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dc.contributor.advisorChairperson, Graduate Committee: Brendan Mumeyen
dc.contributor.authorSalinas Duron, Danielen
dc.date.accessioned2018-10-12T21:10:07Z
dc.date.available2018-10-12T21:10:07Z
dc.date.issued2018en
dc.identifier.urihttps://scholarworks.montana.edu/xmlui/handle/1/14584en
dc.description.abstractChanges in cellular metabolism can be deduced from how they affect the measurable metabolites in cell samples. We provide methods to compute metabolic reaction rates from changes in measurable metabolites over time. The methods provided are intended to overcome technical challenges, such as the inapplicability of a steady state assumption, heterogeneity of samples from different donors, and the lack of targeted metabolomics data. Solutions to these challenges involve identifying metabolites constrained even under non-steady state, using components analysis to find the donor consensus, and using an integer linear program to solve a set cover variant designed to generate targeted data from untargeted data. The methods are applied on data derived from diseased articular cells. The results show that the reaction rates inferred from the incomplete data are biologically relevant, and that the minimal pathways captured ancillary processes that alternative approaches ignored. We conclude that, although the resulting rates and pathways are not conclusive, they provide useful guidance on experiments to pursue. On the experimental side, our findings have lead us to believe that osteoarthritic chondrocytes respond to compression by initiating protein synthesis, opening the possibility of physical therapy as a stimulus for cartilage regeneration.en
dc.language.isoenen
dc.publisherMontana State University - Bozeman, College of Engineeringen
dc.subject.lcshMicrobial metabolitesen
dc.subject.lcshMathematical optimizationen
dc.subject.lcshNP-complete problemsen
dc.subject.lcshCartilageen
dc.subject.lcshJointsen
dc.titleNew methods in computation of reaction fluxes from metabolomics dataen
dc.typeDissertationen
dc.rights.holderCopyright 2018 by Daniel Salinas Duronen
thesis.degree.committeemembersMembers, Graduate Committee: Ronald K. June II; Binhai Zhu; Brittany Fasy.en
thesis.degree.departmentComputer Science.en
thesis.degree.genreDissertationen
thesis.degree.namePhDen
thesis.format.extentfirstpage1en
thesis.format.extentlastpage143en
mus.data.thumbpage47en


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