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Last Update:
September 27, 2017

Names	Position	Research area	Telephone	e-mail

Sætrom, Pål	Professor	ncRNA-based regulation	72573011

Other members

Pål Sætrom received the M.Sc. degree in Computer Science from the Norwegian University of Science and Technology (NTNU) in 2001. In 2002, he co-founded Interagon AS, Trondheim, Norway, where he worked on hardware search technologies, machine learning, and nucleic acid pattern mining. He completed his DPhil (NTNU, 2005) as a result of this work. Pål Sætrom then joined Prof. John J. Rossi's HIV therapy lab at the Beckman Research Institute of The City of Hope, Duarte, California, where he worked on algorithms for predicting microRNA genes and target sites.

Sætrom returned to NTNU in 2006 and has since then headed several research projects on ncRNA-based gene regulation. On March 2011, he was appointed full professor in bioinformatics at NTNU's Department of Computer and Information Science.

The long-term goal of Pål Sætrom's research is to develop and use computational models to predict how changes in gene regulation can control development and cause disease.

Publications

(2017) "Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation"
Landfors, M.; Johansen, J.; Aronsen, J.M.; Vagbo, C.B.; Dore, L.C.; He, C.; Sjaastad, I.; Saetrom, P.; Fedorcsak, P.; Dahl, J.A.; Aanes, H.; Fusser, M.; Klungland, A.
Cell discovery 3():17013 view article

(2015) "RNA motif discovery: a computational overview"
Achar, A.; Saetrom, P.
Biology direct 10():61 view article

(2015) "Cell cycle regulation of human DNA repair and chromatin remodeling genes"
Mjelle, R.; Hegre, S.A.; Aas, P.A.; Slupphaug, G.; Drablos, F.; Saetrom, P.; Krokan, H.E.
DNA repair 30():53-67 view article

(2015) "A novel POLE mutation associated with cancers of colon, pancreas, ovaries and small intestine"
Hansen, M.F.; Johansen, J.; Bjornevoll, I.; Sylvander, A.E.; Steinsbekk, K.S.; Saetrom, P.; Sandvik, A.K.; Drablos, F.; Sjursen, W.
Familial cancer (): view article

(2015) "AID expression in B-cell lymphomas causes accumulation of genomic uracil and a distinct AID mutational signature"
Pettersen, H.S.; Galashevskaya, A.; Doseth, B.; Sousa, M.M.L.; Sarno, A.; Visnes, T.; Aas, P.A.; Liabakk, N.-B.; Slupphaug, G.; Saetrom, P.; Kavli, B.; Krokan, H.E.
DNA repair 25():60-71 view article

(2014) "Exploiting human CD34+ stem cell-conditioned medium for tissue repair"
Mintz, P.J.; Huang, K.-W.; Reebye, V.; Nteliopoulos, G.; Lai, H.-S.; Saetrom, P.; Kasahara, N.; Jensen, S.; Pai, M.; Gordon, M.Y.A.; Marley, S.B.; Behan, R.; Spalding, D.R.; Haoudi, A.; Emara, M.M.; Nicholls, J.; Rossi, J.J.; Habib, N.A.
Molecular therapy : the journal of the American Society of Gene Therapy 22(1):149-159 view article

(2014) "Novel RNA oligonucleotide improves liver function and inhibits liver carcinogenesis in vivo"
Reebye, V.; Saetrom, P.; Mintz, P.J.; Huang, K.-W.; Swiderski, P.; Peng, L.; Liu, C.; Liu, X.; Lindkaer-Jensen, S.; Zacharoulis, D.; Kostomitsopoulos, N.; Kasahara, N.; Nicholls, J.P.; Jiao, L.R.; Pai, M.; Spalding, D.R.; Mizandari, M.; Chikovani, T.; Emara, M.M.; Haoudi, A.; Tomalia, D.A.; Rossi, J.J.; Habib, N.A.
Hepatology (Baltimore, Md.) 59(1):216-227 view article

