Browsing NTNU Open by Author "Drabløs, Finn"
Now showing items 1-20 of 50
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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 ... -
A Computational Analysis of Motif-Negative VDR-DNA Interaction and Possible Explanations of Its Mechanism of Interaction
Hayford, Claude Fiifi (Master thesis, 2014)Transcription factor binding to DNA has generally been assumed to be as a result of the recognition of sequence-specific motifs in the transcription factor binding sites. Recent studies have however shown several examples ... -
A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
Rye, Morten Beck; Sætrom, Pål; Drabløs, Finn (Journal article; Peer reviewed, 2011)Chromatin immunoprecipitation (ChIP) followed by high throughput sequencing (ChIP-seq) is rapidly becoming the method of choice for discovering cell-specific transcription factor binding locations genome wide. By aligning ... -
A property-based analysis of human transcription factors
Bahrami, Shahram; Ehsani, Rezvan; Drabløs, Finn (Journal article; Peer reviewed, 2015)Background Transcription factors are essential proteins for regulating gene expression. This regulation depends upon specific features of the transcription factors, including how they interact with DNA, how they interact ... -
Assessment of composite motif discovery methods
Klepper, Kjetil; Sandve, Geir Kjetil; Abul, Osman; Johansen, Jostein; Drabløs, Finn (Journal article; Peer reviewed, 2008)Background: Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have ... -
c-Myb Binding Sites in Haematopoietic Chromatin Landscapes
Bengtsen, Mads; Klepper, Kjetil; Gundersen, Sveinung; Cuervo, Ignacio; Drabløs, Finn; Hovig, Johannes Eivind; Sandve, Geir Kjetil F.; Gabrielsen, Odd Stokke; Eskeland, Ragnhild (Journal article, 2015)Strict control of tissue-specific gene expression plays a pivotal role during lineage commit- ment. The transcription factor c-Myb has an essential role in adult haematopoiesis and func- tions as an oncogene when rearranged ... -
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 ... -
Cholesterol synthesis pathway genes in prostate cancer are transcriptionally downregulated when tissue confounding is minimized
Rye, Morten Beck; Bertilsson, Helena; Andersen, Maria Karoline; Rise, Kjersti; Bathen, Tone Frost; Drabløs, Finn; Tessem, May-Britt (Journal article; Peer reviewed, 2018)Background The relationship between cholesterol and prostate cancer has been extensively studied for decades, where high levels of cellular cholesterol are generally associated with cancer progression and less favorable ... -
Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines
Rye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, H; Carninci, P; Forrest, A; Drabløs, Finn (Journal article; Peer reviewed, 2014)Background Deciphering the most common modes by which chromatin regulates transcription, and how this is related to cellular status and processes is an important task for improving our understanding of human cellular ... -
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 ... -
Comparative genomics to delineate pathogenic potential in Non-O157 Shiga toxin-producing Escherichia coli (STEC) from patients with and without haemolytic uremic syndrome (HUS) in Norway
Haugum, Kjersti; Johansen, Jostein; Gabrielsen, Christina; Brandal, Lin Thorstensen; Bergh, Kåre; Ussery, David Wayne; Drabløs, Finn; Afset, Jan Egil (Journal article; Peer reviewed, 2014)Shiga toxin-producing Escherichia coli (STEC) cause infections in humans ranging from asymptomatic carriage to bloody diarrhoea and haemolytic uremic syndrome (HUS). Here we present whole genome comparison of Norwegian ... -
Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli
Ås, Christina Gabrielsen; Drabløs, Finn; Haugum, Kjersti; Afset, Jan Egil (Journal article; Peer reviewed, 2018)Shiga toxin-producing Escherichia coli (STEC) cause both sporadic infections and outbreaks of enteric disease in humans, with symptoms ranging from asymptomatic carriage to severe disease like haemolytic uremic syndrome ... -
Compo: composite motif discovery using discrete models
Sandve, Geir Kjetil; Abul, Osman; Drabløs, Finn (Journal article; Peer reviewed, 2008)Background: Computational discovery of motifs in biomolecular sequences is an established field, with applications both in the discovery of functional sites in proteins and regulatory sites in DNA. In recent years there ... -
Computational Analysis of DNA Methylation and Gene Expression Patterns in Prostate Cancer
Rauluševičiūtė, Ieva (Master thesis, 2018)DNA methylation is an important contributor for prostate cancer development and progression. It has been studied experimentally for years, but, lately, high-throughput technologies are able to produce genome-wide DNA ... -
Cytosolic scaffold functions of PCNA
Olaisen, Camilla (Doctoral theses at NTNU;2017:203, Doctoral thesis, 2017)PCNA som et plattform-protein i cytosol Kroppen vår består av millioner av celler som alle stammer fra en enkelt celle. For hver celledeling må arvestoffet, DNA-et, kopieres feilfritt i et samarbeid mellom mange ulike ... -
Discovery of approximate composite motifs in biological sequences
Valebjørg, Vetle Søraas (Master thesis, 2006)Mapping the regulatory system in living organisms is a great challenge, and many methods have been created during the last 15 years to solve this problem. The biological processes are however more flexible and complex than ... -
DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation
Rauluseviciute, Ieva; Drabløs, Finn; Rye, Morten Beck (Journal article; Peer reviewed, 2020)Background Prostate cancer (PCa) has the highest incidence rates of cancers in men in western countries. Unlike several other types of cancer, PCa has few genetic drivers, which has led researchers to look for additional ... -
DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis
Rauluseviciute, Ieva; Drabløs, Finn; Rye, Morten Beck (Journal article; Peer reviewed, 2019)Sequencing technologies have changed not only our approaches to classical genetics, but also the field of epigenetics. Specific methods allow scientists to identify novel genome-wide epigenetic patterns of DNA methylation ... -
Enhanced efficacy of bleomycin in bladder cancer cells by photochemical internalization
Baglo, Yan; Hagen, Lars; Høgset, Anders; Drabløs, Finn; Otterlei, Marit; Gederaas, Odrun Arna (Journal article; Peer reviewed, 2014)Bleomycin is a cytotoxic chemotherapeutic agent widely used in cancer treatment. However, its efficacy in different cancers is low, possibly due to limited cellular internalization. In this study, a novel approach known ... -
Enhanced identification of significant regulators of gene expression
Ehsani, Rezvan; Drabløs, Finn (Peer reviewed; Journal article, 2020)Background Diseases like cancer will lead to changes in gene expression, and it is relevant to identify key regulatory genes that can be linked directly to these changes. This can be done by computing a Regulatory Impact ...