My proteomics journal watch - year 2000 [ this week | 2004 Jul-Dec | 2004 Jan-Jun | 2003 Jul-Dec | 2003 Jan-Jun | 2002 | 2001 | 2000 | 1999 ]

General
Nature Structural Biology volume 7, Supplement (2000) Structural Genomics
2-d gel electrophoresis and mass spectroscopy applications in expression profiling
Protein-protein interaction
Structural genomics
Technical issues

* Protein chip related articles are put under the microarray section of My functional genomics journal watch

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General

  1. Rudert F. Genomics and proteomics tools for the clinic.  Curr Opin Mol Ther. 2000 Dec;2(6):633-42. [PubMed]
  2. Banks RE, Dunn MJ, Hochstrasser DF, Sanchez JC, Blackstock W, Pappin DJ, Selby PJ. Proteomics: new perspectives, new biomedical opportunities. Lancet. 2000 Nov 18;356(9243):1749-56. [PubMed]
  3. Heinrichs A. Protein science in the postgenomic era. Trends Biotech. 2000; Nov, 25: 541-3
  4. Chakravarti DN, Fiske MJ, Fletcher LD, Zagursky RJ. Application of genomics and proteomics for identification of bacterial gene products as potential vaccine candidates. Vaccine. 2000 Nov 8;19(6):601-12. [PubMed]
  5. Chambers G, Lawrie L, Cash P, Murray GI. Proteomics: a new approach to the study of disease. J Pathol. 2000 Nov;192(3):280-288. [PubMed]
  6. Jain KK. Applications of proteomics in oncology.  Pharmacogenomics. 2000 Nov;1(4):385-93. [PubMed]
  7. Smith RD. Probing proteomes-seeing the whole picture? Nat Biotechnol. 2000 Oct;18(10):1041-1042. [PubMed]
  8. Sansom C. Proteomics may aid bladder cancer diagnosis. Lancet Oncol. 2000 Sep;1(1):5. [PubMed]
  9. Steely HT Jr, Clark AF.  The use of proteomics in ophthalmic research.  Pharmacogenomics. 2000 Aug;1(3):267-80. [PubMed]
  10. Cunningham MJ.  Genomics and proteomics. The new millennium of drug discovery and development.  J Pharmacol Toxicol Methods. 2000 Jul;44(1):291-300. [PubMed]
  11. Haynes PA, Yates JR 3rd. Proteome profiling-pitfalls and progress. Yeast. 2000 Jun 30;17(2):81-7. Review. [PubMed]
  12. Pandey A, Mann M. Proteomics to study genes and genomes. Nature. 2000 Jun 15;405(6788):837-46. Review. [PubMed]
  13. Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-genomic era.  Nature. 2000 Jun 15;405(6788):823-6. Review. [PubMed]
  14. Washburn MP, Yates JR.  Analysis of the microbial proteome. Curr Opin Microbiol. 2000 Jun;3(3):292-7. Review. [PubMed]
  15. Liotta LA, Petricoin EF. Beyond the genome to tissue proteomics.  Breast Cancer Res. 2000;2(1):13-4. [PubMed]

