Literature DB >> 22253257

On the discordance of metabolomics with proteomics and transcriptomics: coping with increasing complexity in logic, chemistry, and network interactions scientific correspondence.

Alisdair R Fernie1, Mark Stitt.   

Abstract

Mesh：

Year:  2012        PMID： 22253257      PMCID： PMC3291261          DOI： 10.1104/pp.112.193235

Source DB:  PubMed          Journal:  Plant Physiol        ISSN： 0032-0889            Impact factor:   8.340


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  63 in total

Review 1.  Network biology: understanding the cell's functional organization.

Authors:  Albert-László Barabási; Zoltán N Oltvai
Journal:  Nat Rev Genet       Date:  2004-02       Impact factor: 53.242

2.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

Authors:  Jan Schellenberger; Richard Que; Ronan M T Fleming; Ines Thiele; Jeffrey D Orth; Adam M Feist; Daniel C Zielinski; Aarash Bordbar; Nathan E Lewis; Sorena Rahmanian; Joseph Kang; Daniel R Hyduke; Bernhard Ø Palsson
Journal:  Nat Protoc       Date:  2011-08-04       Impact factor: 13.491

3.  Dynamic imaging of glucose flux impedance using FRET sensors in wild-type Arabidopsis plants.

Authors:  Bhavna Chaudhuri; Friederike Hörmann; Wolf B Frommer
Journal:  J Exp Bot       Date:  2011-01-25       Impact factor: 6.992

4.  High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions.

Authors:  Camila Caldana; Thomas Degenkolbe; Alvaro Cuadros-Inostroza; Sebastian Klie; Ronan Sulpice; Andrea Leisse; Dirk Steinhauser; Alisdair R Fernie; Lothar Willmitzer; Matthew A Hannah
Journal:  Plant J       Date:  2011-07-11       Impact factor: 6.417

5.  Lysine acetylation is a widespread protein modification for diverse proteins in Arabidopsis.

Authors:  Xia Wu; Man-Ho Oh; Eliezer M Schwarz; Clayton T Larue; Mayandi Sivaguru; Brian S Imai; Peter M Yau; Donald R Ort; Steven C Huber
Journal:  Plant Physiol       Date:  2011-02-10       Impact factor: 8.340

6.  Deciphering the transcriptional regulatory logic of amino acid metabolism.

Authors:  Byung-Kwan Cho; Stephen Federowicz; Young-Seoub Park; Karsten Zengler; Bernhard Ø Palsson
Journal:  Nat Chem Biol       Date:  2011-11-13       Impact factor: 15.040

7.  The metabolic response of heterotrophic Arabidopsis cells to oxidative stress.

Authors:  Charles J Baxter; Henning Redestig; Nicolas Schauer; Dirk Repsilber; Kiran R Patil; Jens Nielsen; Joachim Selbig; Junli Liu; Alisdair R Fernie; Lee J Sweetlove
Journal:  Plant Physiol       Date:  2006-11-22       Impact factor: 8.340

Review 8.  'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.

Authors:  Andrew D Hanson; Anne Pribat; Jeffrey C Waller; Valérie de Crécy-Lagard
Journal:  Biochem J       Date:  2009-12-14       Impact factor: 3.857

9.  Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes.

Authors:  Yves Gibon; Bjoern Usadel; Oliver E Blaesing; Beate Kamlage; Melanie Hoehne; Richard Trethewey; Mark Stitt
Journal:  Genome Biol       Date:  2006-08-17       Impact factor: 13.583

10.  Metabolite annotations based on the integration of mass spectral information.

Authors:  Yoko Iijima; Yukiko Nakamura; Yoshiyuki Ogata; Ken'ichi Tanaka; Nozomu Sakurai; Kunihiro Suda; Tatsuya Suzuki; Hideyuki Suzuki; Koei Okazaki; Masahiko Kitayama; Shigehiko Kanaya; Koh Aoki; Daisuke Shibata
Journal:  Plant J       Date:  2008-02-07       Impact factor: 6.417
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  67 in total

1.  Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation.

