Morten Beck Rye
+4773598591
+4772573415
Laboratoriesenteret, 5.etg øst, Øya, Erling Skjalgssons g 1
About
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.
Publications
2022
-
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.
Abstract
-
Emdal, Elisabeth Fritzke;
Ottestad, Anine Larsen;
Vågbø, Cathrine Broberg;
Skarpeteig, Veronica;
Rye, Morten Beck.
(2022)
Prøv deg som en DNA-detektiv.
Forskningstorget 2022
[Kunstnerisk og museal presentasjon] . NTNU Vitenskapsmuseet; Kalvskinnet, Trondheim. 2022-09-22 - 2022-09-23.
Other presentation
-
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.
(2022)
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7).
Nature Communications.
volum 13 (1).
Errata
-
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.
Academic article
-
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.
Abstract
-
Misund, Kristine;
Hofste op Bruinink, Davine;
Coward, Eivind;
Hoogenboezem, Remco M.;
Rustad, Even Holth;
Sanders, Mathijs A.;
Rye, Morten Beck;
Sponaas, Anne-Marit;
van der Holt, Bronno;
Zweegman, Sonja;
Hovig, Eivind;
Meza, Leonardo Zepeda;
Sundan, Anders;
Myklebost, Ola;
Sonneveld, Pieter;
Waage, Anders.
(2022)
Clonal evolution after treatment pressure in multiple myeloma: heterogenous genomic aberrations and transcriptomic convergence.
Leukemia.
volum 36 (7).
Academic article
-
Pedersen, Christine Aaserød;
Cao, Maria Dung;
Fleischer, Thomas;
Rye, Morten Beck;
Knappskog, Stian;
Eikesdal, Hans Petter;
Lønning, Per Eystein;
Tost, Jörg;
Kristensen, Vessela N.;
Tessem, May-Britt;
Giskeødegård, Guro F.;
Bathen, Tone Frost.
(2022)
DNA methylation changes in response to neoadjuvant chemotherapy are associated with breast cancer survival.
Breast Cancer Research.
volum 24:43 (1).
Academic article
-
Rise, Kjersti;
Tessem, May-Britt;
Drabløs, Finn;
Rye, Morten Beck.
(2022)
FunHoP analysis reveals upregulation of mitochondrial genes in prostate cancer.
PLOS ONE.
volum 17 (10).
Academic article
-
Rye, Morten Beck;
Krossa, Sebastian;
Hall, Martina;
van Mourik, Casper;
Bathen, Tone Frost;
Drabløs, Finn;
Tessem, May-Britt;
Bertilsson, Helena.
(2022)
The genes controlling normal function of citrate and spermine secretion are lost in aggressive prostate cancer and prostate model systems.
iScience.
volum 25 (6).
Academic article
2021
-
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.
Academic article
-
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.
Academic article
-
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.
volum 288 (23).
Academic article
2020
-
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.
volum 21 (3).
Academic article
-
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.
volum 13 (1).
Academic article
-
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.
(2020)
LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium.
Science Advances.
volum 6 (37).
Academic article
2019
-
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.
volum 21 (1).
Academic article
-
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.
volum 11:193.
Academic literature review
-
Vardaxis, Ioannis;
Drabløs, Finn;
Rye, Morten Beck;
Lindqvist, Bo Henry.
(2019)
MACPET: model-based analysis for ChIA-PET.
Biostatistics.
Academic article
2018
-
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.
volum 8:14269.
Academic article
-
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.
volum 18 (478).
Academic article
-
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.
volum 9 (14).
Academic article
-
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.
(2018)
Norwegian e-Infrastructure for Life Sciences (NeLS).
F1000 Research.
volum 7:968.
Academic article
2017
-
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.
volum 7.
Academic article
2016
-
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.
Academic article
-
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.
volum 8 (6).
Academic article
-
Tessem, May-Britt;
Bertilsson, Helena;
Angelsen, Anders;
Bathen, Tone Frost;
Drabløs, Finn Sverre;
Rye, Morten Beck.
(2016)
A balanced tissue composition reveals new metabolic and gene expression markers in prostate cancer.
PLOS ONE.
volum 11 (4).
Academic article
-
Vandsemb, Esten Nymoen;
Bertilsson, Helena;
Abdollahi, Pegah;
Størkersen, Øystein;
Våtsveen, Thea Kristin;
Rye, Morten Beck;
Rø, Torstein Baade;
Børset, Magne;
Slørdahl, Tobias Schmidt.
(2016)
Phosphatase of regenerating liver 3 (PRL-3) is overexpressed in human prostate cancer tissue and promotes growth and migration.
Journal of Translational Medicine.
volum 14 (71).
Academic article
2015
-
Rydbeck, Halfdan;
Sandve, Geir Kjetil F.;
Ferkingstad, Egil;
Simovski, Boris;
Rye, Morten Beck;
Hovig, Johannes Eivind.
(2015)
ClusTrack: Feature extraction and similarity measures for clustering of genome-wide data sets.
PLOS ONE.
volum 10 (4).
Academic article
-
Hurst, Laurence D.;
Ghanbarian, Avazeh T.;
Forrest, Alistair R.R.;
Huminiecki, Lukasz;
Haberle, Vanja;
Drabløs, Finn Sverre;
Rye, Morten Beck.
(2015)
The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome.
PLoS Biology.
volum 13:e1002315 (12).
Academic article
2014
-
Forest, Alistair R.R.;
Kawaji, Hideya;
Rehli, Michael;
Baillie, John Kenneth;
de Hoon, Michiel;
Haberle, Vanja;
Lassmann, Timo;
Kulakovskiy, Ivan;
Lizio, Marina;
Itoh, Masayoshi;
Andersson, Robin;
Mungall, Christopher;
Meehan, Terrence;
Schmeier, Sebastian;
Bertin, Nicolas;
Jørgensen, Mette Kristine;
Dimont, Emmanuel;
Arner, Erik;
Schmidl, Christian.
