Lab Projects

From Glabwiki

Contents 1 Current Projects 1.1 Genome-Based Peptide Fingerprint Scanning 1.2 PROCLAME 1.3 Agent Based Modelling 1.4 Ultra-Structure for Biology and Proteomics Research 1.5 Top-down Proteomic Analysis of Compensatory Mutations in Bacteria 1.6 BaseFinder 1.7 Francisella FUGE 1.8 GFS Extension 2 Past Projects and Software Links

Current Projects

Genome-Based Peptide Fingerprint Scanning

• GFS: A software system for identifying proteins by comparison of MS and MS/MS data to unannotated genome sequence. The official GFS website is here. Related Publications:
  
  • 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

• The official Proclame: website: Protein Cleavage and Modification Engine. This program predicts possible combinations of post translational modifications given a top-down intact mass measurement and a sequence from the gene. Relevant publications:
  
  • 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.
• The project page for PROCLAME

Agent Based Modelling

• Agent-Based Modeling of Intracellular Signalling: We are modeling many aspects of the bacterial chemotaxis pathway using Agent Based Modeling
  

Ultra-Structure for Biology and Proteomics Research

• CORE576: Ultra-Structure for Biology: A system for universal storage of biological information, and deductive inference.
  

Top-down Proteomic Analysis of Compensatory Mutations in Bacteria

• Protocol to Extract Ribosomal Proteins for LC/MS analysis: Ribosomal proteins make up to approximately 45% of the raw weight of fastly dividing prokaryotic cells. Using this method, a holoribosome protein complement can be adequately isolated and purified for analysis on LC/MS.
• Analysis of Compensatory Mutations by Mass Spectrometry: We are using a top-down mass spec approach to analyze proteome-level changes that occur in response to environmental pressures that may result in compensatory mutations within bacterial genomes.
  

BaseFinder

• BaseFinder: BaseFinder is software for the analysis of trace data from fluorescence-based sequencers. It is a flexible and modular system, allowing easy addition of processing tools (modules), and macro-like scripting abilities to define common processing sequences. It includes tools for tasks like multi-component transform, baseline correction, noise filtering, deconvolution, and base-calling. This program should be particularly useful to those exploring new instruments or chemistries for DNA sequencing. Can also be used to analyze SHAPE data. Publications:
  
  • 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.

Francisella FUGE

• Francisella-FUGUE: Gene function prediction by alignment of gene sequence and protein structure profiles.

GFS Extension

• GFS Development and Management: Projects to improve and extend GFS functionality.

Past Projects and Software Links

• Recode: A database of recoding events. Currently maintained by the Gesteland Lab.
  • 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: this work was performed in the Gesteland Lab, and is no longer being maintained.
  • 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

• Frameshift prediction using heptamer statistics. The original program is here.
  • 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.