Oliver Bonham-carter

Oliver Bonham-carter
Allegheny College · Department of Computer Science

BS, MS, PhD

About

18
Publications
2,683
Reads
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248
Citations
Introduction
I am currently working on data analytics in different programming languages (Python, R, for example) for bioinformatics-based protein data. This research comprises post-translational modifications and is to determine the types of stresses that protein types can tolerate before protein domains become over-loaded or fail. In addition to this work, i am also using python to further develop a tool for data-analysis and text analysis. The tool is called "Lister" and parts of its functionality and results have been published. The manuscript can be found in my listing of papers on Researchgate.
Additional affiliations
January 2018 - February 2019
Allegheny College
Position
  • Professor (Assistant)
August 2016 - November 2016
Allegheny College
Position
  • Visiting Assistant Professor

Publications

Publications (18)
Chapter
Full-text available
Interaction between genes is one driving force that can influence a biological outcome. In a genetic disease such as cancer, understanding genetic interactions may help us elucidate mechanisms sustaining cancer growth. A computational approach is one way to detect genetic interactions in the context of cancer. In this article, we introduce a tool,...
Chapter
Full-text available
Investigators in bioinformatics are often confronted with the difficult task of connecting ideas, which are found scattered around the literature, using robust keyword searches. It is often customary to identify only a few keywords in a research article to facilitate search algorithms, which is usually completed in absence of a general approach tha...
Preprint
Full-text available
Cancer results from complex interactions between genes that are misregulated. Although our understanding of the contribution of single genes to cancer is expansive, the interplay between genes in the context of this devastating disease remains to be understood. Using the Genomic Data Commons Data Portal through National Cancer Institute, we randoml...
Article
Full-text available
Post-translational modifications (PTMs) are important steps in the biosynthesis of proteins. Aside from their integral contributions to protein development, i.e. perform specialized proteolytic cleavage of regulatory subunits, the covalent addition of functional groups of proteins or the degradation of entire proteins, PTMs are also involved in ena...
Conference Paper
Full-text available
In the proteome, stresses may work against optimal protein function and PTMs play roles in protein stress responses. Many peer-reviewed articles are available to bioinformatics research in the literature, however, the details of stress, protein and their PTM interactions have been scattered throughout the literature and these concepts are mentioned...
Conference Paper
Full-text available
Due to the expanding growth of information in the biomedical literature and biomedical databases, researchers and practitioners in the biomedical field require efficient methods of handling and extracting useful information. We present a novel framework for biomedical text mining based on a learning multi-agent system. Our distributed system compri...
Article
Full-text available
Exposure to weightlessness (microgravity) or other protein stresses are detrimental to animal and human protein tissue health. Protein damage has been associated with stress and is linked to aging and the on-set of diseases such as Alzheimer's, Parkinsons, sepsis, and others. Protein stresses may cause alterations to physical protein structure, alt...
Conference Paper
Full-text available
A post-translational modification (PTM) describes a form of biosynthesis for the task of initializing proteins for specific functions. PTMs are complexes which are involved in developing or customizing proteins to increase their functional diversity. In times of protein stress, PTMs may be involved in altering protein structures to allow for better...
Article
Full-text available
Exposure to microgravity conditions is detrimental to animal and human protein tissue and is linked to ailments associated with aging, disease and other disorders originating at the protein level. With exposure, dangerously low blood pressure results from diminished blood production forces the heart to beat at abnormal rates and causes damage. The...
Article
Full-text available
On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool uses these natural patterns to determine relatedness across sequence data. We introduce spectrum sets (sets of motifs) which are permutation...
Conference Paper
Full-text available
Occurring naturally along the genomes of many viruses and other pathogens, short palindromic restriction sites (<14bps) are often exploited by bacterial restriction enzymes as autoimmune defenses to end pathogen threats. These motifs may also appear in the host's genome where they are methylated so as not to attract restriction enzymes to the host'...
Article
Full-text available
Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing...
Conference Paper
Full-text available
Abstract—We present a new conceptual methodology for realizing encryption involving trap-door functions built from biological processes. Many standard encryption methods such as RSA security, for example, utilize functions that are easy to compute in one direction but the reverse is a computationally hard problem without a key. In biology, a trap-d...
Conference Paper
Full-text available
We present a new conceptual methodology for realizing encryption involving trap-door functions built from biological processes. Many standard encryption methods such as RSA security, for example, utilize functions that are easy to compute in one direction but the reverse is a computationally hard problem without a key. In biology, a trap-door like...
Conference Paper
Full-text available
Motivation: In meta-genome sequencing and assembly projects, where there are different types of contigs mixed together in a single pool, the task of assembling its different organisms is a complex and challenging problem. It is therefore desirable to sort the contigs by origins into separate bins from which to work. We propose a framework of using...
Article
Full-text available
On the basis of our investigation of the premalignant crypt phenotype in familial adenomatous polyposis patients, the hypothesis is developed that tumor initiation in the colon is caused by crypt stem cell overproduction. A novel kinetic model for the colonic crypt was used to investigate how the earliest tissue abnormality (altered crypt labeling...

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