Protein Inference Engine (PIE): protein post-translational modifications from top-down and bottom-up data

  • Jefferys, S., and Giddings, M.C., Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data. Bioinformatics (2011) 27 (6): 844-852. Abstract.

    GFS: A software system for identifying proteins by comparison of MS and MS/MS data to unannotated genome sequence.

  • 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.
  • 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.
  • PROCLAME: Protein Cleavage and Modification Engine.

  • 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.
  • BaseFinder: a flexible software for the analysis of trace data from fluorescence-based sequencers.

  • 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.
  • 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.
  • Recode: A database of recoding events.

  • 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.
  • Antisense oligo efficacy predictions by neural networks, and a database of antisense oligos.

  • 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.
  • 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
  • freqAnalysis: frameshift prediction using heptamer statistics.

  • 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.
  • Antibiotic Resistance

  • Su, H.c., Ramkisson, K., Doolittle, J., Clark, M., Khatun, J., Secrest, A., Wolfgang, M.C., and Giddings, M.C., The development of ciprofloxacin resistance in Pseudomonas aeruginosa involves multiple response stages and multiple proteins. Antimicrob. Agents Chemother, 2010. doi:10.1128/AAC.00762-10. Abstract.


  • Maier, C., Long, J.g., Hemminger, B.M., Giddings, M.C., Ultra-Structure database design methodology for managing systems biology data and analyses. BMC Bioinformatics 2009, 10:254. Full Text.
  • Other

  • Holmes, M.R., Ramkissoon, K., and Giddings, M.C., Proteomics and Protein Identification, in “Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Third Edition”, Edited by Andreas D. Baxevanis and B. F. Francis Ouellette, 2005. Hoboken, NJ: John Wiley & Sons. ISBN: 0-471-47878-4. Link to purchase book.
  • Khatun, J., Ramkissoon, K., and Giddings, M.C., Fragmentation Characteristics of Collision-Induced Dissociation in MALDI TOF/TOF Mass Spectrometry. Anal. Chem., 2007, 79 (8), pp 3032–3040. Abstract.
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