Mark P. Styczynski

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Analysis of metabolomic profiling data from gas chromatography-mass spectrometry (GC/MS) measurements usually relies upon reference libraries of metabolite mass spectra to structurally identify and track metabolites. In general, techniques to enumerate and track unidentified metabolites are nonsystematic and require manual curation. We present a method and(More)
Jerome Amir Singh1,2 & Abdallah S Daar3 1CAPRISA, Private Bag X7, Congella, 4013, Durban, South Africa, and Howard College School of Law, University of KwaZulu-Natal, King George V Avenue, Durban, South Africa. 2Department of Public Health Sciences and Joint Center for Bioethics, University of Toronto, 88 College Street, Toronto, Canada. 3McLaughlin-Rotman(More)
Biologists pioneering the new field of comparative functional genomics attempt to infer the mechanisms of gene regulation by looking for similarities and differences of gene activity over time across multiple species. They use three kinds of data: functional data such as gene activity measurements, pathway data that represent a series of reactions within a(More)
The (l,d)-motif challenge problem, as introduced by Pevzner and Sze, is a mathematical abstraction of the DNA functional site discovery task. Here we expand the (l,d)-motif problem to more accurately model this task and present a novel algorithm to solve this extended problem. This algorithm is guaranteed to find all (l,d)-motifs in a set of input sequences(More)
In the last 10 years, Inference of Gene Regulatory Networks from Microarray data has become an important research area in Bioinformatics. Several algorithms have been proposed and Regulatory networks have been inferred with good accuracy for Saccromycin cervisea, Escherichia coli, Hela cells etc. A large amount of knowledge on various biological systems,(More)
INTRODUCTION Recently, multicellular spheroids were isolated from a well-established epithelial ovarian cancer cell line, OVCAR-3, and were propagated in vitro. These spheroid-derived cells displayed numerous hallmarks of cancer stem cells, which are chemo- and radioresistant cells thought to be a significant cause of cancer recurrence and resultant(More)
Cancer metabolism is emerging as an important focus area in cancer research. However, the in vitro cell culture conditions under which much cellular metabolism research is performed differ drastically from in vivo tumor conditions, which are characterized by variations in the levels of oxygen, nutrients like glucose, and other molecules like(More)
The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target(More)
The first discovery of metabolic changes in cancer occurred almost a century ago. While the genetic underpinnings of cancer have dominated its study since then, altered metabolism has recently been acknowledged as a key hallmark of cancer and metabolism-focused research has received renewed attention. The emerging field of metabolomics - which attempts to(More)
Metabolic engineering is generally focused on static optimization of cells to maximize production of a desired product, though recently dynamic metabolic engineering has explored how metabolic programs can be varied over time to improve titer. However, these are not the only types of applications where metabolic engineering could make a significant impact.(More)