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1. Full Text MicroRNA-Directed Transcriptional Gene Silencing in Mammalian Cells
by Daniel H. Kim and Pål Sætrom and Ola Snøve and John J. Rossi
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2008, Volume 105, Issue 42, pp. 16230 - 16235
MicroRNAs (miRNAs) regulate gene expression at the posttranscriptional level in the cytoplasm, but recent findings suggest additional roles for miRNAs in the... 
Biotechnology | Transcriptional regulatory elements | MicroRNA | Messenger RNA | RNA | Genes | Cell cycle | Cell lines | HeLa cells | Promoter regions | miRNA | RNAi | Epigenetic | POLR3D | Argonaute | METHYLATION | epigenetic | MULTIDISCIPLINARY SCIENCES | GENOME | Cell Line | Animals | Base Sequence | Humans | Gene Silencing | MicroRNAs - genetics | Transcription, Genetic - genetics | Promoter Regions, Genetic - genetics | Gene silencing | Evaluation | Genetic aspects | Research | Genetic transcription | Properties | Mammals | Proteins | Ribonucleic acid--RNA | Cells | Post-transcription | Transcription | RNA-mediated interference | Antisense | Genomes | polycomb group proteins | Nuclei | Promoters | epigenetics | Mammalian cells | Lysine | Cytoplasm | Histone H3 | Biological Sciences
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2. Full Text MicroRNAs in Disease and Potential Therapeutic Applications
by Soifer, Harris S and Rossi, John J and Sætrom, Pål
Molecular Therapy, ISSN 1525-0016, 12/2007, Volume 15, Issue 12, pp. 2070 - 2079
MicroRNAs (miRNAs) are 21–24 nucleotide (nt) duplex RNAs that are created from precursor transcripts by subsequent processing steps mediated by members of the... 
RNA-POLYMERASE-II | MEDICINE, RESEARCH & EXPERIMENTAL | DOUBLE-STRANDED-RNA | SARCOMA-ASSOCIATED HERPESVIRUS | MUSCLE-SPECIFIC MICRORNA | MICROPROCESSOR COMPLEX | SHORT HAIRPIN RNAS | X MENTAL-RETARDATION | SMALL INTERFERING RNA | MESSENGER-RNA | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | IN-VIVO | GENETICS & HEREDITY | MicroRNAs - genetics | MicroRNAs - physiology | RNA Interference | Humans | RNA, Messenger - genetics
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3. Full Text MicroRNAs – targeting and target prediction
by Saito, Takaya and Sætrom, Pal
New BIOTECHNOLOGY, ISSN 1871-6784, 2010, Volume 27, Issue 3, pp. 243 - 249
MicroRNAs (miRNAs) are a class of small noncoding RNAs that can regulate many genes by base pairing to sites in mRNAs. The functionality of miRNAs overlaps... 
BIOGENESIS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | CODING REGION | SEQUENCE | BIOCHEMICAL RESEARCH METHODS | 3'-UTR | SIRNAS | MAMMALIAN MESSENGER-RNAS | BINDING-SITES | IDENTIFICATION | ANIMAL MICRORNAS | EXPRESSION | Gene Targeting | RNA, Small Interfering - genetics | Animals | Base Sequence | Humans | MicroRNAs - metabolism | MicroRNAs - genetics | 3' Untranslated Regions | RNA, Small Interfering - metabolism | Quantitative Biology - Genomics
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4. Full Text Distance constraints between microRNA target sites dictate efficacy and cooperativity
by Sætrom, Pål and Heale, Bret S.E and Snøve, Ola and Aagaard, Lars and Alluin, Jessica and Rossi, John J
Nucleic Acids Research, ISSN 0305-1048, 4/2007, Volume 35, Issue 7, pp. 2333 - 2342
MicroRNAs (miRNAs) have the potential to regulate the expression of thousands of genes, but the mechanisms that determine whether a gene is targeted or not are... 
CAENORHABDITIS-ELEGANS | HUMAN GENOME | MESSENGER-RNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENES | LET-7 | MIRNAS | BINDING-SITES | IDENTIFICATION | CLEAVAGE | EXPRESSION | RNA, Small Interfering - chemistry | Cell Line | Sequence Analysis, RNA | Down-Regulation | Humans | MicroRNAs - metabolism | HeLa Cells | Binding Sites | MicroRNAs - chemistry | 3' Untranslated Regions - chemistry | RNA, Small Interfering - metabolism | RNA
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5. Full Text Circular RNAs are depleted of polymorphisms at microRNA binding sites
by Thomas, Laurent F and Sætrom, Pål
Bioinformatics, ISSN 1367-4803, 08/2014, Volume 30, Issue 16, pp. 2243 - 2246
Motivation: Circular RNAs (circRNAs) are an abundant class of highly stable RNAs that can affect gene regulation by binding and preventing microRNAs (miRNAs)... 
