Morgan C. Giddings

Formerly: Research Professor

College of Arts and Sciences, Boise State University

Formerly: Adjunct Associate Professor
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill

Morgan C. Giddings, Principal Investigator
Morgan C. Giddings, Principal Investigator
Contact Information:
(208) 514-1639
morgan AT giddingslab DOT org

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 her focus on development of new computational and bionformatics tools for proteomics. She developed the Genome Fingerprint Scanning system, designed to identify the coding loci of proteins directly within a raw, unannotated genomic sequence. She also guided the development of PROCLAME, the first tool for de novo exploration of possible post-translational events that modify the masses of intact proteins measured by electrospray mass spectrometry.

The Giddings Lab’s general interest is in improving the functional understanding of how genomes encode diversity in the encoded proteome. The lab continues an ongoing development of tools for the interpretation of mass-spectrometry based proteomics data, including improved MS/MS database search accuracy, improved peptide mass fingerprint accuracy using peak height statistics, and integration of bottom-up with top-down proteomic data sets. Additional projects include cancer biomarker research, and an examination of antibiotic drug resistance in E. coli and P. aeruginosa using a systems biology approach.

Publications

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.

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.

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

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.

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.

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

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. Abstract.

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. Article’s first page.

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. Abstract.

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. Abstract.

2 thoughts on “Morgan C. Giddings”

  1. Dear Dr.Giddings,

    I just got a chance to read your article “On the Process of Becoming a Great Scientist”. It’s such a great and inspiring article! Just want to stop by to thank you for writing it.

    Best regards,
    Aopeau Imvittaya

  2. You inspire me.
    Thank you, for your article “On the Process of Becoming a Great Scientist.”
    Best wishes,
    Angela Lane

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