author/s	title	publication
Databases
MIPS
Mewes, et al.	MIPS: a database for genomes & protein sequences	NAR 2002, vol.30, no.1, p.31-34
YPD (Old-1997)
Payne & Garrels	Yeast Protein Database: a database for the complete proteome of Saccharomyces cerevisiae	NAR 1997, vol. 25, no. 1, p. 57-62
BIND
Bader & Hogue	BIND: A data specification for storing & describing biomolecular interactions, molecular complexes & pathways	Bioinformatics 2000, vol.16, no.30 p.465-477
TRIPLES
Kunmar, et al.	The triples database:A community resource for yeast molecular biology	NAR 2002, vol.30, no.1, p.73-75
Live DIP
Duan, et al.	Describing biological protein interactions in terms of protein states & state transitions	Mol. & Cell Proteomics 1.2, 2002, p. 104-116
Xenarios, et al.	DIP, The database of interacting proteins:a research tool for studying cellular networks of protein interactions	NAR 2002, vol. 30, no. 1 p 303-305
Xenarios, et al.	DIP: The database of interacting proteins: 2001 Update	NAR 2001, vol. 29, no. 1 p 239-241
Gene/Protein Function
Marcotte, et al.	Detecting protein function & protein-protein interactions from genome sequences	Science, July 1999, 285751-753:929-934
Huynen, et al.	Predicting protein function by genomic context:quantitative evaluation & qualitative inferences	GenomeResearch 2000, 10:1204-1210
Brent, Roger	Genomic biology	Cell, Jan 2000 vol. 100: 169-183
Cho, et al.	Parallel analysis of genetic selections using whole genome oligonucleotide arrays	PNAS, Mar 1998, v.95 p.3752-3757
Nguyen, et al.	DNA microarray experiments:biological & technological aspects	Biometrics, Dec 2002, 58:701-717
Gullans, Steven	Of microarrays & meandering data points	NatureGenetics Sep 2000, 26:4-5
Irving & Hudson	Proteins emerge from disarray	NatureBioTech, Sep 2000, 18:932-933
Gygi, et al.	Quantitative analysis of complex protein mixtures using isotope-coded affinity tags	NatureBioTech, Oct 1999, 17:994-999
Service, Robt	Protein arrays step out of DNA's shadow	Science
Yaffe, et al.	A motif-based profile scanning approach for genome-wide prediction of signaling pathways	NatureBioTech, Apr 2001, 19:348-353
Periwal & Szallasi	Trading "wet-work" for network	NatureBioTech, Apr 2002, 20:345-346
Fuente, et al.	Linking the genes:inferring quantitative gene networks from microarray data	TIG Aug 2002, 18:395-398
Oliver, Stephen	Functional genomics: lessons from yeast	TheRoyalSociety, Jan 2002,
Qian, et al.	Beyond synexpression relationships: local clustering of time-shifted & inverted gene expression profiles identifies new, biologically relevant interactions	JMB, 2001, 314:1053-1066
Lander, Eric	Array of hope	NatureGenetics supplement, Jan 1999, v. 21
Baker & Sali	Protein structure prediction & structural genomics	Science, Oct 2001, 294:93-96
Burley, Stephen	An overview of structural genomics	StructuralGenomics supplement, Nov 2000
Yeung & Ruzzo	Principal component analysis for clustering gene expression data	Bioinformatics, 2001, 17:9:763-774
Alter, et al.	Singular value decomposition for genome-wide expression data processing & modeling	PNAS, Aug 2000, 97:18:10101-10106
Blundell & Mizuguchi	Structural genomics: an overview	Progress in Biophysics & MolBio, 2000, 73:289-295
Knight, Jonathan	When the chips are down:DNA microarrays are transforming studies of gene expression	Nature, Apr 2001, 410:860-861
Papers on Cancer
Berns, Anton	Gene expression in diagnosis	Nature, 3 Feb 2000, 403:491492
Perou, et al.	Molecular portraits of human breast tumors	Nature, 17 Aug 2000, 406:747-752
Staunton, et al.	Chemosensitivity prediction by transcriptional profiling	PNAS, 11 Sep 2001, 98:10787-10792
Scherf, et al.	A gene expression database for the molecular pharmacology of cancer	NatureGenetics, Mar 2000 24:236-244
Protein-Protein Interactions Background
Zhou & Shan	Prediction of protein interaction sites from sequence profile & residue neighgbor list	Proteins, 2001, 44:336-343
Pazos, et al.	Correlated mutations contain information about protein-protein interaction	JMB 1997;271:511-523
Sprinzak & Margalit	Correlated sequence-signatures as markers of protein-protein interaction	JMB 2001;311:681-692
Mellor, et al.	Predictome: a database of putative functional links between proteins	NAR 2002;30:1:306-309
Various Fun
Park, et al.	Estimating the significance of sequence order in protein secondary structure & prediction	Bioinformatics, 2000, 16:11:978-987
Enright, et al.	An algorithm for large-scale detection of protein families	NAR, 2002 30:7:1575-1584
Casari, et al.	A method to predict functional residues in proteins	StructualBiology, Feb 1995, 2:2:171-178
Grabowski, Paula	Alternative splicing in parallel	NatureBioTech, Apr 2002, 20:346-347
Other Related Papers
Matthews, et al.	Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs"	GenomeResearch 2001, 11:2120-2126
Bernstein, et al.	Analyzing mRNA-protein complexes using a yeast three-hybrid system	Methods, 2002, 26:123-141
Teichman, Sarah	Principles of protein-protein interactions	Bioinformatics, 2002, 18:249
von Mering, et al.	Supplementary information
Protein Chips
Zhu, et al.	Global analysis of protein activities using proteome chips	Science 14 Sep 2001, 293:2101-2150
Zhu, et al.	Analysis of yeast protein kinases using protein chips	NatureGenetics, Nov 2000 26:283-289
Even More Marginally Related
Giaever, et al.	Functional profiling of the Saccharomyces cerevisiae genome	Nature 25 Jul 2002 418:387-391
Bock & Gough	Predicting protein-protein interactions from primary structure	Bioinformatics 2001, 17:5:455-460
Gygi, et al.	Evaluation of two dimensional gel electrophoresis-based proteome analysis technology	PNAS, 15 Aug 2000, 97:17:9390-9395
Rain, et al.	The protein-protein interaction map of Helicobacter pylori	Nature, 11 Jan 2001, 409:211-215
Hu, James	A guided tour in protein interaction space: coiled coils from the yeast proteome	PNAS, 21 Nov 2000, 97:24:12935-12936
Wojcik & Schachter	Protein-protein interaction map inference using interacting domain profile pairs	Bioinformatics 2001, pp. s296-s305
Clean Copies for Dannie
Maslov & Sneppen	Specificity & stability in topology of protein networks	Science 3 May 2002;296:910-913