Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release

Keywords

Biology, Arabidopsis, Computational biology, Genome, Genetics

References

• Polycistronic expression and RNA-binding specificity of the C. elegans homologue of the spliceosome-associated protein SAP49.Waltraud Schreiber, Stefan Bleitzhofer, Michael Herrler — 1997
• A global analysis of Caenorhabditis elegans operonsJosé María Merino — 2002
• Annotation of parasite genomes.Matthew Berriman, Midori A. Harris — 2004
• Dynamics and Evolution of Transposable ElementsPierre Capy — 1996
• Analysis of the genome sequence of the flowering plant Arabidopsis thalianaArabidopsis Genome Initiative — 2000
• Computational gene finding in plantsMihaela Pertea, Steven L. Salzberg — 2004
• Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resourceMidori A. Harris — 2004
• The Arabidopsis splicing factor SR1 is regulated by alternative splicingG. Lázár, Howard M. Goodman — 2000
• Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure.Elaine K. Round, Susan K. Flowers, Eric J. Richards — 1997
• The stoned locus of Drosophila melanogaster produces a dicistronic transcript and encodes two distinct polypeptides.J. Macpherson Andrew, Michiko Smith, John Merakovsky — 1996
• Database and analyses of known alternatively spliced genes in plants.Yan Zhou, Chunlong Zhou, Lin Ye — 2003
• Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: Implication for land plant evolutionTomoaki Nishiyama, Tomomichi Fujita, Tadasu Shin‐I — 2003
• The leucine-rich repeat as a protein recognition motif.Boštjan Kobe — 2001
• Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.Julia C. Redman, Brian J. Haas, Gene Tanimoto — 2004
• EyeSite: a semi-automated database of protein families in the eyeDavid A. Lee — 2004
• Cyclophilin and Protein Disulfide Isomerase Genes Are Co-Transcribed in a Functionally Related Manner in Caenorhabditis elegansAntony P. Page — 1997
• Do natural antisense transcripts make sense in eukaryotes?Christine Vanhée-Brossollet, Catherine Vaquero — 1998
• Does this have a familiar RING?Andrew J. Saurin, Katherine L. B. Borden, Michael N. Boddy — 1996
• Alternative splicing: combinatorial output from the genome.Gavin C Roberts, Christopher W. J. Smith — 2002
• Similar amino acid sequences: chance or common ancestry?Russell F. Doolittle — 1981

Cited by

• A Survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana.Chang Pyo Hong, P. Plaha, Dal-Hoe Koo — 2006
• Targeting of nucleus-encoded proteins to chloroplasts in plants.Ayodele Samuel Jegede — 2008
• Analysis of alternative splicing in plants with bioinformatics tools.Brian J. Haas — 2008
• Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactisShamrahayu Abd Aziz — 2014
• Plant genome annotation methods.Shu Ouyang, Françoise Thibaud‐Nissen, Kevin L. Childs — 2009
• Prediction and Annotation of Plant Protein Interaction NetworksJason McDermott, Jun Wang, Jun Yu — 2009
• Molecular mechanism of Arabidopsis CBF mediated plant cold-regulated gene transcriptional activationZhibin Wang — 2006
• 2D PAGE: Sample Preparation and FractionationAnton Posch — 2008
• Plant Genome Diversity Volume 1Jonathan F. Wendel, Ilia J. Leitch, Jaroslav Doležel — 2012
• Régulation de l'expression des gènes dupliqués chez les polyploïdes : approche protéomique appliquée à l'analyse de Brassicacées autopolyploïdes et allopolyploïdesWarren Albertin — 2005
• Mu in vitro Transposition Technology in Functional Genetics and Genomics: Applications on Mouse and BacteriophagesHeikki Vilén — 2006
• Studies of epigenetic mechanisms affecting transcription in "Arabidopsis thaliana"M. Čaikovski — 2008
• Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populationsJan Lisec, Rhonda C. Meyer, Matthias Steinfath — 2007
• Bioinformatics for plant genome annotationMark Fiers — 2006
• Approaches to Fungal Genome AnnotationBrian J. Haas, Qiandong Zeng, Matthew D. Pearson — 2011
• Experimental validation of novel genes predicted in the un-annotated regions of the Arabidopsis genomeWilliam A. Moskal, Hank Wu, Beverly A. Underwood — 2007
• Significant Pattern Discovery in Gene Location and PhylogenyMichael C. Riley — 2009
• PlnTFDB: an integrative plant transcription factor databaseDiego Mauricio Riaño‐Pachón, Slobodan Ruzicic, Ingo Drèyer — 2007
• The outer membrane protein Omp35 affects the reduction of Fe(III), nitrate, and fumarate by Shewanella oneidensis MR-1Tamara M. Maier, Charles R. Myers — 2004
• Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants.Kevin A.T. Silverstein, William A. Moskal, Hank Wu — 2007

Related papers

• ИСПОЛЬЗОВAНИЕ ПОТЕНЦИAЛA СОЦИAЛЬНЫХ ПAРТНЕРОВ В ПОДГОТОВКЕ БУДУЩИХ ПЕДAГОГОВБ.Б. Атaбекова — 2024
• Cloning and Characterization of Rat BAT3 cDNAToshinori Ozaki, Eiji Hanaoka, Masahiko Naka — 1999
• Expression of a rice OsARGOS gene in Arabidopsis promotes cell division and expansion and increases organ sizeBao, Wang, Yal�in — 2009
• EFFECT OF THE NEMATODE PHASMARHABDITIS HERMAPHRODITA ON YOUNG STAGES OF THE PEST SLUG ARION LUSITANICUSB. Grimm — 2002
• HLA-B-associated transcript 3 (Bat3)/Scythe is essential for p300-mediated acetylation of p53.Toru Sasaki, Eugene Gan, Andrew Wakeham — 2007
• Anthoxanthum Mosaic VirusP. L. Catherall — 1970
• Ecological and evolutionary importance of neighbors in the grass Anthoxanthum odoratumGerrit A. J. Platenkamp, T. C. Foin — 1990
• Salinity tolerance of Arabidopsis: a good model for cereals?Inge Skrumsager Møller, Mark Tester — 2007
• European Sweet Vernal Grasses (Anthoxanthum: Poaceae, Pooideae, Aveneae): A Morphometric Taxonomical ApproachManuel Pimentel Pereira, Graciela Estévez‐Pérez, Elvira Sahuquillo — 2007
• Memoirs: The Structure and Biology of Schizoneura Lanigera, Hausmann or Woolly Aphis of the Apple Tree: Part I.--The Apterous Viviparous FemaleJ. Dswidson — 1913