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Last Update:
September 27, 2017

Names	Position	Research area	Telephone	e-mail

Rye, Morten	Post doc.	Prostate cancer transcriptomics	72573415

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Publications

(2016) "Phosphatase of regenerating liver 3 (PRL-3) is overexpressed in human prostate cancer tissue and promotes growth and migration"
Vandsemb, E.N.; Bertilsson, H.; Abdollahi, P.; Storkersen, O.; Vatsveen, T.K.; Rye, M.B.; Ro, T.B.; Borset, M.; Slordahl, T.S.
Journal of translational medicine 14():71 view article

(2016) "A Balanced Tissue Composition Reveals New Metabolic and Gene Expression Markers in Prostate Cancer"
Tessem, M.-B.; Bertilsson, H.; Angelsen, A.; Bathen, T.F.; Drablos, F.; Rye, M.B.
PloS one 11(4):e0153727 view article

(2016) "Presence of TMPRSS2-ERG is associated with alterations of the metabolic profile in human prostate cancer"
Hansen, A.F.; Sandsmark, E.; Rye, M.B.; Wright, A.J.; Bertilsson, H.; Richardsen, E.; Viset, T.; Bofin, A.M.; Angelsen, A.; Selnaes, K.M.; Bathen, T.F.; Tessem, M.-B.
Oncotarget 7(27):42071-42085 view article

(2016) "A novel non-canonical Wnt signature for prostate cancer aggressiveness"
Sandsmark, E.; Hansen, A.F.; Selnaes, K.M.; Bertilsson, H.; Bofin, A.M.; Wright, A.J.; Viset, T.; Richardsen, E.; Drablos, F.; Bathen, T.F.; Tessem, M.-B.; Rye, M.B.
Oncotarget (): view article

(2015) "ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets"
Rydbeck, H.; Sandve, G.K.; Ferkingstad, E.; Simovski, B.; Rye, M.; Hovig, E.
PloS one 10(4):e0123261 view article

(2014) "A promoter-level mammalian expression atlas"
Forrest, A.R.R.; Kawaji, H.; Rehli, M.; Baillie, J.K.; de Hoon, M.J.L.; Haberle, V.; Lassman, T.; Kulakovskiy, I.V.; Lizio, M.; Itoh, M.; Andersson, R.; Mungall, C.J.; Meehan, T.F.; Schmeier, S.; Bertin, N.; Jorgensen, M.; Dimont, E.; Arner, E.; Schmidl, C.; Schaefer, U.; Medvedeva, Y.A.; Plessy, C.; Vitezic, M.; Severin, J.; Semple, C.A.; Ishizu, Y.; Young, R.S.; Francescatto, M.; Alam, I.; Albanese, D.; Altschuler, G.M.; Arakawa, T.; Archer, J.A.C.; Arner, P.; Babina, M.; Rennie, S.; Balwierz, P.J.; Beckhouse, A.G.; Pradhan-Bhatt, S.; Blake, J.A.; Blumenthal, A.; Bodega, B.; Bonetti, A.; Briggs, J.; Brombacher, F.; Burroughs, A.M.; Califano, A.; Cannistraci, C.V.; Carbajo, D.; Chen, Y.; Chierici, M.; Ciani, Y.; Clevers, H.C.; Dalla, E.; Davis, C.A.; Detmar, M.; Diehl, A.D.; Dohi, T.; Drablos, F.; Edge, A.S.B.; Edinger, M.; Ekwall, K.; Endoh, M.; Enomoto, H.; Fagiolini, M.; Fairbairn, L.; Fang, H.; Farach-Carson, M.C.; Faulkner, G.J.; Favorov, A.V.; Fisher, M.E.; Frith, M.C.; Fujita, R.; Fukuda, S.; Furlanello, C.; Furino, M.; Furusawa, J.-ichi; Geijtenbeek, T.B.; Gibson, A.P.; Gingeras, T.; Goldowitz, D.; Gough, J.; Guhl, S.; Guler, R.; Gustincich, S.; Ha, T.J.; Hamaguchi, M.; Hara, M.; Harbers, M.; Harshbarger, J.; Hasegawa, A.; Hasegawa, Y.; Hashimoto, T.; Herlyn, M.; Hitchens, K.J.; Ho Sui, S.J.; Hofmann, O.M.; Hoof, I.; Hori, F.; Huminiecki, L.; Iida, K.; Ikawa, T.; Jankovic, B.R.; Jia, H.; Joshi, A.; Jurman, G.; Kaczkowski, B.; Kai, C.; Kaida, K.; Kaiho, A.; Kajiyama, K.; Kanamori-Katayama, M.; Kasianov, A.S.; Kasukawa, T.; Katayama, S.; Kato, S.; Kawaguchi, S.; Kawamoto, H.; Kawamura, Y.I.; Kawashima, T.; Kempfle, J.S.; Kenna, T.J.; Kere, J.; Khachigian, L.M.; Kitamura, T.; Klinken, S.P.; Knox, A.J.; Kojima, M.; Kojima, S.; Kondo, N.; Koseki, H.; Koyasu, S.; Krampitz, S.; Kubosaki, A.; Kwon, A.T.; Laros, J.F.J.; Lee, W.; Lennartsson, A.; Li, K.; Lilje, B.; Lipovich, L.; Mackay-Sim, A.; Manabe, R.-ichiroh; Mar, J.C.; Marchand, B.; Mathelier, A.; Mejhert, N.; Meynert, A.; Mizuno, Y.; de Lima Morais, D.A.; Morikawa, H.; Morimoto, M.; Moro, K.; Motakis, E.; Motohashi, H.; Mummery, C.L.; Murata, M.; Nagao-Sato, S.; Nakachi, Y.; Nakahara, F.; Nakamura, T.; Nakamura, Y.; Nakazato, K.; van Nimwegen, E.; Ninomiya, N.; Nishiyori, H.; Noma, S.; Noma, S.; Noazaki, T.; Ogishima, S.; Ohkura, N.; Ohimiya, H.; Ohno, H.; Ohshima, M.; Okada-Hatakeyama, M.; Okazaki, Y.; Orlando, V.; Ovchinnikov, D.A.; Pain, A.; Passier, R.; Patrikakis, M.; Persson, H.; Piazza, S.; Prendergast, J.G.D.; Rackham, O.J.L.; Ramilowski, J.A.; Rashid, M.; Ravasi, T.; Rizzu, P.; Roncador, M.; Roy, S.; Rye, M.B.; Saijyo, E.; Sajantila, A.; Saka, A.; Sakaguchi, S.; Sakai, M.; Sato, H.; Savvi, S.; Saxena, A.; Schneider, C.; Schultes, E.A.; Schulze-Tanzil, G.G.; Schwegmann, A.; Sengstag, T.; Sheng, G.; Shimoji, H.; Shimoni, Y.; Shin, J.W.; Simon, C.; Sugiyama, D.; Sugiyama, T.; Suzuki, M.; Suzuki, N.; Swoboda, R.K.; 't Hoen, P.A.C.; Tagami, M.; Takahashi, N.; Takai, J.; Tanaka, H.; Tatsukawa, H.; Tatum, Z.; Thompson, M.; Toyodo, H.; Toyoda, T.; Valen, E.; van de Wetering, M.; van den Berg, L.M.; Verado, R.; Vijayan, D.; Vorontsov, I.E.; Wasserman, W.W.; Watanabe, S.; Wells, C.A.; Winteringham, L.N.; Wolvetang, E.; Wood, E.J.; Yamaguchi, Y.; Yamamoto, M.; Yoneda, M.; Yonekura, Y.; Yoshida, S.; Zabierowski, S.E.; Zhang, P.G.; Zhao, X.; Zucchelli, S.; Summers, K.M.; Suzuki, H.; Daub, C.O.; Kawai, J.; Heutink, P.; Hide, W.; Freeman, T.C.; Lenhard, B.; Bajic, V.B.; Taylor, M.S.; Makeev, V.J.; Sandelin, A.; Hume, D.A.; Carninci, P.; Hayashizaki, Y.
Nature 507(7493):462-470 view article

