History of Correlation btwn Protein and mRNA

From Networkbiology.net

1982
Ikemura T.  Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs.J Mol Biol. 1982 Jul 15;158(4):573-97.  PMID: 6750137

1985
Sharp PM. Does the 'non-coding' strand code?Nucleic Acids Res. 1985 Feb 25;13(4):1389-97. PMID: 3889840

1986
Sharp PM, Tuohy TM, Mosurski KR. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986 Jul 11;14(13):5125-43.PMID: 3526280

1989
Krek W, Nigg EA.  Structure and developmental expression of the chicken CDC2 kinase. EMBO J. 1989 Oct;8(10):3071-8. PMID: 2684635

1990
Malbon CC, Hadcock JR, Rapiejko PJ, Ros M, Wang HY, Watkins DC.  Regulation of transmembrane signalling elements: transcriptional, post-transcriptional and post-translational controls. Biochem Soc Symp. 1990;56:155-64. PMID: 256960

1991
Xu H, Boeke JD. Host genes that influence transposition in yeast: the abundance of a rare tRNA regulates Ty1 transposition frequency. Proc Natl Acad Sci U S A. 1990 Nov;87(21):8360-4. Erratum in: Proc Natl Acad Sci U S A 1991 Mar 15;88(6):2612. PMID: 2172984
Colasanti J, Tyers M, Sundaresan V. Isolation and characterization of cDNA clones encoding a functional p34cdc2 homologue from Zea mays. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3377-81. PMID: 2014258

1999
Gygi SP, Rochon Y, Franza BR, Aebersold R.  Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 1999 Mar;19(3):1720-30. PMID: 10022859
Futcher B, Latter GI, Monardo P, McLaughlin CS, Garrels JI.  A sampling of the yeast proteome. Mol Cell Biol. 1999 Nov;19(11):7357-68. PMID: 10523624

2001
Reichler SA, Balk J, Brown ME, Woodruff K, Clark GB, Roux SJ.  Light differentially regulates cell division and the mRNA abundance of peanucleolin during de-etiolation. Plant Physiol. 2001 Jan;125(1):339-50.
Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 2001 May 4;292(5518):929-34. PMID: 11340206
Bai Y, Hajek P, Chomyn A, Chan E, Seo BB, Matsuno-Yagi A, Yagi T, Attardi G. Lack of complex I activity in human cells carrying a mutation in MtDNA-encoded ND4 subunit is corrected by the Saccharomyces cerevisiae NADH-quinone oxidoreductase (NDI1) gene. J Biol Chem. 2001 Oct 19;276(42):38808-13. Epub 2001 Jul 30. PMID: 11479321Huang JX, Mehrens D, Wiese R, Lee S, Tam SW, Daniel S, Gilmore J, Shi M, Lashkari D.  High-throughput genomic and proteomic analysis using microarray technology.
Clin Chem. 2001 Oct;47(10):1912-6. PMID: 11568118

2002
Miller JL.  Hemoglobin switching and modulation: genes, cells, and signals. Curr Opin Hematol. 2002 Mar;9(2):87-92. Review. PMID: 11844989
Greenbaum D, Jansen R, Gerstein M.  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. Bioinformatics. 2002 Apr;18(4):585-96. PMID: 12016056
Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5860-5. Epub 2002 Apr 23. PMID: 11972065
Yang C, Hua Q, Shimizu K.  Integration of the information from gene expression and metabolic fluxes for the  analysis of the regulatory mechanisms in Synechocystis. Appl Microbiol Biotechnol. 2002 May;58(6):813-22. Epub 2002 Mar 15. PMID: 12021803
Analytical and biological variances associated with proteomic studies of Medicago truncatula by two-dimensional polyacrylamide gel electrophoresis. Proteomics. 2002 Aug;2(8):960-8. PMID: 12203891
Rushmore TH, Kong AN.  Pharmacogenomics, regulation and signaling pathways of phase I and II drug metabolizing enzymes. Curr Drug Metab. 2002 Oct;3(5):481-90.  Review. PMID: 12369894

2003
Jansen R, Bussemaker HJ, Gerstein M.  Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res. 2003 Apr 15;31(8):2242-51. PMID: 12682375 
Greenbaum D, Colangelo C, Williams K, Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 2003;4(9):117. Epub 2003 Aug 29. PMID: 12952525
Allen TE, Herrgård MJ, Liu M, Qiu Y, Glasner JD, Blattner FR, Palsson BØ.  Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. J Bacteriol. 2003 Nov;185(21):6392-9. PMID: 14563874
Hegde PS, White IR, Debouck C. Interplay of transcriptomics and proteomics. Curr Opin Biotechnol. 2003 Dec;14(6):647-51. Review. PMID: 14662396

