My bioinformatics research interests include protein-protein interactions in the muscles, under the influences of microgravity (weightlessness) and of other cellular stresses, which may result in crippling microbiological oxidative activities. These lethal effects may lead to a general unraveling of protein structure and hence, function, during a course of functional protein degradation. For this post translational modification research, I have created analytical tools using knowledge from biology, mathematics and computer science to help to discover points of failure across mitochondrial and non-mitochondrial protein sequence data. This work is to further investigate protein longevity and to be able to predict the initiation of ailments stemming from protein malfunctions which are suffered by astronauts and people on Earth, alike. In my research I address different aspects leading to the breaking of protein constituents which cause major losses of muscular mass, ability and control. In addition, the knowledge from my work may lead to the discovery of causes for the onset of diseases associated with ageing including: Alzheimers, Huntingtons and Parkinsons disease.
The following are some of the projects in which I was, or am still involved. Many of the projects involved tool-development and data analysis for my publications.
BeagleTM: An adaptable text mining method for relationship discovery in literature
- Owing to the growing size of the literature, we introduce a text mining method and tool, (BeagleTM ), for knowledge harvesting from papers in a literature corpus without the use of article meta-data. Unlike other text mining tools that only highlight found keywords in articles, our method allows users to visually ascertain which keywords have been featured in studies together with others in peer-reviewed work. Drawing from an arbitrarily-sized corpus, BeagleTM creates visual networks describing interrelationships between user-defined terms to facilitate the discovery of connected or parallel studies.
Clone this repository: git clone email@example.com:developmentAC/beagleTM.git
PTM Tracker: A system for determining trends of PTM modification sites relative to protein domains
- We introduce a new methodology for detecting conserved regions of protein code between PTM modification sites and the domains that with which they are involved. In this work, we note that many related domains appear to have similar numbers of amino acids between the domains and the modification site to suggest that this distance is not arbitrary, and may be due to the mechanism of the domain's activation via PTMs.
A text mining application for linking functionally stressed-proteins to their post-translational modifications
- We introduce our own text mining system which is able to determine relationships between stresses, proteins and the PTMs that they summon. The results are direct and indirect links which are found by a powerful query-based approach using local databases.
Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organisms
- We study the bias that exists in PTM usage across diverse organisms. We find that there appears to be a complex and alternative mechanism between organisms in terms of their natural PTMs, tRNA, amino acids and other biases.
Slides from the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB)
Modeling the Effects of Microgravity On Oxidation in Mitochondria: A Protein Damage Assessment Across a Diverse Set of Life Forms
- We study the content of regions which are likely causes to protein failure in protein. We find that mitochondria has some protection against protein failure which is not detected in non-mitochondrial protein.
A (nucleotide) base composition analysis tool for sequence grouping.
- A tool that gathers frequencies of subwords in a pool of many different genetic sequences (DNA or protein) to determine general resemblances between them using information theoretic approaches. By measuring the information quantities and qualities across sequences in a pool, this tool is able to organize them according to this information. Its main applications have been in sequence or gene assembly projects.
sEncrypt: An Encryption Tool using biological data to encrypt information
- We propose a conceptual encryption framework which uses the wealth of data available from bioinformatics research projects (DNA, codon bias tables for specific organisms) to render plain text unreadable. The plain text is recovered with the knowledge of which data was used. Since there is so much data available form so many different research projects, the text may never be recovered without specific information. Furthermore, since biology does not follow logical rules, brute-force approaches may prove ineffective in this system.
Slides from the 12th IEEE International Conference on Trust, Security and Privacy in Computing and Communications (IEEE TrustCom-13), 2013
Evidence of a Pathway of Reduction in Bacteria: Reduced Quantities of Restriction Sites Impact tRNA Activity in a Trial Set
- We apply information theory to biology to determine that naturally missing regions of DNA which make-up restriction site are impacting more than just the DNA. Here we suggest that these missing regions create absent tRNAs which are important to the creation of specific proteins. In summary, the evolution of protein material begins with the the information quality (including its noise) of DNA.
Other projects in which I was involved: