Morten Beck Rye
Om
Jeg driver translasjonell forskning innen beregningsbiologi med fokus på integrasjon av storskaladata fra genekspresjon, metabolisme, epigenetikk og genregulering for å forbedre diagnostikk og behandlingsvalg for pasienter med prostatakreft. Dette gjøres i et forskningssamarbeid mellom BiGR og MR-Senteret på NTNU og Urologisk institutt ved St.Olavs hospital. Gjennom vår forsking prøver vi å finne ut hva som skiller aggressiv fra ufarlig prostatakreft på molekylært nivå gjennom integrasjon av data generert fra ulike høykapasitetsteknologier.
Det har i de senere år vært økt fokus på menns helse i kampanjer og offentlige debatter, noe som har ført en økning i antall menn som testes for prostatakreft. En utfordring inne prostatakreftdiagnostikk er å kunne skille de kreftformene som er aggressive og livstruende, fra se som er ufarlige. Dette gjøres i dag ved å vurdere innsamlede kliniske data fra MR-bilder, blodprøver og vevsprøver fra prostata. På grunn av begrensinger i klassifiseringssystemet, har overbehandling av ufarlig prostatakreft blitt en økende belastning for både pasienter og helsesystemet. I tillegg kommer det at dagens klassifisering i enkelt tilfeller også mislykkes med å detektere aggressive kreftformer. Målet for vår forskning er derfor å forbedre klassifiseringen av aggressiv og ufarlig prostatakreft, både ved første diagnose og for pasienter under aktiv overvåkning av sykdommen.
Vi utvikler for tiden en robust klassifikator for aggressiv prostatakreft baser på molekylære data fra vevsbiopsier, som er invasiv i prostata. Vår visjon derimot, er at aggressiv prostatakreft skal kunne detekteres kun ved minimalt invasive metoder (f.eks blodprøver) eller ikke-invasive metoder som MR-avbilding. For å oppnå dette har vi valgt å fokusere vår forskning på detaljert storskala analyse av frosset vev donert av pasienter med prostatkreft. Vi analysere prøvene molekylært med nye avanserte målemetoder for å få en forståelse av hvordan vevsstrukturer, molekylære sammensetninger og bildesegmenter kan knyttes mot hverandre. Dette er hovedtema i ProstOmics, et pågående samarbeidsprosjekt hvor Gruppe for bioinformatikk bidrar med beregningsbaserte analyser.
Forskningsaktivitet og retninger
Utvikling og validering av en robust geneskpresjonssignatur som kan skille aggressiv og ufarlig prostatakreft fra kliniske pasientprøver
Integrasjon av data fra ProstOmics med store mengder fritt tilgjengelige data for å knytte molekylære signaturesr med vev og MR-bilde-strukturer. Dette for å forbedre ikke-invasiv klassifisering av aggressiv prostatakreft
Undersøke potensialet for epigenetiske markører for deteksjon av aggressiv prostatakreft i blod, urin og sekret fra prostata.
I tillegg er jeg involvert i kjernefasiliteten for bioinformatikk (BioCore) og tilsvarende tjenester for bioinformatikk gjennom Elixir, der jeg assisterer andre forskere med bioinformatikk-analyser i ulike prosjekter. Jeg er også ansvarlig for et årlig kurs i sekvenseringsanalyse (arrangert annethvert år gjennom NORBIS).
Publikasjoner
2026
-
Taylor, Kristofer G.;
Johannessen, Bjarne;
Mills, Ian Geoffrey;
Rye, Morten Beck;
Axcrona, Karol;
Skotheim, Rolf.
(2026)
Spatial Robustness of Prostate Cancer Biomarkers Evaluated by Spatial Transcriptomics.
The Prostate
Vitenskapelig artikkel
2025
-
Krossa, Sebastian;
Andersen, Maria K.;
Midtbust, Elise;
Wess, Maximilian;
Antti, Kiviaho,;
Sharma, Abhibhav;
Sini, Hakkola,;
Yangyang, Hao,;
Mohammed, Alshalalfa,;
Elai, Davicioni,.
(2025)
Spatial multi-omics identifies aggressive prostate cancer signatures highlighting pro-inflammatory chemokine activity in the tumor microenvironment | Nature Communications.
Nature Communications
Vitenskapelig artikkel
-
Pedersen, Christine Aaserød;
Tessem, May-Britt;
Rye, Morten Beck;
Fleischer, Thomas.
(2025)
From methylation to mechanism: DNA methylation and multi-omics analysis of breast and prostate cancer aggressiveness.