Nature Structural Biology volume 7, Supplement (2000) Structural Genomics

  1. Smith T. A new era. Nat Struct Biol. 2000 Nov;7 Suppl:927. [pdf]
  2. Russell RB, Eggleston DS. New roles for structure in biology and drug discovery. Nat Struct Biol. 2000 Nov;7 Suppl:928-30. [PubMed][pdf]
  3. Norvell JC, Machalek AZ. Structural genomics programs at the US National Institute of General Medical Sciences.  Nat Struct Biol. 2000 Nov;7 Suppl:931. [PubMed][pdf]
  4. Burley SK. An overview of structural genomics. Nat Struct Biol. 2000 Nov;7 Suppl:932-4. [PubMed][pdf]
  5. Terwilliger TC. Structural genomics in North America. Nat Struct Biol. 2000 Nov;7 Suppl:935-9. [PubMed][pdf]
  6. Heinemann U. Structural genomics in Europe: slow start, strong finish? Nat Struct Biol. 2000 Nov;7 Suppl:940-2. [PubMed][pdf]
  7. Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S.  Structural genomics projects in Japan. Nat Struct Biol. 2000 Nov;7 Suppl:943-5. [PubMed][pdf]
  8. Dry S, McCarthy S, Harris T. Structural genomics in the biotechnology sector. Nat Struct Biol. 2000 Nov;7 Suppl:946-9. [PubMed][pdf]
  9. Meyers TC, Turano TA, Greenhalgh DA, Waller PR. Patent protection for protein structures and databases.  Nat Struct Biol. 2000 Nov;7 Suppl:950-2. [PubMed][pdf]
  10. Williamson AR. Creating a structural genomics consortium. Nat Struct Biol. 2000 Nov;7 Suppl:953. [PubMed][pdf]
  11. Doudna JA.  Structural genomics of RNA. Nat Struct Biol. 2000 Nov;7 Suppl:954-6. [PubMed][pdf]
  12. Berman HM, Bhat TN, Bourne PE, Feng Z, Gilliland G, Weissig H, Westbrook J. The Protein Data Bank and the challenge of structural genomics.  Nat Struct Biol. 2000 Nov;7 Suppl:957-9. [PubMed][pdf]
  13. Gerstein M.  Integrative database analysis in structural genomics.  Nat Struct Biol. 2000 Nov;7 Suppl:960-3. [PubMed][pdf]
  14. Hol WG. Structural genomics for science and society.  Nat Struct Biol. 2000 Nov;7 Suppl:964-6. [PubMed][pdf]
  15. Brenner SE. Target selection for structural genomics.  Nat Struct Biol. 2000 Nov;7 Suppl:967-9. [PubMed][pdf]
  16. Edwards AM, Arrowsmith CH, Christendat D, Dharamsi A, Friesen JD, Greenblatt JF, Vedadi M.  Protein production: feeding the crystallographers and NMR spectroscopists.  Nat Struct Biol. 2000 Nov;7 Suppl:970-2. [PubMed][pdf]
  17. Abola E, Kuhn P, Earnest T, Stevens RC. Automation of X-ray crystallography.  Nat Struct Biol. 2000 Nov;7 Suppl:973-7. [PubMed][pdf]
  18. Lamzin VS, Perrakis A.  Current state of automated crystallographic data analysis.  Nat Struct Biol. 2000 Nov;7 Suppl:978-81. [PubMed][pdf]
  19. Montelione GT, Zheng D, Huang YJ, Gunsalus KC, Szyperski T.  Protein NMR spectroscopy in structural genomics.  Nat Struct Biol. 2000 Nov;7 Suppl:982-5. [PubMed][pdf]
  20. Sanchez R, Pieper U, Melo F, Eswar N, Marti-Renom MA, Madhusudhan MS, Mirkovic N, Sali A.  Protein structure modeling for structural genomics. Nat Struct Biol. 2000 Nov;7 Suppl:986-90. [PubMed][pdf]
  21. Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA.  From structure to function: approaches and limitations.  Nat Struct Biol. 2000 Nov;7 Suppl:991-4. [PubMed][pdf]

2-d gel electrophoresis and mass spectroscopy applications in expression profiling

  1. O'Shaughnessy RF, Seery JP, Celis JE, Frischauf A, Watt FM. PA-FABP, a novel marker of human epidermal transit amplifying cells revealed by 2D protein gel electrophoresis and cDNA array hybridisation. FEBS Lett. 2000 Dec 8;486(2):149-154. [PubMed]
  2. Gerner C, Frohwein U, Gotzmann J, Bayer E, Gelbmann D, Bursch W, Schulte-Hermann R. The Fas-induced apoptosis analyzed by high-throughput proteome analysis. J Biol Chem. 2000 Dec 15; 275(50):39018-39025 [PubMed]
  3. Kovarova H, Hajduch M, Korinkova G, Halada P, Krupickova S, Gouldsworthy A, Zhelev N, Strnad M. Proteomics approach in classifying the biochemical basis of the anticancer activity of the new olomoucine-derived synthetic cyclin-dependent kinase  inhibitor, bohemine.  Electrophoresis. 2000 Nov;21(17):3757-64. [PubMed]
  4. Regula JT, Ueberle B, Boguth G, Gorg A, Schnolzer M, Herrmann R, Frank R. Towards a two-dimensional proteome map of Mycoplasma pneumoniae. Electrophoresis. 2000 Nov;21(17):3765-80. [PubMed]
  5. Nouwens AS, Cordwell SJ, Larsen MR, Molloy MP, Gillings M, Willcox MD, Walsh BJ.  Complementing genomics with proteomics: the membrane subproteome of Pseudomonas aeruginosa PAO1.  Electrophoresis. 2000 Nov;21(17):3797-809. [PubMed]
  6. Jain KK. Applications of proteomics in oncology.  Pharmacogenomics. 2000 Nov;1(4):385-93 [PubMed]
  7. Clarke BC, Hobbs M, Skylas D, Appels R. Genes active in developing wheat endosperm. Funct Integr Genomics. 2000 1:44-55 [link to journal]
  8. Emslie KR. Molloy MP, Barardi CRM, Jardine D, Wilkins MR, Bellamy AR. Williams KL. Serotype classification and characterisation of the rotavirus SA11 VP6 protein using mass spectrometry and two-dimensional gel electrophoresis. Funct Integr Genomics. 2000 1:12-24 [link to journal]
  9. Celisa JE, Kruhofferb M, Gromovaa I, Frederiksenb C, Ostergaarda M, Thykjaerb T, Gromova P, Yub J, Palsdottira H, Magnussona N, Orntoftb TF. Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics. FEBS Lett. 2000 Aug 25;480(1):2-16. [PubMed]
  10. Andersen JS, Mann M. Functional genomics by mass spectrometry. FEBS Lett. 2000 Aug 25;480(1):25-31. [PubMed]
  11. Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9390-5. [PubMed][pdf]
  12. Uetz P, Hughes RE.  Systematic and large-scale two-hybrid screens.  Curr Opin Microbiol. 2000 Jun;3(3):303-8. Review. [PubMed]