(2014) "Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol"
Lange, L.A.; Hu, Y.; Zhang, H.; Xue, C.; Schmidt, E.M.; Tang, Z.-Z.; Bizon, C.; Lange, E.M.; Smith, J.D.; Turner, E.H.; Jun, G.; Kang, H.M.; Peloso, G.; Auer, P.; Li, K.-P.; Flannick, J.; Zhang, J.; Fuchsberger, C.; Gaulton, K.; Lindgren, C.; Locke, A.; Manning, A.; Sim, X.; Rivas, M.A.; Holmen, O.L.; Gottesman, O.; Lu, Y.; Ruderfer, D.; Stahl, E.A.; Duan, Q.; Li, Y.; Durda, P.; Jiao, S.; Isaacs, A.; Hofman, A.; Bis, J.C.; Correa, A.; Griswold, M.E.; Jakobsdottir, J.; Smith, A.V.; Schreiner, P.J.; Feitosa, M.F.; Zhang, Q.; Huffman, J.E.; Crosby, J.; Wassel, C.L.; Do, R.; Franceschini, N.; Martin, L.W.; Robinson, J.G.; Assimes, T.L.; Crosslin, D.R.; Rosenthal, E.A.; Tsai, M.; Rieder, M.J.; Farlow, D.N.; Folsom, A.R.; Lumley, T.; Fox, E.R.; Carlson, C.S.; Peters, U.; Jackson, R.D.; van Duijn, C.M.; Uitterlinden, A.G.; Levy, D.; Rotter, J.I.; Taylor, H.A.; Gudnason, V.J.; Siscovick, D.S.; Fornage, M.; Borecki, I.B.; Hayward, C.; Rudan, I.; Chen, Y.E.; Bottinger, E.P.; Loos, R.J.F.; Saetrom, P.; Hveem, K.; Boehnke, M.; Groop, L.; McCarthy, M.; Meitinger, T.; Ballantyne, C.M.; Gabriel, S.B.; O'Donnell, C.J.; Post, W.S.; North, K.E.; Reiner, A.P.; Boerwinkle, E.; Psaty, B.M.; Altshuler, D.; Kathiresan, S.; Lin, D.-Y.; Jarvik, G.P.; Cupples, L.A.; Kooperberg, C.; Wilson, J.G.; Nickerson, D.A.; Abecasis, G.R.; Rich, S.S.; Tracy, R.P.; Willer, C.J.
American journal of human genetics 94(2):233-245 view article

(2014) "Error-free versus mutagenic processing of genomic uracil--relevance to cancer"
Krokan, H.E.; Saetrom, P.; Aas, P.A.; Pettersen, H.S.; Kavli, B.; Slupphaug, G.
DNA repair 19():38-47 view article

(2014) "Circular RNAs are depleted of polymorphisms at microRNA binding sites"
Thomas, L.F.; Saetrom, P.
Bioinformatics (Oxford, England) 30(16):2243-2246 view article

(2014) "Regulation of inflammatory phenotype in macrophages by a diabetes-induced long noncoding RNA"
Reddy, M.A.; Chen, Z.; Park, J.T.; Wang, M.; Lanting, L.; Zhang, Q.; Bhatt, K.; Leung, A.; Wu, X.; Putta, S.; Saetrom, P.; Devaraj, S.; Natarajan, R.
Diabetes 63(12):4249-4261 view article

(2014) "The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences"
Razick, S.; Mocnik, R.; Thomas, L.F.; Ryeng, E.; Drablos, F.; Saetrom, P.
Database : the journal of biological databases and curation 2014():bau027 view article

(2013) "Novel long noncoding RNAs are regulated by angiotensin II in vascular smooth muscle cells"
Leung, A.; Trac, C.; Jin, W.; Lanting, L.; Akbany, A.; Saetrom, P.; Schones, D.E.; Natarajan, R.
Circulation research 113(3):266-278 view article

