Full Text Journal Articles by
Author Morten Rye

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Genomic selection for white spot syndrome virus resistance in whiteleg shrimp boosts survival under an experimental challenge test.

Marie Lillehammer, Rama Bangera, Marcela Salazar, Sergio Vela, Edna C Erazo, Andres Suarez, James Cock, Morten Rye, Nicholas Andrew Robinson,

White spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The development of resistant shrimp populations is an attractive option for management of the disease. However, heritability for WSSV resistance is generally low and genetic improvement by conventional selection has been slow. This study was designed to determine ... Read more >>

Sci Rep (Scientific reports)
[2020, 10(1):20571]

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LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium.

Rosalie T Zwiggelaar, Håvard T Lindholm, Madeleine Fosslie, Marianne Terndrup Pedersen, Yuki Ohta, Alberto Díez-Sánchez, Mara Martín-Alonso, Jenny Ostrop, Mami Matano, Naveen Parmar, Emilie Kvaløy, Roos R Spanjers, Kamran Nazmi, Morten Rye, Finn Drabløs, Cheryl Arrowsmith, John Arne Dahl, Kim B Jensen, Toshiro Sato, Menno J Oudhoff,

Intestinal epithelial homeostasis is maintained by adult intestinal stem cells, which, alongside Paneth cells, appear after birth in the neonatal period. We aimed to identify regulators of neonatal intestinal epithelial development by testing a small library of epigenetic modifier inhibitors in Paneth cell-skewed organoid cultures. We found that lysine-specific demethylase ... Read more >>

Sci Adv (Science advances)
[2020, 6(37):]

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MACPET: model-based analysis for ChIA-PET.

Ioannis Vardaxis, Finn Drabløs, Morten B Rye, Bo Henry Lindqvist,

We present model-based analysis for ChIA-PET (MACPET), which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels in ... Read more >>

Biostatistics (Biostatistics (Oxford, England))
[2020, 21(3):625-639]

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Genetic variation in growth pattern within a population of farmed Atlantic salmon (Salmo salar) during a standard production cycle

Ingunn Thorland, Jørn Thodesen, Terje Refstie, Ole Folkedal, Lars Helge Stien, Jonatan Nilsson, Rudi Ripman Seim, Tore S Kristiansen, Morten Rye,

Selection for faster growth to market size has a long history in selective breeding programs for aquaculture species. In Atlantic salmon, selection for faster growth has been carried out for more than four decades, i.e. about ten generations. Genetic improvement of growth rate is indicated as favourable correlated to improved ... Read more >>

Aquaculture (Aquaculture (Amsterdam, Netherlands))
[2020, 518:Not Available]

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LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium

Rosalie Zwiggelaar, Håvard Lindholm, Madeleine Fosslie, Marianne Pedersen, Yuki Ohta, Alberto Díez-Sánchez, Mara Martín-Alonso, Jenny Ostrop, Mami Matano, Naveen Parmar, Emilie Kvaløy, Roos Spanjers, Kamran Nazmi, Morten Rye, Finn Drabløs, Cheryl Arrowsmith, John Arne Dahl, Kim Jensen, Toshiro Sato, Menno Oudhoff,

ABSTRACT Intestinal epithelial homeostasis is maintained by adult intestinal stem cells, which, alongside Paneth cells, appear after birth in the neonatal period. We aimed to identify new regulators of neonatal intestinal epithelial development by testing a small library of epigenetic modifier inhibitors in Paneth cell-skewed organoid cultures. We found that ... Read more >>

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DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation.

Ieva Rauluseviciute, Finn Drabløs, Morten Beck Rye,

BACKGROUND:Prostate cancer (PCa) has the highest incidence rates of cancers in men in western countries. Unlike several other types of cancer, PCa has few genetic drivers, which has led researchers to look for additional epigenetic and transcriptomic contributors to PCa development and progression. Especially datasets on DNA methylation, the most ... Read more >>

BMC Med Genomics (BMC medical genomics)
[2020, 13(1):6]

Cited: 2 times

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DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis.

