Background and activities

My research activity is in the translational field between computational transcriptomics, metabolomics, epigenetics and gene regulation to improve disease outcome predictions and treatment decisions for prostate cancer. This is achieved through a collaboration between BiGR and the MR Cancer Group at NTNU and Department of Urology at St. Olavs Hospital. In our research, I and my colleagues are trying to understand what separates aggressive from indolent prostate cancers at the molecular level through integration of data from various high throughput technologies.

Due to increased focus on men’s health through campaigns and public debate, it is expected that the number of men tested for prostate cancer will increase. A challenge in current prostate cancer diagnostics is the separation of prostate cancer in low, intermediate and high risk groups based on the acquired clinical data, which includes MR-images, tissue biopsies and blood-samples. Limitations in the classification system sometimes lead to undertreatment of high risk cancers. However, a more common problem is probably the tendency to overtreat low risk cancers resulting in unwanted side-effects from treatment for a large group of patients. The goal of our research is to improve the detection of high and low risk prostate cancer in clinical care, both at initial diagnosis and during active surveillance of the disease.     

We are currently developing robust classifiers for aggressive prostate cancer based on molecular data from tissue biopsies. However, our long term vision is that aggressive prostate cancer should be classified through minimally invasive blood-samples or non-invasively through MR-imaging. To achieve this we need to focus on extensive analysis of patient tissue samples using state-of-the-art technology improve our understanding on how prostate tissue characteristics, molecular signals and image features are connected. This is currently the focus of the ongoing ProstOmics project.

Current research directions:

Development and validation of a gene expression signature which can robustly separate indolent and aggressive prostate cancer from clinical patient biopsies.

Inegrating data produced in the ProstOmics project with other huge resources of publicly available data to connect molecular data with tissue and image features. The long-term goal is to improve non-invasive classification of aggressive prostate cancer

Investigating the potential of epigenetic markers for detection of aggressive prostate cancer in blood, urine and prostatic fluid.

In addition I am also involved in the Bioinformatics Core Facility and the Bioinformatics Helpdesk for Elixir Norway, where I am assisting other researchers with bioinformatics analysis, particularly involving Next Generation Sequencing (NGS) data. I am also responsible for an annual course in NGS analysis, hosted biannually by NORBIS.  

Scientific, academic and artistic work

A selection of recent journal publications, artistic productions, books, including book and report excerpts. See all publications in the database