(2014)
A promoter-level mammalian expression atlas.
Nature.
volum 507 (7493).
Academic article
-
Rye, Morten Beck;
Bertilsson, Helena;
Drabløs, Finn;
Angelsen, Anders;
Bathen, Tone Frost;
Tessem, May-Britt.
(2014)
Gene signatures ESC, MYC and ERG-fusion are early markers of a potentially dangerous subtype of prostate cancer.
BMC Medical Genomics.
volum 7 (50).
Academic article
-
Rye, Morten Beck;
Sandve, Geir Kjetil F.;
Daub, Carsten O;
Kawaji, H;
Carninci, P;
Forrest, A;
Drabløs, Finn.
(2014)
Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines.
BMC Genomics.
volum 15 (1).
Academic article
-
Tessem, May-Britt;
Rye, Morten Beck.
(2014)
Early markers of a potentially dangerous type of prostate cancer.
Website (informational material)
2013
-
Sandve, Geir Kjetil;
Gundersen, Sveinung;
Johansen, Morten;
Glad, Ingrid Kristine;
Gunathasan, Krishanthi;
Holden, Lars;
Holden, Marit;
Liestøl, Knut;
Nygård, Ståle;
Nygaard, Vegard;
Paulsen, Jonas;
Rydbeck, Halfdan;
Trengereid, Kai;
Clancy, Trevor;
Drabløs, Finn;
Ferkingstad, Egil;
Kalaš, Matúš;
Lien, Tonje Gulbrandsen;
Rye, Morten Beck.
(2013)
The Genomic HyperBrowser: an analysis web server for genome-scale data.
Nucleic Acids Research (NAR).
volum 41 (W1).
Academic article
-
Hofsli, Eva;
Sjursen, Wenche;
Prestvik, Wenche S;
Johansen, Jostein;
Rye, Morten Beck;
Tranø, Gerd;
Wasmuth, Hans;
Hatlevoll, Ingunn;
Thommesen, Liv.
(2013)
Identification of serum microRNA profiles in colon cancer.
British Journal of Cancer.
volum 108 (8).
Academic article
2012
-
Håndstad, Tony;
Rye, Morten Beck;
Mocnik, Rok;
Drabløs, Finn;
Sætrom, Pål.
(2012)
Cell-type specificity of ChIP-predicted transcription factor binding sites.
BMC Genomics.
volum 13.
Academic article
-
Kornacker, K;
Rye, Morten Beck;
Håndstad, Tony;
Drabløs, Finn.
(2012)
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.
BMC Bioinformatics.
volum 13.
Academic article
-
Rye, Morten Beck;
Færgestad, Ellen Mosleth.
(2012)
Preprocessing of electrophoretic images in 2-DE analysis.
Chemometrics and Intelligent Laboratory Systems.
volum 117 (August).
Academic article
2011
-
Færgestad, Ellen Mosleth;
Rye, Morten Beck;
Nhek, Sarin;
Hollung, Kristin;
Grove, Harald.
(2011)
The Use of Chemometrics to Analyse Protein Patterns from Gel Electrophoresis.
Acta Chromatographica.
volum 23 (1).
Academic literature review
-
Håndstad, Tony;
Rye, Morten Beck;
Drabløs, Finn;
Sætrom, Pål.
(2011)
A ChIP-Seq Benchmark Shows That Sequence Conservation Mainly Improves Detection of Strong Transcription Factor Binding Sites.
PLOS ONE.
volum 6 (4).
Academic article
-
Rye, Morten Beck;
Sætrom, Pål;
Drabløs, Finn.
(2011)
A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs.
Nucleic Acids Research (NAR).
volum 39 (4).
Academic article
-
Rye, Morten Beck;
Sætrom, Pål;
Håndstad, Tony;
Drabløs, Finn.
(2011)
Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.
BMC Biology.
volum 9.
Academic article
-
Sun, Cheng;
Fiksdal, Liv;
Hanssen-Bauer, Audun;
Rye, Morten Beck;
Leiknes, TorOve.
(2011)
Characterization of membrane biofouling at different operating conditions (flux) in drinking water treatment using confocal laser scanning microscopy (CLSM) and image analysis.
Journal of Membrane Science.
volum 382 (1-2).
Academic article
2008
-
Rye, Morten Beck;
Færgestad, Ellen Mosleth;
Martens, Harald;
Wold, Jens-Petter;
Alsberg, Bjørn Kåre.
(2008)
An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis.
Electrophoresis.
volum 29 (6).
Academic article
-
Rye, Morten Beck;
Alsberg, Bjørn Kåre.
(2008)
A multivariate spot filtering model for two-dimensional gel electrophoresis.
Electrophoresis.
volum 29 (6).
Academic article
-
Rye, Morten Beck;
Feargestad, EM;
Martens, H;
Wold, JP;
Alsberg, Bjørn Kåre.
(2008)
An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis.
Electrophoresis.
volum 29.
Academic article
-
Rye, Morten Beck;
Mosleth, Ellen Færgestad;
Alsberg, Bjørn Kåre.
(2008)
A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis.
Electrophoresis.
volum 29.
Academic article
2007
-
Mosleth, Ellen Færgestad;
Rye, Morten Beck;
Walczak, Beata;
Gidskehaug, Lars;
Wold, Jens Petter;
Grove, Harald;
Jia, X;
Hollung, Kristin;
Indahl, Ulf;
Westad, Frank;
Van Der Berg, Franz;
Martens, Harald Aagaard.