Norges teknisk-naturvitenskapelige universitet
Doktoravhandling
-
Wess, Maximilian;
Andersen, Maria Karoline;
Midtbust, Elise;
Guillem, Juan Carlos Cabellos;
Viset, Trond;
Størkersen, Øystein;
Krossa, Sebastian;
Rye, Morten Beck;
Tessem, May-Britt.
(2025)
Spatial integration of multi-omics data from serial sections using the novel Multi-Omics Imaging Integration Toolset.
GigaScience
Vitenskapelig artikkel
-
Pedersen, Christine Aaserød;
Fleischer, Thomas;
Wess, Maximilian;
Midtbust, Elise;
Andersen, Maria Karoline;
Viset, Trond;
Størkersen, Øystein;
Rye, Morten Beck;
Tessem, May-Britt.
(2025)
DNA methylation in normal-appearing tissue associated with prostate cancer recurrence and metastasis.
Clinical Epigenetics
Vitenskapelig artikkel
2024
-
Wess, Maximilian;
Andersen, Maria Karoline;
Midtbust, Elise;
Guillem, Juan Carlos Cabellos;
Viset, Trond;
Størkersen, Øystein;
Krossa, Sebastian;
Rye, Morten Beck;
Tessem, May-Britt.
(2024)
Spatial Integration of Multi-Omics Data using the novel Multi-Omics Imaging Integration Toolset.
BioRxiv
Vitenskapelig artikkel
-
Behsen, Alenka Djarmila;
Holien, Toril;
Micci, Francesca;
Rye, Morten Beck;
Rasmussen, Jenny Malm;
Andersen, Kristin;
Hess, Eli Svorkdal;
Børset, Magne;
Keats, Jonathan;
Våtsveen, Thea Kristin.
(2024)
Cell surface marker heterogeneity in human myeloma cell lines for modeling of disease and therapy.
Scientific Reports
Vitenskapelig artikkel
-
Andersen, Maria K.;
Krossa, Sebastian;
Midtbust, Elise;
Pedersen, Christine Aaserød;
Wess, Maximilian;
Høiem, Therese Stork;
Viset, Trond;
Størkersen, Øystein;
Nervik, Ingunn;
Sandsmark, Elise.
(2024)
Spatial transcriptomics reveals strong association between SFRP4 and extracellular matrix remodeling in prostate cancer.
Communications Biology
Vitenskapelig artikkel
-
Kiviaho, Antti;
Eerola, Sini K.;
Kallio, Heini M.L.;
Andersen, Maria K.;
Hoikka, Miina;
Salonen, Iida;
Spotbeen, Xander;
Giesen, Alexander;
Parker, Charles T.A.;
Taavitsainen, Sinja.
(2024)
Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer.
Nature Communications
Vitenskapelig artikkel
-
Bergum, Olaug Elisabeth Torheim;
Singleton, Amanda Holstad;
Røst, Lisa Marie Ivarsdatter;
Bodein, Antoine;
Scott-Boyer, Marie-Pier;
Rye, Morten Beck;
Droit, Arnaud;
Bruheim, Per;
Otterlei, Marit.
(2024)
SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated.
Frontiers in Microbiology
Vitenskapelig artikkel
2023
-
Andersen, Maria Karoline;
Krossa, Sebastian;
Midtbust, Elise;
Pedersen, Christine Aaserød;
Wess, Maximilian;
Høiem, Therese Stork;
Viset, Trond;
Størkersen, Øystein;
Nervik, Ingunn;
Sandsmark, Elise.
(2023)
Spatial transcriptomics reveals strong association between SFRP4 and extracellular matrix remodeling in prostate cancer.
Research Square
Vitenskapelig artikkel
2022
-
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
Konferanseabstract
-
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.
(2022)
Prediction of recurrence from metabolites and expression of TOP2A and EZH2 in prostate cancer patients treated with radiotherapy.
NMR in Biomedicine
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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.
(2022)
DNA methylation changes in response to neoadjuvant chemotherapy are associated with breast cancer survival.
Breast Cancer Research
Vitenskapelig artikkel
-
Misund, Kristine;
Bruinink, Davine Hofste op;
Coward, Eivind;
Hoogenboezem, Remco M.;
Rustad, Even Holth;
Sanders, Mathijs A.;
Rye, Morten Beck;
Sponaas, Anne-Marit;
Holt, Bronno van der;
Zweegman, Sonja.
(2022)
Clonal evolution after treatment pressure in multiple myeloma: heterogenous genomic aberrations and transcriptomic convergence.
Leukemia
Vitenskapelig artikkel
-
Rise, Kjersti;
Tessem, May-Britt;
Drabløs, Finn;
Rye, Morten Beck.
(2022)
FunHoP analysis reveals upregulation of mitochondrial genes in prostate cancer.
