| author/s | title | publication | ||
| I. Key papers reviewed (analysis of yeast protein interaction data) | ||||
| Fellenberg, et al | Integrative Analysis of Protein Interaction Data | AAAI 2000, p.152-161 | ||
| Gygi, et al | Correlation b/w Protein and mRNA Abundance in Yeast | Mol & Cel Biology Mar. 1999, vol.19, p.1720-1730 | ||
| Walhout, et al | Protein Interaction Mapping in C.elegans Using Proteins Involved in Vulval Development | Science, 7 January 2000, 287:116-122 | ||
| Ideker, et al | Integrated Genomic and Proteomic Analysis of a Systematically Perturbed Metabolic Network | Science, 4 May 2001, 292:929-934 | ||
| Washburn, et al | Large-scale analysis of the yeast proteome by multidimensional protein identification technology | Nature Biotechnology, Mar 2001, 19:242-247 | ||
| Maslov and Sneppen | Specificity and Stability in Topology of Protein Networks | Science, 3 May 2002, 296:910-913 | ||
| Edwards, et al | Bridging structural biology and genomics: assessing protein interaction data with known complexes. | TIG 2002 | ||
| Jansen, et al | Relating Whole-Genome Expression Data with Protein-Protein Interactions | Genome Research, 2002 12:37-46 | ||
| Tong, et al | A Combined Experimental & Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules | Science, 11 Jan 2002, 295:321-324 | ||
| Mrowka, et al | Is there a Bias in Proteome Research? | Genome Research, 2001 11:1971-1973 | ||
| Grigoriev | A Relationshiop between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 & the yeast Saccharomyces cerevisiae | NAR 2001, vol.29, no.17, p.3513-3519 | ||
| Ge, et al | Correlation b/w transcriptome & interactome mapping data from Saccharomyces cerevisiae | Nature Genetics, Dec 2001, 29:482-486 | ||
| Kemmeren, et al | Protein Interaction Verification & Functional Annotation by Integrated Analysis of Genome-Scale Data | Molecular Cell, May 2002, 9:1133-1143 | ||
| Washburn, et al | Comparative Analysis of Multiple Genome-Scale Data Sets | Genome Research, 2002 12:1564-1573 | ||
| Bader & Hogue | Analyzing yeast protein-protein interaction data obtained from different sources | Nature biotechnology, Oct 2002, 20:991-997 | ||
| Deane, et al | Protein Interactons: Two methods for assessment of the reliability of high throughput observations | Mol & Cel Proteomics, 2002, p.349-356 | ||
| von Mering, et al | Comparative assessment of large-scale data sets of protein-protein interactions | Nature, 23 May 2002, 417:399-403 | ||
| Lappe, et al | Generating protein interaction maps from incomplete data: application to fold assignment | Bioinformatics 2001, p.S149-S156 | ||
| Aloy & Russell | Interrogating protein interaction networks through structural biology | PNAS, Apr 2002, v.9,no.9,p.5896-5901 | ||
| Gerstein, et al | Interating interactions | Science, 11 Jan 2002, 295:284-285 | ||
| II. Descriptions/Reviews (of Data/Studies… | ||||
| Tucker, et al | Towards an understanding of complex protein networks | Trends in Cell Biology March 2001, 11:3:102-106 | ||
| Legrain & Selig | Genome-wide protein interaction maps using two-hybrid systems | FEBS Letters, 2000, 480:32-36 | ||
| Chen & Han | Building a protein interaction map: research in the post-genome era | BioEssays 2000, 22:503-503 | ||
| III. Key Data Papers | ||||
| Schwikowski, et al | A network of protein-protein interactions in yeast | Nature Biotechnology December 2000, 18:1257-1261 | ||
| Fromont-Racine, et al | Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens | Nature Genetics, July 1997, 16:277-282 | ||
| A. Two-hybrid Studies | ||||
