The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

Keywords

Arabidopsis, Biology, Genome, Arabidopsis thaliana, Computational biology

References

• Can plant biotechnology help in solving our food and energy shortage in the future?Maria Teresa Santos Soares da Silva — 2011
• The Gene Ontology in 2010: extensions and refinementsThe Gene Ontology Consortium — 2009
• Using the Generic Synteny Browser (GBrowse_syn)Sheldon McKay, Ismael A. Vergara, Jason Stajich — 2010
• Arabidopsis thaliana- the model plant to study host-pathogen interactions.Nikolaus L. Schlaich — 2011
• AUGUSTUS: ab initio prediction of alternative transcriptsMario Stanke, O. Keller, Irfan Gunduz — 2006
• Features of Arabidopsis Genes and Genome Discovered using Full-length cDNAsNickolai Alexandrov, Maxim Troukhan, Vyacheslav Brover — 2005
• The BioGRID interaction database: 2013 updateAndrew Chatr‐aryamontri, Bobby‐Joe Breitkreutz, Sven Heinicke — 2012
• Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.Nicolas Buisine, Hadi Quesneville, Vincent Colot — 2008
• A stress-free walk from Arabidopsis to crops.Yin Hoon Chew, Karen Halliday — 2011
• Discovery and revision of Arabidopsis genes by proteogenomicsNatalie Castellana, Samuel Payne, Zhouxin Shen — 2008
• Disease induction by human microbial pathogens in plant-model systems: potential, problems and prospects.Peter van Baarlen, Alex van Belkum, Bart P. H. J. Thomma — 2007
• InterProScan - an integration platform for the signature-recognition methods in InterProEvgeny M. Zdobnov, Rolf Apweiler — 2001
• A cross-species alignment tool (CAT)Heng Li, Liang Guan, Tao Liu — 2007
• pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana.Katja Baerenfaller, Matthias Hirsch‐Hoffmann, Julia Svozil — 2011
• The value of Arabidopsis research in understanding human disease states.Xiang Xu, Simon Geir Møller — 2011
• Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genomeSébastien Aubourg, Marie‐Laure Martin‐Magniette, Véronique Brunaud — 2007
• Arabidopsis as a model for wood formation.Jing Zhang, Annakaisa Elo, Ykä Helariutta — 2011
• Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological LiteratureHans‐Michael Müller, Eimear E. Kenny, Paul W. Sternberg — 2004
• Sequencing of natural strains of Arabidopsis thaliana with short reads.Stephan Ossowski, Korbinian Schneeberger, Richard M. Clark — 2008
• Highly integrated single-base resolution maps of the epigenome in Arabidopsis.Ryan Lister, Ronan C. O’Malley, Julian Tonti‐Filippini — 2008

Cited by

• The Evolution of the Glucosinolate Pathway in the BrassicaceaeCarrie Olson-Manning — 2013
• CONSERVED NONCODING SEQUENCES REGULATE STEADY-STATE mRNA LEVELS IN Arabidopsis thalianaJacob B. Spangler — 2013
• Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis.智美 藤澤, 香奈 村瀬, 真理子 齋藤 — 2013
• Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants[W]Alison Brettle, Michelle Maden, Jenny Tancock — 2013
• Transcriptome-Mining for Single-Copy Nuclear Markers in FernsShalini Chandra, Shirish C. Srivastava, Yin Leng Theng — 2013
• An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data AnalysisG Turazza — 2013
• Techniques for transferring host-pathogen protein interactions knowledge to new tasksKim Massey — 2015
• Transcriptional transitions in Nicotiana benthamiana leaves upon induction of oil synthesis by WRINKLED1 homologs from diverse species and tissuesDavid A. DeCoster — 2015
• Tissue specific and abiotic stress regulated transcription of histidine kinases in plants is also influenced by diurnal rhythmA. Romano — 2015
• A cis-regulatory sequence from a short intergenic region gives rise to a strong microbe-associated molecular pattern-responsive synthetic promoterMona Lehmeyer, Erik K. R. Hanko, Lena Roling — 2016
• Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchaticaJ. Moret, Michel Piotin, L Spelle — 2016
• Unveiling the functional diversity of the Alpha-Beta hydrolase fold in plantsRoberto López del Campo — 2016
• Signatures of local adaptation in candidate genes of oaks (Quercus spp.) with respect to present and future climatic conditionsLuis T. Villa, Domingo A. Tarzia — 2016
• Transcriptional Analysis of serk1 and serk3 Coreceptor Mutants1D.J. Gould, T.M. Massis, E.A. Kjeldgaard — 2016
• CSDB_GT: a new curated database on glycosyltransferasesHaohao Gu, He Zhang — 2016
• Main and epistatic loci studies in soybean for Sclerotinia sclerotiorum resistance reveal multiple modes of resistance in multi-environmentsTara C. Moellers, Arti Singh, Jiaoping Zhang — 2017
• Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza淳一 藤田 — 2018
• Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thalianaИ. К. Гималтдинов, В. Л. Дмитриев, Л. Ф. Ситдикова — 2019
• The genomics and physiology of abiotic stressors associated with global elevational gradients in Arabidopsis thalianaMaria Yau — 2024
• Plant proteomics: from genome sequencing to proteome databases and repositories.Katsumi Sakata, Setsuko Komatsu — 2014

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