Ieva Rauluseviciute, Finn Drabløs, Morten Beck Rye,

Sequencing technologies have changed not only our approaches to classical genetics, but also the field of epigenetics. Specific methods allow scientists to identify novel genome-wide epigenetic patterns of DNA methylation down to single-nucleotide resolution. DNA methylation is the most researched epigenetic mark involved in various processes in the human cell, ... Read more >>

Clin Epigenetics (Clinical epigenetics)
[2019, 11(1):193]

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Selection response for Streptococcus agalactiae resistance in Nile tilapia Oreochromis niloticus.

Wasana Suebsong, Supawadee Poompuang, Prapansak Srisapoome, Skorn Koonawootrittriron, Amorn Luengnaruemitchai, Harry Johansen, Morten Rye,

The potential of selection to improve resistance to streptococcosis was evaluated in a commercial population of Nile tilapia in Thailand. The base generation (G0) consisted of offspring from 98 sires and 149 dams using a partly nested design. At 60 days post-hatch, 30 fish from each family were injected intraperitoneally with ... Read more >>

J Fish Dis (Journal of fish diseases)
[2019, 42(11):1553-1562]

Cited: 1 time

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Glutamine to proline conversion is associated with response to glutaminase inhibition in breast cancer.

Maria T Grinde, Bylgja Hilmarsdottir, Hanna Maja Tunset, Ida Marie Henriksen, Jana Kim, Mads H Haugen, Morten Beck Rye, Gunhild M Mælandsmo, Siver A Moestue,

INTRODUCTION:Glutaminase inhibitors target cancer cells by blocking the conversion of glutamine to glutamate, thereby potentially interfering with anaplerosis and synthesis of amino acids and glutathione. The drug CB-839 has shown promising effects in preclinical experiments and is currently undergoing clinical trials in several human malignancies, including triple-negative breast cancer (TNBC). ... Read more >>

Breast Cancer Res (Breast cancer research : BCR)
[2019, 21(1):61]

Cited: 3 times

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Genetic parameters for growth and survival in rohu carp (Labeo rohita)

Bjarne Gjerde, Kanta D Mahapatra, Padala V G K Reddy, Jatendra N Saha, Ranjit K Jana, Prem K Meher, Minakshi Sahoo, Hooi Ling Khaw, Trygve Gjedrem, Morten Rye,

Estimates of genetic parameters for growth and survival were obtained from data recorded on 16,718 rohu carp (Labeo rohita), the offspring of 311 sires and 257 dams from seven year-classes. The fish from the first five year-classes (1993 to 1997) were reared in both mono- and polyculture (together with catla ... Read more >>

Aquaculture (Aquaculture (Amsterdam, Netherlands))
[2019, 503:381-388]

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Integrative metabolic and transcriptomic profiling of prostate cancer tissue containing reactive stroma.

Maria K Andersen, Kjersti Rise, Guro F Giskeødegård, Elin Richardsen, Helena Bertilsson, Øystein Størkersen, Tone F Bathen, Morten Rye, May-Britt Tessem,

Reactive stroma is a tissue feature commonly observed in the tumor microenvironment of prostate cancer and has previously been associated with more aggressive tumors. The aim of this study was to detect differentially expressed genes and metabolites according to reactive stroma content measured on the exact same prostate cancer tissue ... Read more >>

Sci Rep (Scientific reports)
[2018, 8(1):14269]

Cited: 4 times

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Norwegian e-Infrastructure for Life Sciences (NeLS)

Kidane Tekle, Sveinung Gundersen, Kjetil Klepper, Lars Ailo Bongo, Inge Alexander Raknes, Xiaxi Li, Wei Zhang, Christian Andreetta, Teshome Dagne Mulugeta, Matúš Kalaš, Morten Rye, Erik Hjerde, Jeevan Karloss Antony Samy, Ghislain Fornous, Abdulrahman Azab, Dag Inge Våge, Eivind Hovig, Nils Peder Willassen, Finn Drabløs, Ståle Nygård, Kjell Petersen, Inge Jonassen,

The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confident ... Read more >>

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Norwegian e-Infrastructure for Life Sciences (NeLS).