(2007)
Pixel-based analysis of multiple images for the identification of changes: A novel approach applied to unravel proteome patters of 2-D electrophoresis gel images.
Proteomics.
volum 7.
Academic article
-
Rye, Morten Beck.
(2007)
Image segmentation and multivariate analysis in two-dimensional gel electrophoresis.
2007. Doktoravhandlinger ved NTNU (200).
Doctoral dissertation
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.
Abstract
-
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.
(2022)
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7).
Nature Communications.
volum 13 (1).
Errata
-
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.
Academic article
-
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.
Abstract
-
Misund, Kristine;
Hofste op Bruinink, Davine;
Coward, Eivind;
Hoogenboezem, Remco M.;
Rustad, Even Holth;
Sanders, Mathijs A.;
Rye, Morten Beck;
Sponaas, Anne-Marit;
van der Holt, Bronno;
Zweegman, Sonja;
Hovig, Eivind;
Meza, Leonardo Zepeda;
Sundan, Anders;
Myklebost, Ola;
Sonneveld, Pieter;
Waage, Anders.
(2022)
Clonal evolution after treatment pressure in multiple myeloma: heterogenous genomic aberrations and transcriptomic convergence.
Leukemia.
volum 36 (7).
Academic article
-
Pedersen, Christine Aaserød;
Cao, Maria Dung;
Fleischer, Thomas;
Rye, Morten Beck;
Knappskog, Stian;
Eikesdal, Hans Petter;
Lønning, Per Eystein;
Tost, Jörg;
Kristensen, Vessela N.;
Tessem, May-Britt;
Giskeødegård, Guro F.;
Bathen, Tone Frost.
(2022)
DNA methylation changes in response to neoadjuvant chemotherapy are associated with breast cancer survival.
Breast Cancer Research.
volum 24:43 (1).
Academic article
-
Rise, Kjersti;
Tessem, May-Britt;
Drabløs, Finn;
Rye, Morten Beck.
(2022)
FunHoP analysis reveals upregulation of mitochondrial genes in prostate cancer.
PLOS ONE.
volum 17 (10).
Academic article
-
Rye, Morten Beck;
Krossa, Sebastian;
Hall, Martina;
van Mourik, Casper;
Bathen, Tone Frost;
Drabløs, Finn;
Tessem, May-Britt;
Bertilsson, Helena.
(2022)
The genes controlling normal function of citrate and spermine secretion are lost in aggressive prostate cancer and prostate model systems.
iScience.
volum 25 (6).
Academic article
-
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.
Academic article
-
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.
Academic article
-
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.
volum 288 (23).
Academic article
-
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.
volum 21 (3).
Academic article
-
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.
volum 13 (1).
Academic article
-
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.
(2020)
LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium.
Science Advances.
volum 6 (37).
Academic article
-
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.
volum 21 (1).
Academic article
-
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.
volum 11:193.
Academic literature review
-
Vardaxis, Ioannis;
Drabløs, Finn;
Rye, Morten Beck;
Lindqvist, Bo Henry.
(2019)
MACPET: model-based analysis for ChIA-PET.
Biostatistics.
Academic article
-
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.
volum 8:14269.
Academic article
-
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.
volum 18 (478).
Academic article
-
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.
volum 9 (14).
Academic article
-
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.
(2018)
Norwegian e-Infrastructure for Life Sciences (NeLS).
F1000 Research.
volum 7:968.
Academic article
-
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.
volum 7.
Academic article
-
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.
Academic article
-
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.
volum 8 (6).
Academic article
-
Tessem, May-Britt;
Bertilsson, Helena;
Angelsen, Anders;
Bathen, Tone Frost;
Drabløs, Finn Sverre;
Rye, Morten Beck.
(2016)
A balanced tissue composition reveals new metabolic and gene expression markers in prostate cancer.
PLOS ONE.
volum 11 (4).
Academic article
-
Vandsemb, Esten Nymoen;
Bertilsson, Helena;
Abdollahi, Pegah;
Størkersen, Øystein;
Våtsveen, Thea Kristin;
Rye, Morten Beck;
Rø, Torstein Baade;
Børset, Magne;
Slørdahl, Tobias Schmidt.
(2016)
Phosphatase of regenerating liver 3 (PRL-3) is overexpressed in human prostate cancer tissue and promotes growth and migration.
Journal of Translational Medicine.
volum 14 (71).
Academic article
-
Rydbeck, Halfdan;
Sandve, Geir Kjetil F.;
Ferkingstad, Egil;
Simovski, Boris;
Rye, Morten Beck;
Hovig, Johannes Eivind.
(2015)
ClusTrack: Feature extraction and similarity measures for clustering of genome-wide data sets.
PLOS ONE.
volum 10 (4).
Academic article
-
Hurst, Laurence D.;
Ghanbarian, Avazeh T.;
Forrest, Alistair R.R.;
Huminiecki, Lukasz;
Haberle, Vanja;
Drabløs, Finn Sverre;
Rye, Morten Beck.
(2015)
The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome.
PLoS Biology.
volum 13:e1002315 (12).
Academic article
-
Forest, Alistair R.R.;
Kawaji, Hideya;
Rehli, Michael;
Baillie, John Kenneth;
de Hoon, Michiel;
Haberle, Vanja;
Lassmann, Timo;
Kulakovskiy, Ivan;
Lizio, Marina;
Itoh, Masayoshi;
Andersson, Robin;
Mungall, Christopher;
Meehan, Terrence;
Schmeier, Sebastian;
Bertin, Nicolas;
Jørgensen, Mette Kristine;
Dimont, Emmanuel;
Arner, Erik;
Schmidl, Christian.
(2014)
A promoter-level mammalian expression atlas.
Nature.
volum 507 (7493).
