Browsing NTNU Open by Author "Sætrom, Pål"
Now showing items 1-20 of 58
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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 Classifier for Microprocessor Processing Site Prediction in Human MicroRNAs
Helvik, Snorre Andreas (Master thesis, 2006)MircoRNAs are ~22nts long non-coding RNA sequences that play a central role in gene regulation. As the microRNAs are temporary and not necessarily expressed when RNA from tissue samples are sequenced, bioinformatics is an ... -
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 short-activating RNA oligonucleotide targeting the islet β-cell transcriptional factor MafA in CD34(+) cells
Reebye, Vikash; Sætrom, Pål; Mintz, Paul J; Rossi, JJ; Kasahara, Noriyuki; Nteliopoulos, G; Nicholls, Joanna P; Haoudi, Abdelali; Gordon, Myrtle YA; Habib, Nagy A (Journal article; Peer reviewed, 2013)Upon functional loss of insulin producing islet β-cells, some patients with diabetes become dependent on life-long insulin supplementation therapy. Bioengineering surrogate insulin producing cells is an alternative replacement ... -
A two-step site and mRNA-level model for predicting microRNA targets
Saito, Takaya; Sætrom, Pål (Journal article; Peer reviewed, 2010)Background: Despite experiments showing that the number of microRNA (miRNA) target sites is critical for miRNA targeting, most existing methods focus on identifying individual miRNA target sites and do not model contributions ... -
AID expression in B-cell lymphomas causes accumulation of genomic uracil and a distinct AID mutational signature
Pettersen, Henrik Sahlin; Galashevskaya, Anastasia; Doseth, Berit; Sousa, Mirta; Sarno, Antonio; Visnes, Torkild; Aas, Per Arne; Liabakk, Nina-Beate; Slupphaug, Geir; Sætrom, Pål; Kavli, Bodil Merete; Krokan, Hans Einar (Journal article; Peer reviewed, 2014)tThe most common mutations in cancer are C to T transitions, but their origin has remained elusive.Recently, mutational signatures of APOBEC-family cytosine deaminases were identified in many com-mon cancers, suggesting ... -
Alkyladenine DNA glycosylase associates with transcription elongation to coordinate DNA repair with gene expression
Montaldo, Nicola Pietro; Bordin, Diana Lilian; Brambilla, Alessandro; Rösinger, Marcel; Martin, Sarah Fordyce; Bjørås, Karine Øian; Bradamante, Stefano; Aas, Per Arne; Furrer, Antonia; Olsen, Lene Christin; Kunath, Nicolas; Otterlei, Marit; Sætrom, Pål; Bjørås, Magnar; Samson, Leona D.; van Loon, Barbara (Journal article; Peer reviewed, 2019)Base excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases, ... -
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 ... -
Classifying Combined MicroRNA Data Sets
Bjørgan, Vegard (Master thesis, 2019)Siden funnene av de første mikroRNA i 1993, har forskere funnet flere tusen forskjellige mikroRNA i det menneskelige genomet gjennom de siste tiårene. MikroRNA som tema har blitt spesielt attraktivt for kreftforskningen ... -
Classifying low confidence miRNA as true and false miRNA
Heggedal, Håkon (Master thesis, 2015)Micro RNAs (miRNAs) are a group of apx. 22 nucleotide (nt) non-coding RNA sequences, playing an important role in gene regulation. The set of known miRNA for humans are grouped as high confidence (HC) miRNA, and low ... -
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 ... -
Comprehensive transcriptomic analyses of tissue, serum, and serum exosomes from hepatocellular carcinoma patients
Mjelle, Robin; Dima, Simona O.; Bacalbasa, Nicolae; Chawla, Konika; Sorop, Andrei; Cucu, Dana; Herlea, Vlad; Sætrom, Pål; Popescu, Irinel (Journal article; Peer reviewed, 2019)Background The expression of microRNAs (miRNAs) is a promising prognostic and diagnostic tool in hepatocellular carcinoma (HCC). Here we performed small RNA sequencing (sRNA-seq) of tissue, serum and serum exosomes to ... -
