Literature DB >> 18591350

Arabidopsis reactome: a foundation knowledgebase for plant systems biology.

Nicolas Tsesmetzis1, Matthew Couchman, Janet Higgins, Alison Smith, John H Doonan, Georg J Seifert, Esther E Schmidt, Imre Vastrik, Ewan Birney, Guanming Wu, Peter D'Eustachio, Lincoln D Stein, Richard J Morris, Michael W Bevan, Sean V Walsh.   

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Year:  2008        PMID: 18591350      PMCID: PMC2483364          DOI: 10.1105/tpc.108.057976

Source DB:  PubMed          Journal:  Plant Cell        ISSN: 1040-4651            Impact factor:   11.277


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  52 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

Review 2.  Mathematical modeling of plant metabolic pathways.

Authors:  John A Morgan; David Rhodes
Journal:  Metab Eng       Date:  2002-01       Impact factor: 9.783

3.  The KEGG databases at GenomeNet.

Authors:  Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Akihiro Nakaya
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

Review 4.  A fortunate choice: the history of Arabidopsis as a model plant.

Authors:  Chris Somerville; Maarten Koornneef
Journal:  Nat Rev Genet       Date:  2002-11       Impact factor: 53.242

5.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.

Authors:  M Remm; C E Storm; E L Sonnhammer
Journal:  J Mol Biol       Date:  2001-12-14       Impact factor: 5.469

6.  The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.

Authors:  Seung Yon Rhee; William Beavis; Tanya Z Berardini; Guanghong Chen; David Dixon; Aisling Doyle; Margarita Garcia-Hernandez; Eva Huala; Gabriel Lander; Mary Montoya; Neil Miller; Lukas A Mueller; Suparna Mundodi; Leonore Reiser; Julie Tacklind; Dan C Weems; Yihe Wu; Iris Xu; Daniel Yoo; Jungwon Yoon; Peifen Zhang
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

7.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Authors:  Ray Ming; Shaobin Hou; Yun Feng; Qingyi Yu; Alexandre Dionne-Laporte; Jimmy H Saw; Pavel Senin; Wei Wang; Benjamin V Ly; Kanako L T Lewis; Steven L Salzberg; Lu Feng; Meghan R Jones; Rachel L Skelton; Jan E Murray; Cuixia Chen; Wubin Qian; Junguo Shen; Peng Du; Moriah Eustice; Eric Tong; Haibao Tang; Eric Lyons; Robert E Paull; Todd P Michael; Kerr Wall; Danny W Rice; Henrik Albert; Ming-Li Wang; Yun J Zhu; Michael Schatz; Niranjan Nagarajan; Ricelle A Acob; Peizhu Guan; Andrea Blas; Ching Man Wai; Christine M Ackerman; Yan Ren; Chao Liu; Jianmei Wang; Jianping Wang; Jong-Kuk Na; Eugene V Shakirov; Brian Haas; Jyothi Thimmapuram; David Nelson; Xiyin Wang; John E Bowers; Andrea R Gschwend; Arthur L Delcher; Ratnesh Singh; Jon Y Suzuki; Savarni Tripathi; Kabi Neupane; Hairong Wei; Beth Irikura; Maya Paidi; Ning Jiang; Wenli Zhang; Gernot Presting; Aaron Windsor; Rafael Navajas-Pérez; Manuel J Torres; F Alex Feltus; Brad Porter; Yingjun Li; A Max Burroughs; Ming-Cheng Luo; Lei Liu; David A Christopher; Stephen M Mount; Paul H Moore; Tak Sugimura; Jiming Jiang; Mary A Schuler; Vikki Friedman; Thomas Mitchell-Olds; Dorothy E Shippen; Claude W dePamphilis; Jeffrey D Palmer; Michael Freeling; Andrew H Paterson; Dennis Gonsalves; Lei Wang; Maqsudul Alam
Journal:  Nature       Date:  2008-04-24       Impact factor: 49.962

8.  An automated method for finding molecular complexes in large protein interaction networks.

Authors:  Gary D Bader; Christopher W V Hogue
Journal:  BMC Bioinformatics       Date:  2003-01-13       Impact factor: 3.169