| Vetz, et al | A comprehesive analysis of protein-protein interactions in Saccharomyces cerevisiae | Nature, 10 Feb 2000, 403:623-627 | ||
| Ito, et al | A comprehensive two-hybrid analysis to explore the yeast protein interactome | PNAS, Apr 2001 98:8:4569-4574 | ||
| Ito, et al | Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations b/w the yeast proteins | PNAS, Feb 2000 97:3:1143-1147 | ||
| B. Protein Complexes | ||||
| Ho, et al | Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry | Nature Jan 2002, 415:180183 | ||
| Gavin, et al | Functional organization of the yeast proteome by systematic analysis of protein complexes | Nature Jan 2002, 415:141-147 | ||
| IV. Commentaries that tell more about the methods | ||||
| Legrain | Protein domain networking: combining data sets from phage & yeast two-hybrid screens offers a more stringent approach for suggesting protein-protein associations | Nature Biotechnology Feb 2002, 20:128-129 | ||
| Eisenber, et al | Protein function in the post-genomic era | look up | ||
| Mayer & Heiter | Protein Networks-built by association | Nature Biotechnology, Dec 2000, 18:1242-1243 | ||
| Hazbun & Fields | Networking proteins in yeast | PNAS Apr 2001 98:8:4277-4278 | ||
| Oliver (background) | Guilt-by-association goes global | Nature Feb 2000, 403:601-603 | ||
| Hieter | What do yeast proteins do? | Nature Nov 1999, 402:362-363 | ||
| Teichmann & Mitchison | Computing protein function | Nature Biotechnology, Jan 2000, 18:27 | ||
| Mann, et al | Analysis of Proteins & proteomes by mass spectrometry | Annu.Rev.Biochem, 2001 70:437-473 | ||
| A. Background on Protein Complexes | ||||
| Puig, et al | The Tandem Affinity Purification (TAP) Method: A General Procedure of Protein Complex Purification | Methods 2001, 24:218-229 | ||
| Rigaut, et al | A generic protein purification method for protein complex characterization & proteome exploration | Nature Biotechnology Oct 1999, 17:1030-1032- | ||
| V. Marginally related-may want to cite | ||||
| Drawid, et al | Genome-wide analysis relating expression level with protein subcellular localization | TIG Oct 2000, 16:10:426-429 | ||
| Marcotte, et al | Localizing proteins in the cell from their phylogenetic profiles | PNAS Oct 2000, 97:22:12115-12120 | ||
| Wojcik, et al | Prediction, assessment & validation of protein interacton maps in bacteria | JMB, 2002 323:763-770 | ||
| Jeong, et al | Lethality & centrality in protein networks | Nature May 2001, 411:41-42 | ||
| Griffin, et al | Complementary profiling of gene expression at the transcriptome & proteome levels in saccharomyces cerevisiae | Mol & Cel Proteomics, 2002, 1.4:323-333 | ||
| Marcotte, et al | Mining literature for protein-protein interactions | Bioinformatics 2001, 17:4:359-363 | ||
| Kumar, et al | Subcellular localiztion of the yeast proteome | Genes & Dev, 2002, 16:707-719 | ||
| Marcotte, et al | A combined algorithm for genome-wide prediction of protein function | Nature Nov 1999, 402:83-86 | ||
| Gerlt | "Fishing" for the functional proteome | Nature biotechnology Aug 2002, 20:786-787 | ||
| Ashburner, et al | Gene ontology: tool for the unification of biology | Nature Genetics, May 2000, 25:25-29 | ||
| Science | High-Speed Biologist Search for gold in proteins | Science Dec 2001, 294:2074-2077 | ||
| Karp | Pathway databases: a case study in computational symbolic theories | Science Sep 2001, 293:2040-2044 | ||
| Ross-MacDonald, et al | Large-scale analysis of the yeast genome by transposon tagging and gene disruption | Nature Nov 1999, 402:413-417 | ||
| Walhout & Vidal | High-Throughput yeast two-hybrid assays for large-scale protein interaction mapping | Methods 2001, 24:297-306 | ||