Journal publications

  • Andersen, Maria Karoline; Krossa, Sebastian; Midtbust, Elise; Viset, Trond; Størkersen, Øystein; Giskeødegård, Guro F.; Rye, Morten Beck; Tessem, May-Britt. (2022) Multiomics spatial mapping of lipid metabolism in prostate cancer. European Urology.
  • Hansen, Ailin Falkmo; Høiem, Therese Stork; Selnæs, Kirsten Margrete; Bofin, Anna M.; Størkersen, Øystein; Bertilsson, Helena; Wright, Alan J.; Giskeødegård, Guro F.; Bathen, Tone Frost; Rye, Morten Beck; Tessem, May-Britt. (2022) Prediction of recurrence from metabolites and expression of TOP2A and EZH2 in prostate cancer patients treated with radiotherapy. NMR in Biomedicine.
  • Krossa, Sebastian; Andersen, Maria Karoline; Midtbust, Elise; Viset, Trond; Størkersen, Øystein; Giskeødegård, Guro; Rye, Morten Beck; Tessem, May-Britt. (2022) Inflammatory chemokines upregulated in the tumor microenvironment of prostate cancer patients experiencing relapse after radical prostatectomy. European Urology.
  • Andersen, Maria Karoline; Høiem, Therese Stork; Claes, Britt S.R.; Balluff, Benjamin; Marta, Martin-Lorenzo; Richardsen, Elin; Krossa, Sebastian; Bertilsson, Helena; Heeren, Ron M.A.; Rye, Morten Beck; Giskeødegård, Guro F.; Bathen, Tone Frost; Tessem, May-Britt. (2021) Spatial differentiation of metabolism in prostate cancer tissue by MALDI-TOF MSI. Cancer & Metabolism.
  • Grapotte, Mathys; Saraswat, Manu; Bessière, Chloé; Menichelli, Christophe; Ramilowski, Jordan A.; Severin, Jessica; Hayashizaki, Yoshihide; Itoh, Masayoshi; Tagami, Michihira; Murata, Mitsuyoshi; Kojima-Ishiyama, Miki; Noma, Shohei; Noguchi, Shuhei; Kasukawa, Takeya; Hasegawa, Akira; Suzuki, Harukazu; Nishiyori-Sueki, Hiromi; Frith, Martin C.; Abugessaisa, Imad; Aitken, Stuart; Aken, Bronwen L.; Alam, Intikhab; Alam, Tanvir; Alasiri, Rami; Alhendi, Ahmad M. N.; Alinejad-Rokny, Hamid; Alvarez, Mariano J.; Andersson, Robin; Arakawa, Takahiro; Araki, Marito; Arbel, Taly; Archer, John; Archibald, Alan L.; Arner, Erik; Arner, Peter; Asai, Kiyoshi; Ashoor, Haitham; Astrom, Gaby; Babina, Magda; Baillie, J. Kenneth; Bajic, Vladimir B.; Bajpai, Archana; Baker, Sarah; Baldarelli, Richard M.; Balic, Adam; Bansal, Mukesh; Batagov, Arsen O.; Batzoglou, Serafim; Beckhouse, Anthony G.; Beltrami, Antonio P.; Beltrami, Carlo A.; Bertin, Nicolas; Bhattacharya, Sharmodeep; Bickel, Peter J.; Blake, Judith A.; Blanchette, Mathieu; Bodega, Beatrice; Bonetti, Alessandro; Bono, Hidemasa; Bornholdt, Jette; Bttcher, Michael; Bougouffa, Salim; Boyd, Mette; Breda, Jeremie; Brombacher, Frank; Brown, James B.; Bult, Carol J.; Burroughs, A. Maxwell; Burt, Dave W.; Busch, Annika; Caglio, Giulia; Califano, Andrea; Cameron, Christopher J.; Cannistraci, Carlo V.; Carbone, Alessandra; Carlisle, Ailsa J.; Carninci, Piero; Carter, Kim W.; Cesselli, Daniela; Chang, Jen-Chien; Chen, Julie C.; Chen, Yun; Chierici, Marco; Christodoulou, John; Ciani, Yari; Clark, Emily