Blar i NTNU Open på forfatter "Rye, Morten Beck"
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A balanced tissue composition reveals new metabolic and gene expression markers in prostate cancer
Tessem, May-Britt; Bertilsson, Helena; Angelsen, Anders; Bathen, Tone Frost; Drabløs, Finn Sverre; Rye, Morten Beck (Journal article; Peer reviewed, 2016)Molecular analysis of patient tissue samples is essential to characterize the in vivo variability in human cancers which are not accessible in cell-lines or animal models. This applies particularly to studies of tumor ... -
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 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 novel non-canonical Wnt signature for prostate cancer aggressiveness
Sandsmark, Elise; Hansen, Ailin Falkmo; Selnæs, Kirsten Margrete; Bertilsson, Helena; Bofin, Anna M.; Wright, Alan J.; Viset, Trond; Richardsen, Elin; Drabløs, Finn Sverre; Bathen, Tone Frost; Tessem, May-Britt; Rye, Morten Beck (Journal article; Peer reviewed, 2016)Activation of the Canonical Wnt pathway (CWP) has been linked to advanced and metastatic prostate cancer, whereas the Wnt5a-induced non-canonical Wnt pathway (NCWP) has been associated with both good and poor prognosis. A ... -
APIM-peptide targeting PCNA improves the efficacy of docetaxel treatment in the TRAMP mouse model of prostate cancer
Søgaard, Caroline Danielsen; Moestue, Siver Andreas; Rye, Morten Beck; Kim, Jana; Nepal, Anala; Liabakk, Nina-Beate; Bachke, Siri; Bathen, Tone Frost; Otterlei, Marit; Hill, Deborah Katherine (Journal article; Peer reviewed, 2018)Docetaxel is the chemotherapeutic choice for metastatic hormone-refractory prostate cancer, however, it only marginally improves the survival rate. The purpose of the present study was to examine if a peptide ... -
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 ... -
Clonal evolution after treatment pressure in multiple myeloma: heterogenous genomic aberrations and transcriptomic convergence
Misund, Kristine; Hofste op Bruinink, Davine; Coward, Eivind; Hoogenboezem, Remco M.; Rustad, Even Holth; Sanders, Mathijs A.; Rye, Morten Beck; Sponaas, Anne-Marit; van der Holt, Bronno; Zweegman, Sonja; Hovig, Eivind; Meza, Leonardo Zepeda; Sundan, Anders; Myklebost, Ola; Sonneveld, Pieter; Waage, Anders (Peer reviewed; Journal article, 2022)We investigated genomic and transcriptomic changes in paired tumor samples of 29 in-house multiple myeloma (MM) patients and 28 patients from the MMRF CoMMpass study before and after treatment. A change in clonal composition ... -
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 ... -
ClusTrack: Feature extraction and similarity measures for clustering of genome-wide data sets
Rydbeck, Halfdan; Sandve, Geir Kjetil F.; Ferkingstad, Egil; Simovski, Boris; Rye, Morten Beck; Hovig, Johannes Eivind (Journal article, 2015)Clustering is a popular technique for explorative analysis of data, as it can reveal subgroupings and similarities between data in an unsupervised manner. While clustering is routinely applied to gene expression data, 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 ... -
Development of an improved pathway analysis - The FunHop story
Rise, Kjersti (Doctoral theses at NTNU;2022:212, Doctoral thesis, 2022)Norsk sammendrag Arbeidet som presenteres i denne avhandlingen omhandler metabolisme i prostatakreft, hovedsakelig i form av bruk og forbedring av analyse av biologiske spor. En stor del av oppgaven handler om utvikling ... -
Differences between targeted and systematic prostate biopsies and their suitability for PRECAST analysis
Iversen, Gabriel (Master thesis, 2022)Bakgrunn: Prostatakreft er den hyppigst diagnostiserte kreftformen i Norge, og det trengs flere verktøy for å predikere prognose for å unngå over- og underbehandling av prostatakreft i intermediærrisikogruppen. Det forventes ... -
Differential Effects of Dietary Supplementation of Krill Meal, Soybean Meal, Butyrate, and Bactocell® on the Gene Expression of Atlantic Salmon Head Kidney
Jalili, Mahsa; Gerdol, Marco; Greco, S.; Pallavicini, Alberto; Buonocore, Francesco; Scapigliati, Giuseppe; Picchietti, Simona; Esteban, Maria Angeles; Rye, Morten Beck; Bones, Atle M. (Peer reviewed; Journal article, 2020)The head kidney is a key organ that plays a fundamental role in the regulation of the fish immune response and in the maintenance of endocrine homeostasis. Previous studies indicate that the supplementation of exogenous ... -
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 changes in response to neoadjuvant chemotherapy are associated with breast cancer survival
Pedersen, Christine Aaserød; Cao, Maria Dung; Fleischer, Thomas; Rye, Morten Beck; Knappskog, Stian; Eikesdal, Hans Petter; Lønning, Per Eystein; Tost, Jörg; Kristensen, Vessela N.; Tessem, May-Britt; Giskeødegård, Guro F.; Bathen, Tone Frost (Peer reviewed; Journal article, 2022)Background Locally advanced breast cancer is a heterogeneous disease with respect to response to neoadjuvant chemotherapy (NACT) and survival. It is currently not possible to accurately predict who will benefit from the ... -
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 ... -
FunHoP analysis reveals upregulation of mitochondrial genes in prostate cancer
Rise, Kjersti; Tessem, May-Britt; Drabløs, Finn; Rye, Morten Beck (Peer reviewed; Journal article, 2022)Mitochondrial activity in cancer cells has been central to cancer research since Otto Warburg first published his thesis on the topic in 1956. Although Warburg proposed that oxidative phosphorylation in the tricarboxylic ... -
FunHoP: Enhanced Visualization and Analysis of Functionally Homologous Proteins in Complex Metabolic Networks
Rise, Kjersti; Tessem, May-Britt; Drabløs, Finn; Rye, Morten Beck (Journal article; Peer reviewed, 2021)Cytoscape is often used for visualization and analysis of metabolic pathways. For example, based on KEGG data, a reader for KEGG Markup Language (KGML) is used to load files into Cytoscape. However, although multiple genes ...