Talk: Current Trends in Proteomics and Mass Spectroscopy: An Overview
(Presented by Todd Wareham)
Journal Papers:
Koopmann et al. (2004) "Serum Diagnosis of Pancreatic Adenocarcinoma Using Surface-Enhanced Laser Desorption and Ionization Mass Spectrometry." Clinical Cancer Research, 10, 860-868. [PDF]
Aebersold and Mann (2003) "Mass spectrometry-based proteomics." Nature, 422, 198-207. [PDF]
Petrocoin et al. (2003) "Serum Proteomic Patterns for Detection of Prostate Cancer." Journal of the National Cancer Institute, 94(20), 1576-1578. [PDF]
Zhu et al. (2003) "Detection of cancer-specific markers amid massive mass spectral data." Proceedings of the National Academy of Sciences, 100(25), 4666-4671. [PDF]
Adam et al. (2002) "Serum Protein Fingerprinting Coupled with a Pattern-matching Algorithm Distinguishes Prostate Cancer from Benign Prostate Hyperplasia and Healthy Men." Cancer Research, 62, 3609-3614. [PDF]
Adkins et al. (2002) "Toward a Human Blood Serum Proteome." Molecular and Cellular Proteomics, 1(12), 947-955. [PDF]
Petrocoin et al. (2002) "Use of proteomic patterns in serum to identify ovarian cancer." The Lancet, 359, 572-577. [PDF]
Conference Papers:
Edwards and Lippert (2004) "Sequence database compression for peptide identification from tandem mass spectra" [WABI][ PDF]
Jaitly et al (2004) "MSMS Peak Identification and Its Applications" [ISMB][PDF]
Lester et al (2004) "Cross-species protein identification in proteomics via protein profiles" [ISMB][PDF]
Bafna and Edwards (2003) "On de novo interpretation of tandem mass spectra for peptide identification" [RECOMB][ PDF]
Colinge et al (2003) "A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring" [WABI] [PDF]
Edwards and Lippert (2002) "Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectroscopy" [WABI][PDF]
Paper: Bowers, P.M., Cokus, S.J., Eisenberg, D., and Yeates,
T.O. (2004) "Use of Logic Relationships to Decipher Protein Network
Organization." Science, 306, 2246-2249.
[PDF]
(presented by Andre Leier)
Talk: Approximate Pattern Matching
(presented by Christoph Richter)
Talk: Evolution of Repeated Sequences by Unequal Crossover
(presented by Bill Langdon)
DNA whose sequence is not maintained by selection will develop periodicities as a result of random crossover (Smith, G.P. (1976)). Does this happen in artificial evolution? ( Movie)
References:
Smith, G.P. (1976) "Evolution of Repeated DNA Sequences by Unequal Crossover." Science, 191(4227), 528-535. [PDF]).
Paper: Wu, F.X., Zhang, W.J., and Kusalik, A.J. (2004) "Modelling Gene
Expression from Microarray Expression Data with State-Space Equations."
In Proceedings of the Ninth Pacific Symposium on Biocomputing.
World Scientific; Singapore. 581-592. [PDF]
(presented by Dwight Kuo)
Paper: Grasso, C., Modrek, B., Xing, Y., and Lee, C. (2004)
"Genome-Wide Detection of Alternative Splicing in Expressed Sequences
Using Partial Order Multiple Sequence Alignment Graphs."
In Proceedings of the Ninth Pacific Symposium on Biocomputing.
World Scientific; Singapore. 29-41. [PDF]
(presented by Todd Wareham)