L.; Coskun, Mehmet; Dalby, Maria; Dalla, Emiliano; Daub, Carsten O.; Davis, Carrie A.; de Hoon, Michiel J. L.; de Rie, Derek; Denisenko, Elena; Deplancke, Bart; Detmar, Michael; Deviatiiarov, Ruslan; Di Bernardo, Diego; Diehl, Alexander D.; Dieterich, Lothar C.; Dimont, Emmanuel; Djebali, Sarah; Dohi, Taeko; Dostie, Jose; Drabløs, Finn; Edge, Albert S. B.; Edinger, Matthias; Ehrlund, Anna; Ekwall, Karl; Elofsson, Arne; Endoh, Mitsuhiro; Enomoto, Hideki; Enomoto, Saaya; Faghihi, Mohammad; Fagiolini, Michela; Farach-Carson, Mary C.; Faulkner, Geoffrey J.; Favorov, Alexander; Fernandes, Ana Miguel; Ferrai, Carmelo; Forrest, Alistair R. R.; Forrester, Lesley M.; Forsberg, Mattias; Fort, Alexandre; Francescatto, Margherita; Freeman, Tom C.; Frith, Martin; Fukuda, Shinji; Funayama, Manabu; Furlanello, Cesare; Furuno, Masaaki; Furusawa, Chikara; Gao, Hui; Gazova, Iveta; Gebhard, Claudia; Geier, Florian; Geijtenbeek, Teunis B. H.; Ghosh, Samik; Ghosheh, Yanal; Gingeras, Thomas R.; Gojobori, Takashi; Goldberg, Tatyana; Goldowitz, Daniel; Gough, Julian; Greco, Dario; Gruber, Andreas J.; Guhl, Sven; Guigo, Roderic; Guler, Reto; Gusev, Oleg; Gustincich, Stefano; Ha, Thomas J.; Haberle, Vanja; Hale, Paul; Hallstrom, Bjrn M.; Hamada, Michiaki; Handoko, Lusy; Hara, Mitsuko; Harbers, Matthias; Harrow, Jennifer; Harshbarger, Jayson; Hase, Takeshi; Hasegawa, Akira; Hashimoto, Kosuke; Hatano, Taku; Hattori, Nobutaka; Hayashi, Ryuhei; Hayashizaki, Yoshihide; Herlyn, Meenhard; Hettne, Kristina; Heutink, Peter; Hide, Winston; Hitchens, Kelly J.; Sui, Shannon Ho; ’t Hoen, Peter A. C.; Hon, Chung Chau; Hori, Fumi; Horie, Masafumi; Horimoto, Katsuhisa; Horton, Paul; Hou, Rui; Huang, Edward; Huang, Yi; Hugues, Richard; Hume, David; Ienasescu, Hans; Iida, Kei; Ikawa, Tomokatsu; Ikemura, Toshimichi; Ikeo, Kazuho; Inoue, Norihiko; Ishizu, Yuri; Ito, Yosuke; Itoh, Masayoshi; Ivshina, Anna V.; Jankovic, Boris R.; Jenjaroenpun, Piroon; Johnson, Rory; Jorgensen, Mette; Jorjani, Hadi; Joshi, Anagha; Jurman, Giuseppe; Kaczkowski, Bogumil; Kai, Chieko; Kaida, Kaoru; Kajiyama, Kazuhiro; Kaliyaperumal, Rajaram; Kaminuma, Eli; Kanaya, Takashi; Kaneda, Hiroshi; Kapranov, Philip; Kasianov, Artem S.; Kasukawa, Takeya; Katayama, Toshiaki; Kato, Sachi; Kawaguchi, Shuji; Kawai, Jun; Kawaji, Hideya; Kawamoto, Hiroshi; Kawamura, Yuki I.; Kawasaki, Satoshi; Kawashima, Tsugumi; Kempfle, Judith S.; Kenna, Tony J.; Kere, Juha; Khachigian, Levon; Kiryu, Hisanori; Kishima, Mami; Kitajima, Hiroyuki; Kitamura, Toshio; Kitano, Hiroaki; Klaric, Enio; Klepper, Kjetil; Klinken, S. Peter; Kloppmann, Edda; Knox, Alan J.; Kodama, Yuichi; Kogo, Yasushi; Kojima, Miki; Kojima, Soichi; Komatsu, Norio; Komiyama, Hiromitsu; Kono, Tsukasa; Koseki, Haruhiko; Koyasu, Shigeo; Kratz, Anton; Kukalev, Alexander; Kulakovskiy, Ivan; Kundaje, Anshul; Kunikata, Hiroshi; Kuo, Richard; Kuo, Tony; Kuraku, Shigehiro; Kuznetsov, Vladimir A.; Kwon, Tae