PubMed link

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Authors

Title

Citation

 

 

 

 

 

 

 

Assess overall quality of major yeast interaction datasets (gives a good sense of the problems inherent to the data)

12000970

link

von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P.

Comparative assessment of large-scale data sets of protein-protein interactions.

Nature 2002 May 23;417(6887):399-403

12118076

link

Deane CM, Salwinski L, Xenarios I, Eisenberg D.

Protein interactions: two methods for assessment of the reliability of high throughput observations.

Mol Cell Proteomics 2002 May;1(5):349-56

12355115

link

Bader GD, Hogue CW.

Analyzing yeast protein-protein interaction data obtained from different sources.

Nat Biotechnol 2002 Oct;20(10):991-7

 

 

 

 

 

 

 

Assess quality of individual interactions

 

12691988

link

Saito R, Suzuki H, Hayashizaki Y.

Construction of reliable protein-protein interaction networks with a new interaction generality measure.

Bioinformatics 2003 Apr 12;19(6):756-63

14555618

link

Bader JS.

Greedily building protein networks with confidence.

Bioinformatics 2003 Oct 12;19(15):1869-74

14564010

link

Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M.

A Bayesian networks approach for predicting protein-protein interactions from genomic data.

Science 2003 Oct 17;302(5644):449-53

14704708

link

Bader JS, Chaudhuri A, Rothberg JM, Chant J.

Gaining confidence in high-throughput protein interaction networks.

Nat Biotechnol 2004 Jan;22(1):78-85

 

 

 

 

 

 

 

Graph clustering

 

12538875

link

Rives AW, Galitski T.

Modular organization of cellular networks.

Proc Natl Acad Sci U S A 2003 Feb 4;100(3):1128-33

12711690

link

Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H, Zhang J, Sun S, Ling L, Zhang N, Li G, Chen R.

Topological structure analysis of the protein-protein interaction network in budding yeast.

Nucleic Acids Res 2003 May 1;31(9):2443-50

14705023

link

Pereira-Leal JB, Enright AJ, Ouzounis CA.

Detection of functional modules from protein interaction networks.

Proteins 2004 Jan 1;54(1):49-57

 

 

 

 

 

 

 

Identify protein complexes from interaction data

 

12525261

link

Bader GD, Hogue CW.

An automated method for finding molecular complexes in large protein interaction networks.

BMC Bioinformatics 2003 Jan 13;4(1):2

14555622

link

Krause R, von Mering C, Bork P.

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.

Bioinformatics 2003 Oct 12;19(15):1901-8

14564010

link

Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M.

A Bayesian networks approach for predicting protein-protein interactions from genomic data.

Science 2003 Oct 17;302(5644):449-53

 

 

 

 

 

 

 

Infer protein function from interactions

 

12740586

link

Vazquez A, Flammini A, Maritan A, Vespignani A.

Global protein function prediction from protein-protein interaction networks.

Nat Biotechnol 2003 Jun;21(6):697-700

12855458

link

Letovsky S, Kasif S.

Predicting protein function from protein/protein interaction data: a probabilistic approach.

Bioinformatics 2003 Jul;19 Suppl 1():I197-I204

14566057

link

Samanta MP, Liang S.

Predicting protein functions from redundancies in large-scale protein interaction networks.

Proc Natl Acad Sci U S A 2003 Oct 28;100(22):12579-83

14751964

link

Deng M, Tu Z, Sun F, Chen T.

Mapping gene ontology to proteins based on protein-protein interaction data.

Bioinformatics 2004 Jan 29;():

 

 

 

 

 

 

 

Predict new interactions from existing data

 

12499302

link

Bock JR, Gough DA.

Whole-proteome interaction mining.

Bioinformatics 2003 Jan;19(1):125-34

12761053

link

Ng SK, Zhang Z, Tan SH.

Integrative approach for computationally inferring protein domain interactions.

Bioinformatics 2003 May 22;19(8):923-9

14871876

link

Iossifov I, Krauthammer M, Friedman C, Hatzivassiloglou V, Bader JS, White KP, Rzhetsky A.

Probabilistic inference of molecular networks from noisy data sources.

Bioinformatics 2004 Feb 10;():

 

 

 

 

 

 

 

Relate graph structure to broad functional properties, such as lethality

 

14668225

link

Chin CS, Samanta MP.

Global snapshot of a protein interaction network-a percolation based approach.

Bioinformatics 2003 Dec 12;19(18):2413-9

14724320

link

Yu H, Zhu X, Greenbaum D, Karro J, Gerstein M.

TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics.

Nucleic Acids Res 2004;32(1):328-37

14960460

link

Przulj N, Wigle DA, Jurisica I.

Functional topology in a network of protein interactions.

Bioinformatics 2004 Feb 12;20(3):340-8

 

 

 

 

 

 

 

Papers that combine multiple data types (very incomplete list)

 

12826619

link

Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D.

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).

Proc Natl Acad Sci U S A 2003 Jul 8;100(14):8348-53

14555958

link

Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Computational discovery of gene modules and regulatory networks.

Nat Biotechnol 2003 Nov;21(11):1337-42

14576317

link

Tornow S, Mewes HW.

Functional modules by relating protein interaction networks and gene expression.

Nucleic Acids Res 2003 Nov 1;31(21):6283-9

11779829

link

Jansen R, Greenbaum D, Gerstein M.

Relating whole-genome expression data with protein-protein interactions.

Genome Res 2002 Jan;12(1):37-46

11694880

link

Ge H, Liu Z, Church GM, Vidal M.

Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae.

Nat Genet 2001 Dec;29(4):482-6

 

 

 

 

 

 

 

Miscellaneous

 

 

11743162

link

Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G.

A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.

Science 2002 Jan 11;295(5553):321-4

11972061

link

Aloy P, Russell RB.

Interrogating protein interaction networks through structural biology.

Proc Natl Acad Sci U S A 2002 Apr 30;99(9):5896-901

12724307

link

Goffard N, Garcia V, Iragne F, Groppi A, de Daruvar A.

IPPRED: server for proteins interactions inference.

Bioinformatics 2003 May 1;19(7):903-4

14642746

link

Hoffmann R, Valencia A.

Protein interaction: same network, different hubs.

Trends Genet 2003 Dec;19(12):681-3

14755292

link

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.

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

Nat Biotechnol 2004 Feb;22(2):177-83