2004
Hanash SM, Beretta LM.  Operomics: integrated genomic and proteomic profiling of cells and tissues. Brief Funct Genomic Proteomic. 2002 Feb;1(1):10-22. PMID: 15251063
Gao F, Foat BC, Bussemaker HJ.  Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics. 2004 Mar 18;5:31. PMID: 15113405
Reif DM, White BC, Moore JH.  Integrated analysis of genetic, genomic and proteomic data. Expert Rev Proteomics. 2004 Jun;1(1):67-75. Review. PMID: 15966800
Beyer A, Hollunder J, Nasheuer HP, Wilhelm T.  Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics. 2004 Nov;3(11):1083-92. Epub 2004 Aug 23. PMID: 15326222
Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, Aebersold R, Collins SJ, Hanlon WA, Hood LE.  Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics. 2004 Oct;3(10):960-9. Epub 2004 Jul 6. PMID: 15238602 

2005
Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A, Christophides GK, James K, Rutherford K, Harris B, Harris D,  Churcher C, Quail MA, Ormond D, Doggett J, Trueman HE, Mendoza J, Bidwell SL, Rajandream MA, Carucci DJ, Yates JR 3rd, Kafatos FC, Janse CJ, Barrell B, Turner  CM, Waters AP, Sinden RE.  A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science. 2005 Jan 7;307(5706):82-6. PMID: 15637271
Lin B, White JT, Lu W, Xie T, Utleg AG, Yan X, Yi EC, Shannon P, Khrebtukova  I, Lange PH, Goodlett DR, Zhou D, Vasicek TJ, Hood L.  Evidence for the presence of disease-perturbed networks in prostate cancer cells  by genomic and proteomic analyses: a systems approach to disease. Cancer Res. 2005 Apr 15;65(8):3081-91. PMID: 15833837
Gianchandani EP, Brautigan DL, Papin JA.  Systems analyses characterize integrated functions of biochemical networks. Trends Biochem Sci. 2006 May;31(5):284-91. Epub 2006 Apr 17. Review. PMID: 16616498
Alter O, Golub GH.  Singular value decomposition of genome-scale mRNA lengths distribution reveals asymmetry in RNA gel electrophoresis band broadening. Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11828-33. Epub 2006 Jul 28. PMID: 16877539
Lafaye A, Junot C, Pereira Y, Lagniel G, Tabet JC, Ezan E, Labarre J.  Combined proteome and metabolite-profiling analyses reveal surprising insights into yeast sulfur metabolism. J Biol Chem. 2005 Jul 1;280(26):24723-30. Epub 2005 Apr 26. PMID: 15855158
Shinkawa T, Taoka M, Yamauchi Y, Ichimura T, Kaji H, Takahashi N, Isobe T.  STEM: a software tool for large-scale proteomic data analyses. J Proteome Res. 2005 Sep-Oct;4(5):1826-31. PMID: 16212438
Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P, Siegel AF, Bolouri H, Aitchison JD, Hood L.  A data integration methodology for systems biology: experimental verification. Proc Natl Acad Sci U S A. 2005 Nov 29;102(48):17302-7. Epub 2005 Nov 21. PMID: 16301536

2006
Segura V, Podhorski A, Guruceaga E, Sevilla JL, Corrales FJ, Rubio A.  GARBAN II: an integrative framework for extracting biological information from proteomic and genomic data. Proteomics. 2006 Apr;6 Suppl 1:S12-5. Review. PMID: 16511812
Liu F, Lu J, Fan HH, Wang ZQ, Cui SJ, Zhang GA, Chi M, Zhang X, Yang PY, Chen Z, Han ZG.  Insights into human CD34+ hematopoietic stem/progenitor cells through a systematically proteomic survey coupled with transcriptome. Proteomics. 2006 May;6(9):2673-92. PMID: 16596711 
Belle A, Tanay A, Bitincka L, Shamir R, O'Shea EK.  Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13004-9. Epub 2006 Aug 17. PMID: 16916930
Waters KM, Pounds JG, Thrall BD.  Data merging for integrated microarray and proteomic analysis. Brief Funct Genomic Proteomic. 2006 Dec;5(4):261-72. Epub 2006 May 10. Review. PMID: 16772273


2007
Su WH, Chao CC, Yeh SH, Chen DS, Chen PJ, Jou YS.  OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci. Nucleic Acids Res. 2007 Jan;35(Database issue):D727-31. Epub 2006 Nov 10. PMID: 17098932
Schmidt MW, Houseman A, Ivanov AR, Wolf DA.  Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Mol Syst Biol. 2007;3:79. Epub 2007 Feb 13. PMID: 17299416
Nie L, Wu G, Culley DE, Scholten JC, Zhang W.  Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications. Crit Rev Biotechnol. 2007 Apr-Jun;27(2):63-75. Review. PMID: 17578703
Kettner C.
Good publication practice as a prerequisite for comparable enzyme data? In Silico Biol. 2007;7(2 Suppl):S57-64. PMID: 17822391
Rawool SB, Venkatesh KV.
Steady state approach to model gene regulatory networks--simulation of microarray experiments. Biosystems. 2007 Nov-Dec;90(3):636-55. Epub 2007 Feb 17. PMID: 17382459
Narsai R, Howell KA, Millar AH, O'Toole N, Small I, Whelan J.  Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. Plant Cell. 2007 Nov;19(11):3418-36. Epub 2007 Nov 16. PMID: 18024567
Tuller T, Kupiec M, Ruppin E. Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol. 2007 Dec;3(12):e248. PMID: 18159940