Academic article
-
Rye, Morten Beck;
Bertilsson, Helena;
Drabløs, Finn;
Angelsen, Anders;
Bathen, Tone Frost;
Tessem, May-Britt.
(2014)
Gene signatures ESC, MYC and ERG-fusion are early markers of a potentially dangerous subtype of prostate cancer.
BMC Medical Genomics.
volum 7 (50).
Academic article
-
Rye, Morten Beck;
Sandve, Geir Kjetil F.;
Daub, Carsten O;
Kawaji, H;
Carninci, P;
Forrest, A;
Drabløs, Finn.
(2014)
Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines.
BMC Genomics.
volum 15 (1).
Academic article
-
Sandve, Geir Kjetil;
Gundersen, Sveinung;
Johansen, Morten;
Glad, Ingrid Kristine;
Gunathasan, Krishanthi;
Holden, Lars;
Holden, Marit;
Liestøl, Knut;
Nygård, Ståle;
Nygaard, Vegard;
Paulsen, Jonas;
Rydbeck, Halfdan;
Trengereid, Kai;
Clancy, Trevor;
Drabløs, Finn;
Ferkingstad, Egil;
Kalaš, Matúš;
Lien, Tonje Gulbrandsen;
Rye, Morten Beck.
(2013)
The Genomic HyperBrowser: an analysis web server for genome-scale data.
Nucleic Acids Research (NAR).
volum 41 (W1).
Academic article
-
Hofsli, Eva;
Sjursen, Wenche;
Prestvik, Wenche S;
Johansen, Jostein;
Rye, Morten Beck;
Tranø, Gerd;
Wasmuth, Hans;
Hatlevoll, Ingunn;
Thommesen, Liv.
(2013)
Identification of serum microRNA profiles in colon cancer.
British Journal of Cancer.
volum 108 (8).
Academic article
-
Håndstad, Tony;
Rye, Morten Beck;
Mocnik, Rok;
Drabløs, Finn;
Sætrom, Pål.
(2012)
Cell-type specificity of ChIP-predicted transcription factor binding sites.
BMC Genomics.
volum 13.
Academic article
-
Kornacker, K;
Rye, Morten Beck;
Håndstad, Tony;
Drabløs, Finn.
(2012)
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.
BMC Bioinformatics.
volum 13.
Academic article
-
Rye, Morten Beck;
Færgestad, Ellen Mosleth.
(2012)
Preprocessing of electrophoretic images in 2-DE analysis.
Chemometrics and Intelligent Laboratory Systems.
volum 117 (August).
Academic article
-
Færgestad, Ellen Mosleth;
Rye, Morten Beck;
Nhek, Sarin;
Hollung, Kristin;
Grove, Harald.
(2011)
The Use of Chemometrics to Analyse Protein Patterns from Gel Electrophoresis.
Acta Chromatographica.
volum 23 (1).
Academic literature review
-
Håndstad, Tony;
Rye, Morten Beck;
Drabløs, Finn;
Sætrom, Pål.
(2011)
A ChIP-Seq Benchmark Shows That Sequence Conservation Mainly Improves Detection of Strong Transcription Factor Binding Sites.
PLOS ONE.
volum 6 (4).
Academic article
-
Rye, Morten Beck;
Sætrom, Pål;
Drabløs, Finn.
(2011)
A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs.
Nucleic Acids Research (NAR).
volum 39 (4).
Academic article
-
Rye, Morten Beck;
Sætrom, Pål;
Håndstad, Tony;
Drabløs, Finn.
(2011)
Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.
BMC Biology.
volum 9.
Academic article
-
Sun, Cheng;
Fiksdal, Liv;
Hanssen-Bauer, Audun;
Rye, Morten Beck;
Leiknes, TorOve.
(2011)
Characterization of membrane biofouling at different operating conditions (flux) in drinking water treatment using confocal laser scanning microscopy (CLSM) and image analysis.
Journal of Membrane Science.
volum 382 (1-2).
Academic article
-
Rye, Morten Beck;
Færgestad, Ellen Mosleth;
Martens, Harald;
Wold, Jens-Petter;
Alsberg, Bjørn Kåre.
(2008)
An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis.
Electrophoresis.
volum 29 (6).
Academic article
-
Rye, Morten Beck;
Alsberg, Bjørn Kåre.
(2008)
A multivariate spot filtering model for two-dimensional gel electrophoresis.
Electrophoresis.
volum 29 (6).
Academic article
-
Rye, Morten Beck;
Feargestad, EM;
Martens, H;
Wold, JP;
Alsberg, Bjørn Kåre.
(2008)
An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis.
Electrophoresis.
volum 29.
Academic article
-
Rye, Morten Beck;
Mosleth, Ellen Færgestad;
Alsberg, Bjørn Kåre.
(2008)
A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis.
Electrophoresis.
volum 29.
Academic article
-
Mosleth, Ellen Færgestad;
Rye, Morten Beck;
Walczak, Beata;
Gidskehaug, Lars;
Wold, Jens Petter;
Grove, Harald;
Jia, X;
Hollung, Kristin;
Indahl, Ulf;
Westad, Frank;
Van Der Berg, Franz;
Martens, Harald Aagaard.
(2007)
Pixel-based analysis of multiple images for the identification of changes: A novel approach applied to unravel proteome patters of 2-D electrophoresis gel images.
Proteomics.
volum 7.
Academic article
Report
-
Rye, Morten Beck.
(2007)
Image segmentation and multivariate analysis in two-dimensional gel electrophoresis.
2007. Doktoravhandlinger ved NTNU (200).
Doctoral dissertation
UTSTILLING
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Emdal, Elisabeth Fritzke;
Ottestad, Anine Larsen;
Vågbø, Cathrine Broberg;
Skarpeteig, Veronica;
Rye, Morten Beck.
