Browsing NTNU Open by Author "Sætrom, Pål"
Now showing items 1-20 of 91
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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, ... -
Applied statistical methods and network analysis for identifying similarities and differences in biological data for various traits.
Hall, Martina (Doctoral theses at NTNU;2024:421, Doctoral thesis, 2024)"Observing differences in various traits, such as differences in human height, why some people are more susceptible to certain diseases, or why some species survive in certain environments, we often question why and how ... -
Associations of gene expression in blood with BMI and weight changes among women in the Norwegian Women and Cancer postgenome cohort
Baiju, Nikita; Rylander, Karin Charlotta Maria; Sætrom, Pål; Sandanger, Torkjel M; Nøst, Therese Haugdahl (Peer reviewed; Journal article, 2023)Objective This study aimed to evaluate associations between blood gene expression profiles and (1) current BMI and (2) past weight changes (WCs) among women who had never been diagnosed with cancer in the Norwegian Women ... -
Bioinformatic analysis of regulatory regions in immediate-early response genes
Blindheim, Magnar (Master thesis, 2020)Denne oppgaven har sett på genetisk og epigenetiske regioner i DNAet som bidrar til å regulere "immidiate-early gener" (IEG). IEG er gener karakterisert ved at de transkriberer mRNA raskt etter stimuli, og er involvert i ... -
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 ... -
Circulating miRNA and Lung Cancer: - a More Comprehensive Analysis of Available Data
Berg, Ole Fredrik Borgundvåg (Master thesis, 2022)Bakgrunn: Denne rapporten ser på mulighetene for å diagnostisere lungekreft ved hjelp av sirkulerende miRNA. Det har vært mye forskning på dette feltet, men lite forskning fra et maskinlæringsperspektiv. Motivasjon: Å ... -
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 genes based on promotors with deep neural networks
Chakroun Jacobsen, William (Master thesis, 2022)Denne oppgaven bruker enkeltcellede RNA-genekspresjonsdata fra 10xGenomics for å studere mulighetene for å bruke et dypt nevralt nettverk for å klassifisere gener basert på transkripsjonssekvenser. Gener i DNA har tilsvarende ... -
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 ... -
Dissecting gene expression networks in the developing hippocampus through the lens of NEIL3 depletion
Bugaj, Anna Maria; Kunath, Nicolas; Saasen, Vidar Langseth; Fernández Berrocal, Marion Silvana; Vankova, Ana; Sætrom, Pål; Bjørås, Magnar; Ye, Jing (Peer reviewed; Journal article, 2024)Gene regulation in the hippocampus is fundamental for its development, synaptic plasticity, memory formation, and adaptability. Comparisons of gene expression among different developmental stages, distinct cell types, and ... -
DNA hydroxymethylation differences underlie phenotypic divergence of somatic growth in Nile tilapia reared in common garden
Konstantinidis, Ioannis; Sætrom, Pål; Brieuc, Marine Servane Ono; Jakobsen, Kjetill Sigurd; Liedtke, Hannes; Pohlmann, Caroline; Tsoulia, Thomais; Fernandes, Jorge Manuel de Oliveira (Journal article; Peer reviewed, 2023)Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the ... -
Enhanced glutathione levels confer resistance to apoptotic and ferroptotic programmed cell death in NEIL DNA glycosylase deficient HAP1 cells
Neurauter, Christine Gran; Pannone, Marco; Sousa, Mirta; Wang, Wei; Kusnierczyk, Anna; Luna, Luisa; Sætrom, Pål; Scheffler, Katja; Bjørås, Magnar (Peer reviewed; Journal article, 2024)The NTHL1 and NEIL1-3 DNA glycosylases are major enzymes in the removal of oxidative DNA base lesions, via the base excision repair (BER) pathway. It is expected that lack of these DNA glycosylases activities would render ...