Literature DB >> 19606149

Systems biology: Untangling the protein web.

Nathan Blow.   

Abstract

Researchers have identified thousands of macromolecular interactions within cells. But, as Nathan Blow finds out, joining them up in networks and figuring out how they work still poses a big challenge.

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Substances：

Year:  2009        PMID： 19606149     DOI： 10.1038/460415a

Source DB:  PubMed          Journal:  Nature        ISSN： 0028-0836            Impact factor:   49.962


  9 in total

1.  Proteome survey reveals modularity of the yeast cell machinery.

Authors:  Anne-Claude Gavin; Patrick Aloy; Paola Grandi; Roland Krause; Markus Boesche; Martina Marzioch; Christina Rau; Lars Juhl Jensen; Sonja Bastuck; Birgit Dümpelfeld; Angela Edelmann; Marie-Anne Heurtier; Verena Hoffman; Christian Hoefert; Karin Klein; Manuela Hudak; Anne-Marie Michon; Malgorzata Schelder; Markus Schirle; Marita Remor; Tatjana Rudi; Sean Hooper; Andreas Bauer; Tewis Bouwmeester; Georg Casari; Gerard Drewes; Gitte Neubauer; Jens M Rick; Bernhard Kuster; Peer Bork; Robert B Russell; Giulio Superti-Furga
Journal:  Nature       Date:  2006-01-22       Impact factor: 49.962

2.  Internal coarse-graining of molecular systems.

Authors:  Jérôme Feret; Vincent Danos; Jean Krivine; Russ Harmer; Walter Fontana
Journal:  Proc Natl Acad Sci U S A       Date:  2009-04-03       Impact factor: 11.205

3.  Life, logic and information.

Authors:  Paul Nurse
Journal:  Nature       Date:  2008-07-24       Impact factor: 49.962

4.  Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Authors:  Nicolas Simonis; Jean-François Rual; Anne-Ruxandra Carvunis; Murat Tasan; Irma Lemmens; Tomoko Hirozane-Kishikawa; Tong Hao; Julie M Sahalie; Kavitha Venkatesan; Fana Gebreab; Sebiha Cevik; Niels Klitgord; Changyu Fan; Pascal Braun; Ning Li; Nono Ayivi-Guedehoussou; Elizabeth Dann; Nicolas Bertin; David Szeto; Amélie Dricot; Muhammed A Yildirim; Chenwei Lin; Anne-Sophie de Smet; Huey-Ling Kao; Christophe Simon; Alex Smolyar; Jin Sook Ahn; Muneesh Tewari; Mike Boxem; Stuart Milstein; Haiyuan Yu; Matija Dreze; Jean Vandenhaute; Kristin C Gunsalus; Michael E Cusick; David E Hill; Jan Tavernier; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2009-01       Impact factor: 28.547

5.  An in vivo map of the yeast protein interactome.

Authors:  Kirill Tarassov; Vincent Messier; Christian R Landry; Stevo Radinovic; Mercedes M Serna Molina; Igor Shames; Yelena Malitskaya; Jackie Vogel; Howard Bussey; Stephen W Michnick
Journal:  Science       Date:  2008-05-08       Impact factor: 47.728

6.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Authors:  Nevan J Krogan; Gerard Cagney; Haiyuan Yu; Gouqing Zhong; Xinghua Guo; Alexandr Ignatchenko; Joyce Li; Shuye Pu; Nira Datta; Aaron P Tikuisis; Thanuja Punna; José M Peregrín-Alvarez; Michael Shales; Xin Zhang; Michael Davey; Mark D Robinson; Alberto Paccanaro; James E Bray; Anthony Sheung; Bryan Beattie; Dawn P Richards; Veronica Canadien; Atanas Lalev; Frank Mena; Peter Wong; Andrei Starostine; Myra M Canete; James Vlasblom; Samuel Wu; Chris Orsi; Sean R Collins; Shamanta Chandran; Robin Haw; Jennifer J Rilstone; Kiran Gandi; Natalie J Thompson; Gabe Musso; Peter St Onge; Shaun Ghanny; Mandy H Y Lam; Gareth Butland; Amin M Altaf-Ul; Shigehiko Kanaya; Ali Shilatifard; Erin O'Shea; Jonathan S Weissman; C James Ingles; Timothy R Hughes; John Parkinson; Mark Gerstein; Shoshana J Wodak; Andrew Emili; Jack F Greenblatt
Journal:  Nature       Date:  2006-03-22       Impact factor: 49.962