(2022)
Prøv deg som en DNA-detektiv.
Forskningstorget 2022
[Kunstnerisk og museal presentasjon] . NTNU Vitenskapsmuseet; Kalvskinnet, Trondheim. 2022-09-22 - 2022-09-23.
Other presentation
INFORMASJONSMATR
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Tessem, May-Britt;
Rye, Morten Beck.
(2014)
Early markers of a potentially dangerous type of prostate cancer.
Website (informational material)
Teaching
Courses
- MOL3022 - Bioinformatics - Method Oriented Project
- MOL3000 - Introduction to Molecular Medicine
- MOL3021 - Bioinformatics - Applied Project
- MOL8001 - Molecular Physiology: Mechanisms and Methods
- MOL3100 - Introduction to Molecular Medicine with Project
- MOL8008 - Bioinformatics Methods for next Generation Sequencing Analysis
Media
2023
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Academic lectureAndersen, Maria Karoline; Midtbust, Elise; Krossa, Sebastian; Viset, Trond; Størkersen, Øystein; Vandenbosch, Michiel; Cleas, Britt S.R.; Giampà , Marco; Høiem, Therese Stork; Heeren, Ron M.A.; Giskeødegård, Guro F.; Rye, Morten Beck; Tessem, May-Britt. (2023) Spatial multiomics show lipid metabolism alterations in prostate cancer. Regional Mass Spectrometry Imaging Spring Workshop ; Uppsala. 2023-04-27 - 2023-04-29.
2022
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PosterAndersen, Maria Karoline; Krossa, Sebastian; Midtbust, Elise; Høiem, Therese Stork; Viset, Trond; Størkersen, Øystein; Giskeødegård, Guro F.; Rye, Morten Beck; Tessem, May-Britt. (2022) Multiomics spatial analysis shows lipid metabolism alterations in prostate cancer. Digital Life Conference 2022 . Digitalt Life; Trondheim. 2022-10-20 - 2022-10-21.
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PosterAndersen, Maria Karoline; Krossa, Sebastian; Midtbust, Elise; Høiem, Therese Stork; Viset, Trond; Størkersen, Øystein; Giskeødegård, Guro F.; Rye, Morten Beck; Tessem, May-Britt. (2022) Multiomics spatial analysis shows lipid metabolism alterations in prostate cancer. 3rd EpiLipidNET Action Meeting . CA19105 EpiLipidNET Cost Action; Aveiro. 2022-09-21 - 2022-09-23.
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Academic lectureAndersen, Maria Karoline; Krossa, Sebastian; Midtbust, Elise; Pedersen, Christine Aaserød; Wess, Maximillian; Viset, Trond; Størkersen, Øystein; Sandsmark, Elise; Bertilsson, Helena; Giskeødegård, Guro F.; Rye, Morten Beck; Tessem, May-Britt. (2022) Spatial transcriptomics reveals biomarker SFRP4 to be strongly associated with extracellular matrix remodeling in prostate cancer stroma. The Norwegian Cancer Symposium 2022 . University of Oslo; Oslo. 2022-09-14 - 2022-09-15.
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Academic lectureKrossa, Sebastian; Andersen, Maria Karoline; Midtbust, Elise; Wess, Maximilian; Viset, Trond; Størkersen, Øystein; Bertilsson, Helena; Giskeødegård, Guro; Rye, Morten Beck; Tessem, May-Britt. (2022) Inflamed normal appearing glands in the tumor microenvironment of prostate cancer are associated with relapse after radical prostatectomy. NBS Contact Meeting 2022 . Norsk Biokjemisk Selskap; Tromsø. 2022-02-10 - 2022-02-12.
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PosterKrossa, Sebastian; Andersen, Maria Karoline; Midtbust, Elise; Wess, Maximilian; Viset, Trond; Størkersen, Øystein; Bertilsson, Helena; Giskeødegård, Guro F.; Rye, Morten Beck; Tessem, May-Britt. (2022) Inflamed normal appearing glands in the tumor microenvironment of prostate cancer are associated with relapse after radical prostatectomy. The Norwegian Cancer Symposium 2022 ; 2022-09-14 - 2022-09-15.
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PosterPedersen, Christine Aaserød; Midtbust, Elise; Krossa, Sebastian; Andersen, Maria Karoline; Viset, Trond; Størkersen, Øystein; Giskeødegård, Guro F.; Rye, Morten Beck; Tessem, May-Britt. (2022) DNA methylation aberrations predicts recurrence both in tumor and normal appearing prostate tissue. European Association of Urology conference 2022 . European Association of Urology; Amsterdam. 2022-06-30 - 2022-07-04.
2020
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Academic lectureRise, Kjersti; Tessem, May-Britt; Drabløs, Finn; Rye, Morten Beck. (2020) How FunHoP changed the picture. MCC International Webinar Series . Mabalacat City College; 2020-10-10.
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Academic lectureRye, Morten Beck; Bertilsson, Helena; Krossa, Sebastian; Bathen, Tone Frost; Drabløs, Finn; Tessem, May-Britt. (2020) A gene signature for citrate and spermine (CS) secretion in the prostate. Swedish Symposium on Prostate Cancer Research . Sahlgrenska Academy, University of Gothenburg; Gøteborg. 2020-02-03 - 2020-02-04.
2019
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PosterAndersen, Maria Karoline; Høiem, Therese Stork; Balluff, Benjamin; Claes, Britt S.R.; Martin-Lorenzo, Marta; Richardsen, Elin; Bertilsson, Helena; Heeren, Ron M.A.; Rye, Morten Beck; Giskeødegård, Guro F.; Bathen, Tone Frost; Tessem, May-Britt. (2019) Altered metabolism in prostate cancer and stroma detected through MALDI-TOF MSI. Metabolomics 2019 . Metabolomics Society; The Hague. 2019-06-23 - 2019-06-27.
