Literature DB >> 12805579

Annotation of the Arabidopsis genome.

Jennifer R Wortman1, Brian J Haas, Linda I Hannick, Roger K Smith, Rama Maiti, Catherine M Ronning, Agnes P Chan, Chunhui Yu, Mulu Ayele, Catherine A Whitelaw, Owen R White, Christopher D Town.   

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Year:  2003        PMID： 12805579      PMCID： PMC166989          DOI： 10.1104/pp.103.022251

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


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  25 in total

1.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

Authors:  A Bairoch; R Apweiler
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  A tool for analyzing and annotating genomic sequences.

Authors:  X Huang; M D Adams; H Zhou; A R Kerlavage
Journal:  Genomics       Date:  1997-11-15       Impact factor: 5.736

3.  GeneMark.hmm: new solutions for gene finding.

Authors:  A V Lukashin; M Borodovsky
Journal:  Nucleic Acids Res       Date:  1998-02-15       Impact factor: 16.971

4.  Pfam: multiple sequence alignments and HMM-profiles of protein domains.

Authors:  E L Sonnhammer; S R Eddy; E Birney; A Bateman; R Durbin
Journal:  Nucleic Acids Res       Date:  1998-01-01       Impact factor: 16.971

5.  A complete BAC-based physical map of the Arabidopsis thaliana genome.

Authors:  T Mozo; K Dewar; P Dunn; J R Ecker; S Fischer; S Kloska; H Lehrach; M Marra; R Martienssen; S Meier-Ewert; T Altmann
Journal:  Nat Genet       Date:  1999-07       Impact factor: 38.330

6.  Interpolated Markov models for eukaryotic gene finding.

Authors:  S L Salzberg; M Pertea; A L Delcher; M J Gardner; H Tettelin
Journal:  Genomics       Date:  1999-07-01       Impact factor: 5.736

7.  Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure.

Authors:  E K Round; S K Flowers; E J Richards
Journal:  Genome Res       Date:  1997-11       Impact factor: 9.043

8.  Prediction of complete gene structures in human genomic DNA.

Authors:  C Burge; S Karlin
Journal:  J Mol Biol       Date:  1997-04-25       Impact factor: 5.469

9.  Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information.

Authors:  S M Hebsgaard; P G Korning; N Tolstrup; J Engelbrecht; P Rouzé; S Brunak
Journal:  Nucleic Acids Res       Date:  1996-09-01       Impact factor: 16.971

10.  Human-mouse alignments with BLASTZ.

Authors:  Scott Schwartz; W James Kent; Arian Smit; Zheng Zhang; Robert Baertsch; Ross C Hardison; David Haussler; Webb Miller
Journal:  Genome Res       Date:  2003-01       Impact factor: 9.043
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  59 in total

1.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.

Authors:  Brian J Haas; Arthur L Delcher; Stephen M Mount; Jennifer R Wortman; Roger K Smith; Linda I Hannick; Rama Maiti; Catherine M Ronning; Douglas B Rusch; Christopher D Town; Steven L Salzberg; Owen White
Journal:  Nucleic Acids Res       Date:  2003-10-01       Impact factor: 16.971

2.  Arabidopsis MPSS. An online resource for quantitative expression analysis.

Authors:  Blake C Meyers; David K Lee; Tam H Vu; Shivakundan Singh Tej; Steve B Edberg; Marta Matvienko; Larry D Tindell
Journal:  Plant Physiol       Date:  2004-06-01       Impact factor: 8.340

3.  Functional annotation of the Arabidopsis genome using controlled vocabularies.

Authors:  Tanya Z Berardini; Suparna Mundodi; Leonore Reiser; Eva Huala; Margarita Garcia-Hernandez; Peifen Zhang; Lukas A Mueller; Jungwoon Yoon; Aisling Doyle; Gabriel Lander; Nick Moseyko; Danny Yoo; Iris Xu; Brandon Zoeckler; Mary Montoya; Neil Miller; Dan Weems; Seung Y Rhee
Journal:  Plant Physiol       Date:  2004-06-01       Impact factor: 8.340

Review 4.  Methods for transcriptional profiling in plants. Be fruitful and replicate.

Authors:  Blake C Meyers; David W Galbraith; Timothy Nelson; Vikas Agrawal
Journal:  Plant Physiol       Date:  2004-06-01       Impact factor: 8.340

5.  High-throughput fluorescent tagging of full-length Arabidopsis gene products in planta.

Authors:  Guo-Wei Tian; Amitabh Mohanty; S Narasimha Chary; Shijun Li; Brigitte Paap; Georgia Drakakaki; Charles D Kopec; Jianxiong Li; David Ehrhardt; David Jackson; Seung Y Rhee; Natasha V Raikhel; Vitaly Citovsky
Journal:  Plant Physiol       Date:  2004-05       Impact factor: 8.340

6.  The use of MPSS for whole-genome transcriptional analysis in Arabidopsis.

Authors:  Blake C Meyers; Shivakundan Singh Tej; Tam H Vu; Christian D Haudenschild; Vikas Agrawal; Steve B Edberg; Hassan Ghazal; Shannon Decola
Journal:  Genome Res       Date:  2004-08       Impact factor: 9.043

7.  Site preferences of insertional mutagenesis agents in Arabidopsis.

Authors:  Xiaokang Pan; Yong Li; Lincoln Stein
Journal:  Plant Physiol       Date:  2004-12-23       Impact factor: 8.340

8.  Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray.

Authors:  Kanako Kawaura; Keiichi Mochida; Yukiko Yamazaki; Yasunari Ogihara
Journal:  Funct Integr Genomics       Date:  2005-11-19       Impact factor: 3.410

Review 9.  New gateways to discovery.

Authors:  Michael M Goodin; Romit Chakrabarty; Rituparna Banerjee; Sharon Yelton; Seth Debolt
Journal:  Plant Physiol       Date:  2007-12       Impact factor: 8.340

10.  Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.

Authors:  C Robin Buell; Qiaoping Yuan; Shu Ouyang; Jia Liu; Wei Zhu; Aihui Wang; Rama Maiti; Brian Haas; Jennifer Wortman; Mihaela Pertea; Kristine M Jones; Mary Kim; Larry Overton; Tamara Tsitrin; Douglas Fadrosh; Jayati Bera; Bruce Weaver; Shaohua Jin; Shivani Johri; Matt Reardon; Kristen Webb; Jessica Hill; Kelly Moffat; Luke Tallon; Susan Van Aken; Matthew Lewis; Teresa Utterback; Tamara Feldblyum; Victoria Zismann; Stacey Iobst; Joseph Hsiao; Aymeric R de Vazeille; Steven L Salzberg; Owen White; Claire Fraser; Yeisoo Yu; HeyRan Kim; Teri Rambo; Jennifer Currie; Kristi Collura; Shelly Kernodle-Thompson; Fusheng Wei; Kudrna Kudrna; Jetty Siva S Ammiraju; Meizhong Luo; Jose Luis Goicoechea; Rod A Wing; David Henry; Ryan Oates; Michael Palmer; Gina Pries; Christopher Saski; Jessica Simmons; Carol Soderlund; William Nelson; Melissa de la Bastide; Lori Spiegel; Lidia Nascimento; Emily Huang; Raymond Preston; Theresa Zutavern; Lance Palmer; Andrew O'Shaughnessy; Sujit Dike; W Richard McCombie; Pat Minx; Holly Cordum; Richard Wilson; Weiwei Jin; Hye-Ran Lee; Jiming Jiang; Scott Jackson
Journal:  Genome Res       Date:  2005-08-18       Impact factor: 9.043
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