Protein-protein interaction

  1. Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol. 2000 Dec;18(12):1257-1261. [PubMed][Web]
  2. Mayer ML, Hieter P. Protein networks-built by association. Nat Biotechnol. 2000 Dec;18(12):1242-1243. [PubMed]
  3. Stanyon CA, Finley RL Jr.  Progress and potential of Drosophila protein interaction maps.  Pharmacogenomics. 2000 Nov;1(4):417-31. [PubMed]
  4. Legrain P, Selig L. Genome-wide protein interaction maps using two-hybrid systems. FEBS Lett. 2000 Aug 25;480(1):32-36. [PubMed]
  5. Zucconi A, Panni S, Paoluzi S, Castagnoli L, Dente L, Cesareni G. Domain repertoires as a tool to derive protein recognition rules. FEBS Lett. 2000 Aug 25;480(1):49-54. [PubMed]
  6. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000 Feb 10;403(6770):623-7. [PubMed][pdf]
  7. Oliver S. Guilt-by-association goes global. Nature. 2000 Feb 10;403(6770):601-3. [PubMed][pdf]
  8. Cagney G, Uetz P, Fields S.  High-throughput screening for protein-protein interactions using two-hybrid assay  Methods Enzymol. 2000;328:3-14. [PubMed]

Structural genomics

  1. Erlandsen H, Abola EE, Stevens RC. Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites. Curr Opin Struct Biol. 2000 Dec 1;10(6):719-730. [PubMed]
  2. Hendrickson WA. Synchrotron crystallography. Trends Biochem Sci. 2000 Dec 1;25(12):637-643. [PubMed]
  3. Baumeister W, Steven AC. Macromolecular electron microscopy in the era of structural genomics. Trends Biochem Sci. 2000 Dec 1;25(12):624-631. [PubMed]
  4. Gershon D. Structural genomics - from cottage industry to industrial revolution. Nature. 2000 Nov 9;408(6809):273-4. [PubMed][pdf]
  5. Abbott A. Structures by numbers. Nature. 2000 Nov 9;408(6809):130-2. [PubMed][pdf]
  6. Structural genomics boost. Nat Biotechnol. 2000 Nov;18(11):1127. [PubMed]
  7. Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku  Y, Miki K, Masui R, Kuramitsu S. Structural genomics projects in Japan. Nat Struct Biol. 2000 Nov;7 Suppl:943-5. [PubMed]
  8. Smaglik P. Genomics initiative to decipher 10000 protein structures. Nature. 2000 Oct 5;407(6804):549 [PubMed][pdf]
  9. Butler D. Wellcome discusses structural genomics effort with industry...but data release remains an open question.  Nature. 2000 Aug 31;406(6799):923-4. [PubMed][pdf]
  10. Peitsch MC, Schwede T, Guex N.  Automated protein modelling--the proteome in 3D. Pharmacogenomics. 2000 Aug;1(3):257-66. [PubMed]
  11. Christendat D, Yee A, Dharamsi A, Kluger Y, Gerstein M, Arrowsmith CH, Edwards AM. Structural proteomics: prospects for high throughput sample preparation. Prog Biophys Mol Biol. 2000 Jan 1;73(5):339-345. [PubMed]

Technical issues

  1. Fung ET, Wright GL Jr, Dalmasso EA.  Proteomic strategies for biomarker identification: progress and challenges.  Curr Opin Mol Ther. 2000 Dec;2(6):643-50. [PubMed]
  2. Li M. Applications of display technology in protein analysis. Nat Biotechnol. 2000 Dec;18(12):1251-1256. [PubMed]
  3. Palmer-Toy DE, Sarracino DA, Sgroi D, LeVangie R, Leopold PE. Direct acquisition of matrix-assisted laser Desorption/Ionization time-of-flight mass spectra from laser capture microdissected tissues. Clin Chem. 2000 Sep;46(9):1513-6. [PubMed]
  4. Aronheim A. Protein Recruitment Systems for the Analysis of Protein-Protein Interactions. Biochemical Pharmacology. 2000 Sep 60:1009-1013.
  5. Horn DM, Zubarev RA, McLafferty FW. Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10313-10317. [PubMed][pdf]
  6. Zucconi A, Panni S, Paoluzi S, Castagnoli L, Dente L, Cesareni G. Domain repertoires as a tool to derive protein recognition rules. FEBS Lett. 2000 Aug 25;480(1):49-54. [PubMed]

last updated: 21 Oct 2001
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