Blar i NTNU Open på forfatter "Sætrom, Pål"
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Optimization of Duplex Stability and Terminal Asymmetry for shRNA Design
Matveeva, OV; Kang, YB; Spiridonov, AN; Sætrom, Pål; Nemtsov, VA; Ogurtsov, AY; Nechipurenko, YD; Shabalina, SA (Journal article; Peer reviewed, 2010)Prediction of efficient oligonucleotides for RNA interference presents a serious challenge, especially for the development of genome-wide RNAi libraries which encounter difficulties and limitations due to ambiguities in ... -
Pathway Analysis of Skin from Psoriasis Patients after Adalimumab Treatment Reveals New Early Events in the Anti-Inflammatory Mechanism of Anti-TNF-α
Langkilde, Ane; Olsen, Lene Christin; Sætrom, Pål; Drabløs, Finn Sverre; Besenbacher, Søren; Raaby, Line; Johansen, Claus; Iversen, Lars (Peer reviewed; Journal article, 2016)Psoriasis is a chronic cutaneous inflammatory disease. The immunopathogenesis is a complex interplay between T cells, dendritic cells and the epidermis in which T cells and dendritic cells maintain skin inflammation. ... -
Predicting MicroRNA targets
Sætrom, Ola (Master thesis, 2005)MicroRNAs are a large family of short non-encoding RNAs that regulated protein production by binding to mRNAs. A single miRNA can regulate an mRNA by itself, or several miRNAs can cooperate in regulating the mRNAs. This ... -
Prediction and analysis of nucleosome positions in yeast
Visnovsky, Marek (Master thesis, 2013)The novel method for a prediction of nucleosome positions in yeast, based on Hidden Markov models extended by duration state modeling, was developed, implemented and tested, using data from Brogaard et al. (Brogaard K, ... -
Prioritization of cell cycle regulated genes
Zakeri, Ghazal (Master thesis, 2013)The cell cycle is an important biological process in which a set of events occurs in a sequential manner progressing to the cell division. Cell cycle is regulated by periodic fluctuations in the expression levels of several ... -
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 ... -
PyRanges: efficient comparison of genomic intervals in Python
Stovner, Endre Bakken; Sætrom, Pål (Journal article; Peer reviewed, 2019)Complex genomic analyses often use sequences of simple set operations like intersection, overlap and nearest on genomic intervals. These operations, coupled with some custom programming, allow a wide range of analyses to ... -
RAFT - Real And False TFBSs
Prasai, Sandesh (Master thesis, 2014)Most prediction methods for finding potential DNA binding sites for a specific transcription factor (TF) use a model for the transcription factor binding site (TFBS), and compare each position of the DNA sequence (e.g. a ... -
Randomised controlled trial of exercise training during lactation on breast milk composition in breastfeeding people with overweight/obesity: a study protocol for the MILKSHAKE trial
Moholdt, Trine; Ashby, Emily Rose; Tømmerdal, Karina Hammer; Lemoine, Maeliss Cynthia Chloe; Holm, Rebecca Lyng; Sætrom, Pål; Iversen, Ann-Charlotte; Ravi, Anuradha; Simpson, Melanie Rae; Giskeødegård, Guro F. (Peer reviewed; Journal article, 2023)Download PDFPDF Protocol Randomised controlled trial of exercise training during lactation on breast milk composition in breastfeeding people with overweight/obesity: a study protocol for the MILKSHAKE trial ... -
RNA motif discovery: a computational overview
Achar, Avinash; Sætrom, Pål (Journal article; Peer reviewed, 2015)Genomic studies have greatly expanded our knowledge of structural non-coding RNAs (ncRNAs). These RNAs fold into characteristic secondary structures and perform specific-structure dependent biological functions. Hence RNA ... -
Separating pseudo-microRNAs from true microRNAs
Holst, Frederik Klokk (Master thesis, 2013)MicroRNAs are small RNA molecules that regulate gene expression in cells. They are derived from hairpin shaped RNA transcripts, and about 50 \% of microRNA genes are localized in genomic regions that are associated with ... -
Shortreads (SR) analysis pipeline and correlation between SR and microRNA (miRNA) expression.
Fadeev, Fedor (Master thesis, 2016)MicroRNA are small non-coding RNA molecules that execute post-transcriptional regulation of gene expression for over half of human and mammalian genes. This report investigates shortreads (11-15 nucleotides) that align to ... -
Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation
Thomas, Laurent; Sætrom, Pål (Journal article; Peer reviewed, 2012)Alternative polyadenylation (APA) can for example occur when a protein-coding gene has several polyadenylation (polyA) signals in its last exon, resulting in messenger RNAs (mRNAs) with different 3′ untranslated region ... -
Small RNA expression from viruses, bacteria and human miRNAs in colon cancer tissue and its association with microsatellite instability and tumor location
Mjelle, Robin; Sjursen, Wenche; Thommesen, Liv; Sætrom, Pål; Hofsli, Eva (Journal article; Peer reviewed, 2019)Background MicroRNAs (miRNA) and other small RNAs are frequently dysregulated in cancer and are promising biomarkers for colon cancer. Here we profile human, virus and bacteria small RNAs in normal and tumor tissue from ... -
sMETASeq: combined profiling of microbiota and host small RNAs
Mjelle, Robin; Aass, Kristin Roseth; Sjursen, Wenche; Hofsli, Eva; Sætrom, Pål (Peer reviewed; Journal article, 2020)Understanding microbial communities' roles in human health and disease requires methods that accurately characterize the microbial composition and their activity and effects within human biological samples. We present ... -
SMUG1 Promotes Telomere Maintenance through Telomerase RNA Processing
Kroustallaki, Pinelopi; Lirussi, Lisa; Carracedo, Sergio; You, Panpan; Esbensen, Qin Ying; Götz, Alexandra; Jobert, Laure; Alsøe, Lene; Sætrom, Pål; Gagos, Sarantis; Nilsen, Hilde (Journal article; Peer reviewed, 2019)Telomerase biogenesis is a complex process where several steps remain poorly understood. Single-strand-selective uracil-DNA glycosylase (SMUG1) associates with the DKC1-containing H/ACA ribonucleoprotein complex, which is ... -
Statistical methods for control of the familywise error rate when testing for genotype-phenotype associations
Halle, Kari Krizak (Doctoral theses at NTNU;2017:060, Doctoral thesis, 2017) -
Studying differential isomiRs in high-throughput sequencing data identifies miRNA end-reads as a novel, putative miRNA degradation product
Mossin, Jan-Preben Silver (Master thesis, 2014)With the advancement of deep-sequencing technologies, it has become clear that individual miRNAs show varying degrees of heterogeneity in the expressed mature sequence. Recent evidence has suggested isomiR variants may be ... -
The eGenVar data management system-cataloguing and sharing sensitive data and metadata for the life sciences
Razick, Sabry; Mocnik, Rok; Thomas, Laurent; Ryeng, Einar; Drabløs, Finn; Sætrom, Pål (Journal article; Peer reviewed, 2014)Systematic data management and controlled data sharing aim at increasing reproducibility, reducing redundancy in work, and providing a way to efficiently locate complementing or contradicting information. One method of ... -
Three investigations of piRNA: Making sense of a new class of molecules
Stovner, Endre Bakken (Master thesis, 2013)This master s thesis is about Piwi-interacting RNA (piRNA) and its object is threefold. We will investigate i) how well a Support Vector Machine (SVM)-based method compares to the currently used software for piRNA cluster ...