Literature DB >> 19060867

PhosphoPep--a database of protein phosphorylation sites in model organisms.

Bernd Bodenmiller, David Campbell, Bertran Gerrits, Henry Lam, Marko Jovanovic, Paola Picotti, Ralph Schlapbach, Ruedi Aebersold.   

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Year:  2008        PMID： 19060867      PMCID： PMC2743685          DOI： 10.1038/nbt1208-1339

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  12 in total

1.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Authors:  Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Journal:  Anal Chem       Date:  2002-10-15       Impact factor: 6.986

2.  Large-scale characterization of HeLa cell nuclear phosphoproteins.

Authors:  Sean A Beausoleil; Mark Jedrychowski; Daniel Schwartz; Joshua E Elias; Judit Villén; Jiaxu Li; Martin A Cohn; Lewis C Cantley; Steven P Gygi
Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-09       Impact factor: 11.205

3.  A probability-based approach for high-throughput protein phosphorylation analysis and site localization.

Authors:  Sean A Beausoleil; Judit Villén; Scott A Gerber; John Rush; Steven P Gygi
Journal:  Nat Biotechnol       Date:  2006-09-10       Impact factor: 54.908

4.  Clustal W and Clustal X version 2.0.

Authors:  M A Larkin; G Blackshields; N P Brown; R Chenna; P A McGettigan; H McWilliam; F Valentin; I M Wallace; A Wilm; R Lopez; J D Thompson; T J Gibson; D G Higgins
Journal:  Bioinformatics       Date:  2007-09-10       Impact factor: 6.937

5.  Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.

Authors:  Xue Li; Scott A Gerber; Adam D Rudner; Sean A Beausoleil; Wilhelm Haas; Judit Villén; Joshua E Elias; Steve P Gygi
Journal:  J Proteome Res       Date:  2007-03       Impact factor: 4.466

6.  Development of human protein reference database as an initial platform for approaching systems biology in humans.

Authors:  Suraj Peri; J Daniel Navarro; Ramars Amanchy; Troels Z Kristiansen; Chandra Kiran Jonnalagadda; Vineeth Surendranath; Vidya Niranjan; Babylakshmi Muthusamy; T K B Gandhi; Mads Gronborg; Nieves Ibarrola; Nandan Deshpande; K Shanker; H N Shivashankar; B P Rashmi; M A Ramya; Zhixing Zhao; K N Chandrika; N Padma; H C Harsha; A J Yatish; M P Kavitha; Minal Menezes; Dipanwita Roy Choudhury; Shubha Suresh; Neelanjana Ghosh; R Saravana; Sreenath Chandran; Subhalakshmi Krishna; Mary Joy; Sanjeev K Anand; V Madavan; Ansamma Joseph; Guang W Wong; William P Schiemann; Stefan N Constantinescu; Lily Huang; Roya Khosravi-Far; Hanno Steen; Muneesh Tewari; Saghi Ghaffari; Gerard C Blobe; Chi V Dang; Joe G N Garcia; Jonathan Pevsner; Ole N Jensen; Peter Roepstorff; Krishna S Deshpande; Arul M Chinnaiyan; Ada Hamosh; Aravinda Chakravarti; Akhilesh Pandey
Journal:  Genome Res       Date:  2003-10       Impact factor: 9.043

7.  Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins.

Authors:  Francesca Diella; Scott Cameron; Christine Gemünd; Rune Linding; Allegra Via; Bernhard Kuster; Thomas Sicheritz-Pontén; Nikolaj Blom; Toby J Gibson
Journal:  BMC Bioinformatics       Date:  2004-06-22       Impact factor: 3.169

8.  PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites.

Authors:  Florian Gnad; Shubin Ren; Juergen Cox; Jesper V Olsen; Boris Macek; Mario Oroshi; Matthias Mann
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

9.  Assessing performance of orthology detection strategies applied to eukaryotic genomes.

Authors:  Feng Chen; Aaron J Mackey; Jeroen K Vermunt; David S Roos
Journal:  PLoS One       Date:  2007-04-18       Impact factor: 3.240

Review 10.  PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells.

Authors:  Bernd Bodenmiller; Johan Malmstrom; Bertran Gerrits; David Campbell; Henry Lam; Alexander Schmidt; Oliver Rinner; Lukas N Mueller; Paul T Shannon; Patrick G Pedrioli; Christian Panse; Hoo-Keun Lee; Ralph Schlapbach; Ruedi Aebersold
Journal:  Mol Syst Biol       Date:  2007-10-16       Impact factor: 11.429
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  103 in total

1.  Cell cycle phosphorylation of mitotic exit network (MEN) proteins.

Authors:  Michele H Jones; Jamie M Keck; Catherine C L Wong; Tao Xu; John R Yates; Mark Winey
Journal:  Cell Cycle       Date:  2011-10-15       Impact factor: 4.534

Review 2.  Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions.

Authors:  Paola Picotti; Ruedi Aebersold
Journal:  Nat Methods       Date:  2012-05-30       Impact factor: 28.547

3.  Musite, a tool for global prediction of general and kinase-specific phosphorylation sites.

Authors:  Jianjiong Gao; Jay J Thelen; A Keith Dunker; Dong Xu
Journal:  Mol Cell Proteomics       Date:  2010-08-11       Impact factor: 5.911

4.  Global molecular dysfunctions in gastric cancer revealed by an integrated analysis of the phosphoproteome and transcriptome.

Authors:  Tiannan Guo; Sze Sing Lee; Wai Har Ng; Yi Zhu; Chee Sian Gan; Jiang Zhu; Haixia Wang; Shiang Huang; Siu Kwan Sze; Oi Lian Kon
Journal:  Cell Mol Life Sci       Date:  2010-10-16       Impact factor: 9.261

Review 5.  Toward a complete in silico, multi-layered embryonic stem cell regulatory network.

Authors:  Huilei Xu; Christoph Schaniel; Ihor R Lemischka; Avi Ma'ayan
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010 Nov-Dec

6.  The role of the Drosophila LAMMER protein kinase DOA in somatic sex determination.

Authors:  Leonard Rabinow; Marie-Laure Samson
Journal:  J Genet       Date:  2010-09       Impact factor: 1.166

7.  HITS-CLIP reveals sex-differential RNA binding and alterative splicing regulation of SRm160 in Drosophila.

Authors:  Chen Qiu; Yu Zhang; Yu-Jie Fan; Ting-Lin Pang; Yan Su; Shuai Zhan; Yong-Zhen Xu
Journal:  J Mol Cell Biol       Date:  2019-02-01       Impact factor: 6.216

8.  Posttranslational regulation impacts the fate of duplicated genes.

Authors:  Grigoris D Amoutzias; Ying He; Jonathan Gordon; Dimitris Mossialos; Stephen G Oliver; Yves Van de Peer
Journal:  Proc Natl Acad Sci U S A       Date:  2009-12-22       Impact factor: 11.205

9.  PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae.

Authors:  Chris Stark; Ting-Cheng Su; Ashton Breitkreutz; Pedro Lourenco; Matthew Dahabieh; Bobby-Joe Breitkreutz; Mike Tyers; Ivan Sadowski
Journal:  Database (Oxford)       Date:  2010-01-28       Impact factor: 3.451

10.  Identification of positive regulators of the yeast fps1 glycerol channel.

Authors:  Sara E Beese; Takahiro Negishi; David E Levin
Journal:  PLoS Genet       Date:  2009-11-26       Impact factor: 5.917
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