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PosterJalili, Mahsa; Gerdol, Marco; Greco, Samuele; Pallavicini, Alberto; Buonocore, Francesco; Scapigliati, Giuseppe; Picchietti, Simona; Esteban, Maria Angeles; Rye, Morten Beck; Bones, Atle M.. (2019) Altered transcription levels of immune markers in head kidney of Atlantic salmon after different feedings. Scandinavian Society of Immunology conference . Scandinavian Society of Immunology; 2019-12-01.
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LectureRye, Morten Beck; Bertilsson, Helena; Krossa, Sebastian; Bathen, Tone Frost; Drabløs, Finn; Tessem, May-Britt. (2019) The genes controlling citrate and spermine secretion in prostate cancer. Norwegian Biochemical Society 55th Contact Meeting . Norsk Biokjemisk Selskap; Røros. 2019-01-24 - 2019-01-27.
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LectureRye, Morten Beck; Nygård, Ståle; Drabløs, Finn; Petersen, Kjell; Våge, Dag Inge; Willassen, Nils Peder; Hovig, Eivind; Jonassen, Inge. (2019) ELIXIR.NO - The national infrastructure of bioinformatics. Norwegian Biochemical Society 55th Contact Meeting . Norsk Biokjemisk Selskap; Røros. 2019-01-24 - 2019-01-27.
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LectureRye, Morten Beck; Tessem, May-Britt; Krossa, Sebastian; Bathen, Tone Frost; Drabløs, Finn; Bertilsson, Helena. (2019) The expression of genes controlling citrate and spermine secretion is lost in aggressive prostate cancer and metastasis. The 32nd NUF Congress . Nordisk Urologisk Forening; Reykjavik. 2019-08-05 - 2019-08-08.
2018
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PosterAndersen, Maria Karoline; Høiem, Therese Stork; Balluff, Benjamin; Martin-Lorenzo, Marta; Richardsen, Elin; Bertilsson, Helena; Heeren, Ron M.A.; Rye, Morten Beck; Giskeødegård, Guro F.; Bathen, Tone Frost; Tessem, May-Britt. (2018) Altered metabolism in prostate cancer and stroma detected through MALDI-TOF MSI. IMSS II & OurCon VI Joint Meeting . IMSS; Charleston. 2018-11-11 - 2018-11-14.
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PosterAndersen, 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. ISMRM Workshop on Advances in Multiscale Cancer Detection: From Micro to Macro . ISMRM; Dublin. 2018-10-07 - 2018-10-10.
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PosterRise, Kjersti; Drabløs, Finn; Rye, Morten Beck. (2018) Cell Lines vs. Tissue - A Comparative Study of Gene Expression Using FunHoP. International Conference on Systems Biology ; 2018-10-28 - 2018-11-01.
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PosterRise, Kjersti; Drabløs, Finn; Rye, Morten Beck. (2018) FunHoP – Enhanced visualisation and analysis of functionally homologous proteins in complex metabolic networks. International Study Group for Systems Biology ; 2018-09-24 - 2018-09-28.
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Popular scientific lectureRye, Morten Beck. (2018) When Prostate Cancer Becomes Dangerous!. Health Innovation Seminar . Medisinsk Fakultet; Trondheim. 2018-03-21 - 2018-03-21.
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PosterRye, Morten Beck; Bertilsson, Helena; Andersen, Maria Karoline; Rise, Kjersti; Bathen, Tone Frost; Drabløs, Finn; Tessem, May-Britt. (2018) Computational minimization of stroma tissue confounding reveals systematic downregulation of cholesterol synthesis pathway genes in prostate cancer. ECCB 2018 - 17th European Conference on Computational Biology . Hellenic Society for Computational Biology and Bioinformatic; Athen. 2018-09-08 - 2918-09-12.
2017
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Academic lectureRise, Kjersti; Drabløs, Finn; Rye, Morten Beck. (2017) Aggregating RNA-Seq reads from multiple genes in KEGG metabolic pathways improves interpretability in gene expression pathway analysis. International Conference on Systems Biology ; Blacksburg, Virginia. 2017-08-06 - 2017-08-12.
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Academic lectureRye, Morten Beck; Bertilsson, Helena; Andersen, Maria Karoline; Rise, Kjersti; Bathen, Tone Frost; Drabløs, Finn; Tessem, May-Britt. (2017) Computational assessment of tissue heterogeneity in patient tissue samples reveals that cholesterol synthesis pathway genes in prostate cancer are consistently downregulated. BC2 Computational Biology Conference . Swiss Institute of Bioinformatics; Basel. 2017-09-12 - 2017-09-15.
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Academic lectureRye, Morten Beck; Bertilsson, Helena; Andersen, Maria Karoline; Rise, Kjersti; Bathen, Tone Frost; Drabløs, Finn; Tessem, May-Britt. (2017) Transcriptional downregulation of cholesterol synthesis pathway genes in prostate cancer. The 53rd Contact Meeting . NBS - Norsk Biokjemisk Selskap; Storefjell Resort Hotel, Gol. 2017-01-19.
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Academic lectureRye, Morten Beck; Tessem, May-Britt; Andersen, Maria Karoline; Rise, Kjersti; Bathen, Tone Frost; Drabløs, Finn; Bertilsson, Helena. (2017) Cholesterol synthesis pathway genes in prostate cancer are downregulated. 31st NUF Congress . Scandinavian Association of Urology; Odense. 2017-06-14 - 2017-06-16.
