User:Giddings
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Revision as of 13:33, 29 June 2006
Contents |
Morgan Giddings
Departments of Microbiology & Immunology and Biomedical Engineering
| Contact Information: |
| CB#7290, 804 Mary Ellen Jones |
| The University of North Carolina at Chapel Hill |
| Chapel Hill, NC 27599-7290 |
| O: 919-843-3513 |
| F: 831-664-4070 |
| E: giddings@remove.these.words.unc.edu |
| To email Morgan, you need to remove "remove.these.words." from the email address |
Morgan's Travel Schedule (restricted page)
How can I reach Michael Giddings?
Background
Morgan became interested in the field of computational biology while working with Professor Lloyd Smith at the University of Wisconsin. Her work focused on the basecalling problem for automated DNA sequencing. A flexible and modular system was developed called BaseFinder, the first program to introduce confidence values on basecalls. In addition, she worked on projects such as automated muli-component determination, dye-encoding schemes to improve throughput and accuracy, and methods for improved trace processing.
In 1998 Morgan joined Ray Gesteland and John Atkins at the University of Utah as a post-doctoral researcher. There she worked to improve targeting efficacy in the analysis of Oligdeoxynucleotides, and then turned to focus on development of new computational and bionformatics tools for proteomics. She developed the Genome Fingerprint Scanning system, which is designed to identify the coding locus of proteins directly within a raw, unannotated genomic sequence. She also guided the development of PROCLAME, the first (and presently, only) tool for de novo exploration of possible post translational events that modify the mass of intact proteins measured by electrospray mass spectrometry.
Interests
My lab continues with a general interest in improving the functional understanding of how genomes encode diversity in the encoded proteome. Focuses include: Ongoing development of tools for the interpretation of mass-spectrometry derived proteomics data, with a focus on methods that bypass the limitations of present genomic annotations, as well as on interpreting and analyzing top-down proteomic data The use of proteomics to study microbial adaptation to adverse conditions such as antibiotic drugs An evolutionary examination of alternatively spliced genes, such as the intriguing Dscam family Modelling of bacterial chemotaxis using a new, agent-based approach
Publications
Reverse Chronology
2007
Yang D, Ramkissoon K, Hamlett E, Giddings MC (2007) High-Accuracy Peptide Mass Fingerprinting Using Peak Intensity Data with Machine Learning. J Proteome Res. Epub ahead of print, Oct 3, 2007. Open access article.
Su HC, Hutchison CA, 3rd, Giddings MC (2007) Mapping phosphoproteins in Mycoplasma genitalium and Mycoplasma pneumoniae. BMC Microbiol 7: 63. Open access article. Noted as "Highly Accessed."
Khatun, J., Ramkissoon, K. and Giddings, M.C. (2007) Fragmentation Characteristics of Collision-Induced Dissociation in MALDI TOF/TOF Mass Spectrometry, Anal Chem, 79, 3032-3040. Link to Pubmed Citation.
2006
Mack E Crayton III, Bradford C Powell, Todd J Vision and Morgan C Giddings. Tracking the evolution of alternatively spliced exons within the Dscam family. BMC Evolutionary Biology 2006, 6:16. Link to open access paper.
2005
Wisz, M.S., Khatun, J., and Giddings, M.C. Computational methods enabling genome-based protein identification from large, complex genomes using mass spectrometry data. in Third IEEE Workshop on Genomic Signal Processing and Statistics (GENSIPS). 2005. Newport, RI. PDF
2004
Wisz, M.S., Suarez, M.K., Holmes, M.R., and Giddings, M.C., GFSWeb: a web tool for genome-based identification of proteins from mass spectrometric samples. J Proteome Res, 2004. 3(6): p. 1292-5. Summary.
Holmes, M.R. and Giddings, M.C., Prediction of posttranslational modifications using intact-protein mass spectrometric data. Anal Chem, 2004. 76(2): p. 276-82. PubMed Abstract.
2003
Giddings, M.C., Shah, A.A., Gesteland, R.F., and Moore, M.B. (2003). “Genome-based peptide fingerprint scanning.” Proc. Nat. Acad. Sci. USA. 100(1):20-25. Abstract.
2002
Giddings, M.C., Shah, A.A., Freier, S., Atkins, J.F., Gesteland, R.F. and Matveeva, O.V. 2002. Artificial neural network prediction of antisense oligodeoxynucleotide activity. Nucleic Acids Res., 30(19), 4295-304 Abstract
Shah, A.A., Giddings, M.C., Parvaz, J.B., Gesteland, R.F., Atkins, J.F., and Ivanov, I.P., Computational identification of putative programmed translational frameshift sites. Bioinformatics, 2002. 18(8): 1046-53. Abstract.
M.V. Buchanan, F.W. Larimer, H.S. Wiley, S.J. Kennel, T.J. Squier, J.M. Ramsey, K.D. Rodland, G.B. Hurst, R.D. Smith, Y. Xu, D. Dixon, M.J. Doktycz, S. Colson, R. Gesteland, C. Giometti, M. Young, and M. Giddings. 2002. Genomes to Life “Center for Molecular and Cellular Systems”: A Research Program for Identification and Characterization of Protein Complexes. Omics, A Journal of Integrative Biology. 6(4):287-304 Abstract
Prior to 2002
Williams P.S., Giddings M.C., Giddings J.C. 2001. A data analysis algorithm for programmed field-flow fractionation. Analytical Chemistry. 73(17):4202-11 Abstract.
Baranov, P.V., Gurvich, O.L., Fayet, O., Prere, M.F., Miller, W.A., Gesteland, R.F., Atkins, J.F., and Giddings M.C. 2001 Recode: A Database of Frameshifting, Bypassing and Codon Redefinition utilized for gene expression. Nucleic Acids Research, 29(1):264-267 Abstract.
Giddings, M., Matveeva, O., Atkins, J., and Gesteland, R. 2000. ODNBase - A web database for antisense oligonucleotide effectiveness studies. Bioinformatics, 16(9):843-844. Abstract.
Matveeva, O.V., Tsodikov, A.D., Giddings, M., Freier, S.M., Wyatt, J.R., Spiridonov, A.N., Shabalina, S.A., Gesteland, R.F., and Atkins, J.F. 2000. Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity. Nucleic Acids Res., 28(15):2862-2865 Abstract.
Giddings, M.C., Severin, J., Westphall, M., Wu, J., and Smith, L.M. 1998. A software system for data analysis in automated DNA sequencing, Genome Research, 8(6):644-665 Abstract.
Yin, Z., Severin, J., Giddings, M., Huang, W., Westphall, M.S., and Smith, L.M. 1996. Automatic matrix determination in 4-dye fluorescence-based DNA sequencing. Electrophoresis. 17, 1143-1150.
Chen, D., Peterson, M.D., Brumley, R. L. Jr., Giddings, M.C., Buxton, E.C., Westphall, M., Smith, L., and Smith, L.M. 1995. Side excitation of fluorescence in ultrathin slab gel electrophoresis. Analytical Chemistry. 67(19), 3405-3411.
Smith, L. M., Brumley, R. L., Buxton, E., Giddings, M., Marchbanks, M. and Tong, X. High speed automated DNA sequencing in ultra thin slab gels. Methods in Enzymology. 1995; 271:219-237.
Giddings, M.C., Brumley, R.L., Haker, M., and Smith, L.M. 1993. An adaptive, object-oriented strategy for base calling in DNA sequence analysis. Nucleic Acids Res. 21(19), 4530-4540.
Go to the Publications page.