Kidane M Tekle, Sveinung Gundersen, Kjetil Klepper, Lars Ailo Bongo, Inge Alexander Raknes, Xiaxi Li, Wei Zhang, Christian Andreetta, Teshome Dagne Mulugeta, Matúš Kalaš, Morten B Rye, Erik Hjerde, Jeevan Karloss Antony Samy, Ghislain Fornous, Abdulrahman Azab, Dag Inge Våge, Eivind Hovig, Nils Peder Willassen, Finn Drabløs, Ståle Nygård, Kjell Petersen, Inge Jonassen,

The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confident ... Read more >>

F1000Res (F1000Research)
[2018, 7:]

Cited: 2 times

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MACPET: Model-based Analysis for ChIA-PET

Ioannis Vardaxis, Finn Drabløs, Morten Rye, Bo Henry Lindqvist,

Abstract We present Model-based Analysis for ChIA-PET (MACPET) which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels ... Read more >>

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APIM-peptide targeting PCNA improves the efficacy of docetaxel treatment in the TRAMP mouse model of prostate cancer.

Caroline K Søgaard, Siver A Moestue, Morten B Rye, Jana Kim, Anala Nepal, Nina-Beate Liabakk, Siri Bachke, Tone F Bathen, Marit Otterlei, Deborah K Hill,

Docetaxel is the chemotherapeutic choice for metastatic hormone-refractory prostate cancer, however, it only marginally improves the survival rate. The purpose of the present study was to examine if a peptide targeting the cellular scaffold protein PCNA could improve docetaxel's efficacy. We found that docetaxel given in combination with a cell ... Read more >>

Oncotarget (Oncotarget)
[2018, 9(14):11752-11766]

Cited: 9 times

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Cholesterol Synthesis Pathway Genes in Prostate Cancer are consistently downregulated when tissue confounding is minimized

Morten Beck Rye, Helena Bertilsson, Maria Andersen, Kjersti Rise, Tone Bathen, Finn Drabløs, May-Britt Tessem,

Abstract The relationship between cholesterol and prostate cancer has been extensively studied for decades, where high levels of cellular cholesterol are generally associated with cancer progression and less favorable outcomes. However, the role of in vivo cellular cholesterol synthesis in this process is unclear, and data on the transcriptional activity ... Read more >>

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SFRP4 gene expression is increased in aggressive prostate cancer.

Elise Sandsmark, Maria K Andersen, Anna M Bofin, Helena Bertilsson, Finn Drabløs, Tone F Bathen, Morten B Rye, May-Britt Tessem,

Increased knowledge of the molecular differences between indolent and aggressive prostate cancer is needed for improved risk stratification and treatment selection. Secreted frizzled-related protein 4 (SFRP4) is a modulator of the cancer-associated Wnt pathway, and previously suggested as a potential marker for prostate cancer aggressiveness. In this study, we investigated ... Read more >>

Sci Rep (Scientific reports)
[2017, 7(1):14276]

Cited: 9 times

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Additive genetic variation in resistance of Nile tilapia (Oreochromis niloticus) to Streptococcus iniae and S. agalactiae capsular type Ib: Is genetic resistance correlated?

Craig A Shoemaker, Benjamin H Beck, Julio C García, Benjamin R LaFrentz, Carlos A Lozano, Morten Rye, Esteban Soto, De-Hai Xu,

Streptococcus iniae and S. agalactiae are both economically important Gram positive bacterial pathogens affecting the globally farmed tilapia (Oreochromis spp.). Historically, control of these bacteria in tilapia culture has included biosecurity, therapeutants and vaccination strategies. Genetic gains in performance traits have been realized for Nile tilapia (Oreochromis niloticus) and interest ... Read more >>

Aquaculture (Aquaculture (Amsterdam, Netherlands))
[2017, 468:193-198]

Cited: 5 times

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A novel non-canonical Wnt signature for prostate cancer aggressiveness.