2016
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LectureRye, Morten Beck; Bertilsson, Helena; Andersen, Maria Karoline; Rise, Kjersti; Bathen, Tone Frost; Drabløs, Finn Sverre; Tessem, May-Britt. (2016) Transcriptional downregulation of cholesterol synthesis revealed as a hallmark for prostate cancer after adjustment for confounding stroma. ESUR16 - 23rd Meeting of the EAU Section of Urological Research . EAU- european Association of Urology; Parma. 2016-10-20 - 2016-10-22.
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Academic lectureSandsmark, Elise; Hansen, Ailin Falkmo; Bertilsson, Helena; Selnæs, Kirsten Margrete; Wright, Alan; Bofin, Anna M.; Bathen, Tone Frost; Tessem, May-Britt; Rye, Morten Beck. (2016) Non-canonicle Wnt5a signalling is associated with EMT and metabolic alterations in human prostate cancer. Current and Future Clinical Biomarkers of Cancer . NTNU; Trondheim. 2016-06-16 - 2016-06-17.
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PosterSandsmark, 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 associated with Gleason score, recurrence, metastases and metabolic alterations in prostate cancer. The 8th National PhD Conference in Medical Imaging ; 2016-11-21 - 2016-11-22.
2015
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Academic lectureHansen, Ailin Falkmo; Sandsmark, Elise; Rye, Morten Beck; Wright, Alan; Bertilsson, Helena; Bofin, Anna M.; Angelsen, Anders; Selnæs, Kirsten Margrete; Bathen, Tone Frost; Tessem, May-Britt. (2015) TMPRSS2:ERG gene fusion and ERG overexpression in human prostate cancer are associated with changed metabolism. ISMRM 2015 ; Toronto. 2015-05-30 - 2015-07-05.
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Academic lectureHansen, Ailin Falkmo; Sandsmark, Elise; Rye, Morten Beck; Wright, Alan; Bertilsson, Helena; Sjøbakk, Torill Eidhammer; Bofin, Anna M.; Angelsen, Anders; Selnæs, Kirsten Margrete; Bathen, Tone Frost; Tessem, May-Britt. (2015) TMPRSS2:ERG gene fusion in human prostate cancer is associated with altered metabolism. NBS contact meeting Svalbard . Norsk Biokjemisk Selskap; Svalbard. 2015-02-09 - 2015-02-13.
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Academic lectureSandsmark, Elise; Hansen, Ailin Falkmo; Bertilsson, Helena; Selnæs, Kirsten Margrete; Wright, Alan J; Axcrona, K; Bofin, Anna M.; Bathen, Tone Frost; Rye, Morten Beck; Tessem, May-Britt. (2015) Non-canonical Wnt5a signalling is associated with EMT and metabolic alterations in human prostate cancer. ESMRMB 2015 Congress ; 2015-10-01 - 2015-10-03.
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PosterSandsmark, Elise; Hansen, Ailin Falkmo; Rye, Morten Beck; Wright, Alan; Bertilsson, Helena; Sjøbakk, Torill Eidhammer; Bofin, Anna M.; Angelsen, Anders; Selnæs, Kirsten Margrete; Bathen, Tone Frost; Tessem, May-Britt. (2015) TMPRSS2:ERG gene fusion in human prostate cancer shows decreased levels of citrate and spermine. Regional forskningskonferanse i Helse Midt-Norge . Helse Nord-Trøndelag; Sjørdal. 2015-06-09 - 2015-06-10.
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PosterSandsmark, Elise; Selnæs, Kirsten Margrete; Bertilsson, Helena; Bofin, Anna M.; Wright, Alan; Viset, Trond; Richardsen, Elin; Drabløs, Finn; Bathen, Tone Frost; Tessem, May-Britt; Rye, Morten Beck. (2015) Non-canonical Wnt5a-Fizzled2 signaling is associated with metabolic reprogramming and biochemical recurrence in human prostate cancer. ESUR-SBUR15 - The 11th World Congress on Urological Research ; Nijmegen. 2015-09-10 - 2015-09-12.
2014
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PosterRye, Morten Beck; Bertilsson, Helena; Bathen, Tone Frost; Drabløs, Finn; Tessem, May-Britt. (2014) Simplifying methods for adjusting tissue heterogeneity pinpoint genes responsible for altered metabolism in prostate cancer samples. ESUR 2014 . EAU Section of Urological Research (ESUR); Glasgow, Scotland. 2014-10-09 - 2014-10-11.
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Academic lectureRye, Morten Beck; Bertilsson, Helena; Bathen, Tone Frost; Drabløs, Finn; Tessem, May-Britt. (2014) Tissue heterogeneity and data integration in prostate cancer. Bioinformatics Network Seminar: Biological networks – from genes to populations . Program for Bioinformatikk (PBI); Sumhuset, Trondheim. 2014-12-08 - 2014-12-08.
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Academic lectureRye, Morten Beck; Bertilsson, Helena; Drabløs, Finn; Angelsen, Anders; Bathen, Tone Frost; Tessem, May-Britt. (2014) Subtype classification of prostate cancer. Onsdagsmøte, IKM . IKM; Kunnskapssenteret, St.Olav. 2014-01-15 - 2014-01-15.
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PosterRye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair; Drabløs, Finn. (2014) Chromatin data integrated with a human reference atlas of experimentally defined promoters reveal repressed promoters located in active chromatin. SocBiN Bioinformatics 2014 . Society for Bioinformatics in Northern Europe (SocBiN); Oslo. 2014-06-11 - 2014-06-13.
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Academic lectureRye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair; Drabløs, Finn. (2014) Repressed promoters in active chromatin. SocBiN Bioinformatics 2014 . Society for Bioinformatics in Northern Europe (SocBiN); Oslo. 2014-06-11 - 2014-06-13.