Jun; Larouche, Matt; Lassmann, Timo; Law, Andy; Le-Cao, Kim-Anh; Lecellier, Charles-Henri; Lee, Weonju; Lenhard, Boris; Lennartsson, Andreas; Li, Kang; Li, Ruohan; Lilje, Berit; Lipovich, Leonard; Lizio, Marina; Lopez, Gonzalo; Magi, Shigeyuki; Mak, Gloria K.; Makeev, Vsevolod; Manabe, Riichiro; Mandai, Michiko; Mar, Jessica; Maruyama, Kazuichi; Maruyama, Taeko; Mason, Elizabeth; Mathelier, Anthony; Matsuda, Hideo; Medvedeva, Yulia A.; Meehan, Terrence F.; Mejhert, Niklas; Meynert, Alison; Mikami, Norihisa; Minoda, Akiko; Miura, Hisashi; Miyagi, Yohei; Miyawaki, Atsushi; Mizuno, Yosuke; Morikawa, Hiromasa; Morimoto, Mitsuru; Morioka, Masaki; Morishita, Soji; Moro, Kazuyo; Motakis, Efthymios; Motohashi, Hozumi; Mukarram, Abdul Kadir; Mummery, Christine L.; Mungall, Christopher J.; Murakawa, Yasuhiro; Muramatsu, Masami; Murata, Mitsuyoshi; Nagasaka, Kazunori; Nagase, Takahide; Nakachi, Yutaka; Nakahara, Fumio; Nakai, Kenta; Nakamura, Kumi; Nakamura, Yasukazu; Nakamura, Yukio; Nakazawa, Toru; Nason, Guy P.; Nepal, Chirag; Nguyen, Quan Hoang; Nielsen, Lars K.; Nishida, Kohji; Nishiguchi, Koji M.; Nishiyori, Hiromi; Nitta, Kazuhiro; Noguchi, Shuhei; Noma, Shohei; Notredame, Cedric; Ogishima, Soichi; Ohkura, Naganari; Ohno, Hiroshi; Ohshima, Mitsuhiro; Ohtsu, Takashi; Okada, Yukinori; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Oksvold, Per; Orlando, Valerio; Ow, Ghim Sion; Ozturk, Mumin; Pachkov, Mikhail; Paparountas, Triantafyllos; Parihar, Suraj P.; Park, Sung-Joon; Pascarella, Giovanni; Passier, Robert; Persson, Helena; Philippens, Ingrid H.; Piazza, Silvano; Plessy, Charles; Pombo, Ana; Ponten, Fredrik; Poulain, Stéphane; Poulsen, Thomas M.; Pradhan, Swati; Prezioso, Carolina; Pridans, Clare; Qin, Xiang-Yang; Quackenbush, John; Rackham, Owen; Ramilowski, Jordan; Ravasi, Timothy; Rehli, Michael; Rennie, Sarah; Rito, Tiago; Rizzu, Patrizia; Robert, Christelle; Roos, Marco; Rost, Burkhard; Roudnicky, Filip; Roy, Riti; Rye, Morten Beck; Sachenkova, Oxana; Sætrom, Pål; Sai, Hyonmi; Saiki, Shinji; Saito, Mitsue; Saito, Akira; Sakaguchi, Shimon; Sakai, Mizuho; Sakaue, Saori; Sakaue-Sawano, Asako; Sandelin, Albin; Sano, Hiromi; Sasamoto, Yuzuru; Sato, Hiroki; Saxena, Alka; Saya, Hideyuki; Schafferhans, Andrea; Schmeier, Sebastian; Schmidl, Christian; Schmocker, Daniel; Schneider, Claudio; Schueler, Marcus; Schultes, Erik A.; Schulze-Tanzil, Gundula; Semple, Colin A.; Seno, Shigeto; Seo, Wooseok; Sese, Jun; Severin, Jessica; Sheng, Guojun; Shi, Jiantao; Shimoni, Yishai; Shin, Jay W.; SimonSanchez, Javier; Sivertsson, Asa; Sjostedt, Evelina; Soderhall, Cilla; Laurent, Georges St; Stoiber, Marcus H.; Sugiyama, Daisuke; Summers, Kim M.; Suzuki, Ana Maria; Suzuki, Harukazu; Suzuki, Kenji; Suzuki, Mikiko; Suzuki, Naoko; Suzuki, Takahiro; Swanson, Douglas J.; Swoboda, Rolf K.; Tagami, Michihira; Taguchi, Ayumi; Takahashi, Hazuki; Takahashi, Masayo; Takamochi, Kazuya; Takeda, Satoru; Takenaka, Yoichi; Tam, Kin