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Literature DB >> 24671625

Plant systems biology: insights, advances and challenges.

Abstract

Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.

Mesh：

Year: 2014 PMID： 24671625 DOI： 10.1007/s00425-014-2059-5

Source DB: PubMed Journal: Planta ISSN： 0032-0935 Impact factor: 4.116

321 in total

Review 1. Proteomics: the first decade and beyond.

Authors: Scott D Patterson; Ruedi H Aebersold
Journal: Nat Genet Date: 2003-03 Impact factor: 38.330

2. Redefining plant systems biology: from cell to ecosystem.

Authors: Joost J B Keurentjes; Gerco C Angenent; Marcel Dicke; Vítor A P Martins Dos Santos; Jaap Molenaar; Wim H van der Putten; Peter C de Ruiter; Paul C Struik; Bart P H J Thomma
Journal: Trends Plant Sci Date: 2011-01-05 Impact factor: 18.313

Review 3. Profiling a plant: expression analysis in Arabidopsis.

Authors: Wolfgang Busch; Jan U Lohmann
Journal: Curr Opin Plant Biol Date: 2007-02-08 Impact factor: 7.834

Review 4. The model organism as a system: integrating 'omics' data sets.

Authors: Andrew R Joyce; Bernhard Ø Palsson
Journal: Nat Rev Mol Cell Biol Date: 2006-03 Impact factor: 94.444

5. Population genomic and genome-wide association studies of agroclimatic traits in sorghum.

Authors: Geoffrey P Morris; Punna Ramu; Santosh P Deshpande; C Thomas Hash; Trushar Shah; Hari D Upadhyaya; Oscar Riera-Lizarazu; Patrick J Brown; Charlotte B Acharya; Sharon E Mitchell; James Harriman; Jeffrey C Glaubitz; Edward S Buckler; Stephen Kresovich
Journal: Proc Natl Acad Sci U S A Date: 2012-12-24 Impact factor: 11.205

6. Two-dimensional electrophoresis of plant proteins and standardization of gel patterns.

Authors: A Tsugita; M Kamo; T Kawakami; Y Ohki
Journal: Electrophoresis Date: 1996-05 Impact factor: 3.535

7. Independently evolved virulence effectors converge onto hubs in a plant immune system network.

Authors: M Shahid Mukhtar; Anne-Ruxandra Carvunis; Matija Dreze; Petra Epple; Jens Steinbrenner; Jonathan Moore; Murat Tasan; Mary Galli; Tong Hao; Marc T Nishimura; Samuel J Pevzner; Susan E Donovan; Lila Ghamsari; Balaji Santhanam; Viviana Romero; Matthew M Poulin; Fana Gebreab; Bryan J Gutierrez; Stanley Tam; Dario Monachello; Mike Boxem; Christopher J Harbort; Nathan McDonald; Lantian Gai; Huaming Chen; Yijian He; Jean Vandenhaute; Frederick P Roth; David E Hill; Joseph R Ecker; Marc Vidal; Jim Beynon; Pascal Braun; Jeffery L Dangl
Journal: Science Date: 2011-07-29 Impact factor: 47.728

Review 8. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond.

Authors: Ryan Lister; Brian D Gregory; Joseph R Ecker
Journal: Curr Opin Plant Biol Date: 2009-01-20 Impact factor: 7.834

9. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.

Authors: Susanna Atwell; Yu S Huang; Bjarni J Vilhjálmsson; Glenda Willems; Matthew Horton; Yan Li; Dazhe Meng; Alexander Platt; Aaron M Tarone; Tina T Hu; Rong Jiang; N Wayan Muliyati; Xu Zhang; Muhammad Ali Amer; Ivan Baxter; Benjamin Brachi; Joanne Chory; Caroline Dean; Marilyne Debieu; Juliette de Meaux; Joseph R Ecker; Nathalie Faure; Joel M Kniskern; Jonathan D G Jones; Todd Michael; Adnane Nemri; Fabrice Roux; David E Salt; Chunlao Tang; Marco Todesco; M Brian Traw; Detlef Weigel; Paul Marjoram; Justin O Borevitz; Joy Bergelson; Magnus Nordborg
Journal: Nature Date: 2010-03-24 Impact factor: 49.962

10. Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing.

Authors: Melissa M L Wong; Charles H Cannon; Ratnam Wickneswari
Journal: BMC Genomics Date: 2011-07-05 Impact factor: 3.969

17 in total

1. A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample.

Authors: Mohamed Salem; Michal Bernach; Krzysztof Bajdzienko; Patrick Giavalisco
Journal: J Vis Exp Date: 2017-06-01 Impact factor: 1.355

Plant systems biology: insights, advances and challenges.

Review 1. Proteomics: the first decade and beyond.

2. Redefining plant systems biology: from cell to ecosystem.

Review 3. Profiling a plant: expression analysis in Arabidopsis.

Review 4. The model organism as a system: integrating 'omics' data sets.

5. Population genomic and genome-wide association studies of agroclimatic traits in sorghum.

6. Two-dimensional electrophoresis of plant proteins and standardization of gel patterns.

7. Independently evolved virulence effectors converge onto hubs in a plant immune system network.

Review 8. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond.

9. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.

10. Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing.

1. A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample.

Review 2. Linking metabolomics data to underlying metabolic regulation.

Review 3. Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance.

4. VESPUCCI: Exploring Patterns of Gene Expression in Grapevine.

5. Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses.

Review 6. Insect Gallers and Their Plant Hosts: From Omics Data to Systems Biology.

7. Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics.

8. The Challenge to Translate OMICS Data to Whole Plant Physiology: The Context Matters.

Review 9. Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs.

Review 10. The female gametophyte: an emerging model for cell type-specific systems biology in plant development.