GENETIC-VARIATION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | MicroRNAs - metabolism | Polymorphism, Single Nucleotide | RNA - chemistry | Binding Sites | Humans | RNA - metabolism | Discovery Note
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6. Full Text PyRanges: efficient comparison of genomic intervals in Python
by Stovner, Endre Bakken and Sætrom, Pål
Bioinformatics (Oxford, England), ISSN 1367-4803, 08/2019
Complex genomic analyses often use sequences of simple set operations like intersection, overlap, and nearest on genomic intervals. These operations, coupled... 
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7. Full Text epic2 efficiently finds diffuse domains in ChIP-seq data
by Stovner, Endre Bakken and Sætrom, Pål
Bioinformatics (Oxford, England), ISSN 1367-4803, 03/2019
Data from chromatin immunoprecipitation (ChIP) followed by high throughput sequencing (ChIP-seq) generally contain either narrow peaks or broad and diffusely... 
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8. Full Text Regulation of inflammatory phenotype in macrophages by a diabetes-induced long noncoding RNA
by Reddy, Marpadga A and Chen, Zhuo and Park, Jung Tak and Wang, Mei and Lanting, Linda and Zhang, Qiang and Bhatt, Kirti and Leung, Amy and Wu, Xiwei and Putta, Sumanth and Sætrom, Pa˚l and Devaraj, Sridevi and Natarajan, Rama
Diabetes, ISSN 0012-1797, 12/2014, Volume 63, Issue 12, pp. 4249 - 4261
The mechanisms by which macrophages mediate the enhanced inflammation associated with diabetes complications are not completely understood. We used RNA... 
RESPONSES | ACTIVATION | OBESITY | HYPERGLYCEMIA | ENDOCRINOLOGY & METABOLISM | SMOOTH-MUSCLE-CELLS | FATTY-ACIDS | EXPRESSION | PROMOTES | ADIPOSE-TISSUE | REVEALS | Up-Regulation | Diabetes Mellitus, Type 2 - genetics | Humans | Middle Aged | Diabetes Mellitus, Experimental - genetics | Gene Expression Regulation | Diabetes Mellitus, Type 1 - genetics | Male | Inflammation - immunology | Monocytes - immunology | RNA, Long Noncoding - genetics | Diabetes Mellitus, Experimental - immunology | RNA, Long Noncoding - immunology | Phenotype | Animals | Diabetes Mellitus, Type 2 - immunology | Inflammation - genetics | Adult | Female | Mice | Diabetes Mellitus, Type 1 - immunology | Macrophages - immunology | Complications and side effects | RNA | Analysis | Inflammation | Research | Diabetes | Macrophages | Risk factors | Bone marrow | Glucose | Ribonucleic acid--RNA | Rodents | Genes | Complications
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9. Full Text Cell cycle regulation of human DNA repair and chromatin remodeling genes
by Mjelle, Robin and Hegre, Siv Anita and Aas, Per Arne and Slupphaug, Geir and Drabløs, Finn and Sætrom, Pål and Krokan, Hans E
DNA Repair, ISSN 1568-7864, 06/2015, Volume 30, pp. 53 - 67
Maintenance of a genome requires DNA repair integrated with chromatin remodeling. We have analyzed six transcriptome data sets and one data set on... 
DNA repair genes | Chromatin remodeling genes | Cell cycle | ICL REPAIR | DOUBLE-STRAND BREAKS | MISMATCH-REPAIR | POLYMERASE-BETA | DAMAGE RESPONSE | FAMILY-MEMBER | BASE EXCISION-REPAIR | MESSENGER-RNA | GENETICS & HEREDITY | S-PHASE | TOXICOLOGY | TUMOR-TRANSFORMING GENE | Gene Expression | Cell Cycle | Humans | DNA Repair - physiology | Chromatin Assembly and Disassembly - genetics | DNA Repair - genetics | Chromatin Assembly and Disassembly - physiology | Chromatin | Analysis | Genes | Genomics | DNA | DNA repair
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10. Full Text A two-step site and mRNA-level model for predicting microRNA targets
by Saito, Takaya and Sætrom, Pål
BMC Bioinformatics, ISSN 1471-2105, 12/2010, Volume 11, Issue 1, pp. 612 - 612
Background: Despite experiments showing that the number of microRNA ( miRNA) target sites is critical for miRNA targeting, most existing methods focus on... 