Authors:  Takayuki Tohge; Federico Scossa; Alisdair R Fernie
Journal:  Plant Physiol       Date:  2015-09-14       Impact factor: 8.340

2.  Genetic and functional investigation of Zn(2)Cys(6) transcription factors RSE2 and RSE3 in Podospora anserina.

Authors:  Elodie Bovier; Carole H Sellem; Adeline Humbert; Annie Sainsard-Chanet
Journal:  Eukaryot Cell       Date:  2013-11-01

3.  Genome-Wide Association Mapping Reveals That Specific and Pleiotropic Regulatory Mechanisms Fine-Tune Central Metabolism and Growth in Arabidopsis.

Authors:  Corina M Fusari; Rik Kooke; Martin A Lauxmann; Maria Grazia Annunziata; Beatrice Enke; Melanie Hoehne; Nicole Krohn; Frank F M Becker; Armin Schlereth; Ronan Sulpice; Mark Stitt; Joost J B Keurentjes
Journal:  Plant Cell       Date:  2017-09-27       Impact factor: 11.277

Review 4.  Transparency in metabolic network reconstruction enables scalable biological discovery.

Authors:  Benjamin D Heavner; Nathan D Price
Journal:  Curr Opin Biotechnol       Date:  2015-01-03       Impact factor: 9.740

5.  Flux profiling of photosynthetic carbon metabolism in intact plants.

Authors:  Robert Heise; Stéphanie Arrivault; Marek Szecowka; Takayuki Tohge; Adriano Nunes-Nesi; Mark Stitt; Zoran Nikoloski; Alisdair R Fernie
Journal:  Nat Protoc       Date:  2014-07-03       Impact factor: 13.491

6.  Characterization of a NADH-dependent glutamate dehydrogenase mutant of Arabidopsis demonstrates the key role of this enzyme in root carbon and nitrogen metabolism.

Authors:  Jean-Xavier Fontaine; Thérèse Tercé-Laforgue; Patrick Armengaud; Gilles Clément; Jean-Pierre Renou; Sandra Pelletier; Manuella Catterou; Marianne Azzopardi; Yves Gibon; Peter J Lea; Bertrand Hirel; Frédéric Dubois
Journal:  Plant Cell       Date:  2012-10-09       Impact factor: 11.277

7.  Proteome analysis of pear reveals key genes associated with fruit development and quality.

Authors:  Jia Ming Li; Xiao San Huang; Lie Ting Li; Dan Man Zheng; Cheng Xue; Shao Ling Zhang; Jun Wu
Journal:  Planta       Date:  2015-02-15       Impact factor: 4.116

8.  Enhanced Secondary- and Hormone Metabolism in Leaves of Arbuscular Mycorrhizal Medicago truncatula.

Authors:  Lisa Adolfsson; Hugues Nziengui; Ilka N Abreu; Jan Šimura; Azeez Beebo; Andrei Herdean; Jila Aboalizadeh; Jitka Široká; Thomas Moritz; Ondřej Novák; Karin Ljung; Benoît Schoefs; Cornelia Spetea
Journal:  Plant Physiol       Date:  2017-07-11       Impact factor: 8.340

9.  Ozone exposure response for U.S. soybean cultivars: linear reductions in photosynthetic potential, biomass, and yield.

Authors:  Amy M Betzelberger; Craig R Yendrek; Jindong Sun; Courtney P Leisner; Randall L Nelson; Donald R Ort; Elizabeth A Ainsworth
Journal:  Plant Physiol       Date:  2012-10-04       Impact factor: 8.340

10.  Seed architecture shapes embryo metabolism in oilseed rape.

Authors:  Ljudmilla Borisjuk; Thomas Neuberger; Jörg Schwender; Nicolas Heinzel; Stephanie Sunderhaus; Johannes Fuchs; Jordan O Hay; Henning Tschiersch; Hans-Peter Braun; Peter Denolf; Bart Lambert; Peter M Jakob; Hardy Rolletschek
Journal:  Plant Cell       Date:  2013-05-24       Impact factor: 11.277
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