7.  Literature-curated protein interaction datasets.

Authors:  Michael E Cusick; Haiyuan Yu; Alex Smolyar; Kavitha Venkatesan; Anne-Ruxandra Carvunis; Nicolas Simonis; Jean-François Rual; Heather Borick; Pascal Braun; Matija Dreze; Jean Vandenhaute; Mary Galli; Junshi Yazaki; David E Hill; Joseph R Ecker; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2009-01       Impact factor: 28.547

8.  An empirical framework for binary interactome mapping.

Authors:  Kavitha Venkatesan; Jean-François Rual; Alexei Vazquez; Ulrich Stelzl; Irma Lemmens; Tomoko Hirozane-Kishikawa; Tong Hao; Martina Zenkner; Xiaofeng Xin; Kwang-Il Goh; Muhammed A Yildirim; Nicolas Simonis; Kathrin Heinzmann; Fana Gebreab; Julie M Sahalie; Sebiha Cevik; Christophe Simon; Anne-Sophie de Smet; Elizabeth Dann; Alex Smolyar; Arunachalam Vinayagam; Haiyuan Yu; David Szeto; Heather Borick; Amélie Dricot; Niels Klitgord; Ryan R Murray; Chenwei Lin; Maciej Lalowski; Jan Timm; Kirstin Rau; Charles Boone; Pascal Braun; Michael E Cusick; Frederick P Roth; David E Hill; Jan Tavernier; Erich E Wanker; Albert-László Barabási; Marc Vidal
Journal:  Nat Methods       Date:  2008-12-07       Impact factor: 28.547

9.  An experimentally derived confidence score for binary protein-protein interactions.

Authors:  Pascal Braun; Murat Tasan; Matija Dreze; Miriam Barrios-Rodiles; Irma Lemmens; Haiyuan Yu; Julie M Sahalie; Ryan R Murray; Luba Roncari; Anne-Sophie de Smet; Kavitha Venkatesan; Jean-François Rual; Jean Vandenhaute; Michael E Cusick; Tony Pawson; David E Hill; Jan Tavernier; Jeffrey L Wrana; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2008-12-07       Impact factor: 28.547
  9 in total
  12 in total

1.  Computational Analysis of Muscular Dystrophy Sub-types Using A Novel Integrative Scheme.

Authors:  Chen Wang; Sook Ha; Jianhua Xuan; Yue Wang; Eric Hoffman
Journal:  Neurocomputing       Date:  2012-09-01       Impact factor: 5.719

2.  Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners.

Authors:  Séverine Boulon; Yasmeen Ahmad; Laura Trinkle-Mulcahy; Céline Verheggen; Andy Cobley; Peter Gregor; Edouard Bertrand; Mark Whitehorn; Angus I Lamond
Journal:  Mol Cell Proteomics       Date:  2009-12-20       Impact factor: 5.911

Review 3.  Cell-based screening: extracting meaning from complex data.

Authors:  Steven Finkbeiner; Michael Frumkin; Paul D Kassner
Journal:  Neuron       Date:  2015-04-08       Impact factor: 17.173

4.  Protein-protein interactions essentials: key concepts to building and analyzing interactome networks.

Authors:  Javier De Las Rivas; Celia Fontanillo
Journal:  PLoS Comput Biol       Date:  2010-06-24       Impact factor: 4.475

5.  A custom correlation coefficient (CCC) approach for fast identification of multi-SNP association patterns in genome-wide SNPs data.

Authors:  Sharlee Climer; Wei Yang; Lisa de las Fuentes; Victor G Dávila-Román; C Charles Gu
Journal:  Genet Epidemiol       Date:  2014-08-28       Impact factor: 2.135

6.  Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes.

Authors:  Binhua Tang; Hang-Kai Hsu; Pei-Yin Hsu; Russell Bonneville; Su-Shing Chen; Tim H-M Huang; Victor X Jin
Journal:  Sci Rep       Date:  2012-11-19       Impact factor: 4.379

7.  Disordered binding regions and linear motifs--bridging the gap between two models of molecular recognition.

Authors:  Bálint Mészáros; Zsuzsanna Dosztányi; István Simon
Journal:  PLoS One       Date:  2012-10-03       Impact factor: 3.240

8.  Assembling a protein-protein interaction map of the SSU processome from existing datasets.

Authors:  Young H Lim; J Michael Charette; Susan J Baserga
Journal:  PLoS One       Date:  2011-03-10       Impact factor: 3.240

9.  A protein interaction map of the LSU processome.

Authors:  Kathleen L McCann; J Michael Charette; Nicholas G Vincent; Susan J Baserga
Journal:  Genes Dev       Date:  2015-04-15       Impact factor: 11.361

Review 10.  Predicting drug side-effects by chemical systems biology.

Authors:  Nicholas P Tatonetti; Tianyun Liu; Russ B Altman
Journal:  Genome Biol       Date:  2009-09-02       Impact factor: 13.583
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