PLOS ONE
Vitenskapelig artikkel
-
Grapotte, Mathys;
Saraswat, Manu;
Bessière, Chloé;
Menichelli, Christophe;
Ramilowski, Jordan A.;
Severin, Jessica;
Hayashizaki, Yoshihide;
Itoh, Masayoshi;
Tagami, Michihira;
Murata, Mitsuyoshi.
(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
Korrigendum
-
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
Konferanseabstract
2021
-
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 (GPB)
Vitenskapelig artikkel
-
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.
(2021)
Spatial differentiation of metabolism in prostate cancer tissue by MALDI-TOF MSI.
Cancer & Metabolism
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
2020
-
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
Vitenskapelig artikkel
-
Zwiggelaar, Rosalie;
Lindholm, Håvard Takle;
Fosslie, Madeleine Lystad;
Pedersen, Marianne Terndrup;
Ohta, Yuki;
Diez Sanchez, Alberto;
Martin Alonso, Mara;
Ostrop, Jenny;
Matano, Mami;
Parmar, Naveen.
(2020)
LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium.
Science Advances
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
2019
-
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
Vitenskapelig oversiktsartikkel
-
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
Vitenskapelig artikkel
-
Vardaxis, Ioannis;
Drabløs, Finn;
Rye, Morten Beck;
Lindqvist, Bo Henry.
(2019)
MACPET: model-based analysis for ChIA-PET.
Biostatistics
Vitenskapelig artikkel
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
Vitenskapelig artikkel
-
Tekle, Kidane M;
Gundersen, Sveinung;
Klepper, Kjetil;
Bongo, Lars Ailo;
Raknes, Inge Alexander;
Li, Xiaxi;
Zhang, Wei;
Andreetta, Christian;
Mulugeta, Teshome Dagne;
Kalaš, Matúš.
(2018)
Norwegian e-Infrastructure for Life Sciences (NeLS).
F1000 Research
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
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
Vitenskapelig artikkel
2016
-
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.
(2016)
A novel non-canonical Wnt signature for prostate cancer aggressiveness.
OncoTarget
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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.
(2016)
Presence of TMPRSS2-ERG is associated with alterations of the metabolic profile in human prostate cancer.
OncoTarget
Vitenskapelig artikkel
2015
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
2014
-
Forest, Alistair R.R.;
Kawaji, Hideya;
Rehli, Michael;
Baillie, John Kenneth;
Hoon, Michiel de;
Haberle, Vanja;
Lassmann, Timo;
Kulakovskiy, Ivan;
Lizio, Marina;
Itoh, Masayoshi.
(2014)
A promoter-level mammalian expression atlas.
Nature
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
2013
-
Sandve, Geir Kjetil;
Gundersen, Sveinung;
Johansen, Morten;
Glad, Ingrid Kristine;
Gunathasan, Krishanthi;
Holden, Lars;
Holden, Marit;
Liestøl, Knut;
Nygård, Ståle;
Nygaard, Vegard.
(2013)
The Genomic HyperBrowser: an analysis web server for genome-scale data.
Nucleic Acids Research (NAR)
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
2012
-
Kornacker, K;
Rye, Morten Beck;
Håndstad, Tony;
Drabløs, Finn.
(2012)
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.
BMC Bioinformatics
Vitenskapelig artikkel
-
Håndstad, Tony;
Rye, Morten Beck;
Mocnik, Rok;
Drabløs, Finn;
Sætrom, Pål.
(2012)
Cell-type specificity of ChIP-predicted transcription factor binding sites.
BMC Genomics
Vitenskapelig artikkel
-
Rye, Morten Beck;
Færgestad, Ellen Mosleth.
(2012)
Preprocessing of electrophoretic images in 2-DE analysis.
Chemometrics and Intelligent Laboratory Systems
Vitenskapelig artikkel
2011
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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)
Vitenskapelig artikkel
-
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
Vitenskapelig oversiktsartikkel
2008
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
Rye, Morten Beck;
Alsberg, Bjørn Kåre.
(2008)
A multivariate spot filtering model for two-dimensional gel electrophoresis.
Electrophoresis
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
2007
-
Rye, Morten Beck.
(2007)
Image segmentation and multivariate analysis in two-dimensional gel electrophoresis.
Norges teknisk-naturvitenskapelige universitet
Doktoravhandling
-
Mosleth, Ellen Færgestad;
Rye, Morten Beck;
Walczak, Beata;
Gidskehaug, Lars;
Wold, Jens Petter;
Grove, Harald;
Jia, X;
Hollung, Kristin;
Indahl, Ulf;
Westad, Frank.
