Literature DB >> 15326280

The plant-specific database. Classification of Arabidopsis proteins based on their phylogenetic profile.

Rodrigo A Gutiérrez1, Matthew D Larson, Curtis Wilkerson.   

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Year:  2004        PMID： 15326280      PMCID： PMC520760          DOI： 10.1104/pp.104.043687

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


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  13 in total

1.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

Authors:  A Krogh; B Larsson; G von Heijne; E L Sonnhammer
Journal:  J Mol Biol       Date:  2001-01-19       Impact factor: 5.469

2.  National Science Foundation-Sponsored Workshop Report: "The 2010 Project" functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them.

Authors:  J Chory; J R Ecker; S Briggs; M Caboche; G M Coruzzi; D Cook; J Dangl; S Grant; M L Guerinot; S Henikoff; R Martienssen; K Okada; N V Raikhel; C R Somerville; D Weigel
Journal:  Plant Physiol       Date:  2000-06       Impact factor: 8.340

3.  Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs.

Authors:  G C MacIntosh; C Wilkerson; P J Green
Journal:  Plant Physiol       Date:  2001-11       Impact factor: 8.340

4.  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

5.  Comparative genomics and evolution of proteins involved in RNA metabolism.

Authors:  Vivek Anantharaman; Eugene V Koonin; L Aravind
Journal:  Nucleic Acids Res       Date:  2002-04-01       Impact factor: 16.971

6.  The phylogenetic extent of metabolic enzymes and pathways.

Authors:  José Manuel Peregrin-Alvarez; Sophia Tsoka; Christos A Ouzounis
Journal:  Genome Res       Date:  2003-03       Impact factor: 9.043

7.  The PEDANT genome database.

Authors:  Dmitrij Frishman; Martin Mokrejs; Denis Kosykh; Gabi Kastenmüller; Grigory Kolesov; Igor Zubrzycki; Christian Gruber; Birgitta Geier; Andreas Kaps; Kaj Albermann; Andreas Volz; Christian Wagner; Matthias Fellenberg; Klaus Heumann; Hans-Werner Mewes
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

8.  Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.

Authors:  O Emanuelsson; H Nielsen; S Brunak; G von Heijne
Journal:  J Mol Biol       Date:  2000-07-21       Impact factor: 5.469

9.  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

10.  Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database.

Authors:  Frédéric Beisson; Abraham J K Koo; Sari Ruuska; Jörg Schwender; Mike Pollard; Jay J Thelen; Troy Paddock; Joaquín J Salas; Linda Savage; Anne Milcamps; Vandana B Mhaske; Younghee Cho; John B Ohlrogge
Journal:  Plant Physiol       Date:  2003-06       Impact factor: 8.340
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  10 in total

1.  Asymmetrical evolution of cytochrome bd subunits.

Authors:  Weilong Hao; G Brian Golding
Journal:  J Mol Evol       Date:  2006-02-10       Impact factor: 2.395

2.  Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis.

Authors:  Joshua L Heazlewood; Julian Tonti-Filippini; Robert E Verboom; A Harvey Millar
Journal:  Plant Physiol       Date:  2005-10       Impact factor: 8.340

3.  Transcription analysis of arabidopsis membrane transporters and hormone pathways during developmental and induced leaf senescence.

Authors:  Eric van der Graaff; Rainer Schwacke; Anja Schneider; Marcelo Desimone; Ulf-Ingo Flügge; Reinhard Kunze
Journal:  Plant Physiol       Date:  2006-04-07       Impact factor: 8.340

4.  Multiple lines of evidence localize signaling, morphology, and lipid biosynthesis machinery to the mitochondrial outer membrane of Arabidopsis.

Authors:  Owen Duncan; Nicolas L Taylor; Chris Carrie; Holger Eubel; Szymon Kubiszewski-Jakubiak; Botao Zhang; Reena Narsai; A Harvey Millar; James Whelan
Journal:  Plant Physiol       Date:  2011-09-06       Impact factor: 8.340

5.  Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature.

Authors:  Stephen J Robinson; Isobel A P Parkin
Journal:  BMC Genomics       Date:  2008-09-22       Impact factor: 3.969

6.  AMPDB: the Arabidopsis Mitochondrial Protein Database.

Authors:  Joshua L Heazlewood; A Harvey Millar
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

7.  Phylogenetic profiling: how much input data is enough?

Authors:  Nives Škunca; Christophe Dessimoz
Journal:  PLoS One       Date:  2015-02-13       Impact factor: 3.240

8.  Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins.

Authors:  Obed Ramírez-Sánchez; Paulino Pérez-Rodríguez; Luis Delaye; Axel Tiessen
Journal:  Genomics Proteomics Bioinformatics       Date:  2016-12-18       Impact factor: 7.691

9.  Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment.

Authors:  Raja Jothi; Teresa M Przytycka; L Aravind
Journal:  BMC Bioinformatics       Date:  2007-05-23       Impact factor: 3.169

10.  SUBA: the Arabidopsis Subcellular Database.

Authors:  Joshua L Heazlewood; Robert E Verboom; Julian Tonti-Filippini; Ian Small; A Harvey Millar
Journal:  Nucleic Acids Res       Date:  2006-10-28       Impact factor: 16.971
  10 in total

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