(2013) "MicroRNAs act complementarily to regulate disease-related mRNA modules in human diseases"
Chavali, S.; Bruhn, S.; Tiemann, K.; Saetrom, P.; Barrenas, F.; Saito, T.; Kanduri, K.; Wang, H.; Benson, M.
RNA (New York, N.Y.) 19(11):1552-1562 view article

(2013) "Designing dual-targeting siRNA duplexes having two active strands that combine siRNA and microRNA-like targeting"
Saetrom, P.
Methods in molecular biology (Clifton, N.J.) 942():169-177 view article

(2013) "Multiple microRNAs may regulate the DNA repair enzyme uracil-DNA glycosylase"
Hegre, S.A.; Saetrom, P.; Aas, P.A.; Pettersen, H.S.; Otterlei, M.; Krokan, H.E.
DNA repair 12(1):80-86 view article

(2013) "Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication"
Pena-Diaz, J.; Hegre, S.A.; Anderssen, E.; Aas, P.A.; Mjelle, R.; Gilfillan, G.D.; Lyle, R.; Drablos, F.; Krokan, H.E.; Saetrom, P.
Nucleic acids research 41(5):2846-2856 view article

(2013) "Novel Long Non-Coding RNAs Are Regulated by Angiotensin II in Vascular Smooth Muscle Cells"
Leung, A.; Trac, C.; Jin, W.; Lanting, L.; Akbany, A.; Saetrom, P.; Schones, D.E.; Natarajan, R.
Circulation research (): view article

(2013) "A Short-activating RNA Oligonucleotide Targeting the Islet beta-cell Transcriptional Factor MafA in CD34(+) Cells"
Reebye, V.; Saetrom, P.; Mintz, P.J.; Rossi, J.J.; Kasahara, N.; Nteliopoulos, G.; Nicholls, J.; Haoudi, A.; Gordon, M.; Habib, N.A.
Molecular therapy. Nucleic acids 2():e97 view article

(2012) "Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation"
Thomas, L.F.; Saetrom, P.
PLoS computational biology 8(8):e1002621 view article

(2012) "Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments"
Saito, T.; Saetrom, P.
Silence 3():3 view article

(2012) "Cell-type specificity of ChIP-predicted transcription factor binding sites"
Handstad, T.; Rye, M.; Mocnik, R.; Drablos, F.; Saetrom, P.
BMC genomics 13():372 view article

(2012) "MicroRNA-181a* Targets Nanog in a Subpopulation of CD34(+) Cells Isolated From Peripheral Blood"
Mintz, P.J.; Saetrom, P.; Reebye, V.; Lundbaek, M.B.; Lao, K.; Rossi, J.J.; Gaensler, K.M.; Kasahara, N.; Nicholls, J.P.; Jensen, S.; Haoudi, A.; Emara, M.M.; Gordon, M.Y.; Habib, N.A.
Molecular therapy. Nucleic acids 1():e34 view article

(2012) "Gene Expression Profile Changes After Short-activating RNA-mediated Induction of Endogenous Pluripotency Factors in Human Mesenchymal Stem Cells"
Voutila, J.; Saetrom, P.; Mintz, P.; Sun, G.; Alluin, J.; Rossi, J.J.; Habib, N.A.; Kasahara, N.
Molecular therapy. Nucleic acids 1():e35 view article

(2011) "Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements"
Rye, M.; Saetrom, P.; Handstad, T.; Drablos, F.
BMC biology 9():80 view article

(2011) "Unconventional RNA interference - recent approaches to robust RNAi"
Lundbaek, M.; Saetrom, P.
European Pharmaceutical Review (5): view article

(2011) "Inferring causative variants in microRNA target sites"
Thomas, L.F.; Saito, T.; Saetrom, P.
Nucleic acids research 39(16):e109 view article

(2011) "A ChIP-Seq Benchmark Shows That Sequence Conservation Mainly Improves Detection of Strong Transcription Factor Binding Sites"
Handstad, T.; Rye, M.B.; Drablos, F.; Saetrom, P.
PloS one 6(4):e18430 view article tool