(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
Vitenskapelig artikkel
Tidsskriftspublikasjoner
-
Taylor, Kristofer G.;
Johannessen, Bjarne;
Mills, Ian Geoffrey;
Rye, Morten Beck;
Axcrona, Karol;
Skotheim, Rolf.
(2026)
Spatial Robustness of Prostate Cancer Biomarkers Evaluated by Spatial Transcriptomics.
The Prostate
Vitenskapelig artikkel
-
Krossa, Sebastian;
Andersen, Maria K.;
Midtbust, Elise;
Wess, Maximilian;
Antti, Kiviaho,;
Sharma, Abhibhav;
Sini, Hakkola,;
Yangyang, Hao,;
Mohammed, Alshalalfa,;
Elai, Davicioni,.
(2025)
Spatial multi-omics identifies aggressive prostate cancer signatures highlighting pro-inflammatory chemokine activity in the tumor microenvironment | Nature Communications.
Nature Communications
Vitenskapelig artikkel
-
Wess, Maximilian;
Andersen, Maria Karoline;
Midtbust, Elise;
Guillem, Juan Carlos Cabellos;
Viset, Trond;
Størkersen, Øystein;
Krossa, Sebastian;
Rye, Morten Beck;
Tessem, May-Britt.
(2024)
Spatial Integration of Multi-Omics Data using the novel Multi-Omics Imaging Integration Toolset.
BioRxiv
Vitenskapelig artikkel
-
Forest, Alistair R.R.;
Kawaji, Hideya;
Rehli, Michael;
Baillie, John Kenneth;
Hoon, Michiel de;
Haberle, Vanja;
Lassmann, Timo;
Kulakovskiy, Ivan;
Lizio, Marina;
Itoh, Masayoshi.
(2014)
A promoter-level mammalian expression atlas.
Nature
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
Andersen, Maria Karoline;
Krossa, Sebastian;
Midtbust, Elise;
Pedersen, Christine Aaserød;
Wess, Maximilian;
Høiem, Therese Stork;
Viset, Trond;
Størkersen, Øystein;
Nervik, Ingunn;
Sandsmark, Elise.
(2023)
Spatial transcriptomics reveals strong association between SFRP4 and extracellular matrix remodeling in prostate cancer.
Research Square
Vitenskapelig artikkel
-
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
Konferanseabstract
-
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 (GPB)
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
Sandve, Geir Kjetil;
Gundersen, Sveinung;
Johansen, Morten;
Glad, Ingrid Kristine;
Gunathasan, Krishanthi;
Holden, Lars;
Holden, Marit;
Liestøl, Knut;
Nygård, Ståle;
Nygaard, Vegard.
(2013)
The Genomic HyperBrowser: an analysis web server for genome-scale data.
Nucleic Acids Research (NAR)
Vitenskapelig artikkel
-
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.
(2022)
Prediction of recurrence from metabolites and expression of TOP2A and EZH2 in prostate cancer patients treated with radiotherapy.
NMR in Biomedicine
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
Rye, Morten Beck;
Alsberg, Bjørn Kåre.
(2008)
A multivariate spot filtering model for two-dimensional gel electrophoresis.
Electrophoresis
Vitenskapelig artikkel
-
Kornacker, K;
Rye, Morten Beck;
Håndstad, Tony;
Drabløs, Finn.
(2012)
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.
BMC Bioinformatics
Vitenskapelig artikkel
-
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.
(2016)
A novel non-canonical Wnt signature for prostate cancer aggressiveness.
OncoTarget
Vitenskapelig artikkel
-
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.
(2022)
DNA methylation changes in response to neoadjuvant chemotherapy are associated with breast cancer survival.
Breast Cancer Research
Vitenskapelig artikkel
-
Wess, Maximilian;
Andersen, Maria Karoline;
Midtbust, Elise;
Guillem, Juan Carlos Cabellos;
Viset, Trond;
Størkersen, Øystein;
Krossa, Sebastian;
Rye, Morten Beck;
Tessem, May-Britt.
(2025)
Spatial integration of multi-omics data from serial sections using the novel Multi-Omics Imaging Integration Toolset.
GigaScience
Vitenskapelig artikkel
-
Håndstad, Tony;
Rye, Morten Beck;
Mocnik, Rok;
Drabløs, Finn;
Sætrom, Pål.
(2012)
Cell-type specificity of ChIP-predicted transcription factor binding sites.
BMC Genomics
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
Misund, Kristine;
Bruinink, Davine Hofste op;
Coward, Eivind;
Hoogenboezem, Remco M.;
Rustad, Even Holth;
Sanders, Mathijs A.;
Rye, Morten Beck;
Sponaas, Anne-Marit;
Holt, Bronno van der;
Zweegman, Sonja.
