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Full-Text Articles in Physical Sciences and Mathematics
Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell
Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell
Faculty Publications
Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the gap open and gap extension penalties for three nuclear ribosomal data sets. Particular attention is given to optimal phylogeny scores for 200 alignments of a range of gap open and gap extension penalties and their respective …
Fibroblast Migration And Collagen Deposition During Dermal Wound Healing: Mathematical Modelling And Clinical Implications, S. Mcdougall, J. A. Sherratt, P. K. Maini, J. C. Dallon
Fibroblast Migration And Collagen Deposition During Dermal Wound Healing: Mathematical Modelling And Clinical Implications, S. Mcdougall, J. A. Sherratt, P. K. Maini, J. C. Dallon
Faculty Publications
The extent to which collagen alignment occurs during dermal wound healing determines the severity of scar tissue formation. We have modelled this using a multiscale approach, in which extracellular materials, for example collagen and fibrin, are modelled as continua, while fibroblasts are considered as discrete units. Within this model framework, we have explored the effects that different parameters have on the alignment process, and we have used the model to investigate how manipulation of transforming growth factor-b levels can reduce scar tissue formation. We briefly review this body of work, then extend the modelling framework to investigate the role played …