(2010) "A two-step site and mRNA-level model for predicting microRNA targets"
Saito, T.; Saetrom, P.
BMC bioinformatics 11():612 view article

(2010) "Rational design of micro-RNA-like bifunctional siRNAs targeting HIV and the HIV coreceptor CCR5"
Ehsani, A.; Saetrom, P.; Zhang, J.; Alluin, J.; Li, H.; Snove, O.J.; Aagaard, L.; Rossi, J.J.
Molecular therapy : the journal of the American Society of Gene Therapy 18(4):796-802 view article

(2010) "MicroRNAs--targeting and target prediction"
Saito, T.; Saetrom, P.
New biotechnology 27(3):243-249 view article

(2010) "Dual-targeting siRNAs"
Tiemann, K.; Hohn, B.; Ehsani, A.; Forman, S.J.; Rossi, J.J.; Saetrom, P.
RNA (New York, N.Y.) 16(6):1275-1284 view article

(2010) "Optimization of duplex stability and terminal asymmetry for shRNA design"
Matveeva, O.V.; Kang, Y.; Spiridonov, A.N.; Saetrom, P.; Nemtsov, V.A.; Ogurtsov, A.Y.; Nechipurenko, Y.D.; Shabalina, S.A.
PloS one 5(4):e10180 view article

(2010) "A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs"
Rye M.B.; Saetrom P.; Drablos F.
Nucleic acids research (): view article tool

(2010) "Rational Design of Micro-RNA-like Bifunctional siRNAs Targeting HIV and the HIV Coreceptor CCR5"
Ehsani, A.; Saetrom, P.; Zhang, J.; Alluin, J.; Li, H.; Snove Jr, O.; Aagaard, L.; Rossi, J.J.
Molecular therapy : the journal of the American Society of Gene Therapy 8(4):796-802 view article

(2009) "miRNA and viral infections in vertebrates"
Saetrom, P.; Klein, J.
European Pharmaceutical Review (1):10-15 view article tool

(2009) "Animal MicroRNA gene prediction"
Snove Jr, O.; Saetrom, P.
Regulation of Gene Expression by Small RNAs ():21-44 view article

(2009) "A risk variant in an miR-125b binding site in BMPR1B is associated with breast cancer pathogenesis"
Saetrom, P.; Biesinger, J.; Li, S.M.; Smith, D.; Thomas, L.F.; Majzoub, K.; Rivas, G.E.; Alluin, J.; Rossi, J.J.; Krontiris, T.G.; Weitzel, J.; Daly, M.B.; Benson, A.B.; Kirkwood, J.M.; O'Dwyer, P.J.; Sutphen, R.; Stewart, J.A.; Johnson, D.; Larson, G.P.
Cancer research 69(18):7459-7465 view article

(2008) "miR-302b maintains "stemness" of human embryonal carcinoma cells by post-transcriptional regulation of Cyclin D2 expression"
Lee, N.S.; Kim, J.S.; Cho, W.J.; Lee, M.R.; Steiner, R.; Gompers, A.; Ling, D.; Zhang, J.; Strom, P.; Behlke, M.; Moon, S.-H.; Salvaterra, P.M.; Jove, R.; Kim, K.-S.
Biochemical and biophysical research communications 377(2):434-440 view article

(2008) "Engineering and optimization of the miR-106b cluster for ectopic expression of multiplexed anti-HIV RNAs"
Aagaard, L.; Zhang, J.; von Eije, K.J.; Li, H; Saetrom, P.; Amarzguioui, M; Rossi, J.J.
Gene therapy 15(23):1536-1549 view article

(2008) "A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs"
Soifer, H.S.; Sano, M.; Sakurai, K.; Chomchan, P.; Saetrom, P.; Sherman, M.A.; Collingwood, M.A.; Behlke, M.A.; Rossi, J.J.
Nucleic acids research 36(20):6511-6522 view article

(2008) "MicroRNA-directed transcriptional gene silencing in mammalian cells"
Kim, D.H.; Saetrom, P.; Snove, O.J.; Rossi, J.J.
Proceedings of the National Academy of Sciences of the United States of America 105(42):16230-16235 view article