(2022)
Clonal evolution after treatment pressure in multiple myeloma: heterogenous genomic aberrations and transcriptomic convergence.
Leukemia
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
Tekle, Kidane M;
Gundersen, Sveinung;
Klepper, Kjetil;
Bongo, Lars Ailo;
Raknes, Inge Alexander;
Li, Xiaxi;
Zhang, Wei;
Andreetta, Christian;
Mulugeta, Teshome Dagne;
Kalaš, Matúš.
(2018)
Norwegian e-Infrastructure for Life Sciences (NeLS).
F1000 Research
Vitenskapelig artikkel
-
Rise, Kjersti;
Tessem, May-Britt;
Drabløs, Finn;
Rye, Morten Beck.
(2022)
FunHoP analysis reveals upregulation of mitochondrial genes in prostate cancer.
PLOS ONE
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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.
(2021)
Spatial differentiation of metabolism in prostate cancer tissue by MALDI-TOF MSI.
Cancer & Metabolism
Vitenskapelig artikkel
-
Rye, Morten Beck;
Færgestad, Ellen Mosleth.
(2012)
Preprocessing of electrophoretic images in 2-DE analysis.
Chemometrics and Intelligent Laboratory Systems
Vitenskapelig artikkel
-
Grapotte, Mathys;
Saraswat, Manu;
Bessière, Chloé;
Menichelli, Christophe;
Ramilowski, Jordan A.;
Severin, Jessica;
Hayashizaki, Yoshihide;
Itoh, Masayoshi;
Tagami, Michihira;
Murata, Mitsuyoshi.
(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
Korrigendum
-
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
Vitenskapelig artikkel
-
Zwiggelaar, Rosalie;
Lindholm, Håvard Takle;
Fosslie, Madeleine Lystad;
Pedersen, Marianne Terndrup;
Ohta, Yuki;
Diez Sanchez, Alberto;
Martin Alonso, Mara;
Ostrop, Jenny;
Matano, Mami;
Parmar, Naveen.
(2020)
LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium.
Science Advances
Vitenskapelig artikkel
-
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
Vitenskapelig oversiktsartikkel
-
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)
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig oversiktsartikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
Pedersen, Christine Aaserød;
Fleischer, Thomas;
Wess, Maximilian;
Midtbust, Elise;
Andersen, Maria Karoline;
Viset, Trond;
Størkersen, Øystein;
Rye, Morten Beck;
Tessem, May-Britt.
(2025)
DNA methylation in normal-appearing tissue associated with prostate cancer recurrence and metastasis.
Clinical Epigenetics
Vitenskapelig artikkel
-
Behsen, Alenka Djarmila;
Holien, Toril;
Micci, Francesca;
Rye, Morten Beck;
Rasmussen, Jenny Malm;
Andersen, Kristin;
Hess, Eli Svorkdal;
Børset, Magne;
Keats, Jonathan;
Våtsveen, Thea Kristin.
(2024)
Cell surface marker heterogeneity in human myeloma cell lines for modeling of disease and therapy.
Scientific Reports
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
Andersen, Maria K.;
Krossa, Sebastian;
Midtbust, Elise;
Pedersen, Christine Aaserød;
Wess, Maximilian;
Høiem, Therese Stork;
Viset, Trond;
Størkersen, Øystein;
Nervik, Ingunn;
Sandsmark, Elise.
(2024)
Spatial transcriptomics reveals strong association between SFRP4 and extracellular matrix remodeling in prostate cancer.
Communications Biology
Vitenskapelig artikkel
-
Kiviaho, Antti;
Eerola, Sini K.;
Kallio, Heini M.L.;
Andersen, Maria K.;
Hoikka, Miina;
Salonen, Iida;
Spotbeen, Xander;
Giesen, Alexander;
Parker, Charles T.A.;
Taavitsainen, Sinja.
(2024)
Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer.
Nature Communications
Vitenskapelig artikkel
-
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
Vitenskapelig artikkel
-
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
Konferanseabstract
-
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.
(2016)
Presence of TMPRSS2-ERG is associated with alterations of the metabolic profile in human prostate cancer.
OncoTarget
Vitenskapelig artikkel
-
Bergum, Olaug Elisabeth Torheim;
Singleton, Amanda Holstad;
Røst, Lisa Marie Ivarsdatter;
Bodein, Antoine;
Scott-Boyer, Marie-Pier;
Rye, Morten Beck;
Droit, Arnaud;
Bruheim, Per;
Otterlei, Marit.
(2024)
SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated.
Frontiers in Microbiology
Vitenskapelig artikkel
-
Vardaxis, Ioannis;
Drabløs, Finn;
Rye, Morten Beck;
Lindqvist, Bo Henry.
