For a list of software projects, please visit the Software page.
1. Finding Protein Biomarkers for Cancer
2. ENcyclopedia Of DNA Elements (ENCODE)
Finding Protein Biomarkers for Cancer
Protein biomarkers – proteins that may be produced from aberrations in the genome – hold great promise in the development of an early diagnostic tool for cancer. A simple, cost-effective blood test for cancer would save lives, as the disease could be treated before it progresses. However, protein biomarker research has not yet lived up to this promise, because many changes in proteins occur in the presence of cancer, and each change may only have a minor correlation with the presence or absence of disease. Our lab is tackling this problem by focusing on measurable genomic changes that underlie protein biomarker changes, examining how they implicate themselves upon proteins that end up in blood plasma. Recently developed whole genome analysis technologies have provided the ability to analyze the entire spectrum of somatic mutations present in any given tumor, providing an unprecedented opportunity for biomarker development. We are using our integrated software Peppy to proteogenomically map from the mutation to its downstream effects on the RNA, proteins, and metabolites.
Read an article in ProteoMonitor about the project.
ENcyclopedia Of DNA Elements (ENCODE)
In 2003, the National Human Genome Research Institute (NHGRI) launched a pilot project called ENCyclopedia Of DNA Elements (ENCODE) to rigorously analyze 44 euchromatic regions of the human genome. The pilot project revealed surprising results such as pervasive intragenic and intergenic transcription, new intronic and intergenic exons, overlapping transcripts, and distant transcriptional start sites. Following the success of the initial pilot phase, the NHGRI expanded ENCODE to study the entire human genome, to provide the scientific community with a comprehensive list of functional elements. As the only member of the ENCODE Consortium focusing on proteomics, we recently proteogenomically mapped (via our integrated software Peppy) the whole human genome to identify protein-coding regions.
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
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 in LC/MS.
Analysis of Compensatory Mutations by Mass Spectrometry: We are using a top-down mass spectrometric approach to analyze proteome-level changes that occur in response to environmental pressures that may result in compensatory mutations within bacterial genomes.