2013
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PosterKornacker, Karl; Rye, Morten Beck; Håndstad, Tony; Drabløs, Finn. (2013) The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. 5th StatSeq Workshop . COST TD801 StatSeq; Helsinki. 2013-04-24 - 2013-04-26.
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Academic lectureRye, Morten Beck. (2013) Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. Faglig besøk til Karolinska Institut . Karolinska Institut; Stockholm. 2013-04-12 - 2013-04-12.
2012
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Academic lectureDrabløs, Finn; Kornacker, Karl; Rye, Morten Beck; Håndstad, Tony. (2012) The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. Norwegian Bioinformatics Forum ; Trondheim. 2012-10-18 - 2012-10-19.
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Academic lectureDrabløs, Finn; Rye, Morten Beck; Klepper, Kjetil; Sætrom, Pål. (2012) Definition and analysis of gene sets from time series data. FANTOM time-courses meeting . FANTOM RIKEN; Yokohama. 2012-10-29 - 2012-11-02.
2011
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Academic lectureRye, Morten Beck. (2011) Chemometrics in Medicine. Seminar i forbindelse med årsmøte i faggruppa for kjemometri . Faggruppa for Kjemometri; NTNU, Trondheim. 2011-04-04.
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Academic lectureRye, Morten Beck. (2011) Epigenetics and SNPs. eGenVar kickoff meating ; NTNU, Trondheim. 2011-03-25.
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Academic lectureRye, Morten Beck. (2011) Transcription factors and histone modifications. BFYS 2011 (Bioinformatics for young scientists) . FUGE, Bergen; Ullensvang. 2011-03-16 - 2011-03-18.
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Academic lectureRye, Morten Beck. (2011) Transcription factors and histone modifications. Joint Friday meeting, Systems Biology and BiGR group ; 2011-03-10.
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PosterRye, Morten Beck; Drabløs, Finn; Sætrom, Pål; Håndstad, Tony. (2011) Epigenetic Influence on Cell-type specific peaks from ChIP-Seq data. Histone code: Fact or fiction? . Keystone Symposia; Midway, Utah. 2011-01-10 - 2011-01-15.
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PosterRye, Morten Beck; Sætrom, Pål; Håndstad, Tony; Drabløs, Finn. (2011) Clusters of ChIP-Seq defined transcription factor binding sites map regulatory elelemnts in the human genome. Unanswered Questions in Transcription, Annual international Symposium . Cambridge Research Institute; Cambridge. 2011-11-04 - 2011-11-05.
2010
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Academic lectureRye, Morten Beck. (2010) A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs. NBF, Norwegian Bioinformatics Forum 2010 ; Radiumhospitalet, Oslo. 2010-11-18 - 2010-11-19.
2009
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Programme participationElvestad, Maiken Bratt; Gjerde, Anne Heidi; Hanssen-Bauer, Audun; Fladvad, Torill; Gilljam, Karin Margaretha; Bergstrøm, Bjarte; Rye, Morten Beck; Muiser, Iwe; Junker, Asbjørn; Hu, Yi; Rakvag, Trude Teoline; Gundersen, Astrid; Olsen, Guro Dalheim; Mundal, Siv Boon; Løset, Mari. (2009) Forskningsdagene 2009. Forskningstorget [TV]. 2009-09-25.
2008
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PosterFærgestad, Ellen Mosleth; Høy, Martin; Grove, Harald; Gidskehaug, Lars; Moldestad, Anette Aamodt; Hollung, Kristin; Walczak, B; Martens, Harald; Rye, Morten Beck. (2008) An improved and rapid method for analysis of 2-DE images; a pixel based approach. FROM GENOME TO PROTEOME: INTEGRATION AND PROTEOME COMPLETION ; Siena, Italy. 2008-08-31 - 2008-09-04.
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PosterMartens, Harald; Høy, Martin; Grove, Harald; Moldestad, Anette; Hollung, Kristin; Rye, Morten Beck. (2008) An improved and rapid method for analysis of 2-DE images; a pixel based approach. 8, Siena Meeting: From genome to proteome ; Siena, italy. 2008-08-28 - 2008-09-04.
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PosterRye, Morten Beck. (2008) Pixel-based approach for identifying significant features in two-dimensional gel electrophoresis. NPC2008, 4th Annual Norwegian Proteomics Conference . Iris; Ulstein. 2008-10-20 - 2008-10-21.
2006
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PosterRye, Morten Beck; Mosleh Færgestad, Ellen; Grove, Harald; Van Der Berg, Franz; Martens, Harald; Hollung, Kristin; Westad, Frank; Bjerke, A H. (2006) Viewing Images As Spectra: A Novel approach of analysing 2DE proteome data. 7th Siena Meeting. From Genome To Proteome ; Siena. 2006-09-03 - 2006-09-07.
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PosterRye, Morten Beck; Alsberg, Bjørn Kåre. (2006) Automatic spot classification in 2DE gel analysis. 7th Siena Meeting From Genome To Proteome ; Siena. 2006-09-03 - 2006-09-07.
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Academic lectureRye, Morten Beck; Alsberg, Bjørn Kåre. (2006) Separering av proteinsegment fra støysegment ved DPLSR i 2D gel elektroforese. 18. norske kjemometrisymposium ; Hafjell. 2006-03-20 - 2006-03-22.
2005
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Academic lectureRye, Morten Beck; Alsberg, Bjørn Kåre. (2005) Comparing Segmentation methods in Two-Dimensional Gel Electrophoresis. BFYS 2005 ; 2005-04-15 - 2005-04-17.
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PosterRye, Morten Beck; Alsberg, Bjørn Kåre. (2005) Protein spot classification by PLSR in two dimensional gel electrophoresis. SSC9 - 9th Scandinavian Symposium on Chemometrics ; 2005-08-21 - 2005-08-25.