Tung; Tanaka, Hiroshi; Tanaka, Rica; Tanaka, Yuji; Tang, Dave; Taniuchi, Ichiro; Tanzer, Andrea; Tarui, Hiroshi; Taylor, Martin S.; Terada, Aika; Terao, Yasuhisa; Testa, Alison C.; Thomas, Mark; Thongjuea, Supat; Tomii, Kentaro; Triglia, Elena Torlai; Toyoda, Hiroo; Tsang, H. Gwen; Tsujikawa, Motokazu; Uhlén, Mathias; Valen, Eivind Dale; van de Wetering, Marc; van Nimwegen, Erik; Velmeshev, Dmitry; Verardo, Roberto; Vitezic, Morana; Vitting-Seerup, Kristoffer; von Feilitzen, Kalle; Voolstra, Christian R.; Vorontsov, Ilya E.; Wahlestedt, Claes; Wasserman, Wyeth W.; Watanabe, Kazuhide; Watanabe, Shoko; Wells, Christine A.; Winteringham, Louise N.; Wolvetang, Ernst; Yabukami, Haruka; Yagi, Ken; Yamada, Takuji; Yamaguchi, Yoko; Yamamoto, Masayuki; Yamamoto, Yasutomo; Yamamoto, Yumiko; Yamanaka, Yasunari; Yano, Kojiro; Yasuzawa, Kayoko; Yatsuka, Yukiko; Yo, Masahiro; Yokokura, Shunji; Yoneda, Misako; Yoshida, Emiko; Yoshida, Yuki; Yoshihara, Masahito; Young, Rachel; Young, Robert S.; Yu, Nancy Y.; Yumoto, Noriko; Zabierowski, Susan E.; Zhang, Peter G.; Zucchelli, Silvia; Zwahlen, Martin; Chatelain, Clément; Carninci, Piero; de Hoon, Michiel J. L.; Wasserman, Wyeth W.; Bréhélin, Laurent; Lecellier, Charles-Henri. (2021) Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications. vol. 12 (1).
  • Rise, Kjersti; Tessem, May-Britt; Drabløs, Finn; Rye, Morten Beck. (2021) FunHoP: Enhanced Visualization and Analysis of Functionally Homologous Proteins in Complex Metabolic Networks. Genomics, proteomics & bioinformatics.
  • Vandsemb, Esten; Rye, Morten Beck; Steiro, Ida Johnsen; Elsaadi, Samah; Rø, Torstein Baade; Slørdahl, Tobias Schmidt; Sponaas, Anne-Marit; Børset, Magne; Abdollahi, Pegah. (2021) PRL-3 induces a positive signaling circuit between glycolysis and activation of STAT1/2. The FEBS Journal. vol. 288 (23).
  • Jalili, Mahsa; Gerdol, Marco; Greco, S.; Pallavicini, Alberto; Buonocore, Francesco; Scapigliati, Giuseppe; Picchietti, Simona; Esteban, Maria Angeles; Rye, Morten Beck; Bones, Atle M.. (2020) Differential Effects of Dietary Supplementation of Krill Meal, Soybean Meal, Butyrate, and Bactocell® on the Gene Expression of Atlantic Salmon Head Kidney. International Journal of Molecular Sciences. vol. 21 (3).
  • Rauluseviciute, Ieva; Drabløs, Finn; Rye, Morten Beck. (2020) DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation. BMC Medical Genomics. vol. 13 (1).
  • Zwiggelaar, Rosalie; Lindholm, Håvard Takle; Fosslie, Madeleine Lystad; Pedersen, Marianne Terndrup; Ohta, Yuki; Sanchez, Alberto Diez; Martin Alonso, Mara; Ostrop, Jenny; Matano, Mami; Parmar, Naveen; Kvaløy, Emilie; Spanjers, Roos; Nazmi, Kamran; Rye, Morten Beck; Drabløs, Finn; Arrowsmith, Cheryl H; Dahl, John Arne; Jensen, Kim B.; Sato, Toshiro; Oudhoff, Menno. (2020) LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium. Science Advances. vol. 6 (37).
