Literature DB >> 21716279

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.

Bruno Aranda, Hagen Blankenburg, Samuel Kerrien, Fiona S L Brinkman, Arnaud Ceol, Emilie Chautard, Jose M Dana, Javier De Las Rivas, Marine Dumousseau, Eugenia Galeota, Anna Gaulton, Johannes Goll, Robert E W Hancock, Ruth Isserlin, Rafael C Jimenez, Jules Kerssemakers, Jyoti Khadake, David J Lynn, Magali Michaut, Gavin O'Kelly, Keiichiro Ono, Sandra Orchard, Carlos Prieto, Sabry Razick, Olga Rigina, Lukasz Salwinski, Milan Simonovic, Sameer Velankar, Andrew Winter, Guanming Wu, Gary D Bader, Gianni Cesareni, Ian M Donaldson, David Eisenberg, Gerard J Kleywegt, John Overington, Sylvie Ricard-Blum, Mike Tyers, Mario Albrecht, Henning Hermjakob.   

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Year:  2011        PMID： 21716279      PMCID： PMC3246345          DOI： 10.1038/nmeth.1637

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  5 in total

1.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

2.  Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France.

Authors:  Sandra Orchard; Luisa Montechi-Palazzi; Eric W Deutsch; Pierre-Alain Binz; Andrew R Jones; Norman Paton; Angel Pizarro; David M Creasy; Jérôme Wojcik; Henning Hermjakob
Journal:  Proteomics       Date:  2007-10       Impact factor: 3.984

3.  The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Authors:  Henning Hermjakob; Luisa Montecchi-Palazzi; Gary Bader; Jérôme Wojcik; Lukasz Salwinski; Arnaud Ceol; Susan Moore; Sandra Orchard; Ugis Sarkans; Christian von Mering; Bernd Roechert; Sylvain Poux; Eva Jung; Henning Mersch; Paul Kersey; Michael Lappe; Yixue Li; Rong Zeng; Debashis Rana; Macha Nikolski; Holger Husi; Christine Brun; K Shanker; Seth G N Grant; Chris Sander; Peer Bork; Weimin Zhu; Akhilesh Pandey; Alvis Brazma; Bernard Jacq; Marc Vidal; David Sherman; Pierre Legrain; Gianni Cesareni; Ioannis Xenarios; David Eisenberg; Boris Steipe; Chris Hogue; Rolf Apweiler
Journal:  Nat Biotechnol       Date:  2004-02       Impact factor: 54.908

4.  DASMI: exchanging, annotating and assessing molecular interaction data.

Authors:  Hagen Blankenburg; Robert D Finn; Andreas Prlić; Andrew M Jenkinson; Fidel Ramírez; Dorothea Emig; Sven-Eric Schelhorn; Joachim Büch; Thomas Lengauer; Mario Albrecht
Journal:  Bioinformatics       Date:  2009-05-15       Impact factor: 6.937

5.  Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

Authors:  Samuel Kerrien; Sandra Orchard; Luisa Montecchi-Palazzi; Bruno Aranda; Antony F Quinn; Nisha Vinod; Gary D Bader; Ioannis Xenarios; Jérôme Wojcik; David Sherman; Mike Tyers; John J Salama; Susan Moore; Arnaud Ceol; Andrew Chatr-Aryamontri; Matthias Oesterheld; Volker Stümpflen; Lukasz Salwinski; Jason Nerothin; Ethan Cerami; Michael E Cusick; Marc Vidal; Michael Gilson; John Armstrong; Peter Woollard; Christopher Hogue; David Eisenberg; Gianni Cesareni; Rolf Apweiler; Henning Hermjakob
Journal:  BMC Biol       Date:  2007-10-09       Impact factor: 7.431
  5 in total
  136 in total

1.  mentha: a resource for browsing integrated protein-interaction networks.

Authors:  Alberto Calderone; Luisa Castagnoli; Gianni Cesareni
Journal:  Nat Methods       Date:  2013-08       Impact factor: 28.547

2.  Optimization criteria and biological process enrichment in homologous multiprotein modules.

Authors:  Luqman Hodgkinson; Richard M Karp
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-11       Impact factor: 11.205

Review 3.  Protein Bioinformatics Databases and Resources.

Authors:  Chuming Chen; Hongzhan Huang; Cathy H Wu
Journal:  Methods Mol Biol       Date:  2017

Review 4.  Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry.

Authors:  Lena Katharina Freudenmann; Ana Marcu; Stefan Stevanović
Journal:  Immunology       Date:  2018-05-08       Impact factor: 7.397

5.  Pathways of Toxicity.

Authors:  Andre Kleensang; Alexandra Maertens; Michael Rosenberg; Suzanne Fitzpatrick; Justin Lamb; Scott Auerbach; Richard Brennan; Kevin M Crofton; Ben Gordon; Albert J Fornace; Kevin Gaido; David Gerhold; Robin Haw; Adriano Henney; Avi Ma'ayan; Mary McBride; Stefano Monti; Michael F Ochs; Akhilesh Pandey; Roded Sharan; Rob Stierum; Stuart Tugendreich; Catherine Willett; Clemens Wittwehr; Jianguo Xia; Geoffrey W Patton; Kirk Arvidson; Mounir Bouhifd; Helena T Hogberg; Thomas Luechtefeld; Lena Smirnova; Liang Zhao; Yeyejide Adeleye; Minoru Kanehisa; Paul Carmichael; Melvin E Andersen; Thomas Hartung
Journal:  ALTEX       Date:  2013-10-15       Impact factor: 6.043

Review 6.  Glycosaminoglycanomics: where we are.

Authors:  Sylvie Ricard-Blum; Frédérique Lisacek
Journal:  Glycoconj J       Date:  2016-11-30       Impact factor: 2.916

7.  Harnessing the heart of big data.

Authors:  Sarah B Scruggs; Karol Watson; Andrew I Su; Henning Hermjakob; John R Yates; Merry L Lindsey; Peipei Ping
Journal:  Circ Res       Date:  2015-03-27       Impact factor: 17.367

Review 8.  Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments.

Authors:  Irina M Armean; Kathryn S Lilley; Matthew W B Trotter
Journal:  Mol Cell Proteomics       Date:  2012-10-15       Impact factor: 5.911

9.  Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT.

Authors:  Hyungwon Choi; Guomin Liu; Dattatreya Mellacheruvu; Mike Tyers; Anne-Claude Gingras; Alexey I Nesvizhskii
Journal:  Curr Protoc Bioinformatics       Date:  2012-09

10.  SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets.

Authors:  Sara J C Gosline; Sarah J Spencer; Oana Ursu; Ernest Fraenkel
Journal:  Integr Biol (Camb)       Date:  2012-11       Impact factor: 2.192
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