Elise Sandsmark, Ailin Falkmo Hansen, Kirsten M Selnæs, Helena Bertilsson, Anna M Bofin, Alan J Wright, Trond Viset, Elin Richardsen, Finn Drabløs, Tone F Bathen, May-Britt Tessem, Morten B Rye,

Activation of the Canonical Wnt pathway (CWP) has been linked to advanced and metastatic prostate cancer, whereas the Wnt5a-induced non-canonical Wnt pathway (NCWP) has been associated with both good and poor prognosis. A newly discovered NCWP, Wnt5/Fzd2, has been shown to induce epithelial-to-mesenchymal transition (EMT) in cancers, but has not ... Read more >>

Oncotarget (Oncotarget)
[2017, 8(6):9572-9586]

Cited: 18 times

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Presence of TMPRSS2-ERG is associated with alterations of the metabolic profile in human prostate cancer.

Ailin Falkmo Hansen, Elise Sandsmark, Morten Beck Rye, Alan J Wright, Helena Bertilsson, Elin Richardsen, Trond Viset, Anna M Bofin, Anders Angelsen, Kirsten M Selnæs, Tone Frost Bathen, May-Britt Tessem,

TMPRSS2-ERG has been proposed to be a prognostic marker for prostate cancer. The aim of this study was to identify changes in metabolism, genes and biochemical recurrence related to TMPRSS2-ERG by using an integrated approach, combining metabolomics, transcriptomics, histopathology and clinical data in a cohort of 129 human prostate samples ... Read more >>

Oncotarget (Oncotarget)
[2016, 7(27):42071-42085]

Cited: 11 times

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Controlled challenge experiment demonstrates substantial additive genetic variation in resistance of Nile tilapia (Oreochromis niloticus) to Streptococcus iniae

Benjamin R LaFrentz, Julio C García, Marie Løvoll, Carlos A Lozano, Morten Rye, Craig A Shoemaker, De-Hai Xu,

Streptococcus iniae is an etiologic agent of streptococcal disease in tilapia and is one of several Streptococcus spp. that negatively impact worldwide tilapia production. Methods for the prevention and control of S. iniae include vaccines, management strategies, and antibiotics. A complimentary preventative approach may include selective breeding for disease resistance, ... Read more >>

Aquaculture (Aquaculture (Amsterdam, Netherlands))
[2016, 458:134-139]

Cited: 1 time

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Phosphatase of regenerating liver 3 (PRL-3) is overexpressed in human prostate cancer tissue and promotes growth and migration.

Esten N Vandsemb, Helena Bertilsson, Pegah Abdollahi, Øystein Størkersen, Thea Kristin Våtsveen, Morten Beck Rye, Torstein Baade Rø, Magne Børset, Tobias S Slørdahl,

PRL-3 is a phosphatase implicated in oncogenesis in multiple cancers. In some cancers, notably carcinomas, PRL-3 is also associated with inferior prognosis and increased metastatic potential. In this study we investigated the expression of PRL-3 mRNA in fresh-frozen samples from patients undergoing radical prostatectomy because of prostate cancer (PC) and ... Read more >>

J Transl Med (Journal of translational medicine)
[2016, 14:71]

Cited: 8 times

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A Balanced Tissue Composition Reveals New Metabolic and Gene Expression Markers in Prostate Cancer.

May-Britt Tessem, Helena Bertilsson, Anders Angelsen, Tone F Bathen, Finn Drabløs, Morten Beck Rye,

Molecular analysis of patient tissue samples is essential to characterize the in vivo variability in human cancers which are not accessible in cell-lines or animal models. This applies particularly to studies of tumor metabolism. The challenge is, however, the complex mixture of various tissue types within each sample, such as ... Read more >>

PLoS One (PloS one)
[2016, 11(4):e0153727]

Cited: 6 times

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The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

Laurence D Hurst, Avazeh T Ghanbarian, Alistair R R Forrest, , Lukasz Huminiecki,

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, ... Read more >>

PLoS Biol (PLoS biology)
[2015, 13(12):e1002315]

Cited: 13 times

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Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage.

Daniel Carbajo, Shigeyuki Magi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Erik Arner, Alistair R R Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub, , Mariko Okada-Hatakeyama, Jessica C Mar,

Understanding how cells use complex transcriptional programs to alter their fate in response to specific stimuli is an important question in biology. For the MCF-7 human breast cancer cell line, we applied gene expression trajectory models to identify the genes involved in driving cell fate transitions. We modified trajectory models ... Read more >>

PLoS One (PloS one)
[2015, 10(12):e0144176]

Cited: 0 times

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