9.  OrthoMCL: identification of ortholog groups for eukaryotic genomes.

Authors:  Li Li; Christian J Stoeckert; David S Roos
Journal:  Genome Res       Date:  2003-09       Impact factor: 9.043

10.  AraCyc: a biochemical pathway database for Arabidopsis.

Authors:  Lukas A Mueller; Peifen Zhang; Seung Y Rhee
Journal:  Plant Physiol       Date:  2003-06       Impact factor: 8.340

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  24 in total

1.  Taking the next step: building an Arabidopsis information portal.

Authors: 
Journal:  Plant Cell       Date:  2012-06-29       Impact factor: 11.277

Review 2.  Computational systems biology of cellular processes in Arabidopsis thaliana: an overview.

Authors:  Pascal Holzheu; Ursula Kummer
Journal:  Cell Mol Life Sci       Date:  2019-11-25       Impact factor: 9.261

3.  Reactome pathway analysis to enrich biological discovery in proteomics data sets.

Authors:  Robin Haw; Henning Hermjakob; Peter D'Eustachio; Lincoln Stein
Journal:  Proteomics       Date:  2011-09       Impact factor: 3.984

Review 4.  Web-queryable large-scale data sets for hypothesis generation in plant biology.

Authors:  Siobhan M Brady; Nicholas J Provart
Journal:  Plant Cell       Date:  2009-04-28       Impact factor: 11.277

5.  PLAZA: a comparative genomics resource to study gene and genome evolution in plants.

Authors:  Sebastian Proost; Michiel Van Bel; Lieven Sterck; Kenny Billiau; Thomas Van Parys; Yves Van de Peer; Klaas Vandepoele
Journal:  Plant Cell       Date:  2009-12-29       Impact factor: 11.277

Review 6.  Gene expression analysis, proteomics, and network discovery.

Authors:  Sacha Baginsky; Lars Hennig; Philip Zimmermann; Wilhelm Gruissem
Journal:  Plant Physiol       Date:  2009-12-11       Impact factor: 8.340

7.  Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses.

Authors:  Janet A Higgins; Paul C Bailey; David A Laurie
Journal:  PLoS One       Date:  2010-04-19       Impact factor: 3.240

8.  Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.

Authors:  Jelle Van Leene; Jens Hollunder; Dominique Eeckhout; Geert Persiau; Eveline Van De Slijke; Hilde Stals; Gert Van Isterdael; Aurine Verkest; Sandy Neirynck; Yelle Buffel; Stefanie De Bodt; Steven Maere; Kris Laukens; Anne Pharazyn; Paulo C G Ferreira; Nubia Eloy; Charlotte Renne; Christian Meyer; Jean-Denis Faure; Jens Steinbrenner; Jim Beynon; John C Larkin; Yves Van de Peer; Pierre Hilson; Martin Kuiper; Lieven De Veylder; Harry Van Onckelen; Dirk Inzé; Erwin Witters; Geert De Jaeger
Journal:  Mol Syst Biol       Date:  2010-08-10       Impact factor: 11.429

9.  Reactome knowledgebase of human biological pathways and processes.

Authors:  Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft; Bernard de Bono; Phani Garapati; Jill Hemish; Henning Hermjakob; Bijay Jassal; Alex Kanapin; Suzanna Lewis; Shahana Mahajan; Bruce May; Esther Schmidt; Imre Vastrik; Guanming Wu; Ewan Birney; Lincoln Stein; Peter D'Eustachio
Journal:  Nucleic Acids Res       Date:  2008-11-03       Impact factor: 16.971

10.  Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine.

Authors:  Ana Rotter; Céline Camps; Marc Lohse; Christian Kappel; Stefania Pilati; Matjaz Hren; Mark Stitt; Pierre Coutos-Thévenot; Claudio Moser; Björn Usadel; Serge Delrot; Kristina Gruden
Journal:  BMC Plant Biol       Date:  2009-08-05       Impact factor: 4.215

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