(2019)
MACPET: model-based analysis for ChIA-PET.
Biostatistics
Vitenskapelig artikkel
-
Mosleth, Ellen Færgestad;
Rye, Morten Beck;
Walczak, Beata;
Gidskehaug, Lars;
Wold, Jens Petter;
Grove, Harald;
Jia, X;
Hollung, Kristin;
Indahl, Ulf;
Westad, Frank.
(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
Vitenskapelig artikkel
Studentoppgave eller avhandling
-
Pedersen, Christine Aaserød;
Tessem, May-Britt;
Rye, Morten Beck;
Fleischer, Thomas.
(2025)
From methylation to mechanism: DNA methylation and multi-omics analysis of breast and prostate cancer aggressiveness.
Norges teknisk-naturvitenskapelige universitet
Doktoravhandling
-
Rye, Morten Beck.
(2007)
Image segmentation and multivariate analysis in two-dimensional gel electrophoresis.
Norges teknisk-naturvitenskapelige universitet
Doktoravhandling
Undervisning
Emner
Formidling
2026
-
Annen presentasjonTelumyan, Elen; Gracia, Beatriz Martín; Sagini, Krizia; Andersen, Maria K.; Tessem, May-Britt; Llorente, Alicia; Rye, Morten Beck. (2026) NOR-EV annual meeting 2026. NOR-EV annual meetibg
2025
-
KonferanseposterSharma, Abhibhav; Wess, Maximilian; Andersen, Maria K.; Rye, Morten Beck; Krossa, Sebastian; Midtbust, Elise; Viset, Trond; Størkersen, Øystein; Kiviaho, Antii; Nykter, Matti. (2025) Spatial Transcriptomics and MSI Uncover ER Stress Mechanisms in Prostate Cancer Progression. 19th Scandinavian Symposium on Chemometrics
-
KonferanseposterTelumyan, Elen; Gracia, Beatriz Martín; Sagini, Krizia; Andersen, Maria K.; Tessem, May-Britt; Rye, Morten Beck; Llorente, Alicia. (2025) Optimizing Protocols for Seminal Extracellular Vesicle Isolation in Prostate Cancer Research. ISEV2025 Annual Meeting
2024
-
KonferanseforedragWess, Maximilian; Andersen, Maria Karoline; Midtbust, Elise; Guillem, Juan Carlos Cabellos; Viset, Trond; Størkersen, Øystein; Rye, Morten Beck; Krossa, Sebastian; Tessem, May-Britt. (2024) Integration of Spatial Transcriptomics and Mass Spectrometry Imaging using MIIT. Spatial Omics
-
KonferanseposterTelumyan, Elen; Gracia, Beatriz Martín; Sagini, Krizia; Andersen, Maria K.; Llorente, Alicia; Tessem, May-Britt; Rye, Morten Beck. (2024) Transcriptomic Biomarker for Prostate Cancer Active Surveillance in Extracellular Vesicles from Liquid Biopsies. The Norwegian Cancer Symposium
-
KonferanseposterTelumyan, Elen; Gracia, Beatriz Martín; Sagini, Krizia; Andersen, Maria K.; Llorente, Alicia; Tessem, May-Britt; Rye, Morten Beck. (2024) A Transcriptomic Biomarker for Prostate Cancer Active Surveillance in Extracellular Vesicles from Liquid Biopsies. CanCell Annual Retreat
-
KonferanseposterTelumyan, Elen; Gracia, Beatriz Martín; Sagini, Krizia; Andersen, Maria K.; Llorente, Alicia; Tessem, May-Britt; Rye, Morten Beck. (2024) Transcriptomic Biomarker for Prostate Cancer Active Surveillance in Extracellular Vesicles from Liquid Biopsies. Precision EV Forum 2024
-
KonferanseforedragSharma, Abhibhav; Wess, Maximilian; Andersen, Maria K.; Rye, Morten Beck; Krossa, Sebastian; Midtbust, Elise; Viset, Trond; Størkersen, Øystein; Kiviaho, Antti; Nykter, Matti. (2024) Spatial multi-omics characterization of epithelial glands reveals novel prognostic signatures in prostate cancer. 4th-Nordic Metabolomic Conference 2024
-
KonferanseforedragSharma, Abhibhav; Wess, Maximilian; Andersen, Maria K.; Rye, Morten Beck; Krossa, Sebastian; Midtbust, Elise; Viset, Trond; Størkersen, Øystein; Kiviaho, Antti; Nykter, Matti. (2024) Spatial multi-omics characterization of epithelial glands reveals novel prognostic signatures in prostate cancer. 20th Annual International Conference of the Metabolomics Society
-
KonferanseposterSingh, Mithlesh Prasad; Wess, Maximilian; Rye, Morten Beck; Lehti, Kaisa Irene; Tessem, May-Britt; Andersen, Maria K.. (2024) Unveiling Spatial Metabolism in Prostate Cancer Tissue: Applying Explainable Machine Learning to Mass Spectrometry Imaging Data. Biomarker Discovery with MSI and Explainable Machine Learning. Spatial Omics 2024 a VIB Tools and Technologies conference
-
KonferanseposterAndersen, Maria Karoline; Krossa, Sebastian; Midtbust, Elise; Pedersen, Christine Aaserød; Wess, Maximilian; Viset, Trond; Størkersen, Øystein; Sandsmark, Elise; Bertilsson, Helena Maria; Giskeødegård, Guro F.. (2024) Spatial transcriptomics reveals biomarker SFRP4 to be strongly associated with extracellular matrix remodeling in prostate cancer stroma. Spatial Omics
