Assessing the limits of genomic data integration for predicting protein networks. Genome Res

Assessing the limits of genomic data integration for predicting protein networks. Genome Res (2005)

Cached

Download Links

by Long J. Lu , Yu Xia , Alberto Paccanaro , Haiyuan Yu , Mark Gerstein

Citations:

BibTeX

@MISC{Lu05assessingthe,
    author = {Long J. Lu and Yu Xia and Alberto Paccanaro and Haiyuan Yu and Mark Gerstein},
    title = {Assessing the limits of genomic data integration for predicting protein networks. Genome Res},
    year = {2005}
}

Bookmark

OpenURL

Abstract

All genomic feature data used in this study can be downloaded at

Citations

3912	CM: Neural Networks for Pattern Recognition - Bishop - 1995
1484	D (2000) Pattern classification - Duda, Hart, et al.
1325	Experiments with a new boosting algorithm - Freund, Schapire - 1996
897	Additive logistic regression: a statistical view of boosting - Friedman, Hastie, et al. - 2000
796	Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25 - Ashburner, CA, et al. - 2000
554	The strenght of weak learnability - Schapire - 1990
475	A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature - Uetz, Giot, et al. - 2000
435	Schapire R: A short introduction to boosting - Freund - 1999
420	A comprehensive two-hybrid analysis to explore the yeast protein interactome - Ito, Chiba, et al. - 2001
321	Molecular Biology of the Cell - Bray, Raff, et al. - 1983
286	Assigning protein functions by comparative genome analysis: protein phylogenetic profiles - Pellegrini, Marcotte, et al. - 1999
279	Transcriptional regulatory networks in Saccharomyces cerevisiae - Lee, Rinaldi, et al. - 2002
270	P: Comparative assessment of large-scale data sets of proteinprotein interactions - Mering, Krause, et al.
269	Knowledge-based analysis of microarray gene expression data by using support vector machines - Brown, Grundy, et al. - 2000
242	A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell - Cho, Campbell, et al. - 1998
232	Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature - Gavin, Bosche, et al. - 2002
202	From molecular to modular cell biology,” Nature 402(suppl.): C47-C52 - Hartwell, Hopfield, et al. - 1999
197	Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature - Ho, Gruhler, et al. - 2002
172	MIPS: a database for genomes and protein sequences - Mewes, Heumann, et al. - 1999
168	Detecting protein function and protein-protein interactions from genome sequences - Marcotte, Pellegrini, et al. - 1999
160	A combined algorithm for genome-wide prediction of protein function. Nature 402: 83–86 - EM, Pellegrini, et al. - 1999
144	Inferring cellular networks using probabilistic graphical models - Friedman - 2004
122	Integrated genomic and proteomic analyses of a systematically perturbed metabolic network - Ideker, Thorsson, et al. - 2001
118	Sali A: Protein structure prediction and structural genomics - Baker
111	A Bayesian networks approach for predicting protein-protein interactions from genomic data - Jansen, Yu, et al. - 2003
102	M: Relating whole-genome expression data with protein-protein interactions - Jansen, Greenbaum, et al.
84	A network of protein-protein interactions in yeast - Schwikowski, Uetz, et al. - 2000
79	A probabilistic functional network of yeast genes - Lee, Date, et al. - 2004
72	Global mapping of the yeast genetic interaction network - Tong, Lesage, et al. - 2004
68	Kasif S: Predicting protein function from protein/ protein interaction data: a probabilistic approach. Bioinformatics 2003 - Letovsky
65	Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae - Ge, Liu, et al. - 2001
51	Computational methods for the prediction of protein interactions - Valencia, Pazos - 2002
50	Global protein function prediction from protein-protein interaction networks - Vazquez, Flammini, et al. - 2003
49	Prolinks: a database of protein functional linkages derived from coevolution - Bowers, Pellegrini, et al. - 2004
41	Information assessment on predicting protein–protein interactions - Lin, Wu, et al. - 2004
37	MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading - Lu, Lu, et al. - 2002
34	Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biology - Greenbaum - 2003
33	Genomic analysis of gene expression relationships in transcriptional regulatory networks - Yu, Luscombe, et al. - 2003
32	M: ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol 2002 - CE, Snyder
30	Conserved clusters of functionally related genes in two bacterial genomes - Tamames, Casari, et al. - 1997
29	Co-evolution of proteins with their interaction partners - Goh, Bogan, et al. - 2000
29	A (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47 - Pazos, Valencia
25	Gerstein M: Genomic analysis of essentiality within protein networks - Yu, Greenbaum, et al.
24	M: Genome-wide analysis relating expression level with protein subcellular localization. Trends Genet 2000 - Drawid, Jansen, et al.
24	M (2002) Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts - Greenbaum, Jansen, et al.
22	Multimeric threading-based prediction of protein–protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome. Genome Res 13 - Lu, AK, et al. - 2003
21	Integration of genomic datasets to predict protein complexes in yeast - Jansen, Lan, et al. - 2002
21	M: Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U - Martone, Euskirchen, et al.
19	FE: Co-evolutionary analysis reveals insights into protein-protein interactions - Goh, Cohen
15	Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell 9: 1133–1143. Copyright © 2003 - Kemmeren, NL, et al. - 2002