Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 4 of 4 for “"Position Weight Matrix"”.
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Simultaneous computational discovery of DNA regulatory motifs and transcription factor binding constraints at high spatial resolution
… noisy ChIP-Seq data. I first present the genome positioning system (GPS) algorithm which predicts protein-DNA interaction events from ChIP-Seq data using a single-base resolution generative probabilistic model. Using synthetic and actual ChIP-Seq data, I show that GPS improves the effective …
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Transcription Factor Binding Dynamics and Spatial Co-localization In Human Genome
… site strength across different TFs based on Position-Weight-Matrices (PWM). While common bioinformatics tools produce scores that can reflect the binding strength between a specific TF and the DNA, these scores are not directly comparable between different TFs. We provided two approaches in …
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Elucidating the mechanistic impact of single nucleotide variants in model organisms
… outperform more rudimentary methods such as the position weight matrix. We further note that models for many TFs with distinct binding specificities were unable to accurately assess the impact of variants. For these TFs, we explore alternative mechanisms underlying TF-binding, such as …
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A bright, sweet evolution: a molecular genetic analysis of Calvin cycle gene expression response to light and sugar in the liverwort marchantia polymorpha, and insights into Calvin cycle promoter motif enrichment in land plants
Higher plants are frequently used as model organisms in Calvin Benson Bassham cycle (CBB) research given their ease of use in the laboratory. The expression of CBB genes in higher plants is well known to be regulated by light, sugar and plant development, yet no focus has been given to lower plant …