2023
-
KonferanseposterWess, Maximilian; Andersen, Maria Karoline; Midtbust, Elise; Guillem, Juan Carlos Cabellos; Krossa, Sebastian; Rye, Morten Beck; Tessem, May-Britt. (2023) Registration-based Integration of Spatially Resolved Multi-Omics Data for Prostate Cancer Classification. PRESIMAL Autumn Research School 2023
-
KonferanseposterWess, Maximilian; Andersen, Maria Karoline; Midtbust, Elise; Krossa, Sebastian; Rye, Morten Beck; Tessem, May-Britt. (2023) Prostate Cancer Classification using Registration-based Integration of Spatial Multi-Omics Data. NTNU Health
-
KonferanseforedragWess, Maximilian; Andersen, Maria Karoline; Midtbust, Elise; Krossa, Sebastian; Rye, Morten Beck; Tessem, May-Britt. (2023) Registration-based Integration of Spatial Multi-Omics Data for Prostate Cancer Classification. The 3rd Nordic Metabolomics Conference
-
KonferanseforedragWess, Maximilian; Andersen, Maria Karoline; Midtbust, Elise; Krossa, Sebastian; Rye, Morten Beck; Tessem, May-Britt. (2023) Integration of Spatial Multi-Omics Data for Prostate Cancer Classification. Regional Mass Spectrometry Imaging Spring Workshop
-
KonferanseforedragAndersen, 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.. (2023) Spatial multiomics show lipid metabolism alterations in prostate cancer. Regional Mass Spectrometry Imaging Spring Workshop
2022
-
KonferanseposterKrossa, 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
-
KonferanseposterPedersen, 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
-
KonferanseposterAndersen, 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
-
KonferanseforedragAndersen, Maria Karoline; Krossa, Sebastian; Midtbust, Elise; Pedersen, Christine Aaserød; Wess, Maximillian; Viset, Trond; Størkersen, Øystein; Sandsmark, Elise; Bertilsson, Helena; Giskeødegård, Guro F.. (2022) Spatial transcriptomics reveals biomarker SFRP4 to be strongly associated with extracellular matrix remodeling in prostate cancer stroma. The Norwegian Cancer Symposium 2022
-
KonferanseforedragKrossa, 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
-
KonferanseposterAndersen, 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
2021
-
KonferanseforedragWess, Maximilian; Andersen, Maria Karoline; Krossa, Sebastian; Rye, Morten Beck; Tessem, May-Britt. (2021) Spatial Integration of Multi-Omics Data for Prostate Cancer Classification. Computational Systems Biology of Cancer multiomics and machine learning
2020
-
KonferanseforedragRise, Kjersti; Tessem, May-Britt; Drabløs, Finn; Rye, Morten Beck. (2020) How FunHoP changed the picture. MCC International Webinar Series
-
KonferanseforedragRye, 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
2019
-
KonferanseposterAndersen, 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.. (2019) Altered metabolism in prostate cancer and stroma detected through MALDI-TOF MSI. Metabolomics 2019
-
ForedragRye, 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
-
KonferanseposterJalili, 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
-
ForedragRye, 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
-
ForedragRye, 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
2018
-
KonferanseposterRye, 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
-
Foredrag
-
KonferanseposterAndersen, 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. (2018) Altered metabolism in prostate cancer and stroma detected through MALDI-TOF MSI. IMSS II & OurCon VI Joint Meeting
-
KonferanseposterAndersen, 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
-
KonferanseposterRise, Kjersti; Drabløs, Finn; Rye, Morten Beck. (2018) Cell Lines vs. Tissue - A Comparative Study of Gene Expression Using FunHoP. International Conference on Systems Biology
-
KonferanseposterRise, 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
2017
-
KonferanseforedragRye, 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
-
KonferanseforedragRye, 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
-
KonferanseforedragRye, 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
-
KonferanseforedragRise, 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
2016
-
KonferanseposterSandsmark, 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. (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
-
KonferanseforedragSandsmark, 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
