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Authors |
Title |
Citation |
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Assess overall quality
of major yeast interaction datasets (gives a good sense of the problems
inherent to the data) |
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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 |
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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 |
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Bader GD, Hogue CW. |
Analyzing yeast
protein-protein interaction data obtained from different sources. |
Nat Biotechnol 2002
Oct;20(10):991-7 |
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Assess quality of
individual interactions |
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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 |
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Bader JS. |
Greedily building protein
networks with confidence. |
Bioinformatics 2003 Oct
12;19(15):1869-74 |
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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 |
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Bader JS, Chaudhuri A,
Rothberg JM, Chant J. |
Gaining confidence in
high-throughput protein interaction networks. |
Nat Biotechnol 2004
Jan;22(1):78-85 |
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Graph clustering |
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Rives AW, Galitski T. |
Modular organization of
cellular networks. |
Proc Natl Acad Sci U S A
2003 Feb 4;100(3):1128-33 |
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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 |
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Pereira-Leal JB, Enright
AJ, Ouzounis CA. |
Detection of functional
modules from protein interaction networks. |
Proteins 2004 Jan 1;54(1):49-57 |
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Identify protein
complexes from interaction data |
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Bader GD, Hogue CW. |
An automated method for
finding molecular complexes in large protein interaction networks. |
BMC Bioinformatics 2003
Jan 13;4(1):2 |
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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 |
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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 |
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Infer protein function
from interactions |
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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 |
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Letovsky S, Kasif S. |
Predicting protein
function from protein/protein interaction data: a probabilistic approach. |
Bioinformatics 2003 Jul;19
Suppl 1():I197-I204 |
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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 |
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Deng M, Tu Z, Sun F, Chen T. |
Mapping gene ontology to
proteins based on protein-protein interaction data. |
Bioinformatics 2004 Jan
29;(): |
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Predict new
interactions from existing data |
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Bock JR, Gough DA. |
Whole-proteome interaction
mining. |
Bioinformatics 2003
Jan;19(1):125-34 |
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Ng SK, Zhang Z, Tan SH. |
Integrative approach for
computationally inferring protein domain interactions. |
Bioinformatics 2003 May
22;19(8):923-9 |
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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;(): |
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Relate graph structure to
broad functional properties, such as lethality |
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Chin CS, Samanta MP. |
Global snapshot of a
protein interaction network-a percolation based approach. |
Bioinformatics 2003 Dec
12;19(18):2413-9 |
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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 |
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Przulj N, Wigle DA, Jurisica
I. |
Functional topology in a
network of protein interactions. |
Bioinformatics 2004 Feb
12;20(3):340-8 |
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Papers that combine
multiple data types (very incomplete list) |
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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 |
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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 |
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Tornow S, Mewes HW. |
Functional modules by
relating protein interaction networks and gene expression. |
Nucleic Acids Res 2003 Nov
1;31(21):6283-9 |
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Jansen R, Greenbaum D,
Gerstein M. |
Relating whole-genome expression
data with protein-protein interactions. |
Genome Res 2002
Jan;12(1):37-46 |
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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 |
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Miscellaneous |
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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 |
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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 |
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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 |
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Hoffmann R, Valencia A. |
Protein interaction: same
network, different hubs. |
Trends Genet 2003
Dec;19(12):681-3 |
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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 |
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