; Tong Hao; Jean-François Rual; Amélie Dricot; Alexei Vazquez; Ryan R Murray; Christophe Simon; Leah Tardivo; Stanley Tam; Nenad Svrzikapa; Changyu Fan; Anne-Sophie de Smet; Adriana Motyl; Michael E Hudson; Juyong Park; Xiaofeng Xin; Michael E Cusick; Troy Moore; Charlie Boone; Michael Snyder; Frederick P Roth; Albert-László Barabási; Jan Tavernier; David E Hill; Marc Vidal
Journal:  Science       Date:  2008-08-21       Impact factor: 47.728

8.  A proteomic strategy for gaining insights into protein sumoylation in yeast.

Authors:  Carilee Denison; Adam D Rudner; Scott A Gerber; Corey E Bakalarski; Danesh Moazed; Steven P Gygi
Journal:  Mol Cell Proteomics       Date:  2004-11-12       Impact factor: 5.911

9.  A comprehensive strategy enabling high-resolution functional analysis of the yeast genome.

Authors:  David K Breslow; Dale M Cameron; Sean R Collins; Maya Schuldiner; Jacob Stewart-Ornstein; Heather W Newman; Sigurd Braun; Hiten D Madhani; Nevan J Krogan; Jonathan S Weissman
Journal:  Nat Methods       Date:  2008-07-11       Impact factor: 28.547

10.  Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.

Authors:  Brian T Wilhelm; Samuel Marguerat; Stephen Watt; Falk Schubert; Valerie Wood; Ian Goodhead; Christopher J Penkett; Jane Rogers; Jürg Bähler
Journal:  Nature       Date:  2008-05-18       Impact factor: 49.962

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  21 in total

1.  Deciphering the Arabidopsis floral transition process by integrating a protein-protein interaction network and gene expression data.

Authors:  Fei He; Yuan Zhou; Ziding Zhang
Journal:  Plant Physiol       Date:  2010-06-07       Impact factor: 8.340

2.  The developmental dynamics of the maize leaf transcriptome.

Authors:  Pinghua Li; Lalit Ponnala; Neeru Gandotra; Lin Wang; Yaqing Si; S Lori Tausta; Tesfamichael H Kebrom; Nicholas Provart; Rohan Patel; Christopher R Myers; Edwin J Reidel; Robert Turgeon; Peng Liu; Qi Sun; Timothy Nelson; Thomas P Brutnell
Journal:  Nat Genet       Date:  2010-10-31       Impact factor: 38.330

3.  Systematic identification of gene annotation errors in the widely used yeast mutation collections.

Authors:  Taly Ben-Shitrit; Nir Yosef; Keren Shemesh; Roded Sharan; Eytan Ruppin; Martin Kupiec
Journal:  Nat Methods       Date:  2012-02-05       Impact factor: 28.547

4.  Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses.

Authors:  Xiyan Li; Tara A Gianoulis; Kevin Y Yip; Mark Gerstein; Michael Snyder
Journal:  Cell       Date:  2010-10-28       Impact factor: 41.582

5.  Physical and genetic-interaction density reveals functional organization and informs significance cutoffs in genome-wide screens.

Authors:  John C Dittmar; Steven Pierce; Rodney Rothstein; Robert J D Reid
Journal:  Proc Natl Acad Sci U S A       Date:  2013-04-15       Impact factor: 11.205

Review 6.  Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries.

Authors:  Kuk-Ki Hong; Jens Nielsen
Journal:  Cell Mol Life Sci       Date:  2012-03-03       Impact factor: 9.261

Review 7.  The future of model organisms in human disease research.

Authors:  Timothy J Aitman; Charles Boone; Gary A Churchill; Michael O Hengartner; Trudy F C Mackay; Derek L Stemple
Journal:  Nat Rev Genet       Date:  2011-07-18       Impact factor: 53.242

Review 8.  A survey of yeast genomic assays for drug and target discovery.

Authors:  Andrew M Smith; Ron Ammar; Corey Nislow; Guri Giaever
Journal:  Pharmacol Ther       Date:  2010-05-28       Impact factor: 12.310

9.  Yeast Systems Biology: The Continuing Challenge of Eukaryotic Complexity.

Authors:  Stephen G Oliver
Journal:  Methods Mol Biol       Date:  2019

Review 10.  Yeast proteomics and protein microarrays.

Authors:  Rui Chen; Michael Snyder
Journal:  J Proteomics       Date:  2010-08-20       Impact factor: 4.044

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