(2008) "Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation"
Smith, D.D.; Saetrom, P.; Snove, O.J.; Lundberg, C.; Rivas, G.E.; Glackin, C.; Larson, G.P.
BMC bioinformatics 9():63 view article

(2007) "Motif kernel generated by genetic programming improves remote homology and fold detection"
Handstad, T.; Hestnes, A.J.H.; Saetrom, P.
BMC bioinformatics 8():23 view article

(2007) "Comparison of approaches for rational siRNA design leading to a new efficient and transparent method"
Matveeva, O.; Nechipurenko, Y.; Rossi, L.; Moore, B.; Saetrom, P.; Ogurtsov, A.Y.; Atkins, J.F.; Shabalina, S.A.
Nucleic acids research 35(8):e63 view article

(2007) "Robust Machine Learning Algorithms Predict MicroRNA Genes and Targets"
Saetrom, P.; Snove, O.J.
Methods Enzymol 427c():25-49 view article

(2007) "Reliable prediction of Drosha processing sites improves microRNA gene prediction"
Helvik, S.A.; Snove, O.J.; Saetrom, P.
Bioinformatics (Oxford, England) 23(2):142-149 view article tool

(2007) "Distance constraints between microRNA target sites dictate efficacy and cooperativity"
Saetrom, P.; Heale, B.S.E.; Snove, O.J.; Aagaard, L.; Alluin, J.; Rossi, J.J.
Nucleic acids research 35(7):2333-2342 view article

(2007) "Epigenetics and microRNAs"
Saetrom, P.; Snove, O.J.; Rossi, J.J.
Pediatric research 61(5 Pt 2):17r-23r view article

(2007) "MicroRNAs in Disease and Potential Therapeutic Applications"
Soifer, HS.; Rossi, JJ.; Saetrom, P.
Molecular Therapy 15(12):2070-2079 view article

(2006) "[Nobel Prize for RNA interference]"
Snove, O.J.; Saetrom, P.
Tidsskrift for den Norske laegeforening 126(24):3252 view article

(2006) "Conserved microRNA characteristics in mammals"
Saetrom, P.; Snove, O.; Nedland, M.; Grunfeld, T.B.; Lin, Y.; Bass, M.B.; Canon, J.R.
Oligonucleotides 16(2):115-144 view article

(2005) "Evolutionary rule mining in time series databases"
Hetland, M.L.; Saetrom, P.
Machine Learning 58(2-3):107-125 view article

(2005) "Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming"
Saetrom, P.; Sneve, R.; Kristiansen, K.I.; Snove, O.J.; Grunfeld, T.; Rognes, T.; Seeberg, E.
Nucleic acids research 33(10):3263-3270 view article

(2005) "Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms"
Saetrom, O.; Snove, O.J.; Saetrom, P.
RNA (New York, N.Y.) 11(7):995-1003 view article tool

(2004) "A recursive MISD architecture for pattern matching"
Halaas, A.; Svingen, B.; Nedland, M.; Saetrom, P.; Snove, O.; Birkeland, O.R.
Ieee Transactions On Very Large Scale Integration (Vlsi) Systems 12(7):727-734 view article

(2004) "Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming"
Saetrom, P.
Bioinformatics (Oxford, England) 20(17):3055-3063 view article

(2004) "A comparison of siRNA efficacy predictors"
Saetrom, P.; Snove, O.J.
Biochemical and biophysical research communications 321(1):247-253 view article

(2004) "Designing effective siRNAs with off-target control"
Snove, O.J.; Nedland, M.; Fjeldstad, S.H.; Humberset, H.; Birkeland, O.R.; Grunfeld, T.; Saetrom, P.
Biochemical and biophysical research communications 325(3):769-773 view article tool

Bioinformatics & Gene Regulation
Department of Cancer Research and Molecular Medicine
Norwegian University of Science and Technology
Trondheim, Norway