-
ForedragRye, 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
2015
-
KonferanseforedragHansen, 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
-
KonferanseposterSandsmark, 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. (2015) TMPRSS2:ERG gene fusion in human prostate cancer shows decreased levels of citrate and spermine. Regional forskningskonferanse i Helse Midt-Norge
-
KonferanseposterSandsmark, Elise; Selnæs, Kirsten Margrete; Bertilsson, Helena; Bofin, Anna M.; Wright, Alan; Viset, Trond; Richardsen, Elin; Drabløs, Finn; Bathen, Tone Frost; Tessem, May-Britt. (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
-
KonferanseforedragSandsmark, 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
-
KonferanseforedragHansen, 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. (2015) TMPRSS2:ERG gene fusion in human prostate cancer is associated with altered metabolism. NBS contact meeting Svalbard
2014
-
KonferanseforedragRye, Morten Beck; Bertilsson, Helena; Drabløs, Finn; Angelsen, Anders; Bathen, Tone Frost; Tessem, May-Britt. (2014) Subtype classification of prostate cancer. Onsdagsmøte, IKM
-
KonferanseposterRye, 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
-
KonferanseposterRye, 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
-
KonferanseforedragRye, 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
-
KonferanseforedragRye, 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
2013
-
KonferanseforedragRye, Morten Beck. (2013) Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. Faglig besøk til Karolinska Institut
-
KonferanseposterKornacker, Karl; Rye, Morten Beck; Håndstad, Tony; Drabløs, Finn. (2013) The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. 5th StatSeq Workshop
2012
-
KonferanseforedragDrabløs, Finn; Rye, Morten Beck; Klepper, Kjetil; Sætrom, Pål. (2012) Definition and analysis of gene sets from time series data. FANTOM time-courses meeting
-
KonferanseforedragDrabløs, Finn; Kornacker, Karl; Rye, Morten Beck; Håndstad, Tony. (2012) The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. Norwegian Bioinformatics Forum
2011
-
KonferanseforedragRye, Morten Beck. (2011) Transcription factors and histone modifications. BFYS 2011 (Bioinformatics for young scientists)
-
KonferanseforedragRye, Morten Beck. (2011) Chemometrics in Medicine. Seminar i forbindelse med årsmøte i faggruppa for kjemometri
-
Konferanseforedrag
-
KonferanseforedragRye, Morten Beck. (2011) Transcription factors and histone modifications. Joint Friday meeting, Systems Biology and BiGR group
-
KonferanseposterRye, 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?
-
KonferanseposterRye, 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
2010
-
KonferanseforedragRye, Morten Beck. (2010) A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs. NBF, Norwegian Bioinformatics Forum 2010
2009
-
Deltakelse i radio- eller TVElvestad, Maiken Bratt; Gjerde, Anne Heidi; Hanssen-Bauer, Audun; Fladvad, Torill; Gilljam, Karin Margaretha; Bergstrøm, Bjarte; Rye, Morten Beck; Muiser, Iwe; Junker, Asbjørn; Hu, Yi. (2009) Forskningsdagene 2009.
2008
-
KonferanseposterFærgestad, 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
-
KonferanseposterMartens, 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
-
KonferanseposterRye, Morten Beck. (2008) Pixel-based approach for identifying significant features in two-dimensional gel electrophoresis. NPC2008, 4th Annual Norwegian Proteomics Conference
2006
-
KonferanseforedragRye, Morten Beck; Alsberg, Bjørn Kåre. (2006) Separering av proteinsegment fra støysegment ved DPLSR i 2D gel elektroforese. 18. norske kjemometrisymposium
-
KonferanseposterRye, Morten Beck; Færgestad, Ellen Mosleh; Grove, Harald; Berg, Franz Van Der; 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
-
KonferanseposterRye, Morten Beck; Alsberg, Bjørn Kåre. (2006) Automatic spot classification in 2DE gel analysis. 7th Siena Meeting From Genome To Proteome
2005
-
KonferanseposterRye, Morten Beck; Alsberg, Bjørn Kåre. (2005) Protein spot classification by PLSR in two dimensional gel electrophoresis. SSC9 - 9th Scandinavian Symposium on Chemometrics
-
KonferanseforedragRye, Morten Beck; Alsberg, Bjørn Kåre. (2005) Comparing Segmentation methods in Two-Dimensional Gel Electrophoresis. BFYS 2005