Blar i NTNU Open på forfatter "Håndstad, Tony"
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A ChIP-Seq Benchmark Shows That Sequence Conservation Mainly Improves Detection of Strong Transcription Factor Binding Sites
Håndstad, Tony; Rye, Morten Beck; Drabløs, Finn; Sætrom, Pål (Journal article; Peer reviewed, 2011)Background: Transcription factors are important controllers of gene expression and mapping transcription factor binding sites (TFBS) is key to inferring transcription factor regulatory networks. Several methods for ... -
Cell-type specificity of ChIP-predicted transcription factor binding sites
Håndstad, Tony; Rye, Morten Beck; Mocnik, Rok; Drabløs, Finn; Sætrom, Pål (Journal article; Peer reviewed, 2012)Background Context-dependent transcription factor (TF) binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing ... -
Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements
Rye, Morten Beck; Sætrom, Pål; Håndstad, Tony; Drabløs, Finn (Journal article; Peer reviewed, 2011)Background Transcription factor binding to DNA requires both an appropriate binding element and suitably open chromatin, which together help to define regulatory elements within the genome. Current methods of identifying ... -
Inferring regulatory networks and dynamical activities of transcription factors and miRNAs
Håndstad, Tony (Doktoravhandlinger ved NTNU, 1503-8181; 2014:182, Doctoral thesis, 2014)Transcription factors (TFs) and miRNAs are fundamental regulators of gene expression. Transcription factors are proteins that regulate the process of transcribing genes in the DNA into mRNA, whereas miRNAs mainly regulate ... -
Motif kernel generated by genetic programming improves remote homology and fold detection
Håndstad, Tony; Hestnes, Arne Johan Husebø; Sætrom, Pål (Journal article; Peer reviewed, 2007)Background: Protein remote homology detection is a central problem in computational biology. Most recent methods train support vector machines to discriminate between related and unrelated sequences and these studies ... -
Protein Remote Homology Detection using Motifs made with Genetic Programming
Håndstad, Tony (Master thesis, 2006)A central problem in computational biology is the classification of related proteins into functional and structural classes based on their amino acid sequences. Several methods exist to detect related sequences when the ... -
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
Kornacker, K; Rye, Morten Beck; Håndstad, Tony; Drabløs, Finn (Journal article; Peer reviewed, 2012)Background: Chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-Seq) is the most frequently used method to identify the binding sites of transcription factors. Active binding sites can be seen ...