Literature DB >> 22303243

Web-based Arabidopsis functional and structural genomics resources.

Yan Lu, Robert L Last.   

Abstract

As plant research moves to a "post-genomic" era, many diverse internet resources become available to the international research community. Arabidopsis thaliana, because of its small size, rapid life cycle and simple genome, has been a model system for decades, with much research funding and many projects devoted to creation of functional and structural genomics resources. Different types of data, including genome, transcriptome, proteome, phenome, metabolome and ionome are stored in these resources. In this chapter, a variety of genomics resources are introduced, with simple descriptions of how some can be accessed by laboratory researchers via the internet.

Entities:  

Year:  2008        PMID: 22303243      PMCID: PMC3243351          DOI: 10.1199/tab.0118

Source DB:  PubMed          Journal:  Arabidopsis Book        ISSN: 1543-8120


  68 in total

1.  Proteome analysis of tobacco bright yellow-2 (BY-2) cell culture plastids as a model for undifferentiated heterotrophic plastids.

Authors:  Sacha Baginsky; Asim Siddique; Wilhelm Gruissem
Journal:  J Proteome Res       Date:  2004 Nov-Dec       Impact factor: 4.466

2.  A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis.

Authors:  Takashi Kuromori; Takuji Wada; Asako Kamiya; Masahiro Yuguchi; Takuro Yokouchi; Yuko Imura; Hiroko Takabe; Tetsuya Sakurai; Kenji Akiyama; Takashi Hirayama; Kiyotaka Okada; Kazuo Shinozaki
Journal:  Plant J       Date:  2006-06-30       Impact factor: 6.417

3.  Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis.

Authors:  O Törjék; D Berger; R C Meyer; C Müssig; K J Schmid; T Rosleff Sörensen; B Weisshaar; T Mitchell-Olds; T Altmann
Journal:  Plant J       Date:  2003-10       Impact factor: 6.417

4.  Rapid array mapping of circadian clock and developmental mutations in Arabidopsis.

Authors:  Samuel P Hazen; Justin O Borevitz; Frank G Harmon; Jose L Pruneda-Paz; Thomas F Schultz; Marcelo J Yanovsky; Sarah J Liljegren; Joseph R Ecker; Steve A Kay
Journal:  Plant Physiol       Date:  2005-05-20       Impact factor: 8.340

5.  ATIDB: Arabidopsis thaliana insertion database.

Authors:  Xiaokang Pan; Hong Liu; Jonathan Clarke; Jonathan Jones; Mike Bevan; Lincoln Stein
Journal:  Nucleic Acids Res       Date:  2003-02-15       Impact factor: 16.971

6.  Genome-wide insertional mutagenesis of Arabidopsis thaliana.

Authors:  José M Alonso; Anna N Stepanova; Thomas J Leisse; Christopher J Kim; Huaming Chen; Paul Shinn; Denise K Stevenson; Justin Zimmerman; Pascual Barajas; Rosa Cheuk; Carmelita Gadrinab; Collen Heller; Albert Jeske; Eric Koesema; Cristina C Meyers; Holly Parker; Lance Prednis; Yasser Ansari; Nathan Choy; Hashim Deen; Michael Geralt; Nisha Hazari; Emily Hom; Meagan Karnes; Celene Mulholland; Ral Ndubaku; Ian Schmidt; Plinio Guzman; Laura Aguilar-Henonin; Markus Schmid; Detlef Weigel; David E Carter; Trudy Marchand; Eddy Risseeuw; Debra Brogden; Albana Zeko; William L Crosby; Charles C Berry; Joseph R Ecker
Journal:  Science       Date:  2003-08-01       Impact factor: 47.728

7.  A map of the interactome network of the metazoan C. elegans.

Authors:  Siming Li; Christopher M Armstrong; Nicolas Bertin; Hui Ge; Stuart Milstein; Mike Boxem; Pierre-Olivier Vidalain; Jing-Dong J Han; Alban Chesneau; Tong Hao; Debra S Goldberg; Ning Li; Monica Martinez; Jean-François Rual; Philippe Lamesch; Lai Xu; Muneesh Tewari; Sharyl L Wong; Lan V Zhang; Gabriel F Berriz; Laurent Jacotot; Philippe Vaglio; Jérôme Reboul; Tomoko Hirozane-Kishikawa; Qianru Li; Harrison W Gabel; Ahmed Elewa; Bridget Baumgartner; Debra J Rose; Haiyuan Yu; Stephanie Bosak; Reynaldo Sequerra; Andrew Fraser; Susan E Mango; William M Saxton; Susan Strome; Sander Van Den Heuvel; Fabio Piano; Jean Vandenhaute; Claude Sardet; Mark Gerstein; Lynn Doucette-Stamm; Kristin C Gunsalus; J Wade Harper; Michael E Cusick; Frederick P Roth; David E Hill; Marc Vidal
Journal:  Science       Date:  2004-01-02       Impact factor: 47.728

8.  Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications.

Authors:  Pierre Hilson; Joke Allemeersch; Thomas Altmann; Sébastien Aubourg; Alexandra Avon; Jim Beynon; Rishikesh P Bhalerao; Frédérique Bitton; Michel Caboche; Bernard Cannoot; Vasil Chardakov; Cécile Cognet-Holliger; Vincent Colot; Mark Crowe; Caroline Darimont; Steffen Durinck; Holger Eickhoff; Andéol Falcon de Longevialle; Edward E Farmer; Murray Grant; Martin T R Kuiper; Hans Lehrach; Céline Léon; Antonio Leyva; Joakim Lundeberg; Claire Lurin; Yves Moreau; Wilfried Nietfeld; Javier Paz-Ares; Philippe Reymond; Pierre Rouzé; Goran Sandberg; Maria Dolores Segura; Carine Serizet; Alexandra Tabrett; Ludivine Taconnat; Vincent Thareau; Paul Van Hummelen; Steven Vercruysse; Marnik Vuylsteke; Magdalena Weingartner; Peter J Weisbeek; Valtteri Wirta; Floyd R A Wittink; Marc Zabeau; Ian Small
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

9.  From genomics to chemical genomics: new developments in KEGG.

Authors:  Minoru Kanehisa; Susumu Goto; Masahiro Hattori; Kiyoko F Aoki-Kinoshita; Masumi Itoh; Shuichi Kawashima; Toshiaki Katayama; Michihiro Araki; Mika Hirakawa
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

10.  An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets.

Authors:  Debbie Winter; Ben Vinegar; Hardeep Nahal; Ron Ammar; Greg V Wilson; Nicholas J Provart
Journal:  PLoS One       Date:  2007-08-08       Impact factor: 3.240

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  3 in total

Review 1.  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

2.  A small zinc finger thylakoid protein plays a role in maintenance of photosystem II in Arabidopsis thaliana.

Authors:  Yan Lu; David A Hall; Robert L Last
Journal:  Plant Cell       Date:  2011-05-17       Impact factor: 11.277

3.  Large-scale reverse genetics in Arabidopsis: case studies from the Chloroplast 2010 Project.

Authors:  Imad Ajjawi; Yan Lu; Linda J Savage; Shannon M Bell; Robert L Last
Journal:  Plant Physiol       Date:  2009-11-11       Impact factor: 8.340

  3 in total

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