Enhanced Ultrasound Interpretation for Use in Neurological Navigation: Developing a Learning Platform for Enhanced Ultrasound Enterpretation
Lislebø, Even; Bjørnstad, Halvor G (Master thesis, 2015)Ultrasound (US) is widely used in medical imaging and boasts several advan- tages over other image modalities such as magnetic resonance imaging (MRI) and X-ray computed tomography (CT). Apart from being free of harmful ... -
Excerpts from the 1st international NTNU symposium on current and future clinical biomarkers of cancer: innovation and implementation, June 16th and 17th 2016, Trondheim, Norway
Robles, Ana I.; Olsen, Karina Standahl; Tsui, Dana W.T.; Georgoulias, Vassilis; Creaney, Jenette; Dobra, Katalin; Vyberg, Mogens; Minato, Nagahiro; Anders, Robert A.; Børresen-Dale, Anne-Lise; Zhou, Jianwei; Sætrom, Pål; Nielsen, Boye Schnack; Kirschner, Michaela B.; Krokan, Hans Einar; Papadimitrakopoulou, Vassiliki; Tsamardinos, Ioannis; Røe, Oluf Dimitri (Journal article; Peer reviewed, 2016)The goal of biomarker research is to identify clinically valid markers. Despite decades of research there has been disappointingly few molecules or techniques that are in use today. The “1st International NTNU Symposium ... -
Gene expression differences between PAXgene and Tempus blood RNA tubes are highly reproducible between independent samples and biobanks
Skogholt, Anne Heidi; Ryeng, Einar; Erlandsen, Sten Even; Skorpen, Frank; Arentz Schønberg, Svanhild Margrethe; Sætrom, Pål (Journal article; Peer reviewed, 2017)Background Gene expression profiling from blood is sensitive to technology choices. For example, the main blood RNA collection systems—the PAXgene and Tempus tubes—differently influence RNA expression signatures. The aim ... -
Gene expression profile changes after short-activating RNA-mediated induction of endogenous pluripotency factors in human mesenchymal stem cells
Voutila, J; Sætrom, Pål; Mintz, Paul J; Sun, Guihua; Alluin, Jessica; Rossi, JJ; Habib, Nagy A.; Kasahara, N. (Journal article; Peer reviewed, 2012)It is now recognized that small noncoding RNA sequences have the ability to mediate transcriptional activation of specific target genes in human cells. Using bioinformatics analysis and functional screening, we screened ... -
Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation
Landfors, Miriam; Johansen, Jostein; Aronsen, Jan Magnus; Vågbø, Cathrine Broberg; Doré, Louis C.; He, Chuan; Sjaastad, Ivar; Sætrom, Pål; Fedorcsák, Péter; Dahl, John Arne; Aanes, Håvard; Fusser, Markus; Klungland, Arne (Journal article; Peer reviewed, 2017)Sertoli cells have dual roles during the cells’ lifetime. In the juvenile mammal, Sertoli cells proliferate and create the structure of the testis, and during puberty they cease to proliferate and take on the adult role ... -
Hardware accelerated genetic programming for pattern mining in strings
Sætrom, Pål (Doktoravhandlinger ved NTNU, 1503-8181; 2005:197, Doctoral thesis, 2005)This thesis considers the problem of mining patterns in strings. Informally, this is the problem of extracting information (patterns) that characterizes parts of, or even the complete, string. The thesis describes a high ... -
Hardware accelerated sequence analysis
Hestnes, Arne Johan (Master thesis, 2005)The thesis evaluates two different techniques for using hardware acceleration in sequence analysis. The problem at hand is to detect remote homologies in protein sequences. This is useful for medical purposes, since protein ... -
Human Breast Milk miRNA, Maternal Probiotic Supplementation and Atopic Dermatitis in Offspring
Simpson, Melanie Rae; Brede, Gaute; Johansen, Jostein; Johnsen, Roar; Storrø, Ola; Sætrom, Pål; Øien, Torbjørn (Peer reviewed; Journal article, 2015)Background: Perinatal probiotic ingestion has been shown to prevent atopic dermatitis (AD) in infancy in a number of randomised trials. The Probiotics in the Prevention of Allergy among Children in Trondheim (ProPACT) trial ...