(2014) "Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines"
Rye, M.; Sandve, G.K.; Daub, C.O.; Kawaji, H.; Carninci, P.; Forrest, A.R.R.; Drablos, F.
BMC genomics 15():120 view article

(2014) "Gene signatures ESC, MYC and ERG-fusion are early markers of a potentially dangerous subtype of prostate cancer"
Rye, M.B.; Bertilsson, H.; Drablos, F.; Angelsen, A.; Bathen, T.F.; Tessem, M.-B.
BMC medical genomics 7():50 view article

(2013) "The Genomic HyperBrowser: an analysis web server for genome-scale data"
Sandve, G.K.; Gundersen, S.; Johansen, M.; Glad, I.K.; Gunathasan, K.; Holden, L.; Holden, M.; Liestol, K.; Nygard, S.; Nygaard, V.; Paulsen, J.; Rydbeck, H.; Trengereid, K.; Clancy, T.; Drablos, F.; Ferkingstad, E.; Kalas, M.; Lien, T.; Rye, M.B.; Frigessi, A.; Hovig, E.
Nucleic acids research 41(Web Server issue):W133-41 view article

(2013) "Identification of serum microRNA profiles in colon cancer"
Hofsli, E.; Sjursen, W.; Prestvik, W.S.; Johansen, J.; Rye, M.; Trano, G.; Wasmuth, H.H.; Hatlevoll, I.; Thommesen, L.
British journal of cancer 108(8):1712-1719 view article

(2012) "The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding"
Kornacker, K.; Rye, M.B.; Handstad, T.; Drablos, F.
BMC bioinformatics 13():176 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

(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) "The Use of Chemometrics to Analyse Protein Patterns from Gel Electrophoresis"
Faergestad, E.M.; Rye, M.B.; Nhek, S.; Hollung, K.; Grove, H.
Acta Chromatographica 23(1):1-40 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 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

(2008) "A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis"
Rye, M.B.; Faergestad, E.M.; Alsberg, B.K.
Electrophoresis 29(6):1359-1368 view article

(2008) "A multivariate spot filtering model for two-dimensional gel electrophoresis"
Rye, M.B.; Alsberg, B.K.
Electrophoresis 29(6):1369-1381 view article

(2008) "An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis"
Rye, M.B.; Faergestad, E.M.; Martens, H.; Wold, J.P.; Alsberg, B.K.
Electrophoresis 29(6):1382-1393 view article

(2007) "Pixel-based analysis of multiple images for the identification of changes: a novel approach applied to unravel proteome patterns [corrected] of 2-D electrophoresis gel images"
Faergestad, E.M.; Rye, M.; Walczak, B.; Gidskehaug, L.; Wold, J.P.; Grove, H.; Jia, X.; Hollung, K.; Indahl, U.G.; Westad, F.; van den Berg, F.; Martens, H.
Proteomics 7(19):3450-3461 view article

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