  • Grinde, Maria Tunset; Hilmarsdòttir, Bylgja; Tunset, Hanna Maja; Henriksen, Ida Marie; Kim, Jana; Haugen, Mads Haugland; Rye, Morten Beck; Mælandsmo, Gunhild Mari; Moestue, Siver Andreas. (2019) Glutamine to proline conversion is associated with response to glutaminase inhibition in breast cancer. Breast Cancer Research. vol. 21 (1).
  • Reuluseviciute, Ieva; Drabløs, Finn; Rye, Morten Beck. (2019) DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis. Clinical Epigenetics. vol. 11:193.
  • Vardaxis, Ioannis; Drabløs, Finn; Rye, Morten Beck; Lindqvist, Bo Henry. (2019) MACPET: model-based analysis for ChIA-PET. Biostatistics.
  • Andersen, Maria Karoline; Rise, Kjersti; Giskeødegård, Guro F.; Richardsen, Elin; Bertilsson, Helena; Størkersen, Øystein; Bathen, Tone Frost; Rye, Morten Beck; Tessem, May-Britt. (2018) Integrative metabolic and transcriptomic profiling of prostate cancer tissue containing reactive stroma. Scientific Reports. vol. 8:14269.
  • Rye, Morten Beck; Bertilsson, Helena; Andersen, Maria Karoline; Rise, Kjersti; Bathen, Tone Frost; Drabløs, Finn; Tessem, May-Britt. (2018) Cholesterol synthesis pathway genes in prostate cancer are transcriptionally downregulated when tissue confounding is minimized. BMC Cancer. vol. 18 (478).
  • Søgaard, Caroline Danielsen; Moestue, Siver Andreas; Rye, Morten Beck; Kim, Jana; Nepal, Anala; Liabakk, Nina-Beate; Bachke, Siri; Bathen, Tone Frost; Otterlei, Marit; Hill, Deborah Katherine. (2018) APIM-peptide targeting PCNA improves the efficacy of docetaxel treatment in the TRAMP mouse model of prostate cancer. OncoTarget. vol. 9 (14).
  • Tekle, Kidane M; Gundersen, Sveinung; Klepper, Kjetil; Bongo, Lars Ailo; Raknes, Inge Alexander; Li, Xiaxi; Zhang, Wei; Andreetta, Christian; Mulugeta, Teshome Dagne; Kalaš, Matúš; Rye, Morten Beck; Hjerde, Erik; Antony Samy, Jeevan Karloss; Fornous, Ghislain; Azab, Abdulrahman; Våge, Dag Inge; Hovig, Eivind; Willassen, Nils Peder; Drabløs, Finn; Nygård, Ståle; Petersen, Kjell; Jonassen, Inge. (2018) Norwegian e-Infrastructure for Life Sciences (NeLS). F1000 Research. vol. 7:968.
  • Sandsmark, Elise; Andersen, Maria Karoline; Bofin, Anna M.; Bertilsson, Helena; Drabløs, Finn; Bathen, Tone Frost; Rye, Morten Beck; Tessem, May-Britt. (2017) SFRP4 gene expression is increased in aggressive prostate cancer. Scientific Reports. vol. 7.
  • Hansen, Ailin Falkmo; Sandsmark, Elise; Rye, Morten Beck; Wright, Alan J; Bertilsson, Helena; Richardsen, Elin; Viset, Trond; Bofin, Anna M.; Angelsen, Anders; Selnæs, Kirsten Margrete; Bathen, Tone Frost; Tessem, May-Britt. (2016) Presence of TMPRSS2-ERG is associated with alterations of the metabolic profile in human prostate cancer. OncoTarget.
  • Sandsmark, Elise; Hansen, Ailin Falkmo; Selnæs, Kirsten Margrete; Bertilsson, Helena; Bofin, Anna M.; Wright, Alan J.; Viset, Trond; Richardsen, Elin; Drabløs, Finn Sverre; Bathen, Tone Frost; Tessem, May-Britt; Rye, Morten Beck. (2016) A novel non-canonical Wnt signature for prostate cancer aggressiveness. OncoTarget. vol. 8 (6).