IMPACT | GENOMICS | PROTEIN | RECOGNITION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | GENE-EXPRESSION | UPDATE | ANIMAL MICRORNAS | TOOLS | CLIP | Computational Biology - methods | Algorithms | Humans | RNA, Messenger - genetics | MicroRNAs - metabolism | MicroRNAs - genetics | Models, Genetic | RNA, Messenger - metabolism | Binding Sites | Physiological aspects | Biological models | MicroRNA | Research | Genetic algorithms | Studies | Medical research | Target recognition | Genomics | Benchmarks | Genomes | Experiments
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11. Full Text Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming
by Sætrom, Pål
Bioinformatics, ISSN 1367-4803, 11/2004, Volume 20, Issue 17, pp. 3055 - 3063
Motivation: Both small interfering RNAs (siRNAs) and antisense oligonucleotides can selectively block gene expression. Although the two methods rely on... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SEQUENCE | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SIRNAS | DUPLEXES | ALGORITHMS | MODEL | SMALL INTERFERING RNAS | THERMODYNAMIC PARAMETERS | Gene Targeting - methods | RNA, Small Interfering - genetics | Algorithms | Oligonucleotides, Antisense - genetics | RNA Interference | Artificial Intelligence | Gene Silencing | Thionucleotides - genetics | Models, Genetic
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12. Full Text Optimization of duplex stability and terminal asymmetry for shRNA design
by Matveeva, Olga V and Kang, Yibin and Spiridonov, Alexey N and Sætrom, Pål and Nemtsov, Vladimir A and Ogurtsov, Aleksey Y and Nechipurenko, Yury D and Shabalina, Svetlana A
PLoS ONE, ISSN 1932-6203, 2010, Volume 5, Issue 4, p. e10180
Prediction of efficient oligonucleotides for RNA interference presents a serious challenge, especially for the development of genome-wide RNAi libraries which... 
SPECIFICITY | BIOLOGY | INTERFERENCE | PARAMETERS | RNA SECONDARY STRUCTURE | KNOCKDOWN | MAMMALIAN-CELLS | EFFICIENCY | EXPRESSION | FUNCTIONAL SIRNAS | SIRNA DESIGN | RNA, Small Interfering - chemistry | Thermodynamics | Algorithms | RNA Interference | Drug Design | Gene Silencing | Nucleic Acid Conformation | RNA Stability | Databases, Nucleic Acid | Messenger RNA | Databases | Analysis | Genomics | Genomes | Gene therapy | National libraries | Target recognition | Structural stability | Oligonucleotides | Science | Order parameters | mRNA | Structure-activity relationships | Parameter identification | Experiments | Optimization | Data bases | Design | Efficiency | Medical research | Statistical analysis | RNA-mediated interference | Antisense RNA | siRNA | Secondary structure | Gene expression | Free energy | Acids | Ribonucleic acids | Asymmetry | Computation | Computer applications | Control stability | Molecular biology | Protein structure
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13. Full Text Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms
by Sætrom, Ola and Snøve Jr, Ola and Sætrom, Pål
RNA, ISSN 1355-8382, 07/2005, Volume 11, Issue 7, pp. 995 - 1003
We present a new microRNA target prediction algorithm called TargetBoost, and show that the algorithm is stable and identifies more true targets than do... 
Boosting | Genetic programming | miRNA target prediction | Machine learning | genetic programming | boosting | BIOCHEMISTRY & MOLECULAR BIOLOGY | ANTISENSE | machine learning | MAMMALIAN-CELLS | DROSOPHILA | REGULATORY RNA | CAENORHABDITIS-ELEGANS | MESSENGER-RNA | COMPUTATIONAL IDENTIFICATION | GENES | C-ELEGANS | EXPRESSION | Caenorhabditis elegans - chemistry | Drosophila - chemistry | Genes, Helminth | Molecular Sequence Data | MicroRNAs - metabolism | Thermodynamics | Sensitivity and Specificity | Binding Sites | Drosophila - genetics | Genes, Insect | Amino Acid Sequence | Reproducibility of Results | Caenorhabditis elegans - metabolism | Caenorhabditis elegans - genetics | Artificial Intelligence | Amino Acid Motifs | Algorithms | Animals | 5' Untranslated Regions |