• Accuracy and efficiency of germline variant calling pipelines for human genome data 

      Zhao, Sen; Agafonov, Oleg; Azab, Abdulrahman; Stokowy, Tomasz; Hovig, Eivind (Journal article; Peer reviewed, 2020)
      Advances in next-generation sequencing technology have enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into ...
    • Cross talk between cytokine and hyperthermia-induced pathways: identification of different subsets of NF-κB-dependent genes regulated by TNFα and heat shock 

      Janus, Patryk; Stokowy, Tomasz; Jaksik, Roman; Szoltysek, Katarzyna; Handschuh, Luiza; Podkowinski, Jan; Widlak, Wieslawa; Kimmel, Marek; Widlak, Piotr (Peer reviewed; Journal article, 2015-05-06)
      Heat shock inhibits NF-κB signaling, yet the knowledge about its influence on the regulation of NF-κB-dependent genes is limited. Using genomic approaches, i.e., expression microarrays and ChIP-Seq, we aimed to establish ...
    • Crosstalk between HSF1 and HSF2 during the heat shock response in mouse testes 

      Korfanty, Joanna; Stokowy, Tomasz; Widlak, Piotr; Gogler-Piglowska, Agnieszka; Handschuh, Luiza; Podkowinski, Jan; Vydra, Natalia; Naumowicz, Anna; Toma-Jonik, Agnieszka; Widlak, Wieslawa (Peer reviewed; Journal article, 2014-12)
      Heat Shock Factor 1 (HSF1) is the primary transcription factor responsible for the response to cellularstress, while HSF2 becomes activated during development and differentiation, including spermatogen-esis. Although both ...
    • Diagnostic accuracy of liquid biopsy in endometrial cancer 

      Łukasiewicz, Marta; Pastuszak, Krzysztof; Łapińska-Szumczyk, Sylwia; Różański, Robert; In ‘T Veld, Sjors G. J. G.; Bieńkowski, Michał; Stokowy, Tomasz; Ratajska, Magdalena; Best, Myron G.; Würdinger, Thomas; Żaczek, Anna J.; Supernat, Anna; Jassem, Jacek (Journal article; Peer reviewed, 2021)
      Background: Liquid biopsy is a minimally invasive collection of a patient body fluid sample. In oncology, they offer several advantages compared to traditional tissue biopsies. However, the potential of this method in ...
    • Genetic variation in 117 myelination-related genes in schizophrenia: Replication of association to lipid biosynthesis genes 

      Stokowy, Tomasz; Polushina, Tatiana; Sønderby, Ida Elken; Karlsson, Robert; Giddaluru, Sudheer; Le Hellard, Stephanie; Bergen, Sarah E; Sullivan, Patrick F; Andreassen, Ole Andreas; Djurovic, Srdjan; Hultman, Christina M.; Steen, Vidar Martin (Peer reviewed; Journal article, 2018-05-02)
      Schizophrenia is a serious psychotic disorder with high heritability. Several common genetic variants, rare copy number variants and ultra-rare gene-disrupting mutations have been linked to disease susceptibility, but there ...
    • Genetic variation in metronidazole metabolism and oxidative stress pathways in clinical giardia lamblia assemblage A and B isolates 

      Saghaug, Christina Skår; Klotz, Christian; Kallio, Juha Pekka; Brattbakk, Hans-Richard; Stokowy, Tomasz; Aebischer, Toni; Kursula, Inari; Langeland, Nina; Hanevik, Kurt (Peer reviewed; Journal article, 2019-05-10)
      Purpose: Treatment-refractory Giardia cases have increased rapidly within the last decade. No markers of resistance nor a standardized susceptibility test have been established yet, but several enzymes and their pathways ...
    • Heat shock factor 1 (Hsf1) cooperates with estrogen receptor α (erα) in the regulation of estrogen action in breast cancer cells 

      Vydra, Natalia; Janus, Patryk; Kuś, Paweł; Stokowy, Tomasz; Mrowiec, Katarzyna; Toma-Jonik, Agnieszka; Krzywon, Aleksandra; Cortez, Alexander Jorge; Wojtaś, Bartosz; Gielniewski, Bartłomiej; Jaksik, Roman; Kimmel, Marek; Widłak, Wiesława (Journal article; Peer reviewed, 2021)
      Heat shock factor 1 (HSF1), a key regulator of transcriptional responses to proteotoxic stress, was linked to estrogen (E2) signaling through estrogen receptor α (ERα). We found that an HSF1 deficiency may decrease ERα ...
    • imPlatelet classifier: image-converted RNA biomarker profiles enable blood-based cancer diagnostics 

      Pastuszak, Krzysztof; Supernat, Anna; Best, Myron G.; In 't Veld, Sjors G.J.G.; Łapińska-Szumczyk, Sylwia; Łojkowska, Anna; Różański, Robert; Zaczek, Anna J; Jassem, Jacek; Würdinger, Thomas; Stokowy, Tomasz (Journal article; Peer reviewed, 2021)
      Liquid biopsies offer a minimally invasive sample collection, outperforming traditional biopsies employed for cancer evaluation. The widely used material is blood, which is the source of tumor-educated platelets. Here, we ...
    • Patient-derived organoids reflect the genetic profile of endometrial tumors and predict patient prognosis 

      Berg, Hege Fredriksen; Hjelmeland, Marta Espevold; Lien, Hilde Eide; Espedal, Heidi; Fonnes, Tina; Srivastava, Aashish; Stokowy, Tomasz; Strand, Elin; Bozickovic, Olivera; Stefansson, Ingunn Marie; Bjørge, Line; Trovik, Jone; Haldorsen, Ingfrid Helene Salvesen; Høivik, Erling Andre; Krakstad, Camilla (Journal article; Peer reviewed, 2021)
      Background: A major hurdle in translational endometrial cancer (EC) research is the lack of robust preclinical models that capture both inter- and intra-tumor heterogeneity. This has hampered the development of new treatment ...
    • Phosphatidylserine receptors enhance SARS-CoV-2 infection 

      Bohan, Dana; Van Ert, Hanora; Ruggio, Natalie; Rogers, Kai J; Badreddine, Mohammad; Aguilar Briseno, José A; Elliff, Jonah; Rojas Chavez, Roberth Anthony; Gao, Boning; Stokowy, Tomasz; Christakou, Eleni; Kursula, Petri; Micklem, David Robert; Gausdal, Gro; Haim, Hillel; Minna, John; Lorens, James Bradley; Maury, Wendy (Journal article; Peer reviewed, 2021)
      Phosphatidylserine (PS) receptors enhance infection of many enveloped viruses through virion-associated PS binding that is termed apoptotic mimicry. Here we show that this broadly shared uptake mechanism is utilized by ...
    • Predictive value of angiogenic proteins in patients with metastatic melanoma treated with bevacizumab monotherapy 

      Schuster, Cornelia; Akslen, Lars A.; Stokowy, Tomasz; Straume, Oddbjørn (Peer reviewed; Journal article, 2019)
      The incidence of malignant melanoma is rising worldwide and survival for metastatic disease is still poor. Recently, new treatment options have become available. Still, predictive biomarkers are needed to optimise treatment ...
    • Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia 

      Aasebø, Elise; Berven, Frode; Bartaula-Brevik, Sushma; Stokowy, Tomasz; Hovland, Randi; Vaudel, Marc; Døskeland, Stein Ove; Mc Cormack, Emmet; Batth, Tanveer S; Olsen, Jesper V; Bruserud, Øystein; Selheim, Frode; Hernandez-Valladares, Maria (Journal article; Peer reviewed, 2020)
      Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly ...
    • Reduced expression of innate immunity-related genes in lymph node metastases of luminal breast cancer patients 

      Popeda, Marta; Markiewicz, Aleksandra; Stokowy, Tomasz; Szade, Jolanta; Niemira, Magdalena; Kretowski, Adam; Bednarz-Knoll, Natalia; Zaczek, Anna J (Journal article; Peer reviewed, 2021)
      Immune system plays a dual role in cancer by either targeting or supporting neoplastic cells at various stages of disease, including metastasis. Yet, the exact immune-related transcriptome profiles of primary tumours (PT) ...
    • Reduced expression of OXPHOS and DNA damage genes is linked to protection from microvascular complications in long-term type 1 diabetes: the PROLONG study 

      Özgümüs, Türküler; Sulaieva, Oksana; Jessen, Leon E.; Jain, Ruchi; Falhammar, Henrik; Nyström, Thomas; Catrina, Sergiu-Bogdan; Jörneskog, Gun; Groop, Leif; Eliasson, Mats; Eliasson, Björn; Brismar, Kerstin; Stokowy, Tomasz; Nilsson, Peter M.; Lyssenko, Valeriya (Journal article; Peer reviewed, 2021)
      Type 1 diabetes is a chronic autoimmune disease requiring insulin treatment for survival. Prolonged duration of type 1 diabetes is associated with increased risk of microvascular complications. Although chronic hyperglycemia ...
    • The role of NF-κB transcription factor in cellular response to ionizing radiation 

      Janus, Patryk; Szoltysek, Katarzyna; Zajac, Gracjana; Widlak, Wieslawa; Stokowy, Tomasz; Wojtas, Bartosz; Widlak, Piotr (Journal article, 2019)
      The NF-κB transcription factor is involved in different aspects of the cellular response to stress, including atypical NF-κB pathway activated by damage induced by ionizing radiation. Moreover, NF-κB could be involved in ...
    • Transcriptomic landscape of blood platelets in healthy donors 

      Supernat, Anna; Popęda, Marta; Pastuszak, Krzysztof; Best, Myron G.; Grešner, Peter; Veld, Sjors In ’t; Siek, Bartłomiej; Bednarz-Knoll, Natalia; Rondina, Matthew T.; Stokowy, Tomasz; Würdinger, Thomas; Jassem, Jacek; Żaczek, Anna J. (Journal article; Peer reviewed, 2021)
      Blood platelet RNA-sequencing is increasingly used among the scientific community. Aberrant platelet transcriptome is common in cancer or cardiovascular disease, but reference data on platelet RNA content in healthy ...