Siste publikasjoner

• Santana-Garcia, Walter; Castro Mondragon, Jaime Abraham; Padilla-Gálvez, Mónica; Nguyen, Nga Thi Thuy; Elizondo-Salas, Ana & Ksouri, Najla [Vis alle 13 forfattere av denne artikkelen] (2022). RSAT 2022: regulatory sequence analysis tools. Nucleic Acids Research (NAR). ISSN 0305-1048. 50(1), s. W670–W676. doi: 10.1093/nar/gkac312.
• Kriener, Birgit; Hu, Hua & Vervaeke, Koen Gerard Alois (2022). Parvalbumin interneuron dendrites enhance gamma oscillations. Cell reports. ISSN 2211-1247. 39(11). doi: 10.1016/j.celrep.2022.110948.
• Guebila, Marouen Ben; Morgan, Daniel C.; Glass, Kimberly; Kuijjer, Marieke; Demeo, Dawn L. & Quackenbush, John (2022). gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. NAR Genomics and Bioinformatics. ISSN 2631-9268. 4(1). doi: 10.1093/nargab/lqac002.
• Strømme, Jonas Meier; Johannessen, Bjarne; Kidd, Susanne Gundersen; Bogaard, Mari; Carm, Kristina Totland & Zhang, Xiaokang [Vis alle 12 forfattere av denne artikkelen] (2022). Expressed prognostic biomarkers for primary prostate cancer independent of multifocality and transcriptome heterogeneity. Cancer Gene Therapy. ISSN 0929-1903. s. 1–9. doi: 10.1038/s41417-022-00444-7.
• Arranz, Lorena (2022). The Hematology of Tomorrow Is Here-Preclinical Models Are Not: Cell Therapy for Hematological Malignancies. Cancers. ISSN 2072-6694. 14(3). doi: 10.3390/cancers14030580. Fulltekst i vitenarkiv
• Lemma, Roza Berhanu; Fleischer, Thomas; Martinsen, Emily; Ledsaak, Marit; Kristensen, Vessela N. & Eskeland, Ragnhild [Vis alle 8 forfattere av denne artikkelen] (2022). Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics & Chromatin. ISSN 1756-8935. 15. doi: 10.1186/s13072-022-00444-9.
• Giliberto, Mariaserena; Thimiri Govinda Raj, Deepak Balaji; Cremaschi, Andrea; Skånland, Sigrid S; Gade, Alexandra & Tjønnfjord, Geir Erland [Vis alle 9 forfattere av denne artikkelen] (2022). Ex vivo drug sensitivity screening in multiple myeloma identifies drug combinations that act synergistically. Molecular Oncology. ISSN 1574-7891. 16(6), s. 1241–1258. doi: 10.1002/1878-0261.13191.
• Spalla, Davide; Treves, Alessandro & Boccara, Charlotte (2022). Angular and linear speed cells in the parahippocampal circuits. Nature Communications. ISSN 2041-1723. 13. doi: 10.1038/s41467-022-29583-z.
• Tran, Vi Ngoc-Nha; Shams, Alireza; Ascioglu, Sinan; Martinecz, Antal; Liang, Jingyi & Clarelli, Fabrizio [Vis alle 9 forfattere av denne artikkelen] (2022). vCOMBAT: a novel tool to create and visualize a computational model of bacterial antibiotic target-binding. BMC Bioinformatics. ISSN 1471-2105. 23(1), s. 1–15. doi: 10.1186/s12859-021-04536-3. Fulltekst i vitenarkiv
• Corkery, Dale P.; Nadeem, Aftab; Aung, Kyaw Min; Hassan, Ahmed; Liu, Tao & Cervantes-Rivera, Ramón [Vis alle 14 forfattere av denne artikkelen] (2021). Vibrio cholerae cytotoxin MakA induces noncanonical autophagy resulting in the spatial inhibition of canonical autophagy. Journal of Cell Science. ISSN 0021-9533. 134(5). doi: 10.1242/jcs.252015.
• Hashem, Hasan; Bucciol, Giorgia; Ozen, Seza; Unal, Sule; Ok Bozkaya, Ikbal & Akarsu, Nurten [Vis alle 51 forfattere av denne artikkelen] (2021). Hematopoietic Cell Transplantation Cures Adenosine Deaminase 2 Deficiency: Report on 30 Patients. Journal of Clinical Immunology. ISSN 0271-9142. doi: 10.1007/s10875-021-01098-0. Fulltekst i vitenarkiv
• Kaustio, Meri; Nayebzadeh, Naemeh; Hinttala, Reetta; Tapiainen, Terhi; Åström, Pirjo & Mamia, Katariina Aino Inkeri [Vis alle 37 forfattere av denne artikkelen] (2021). Loss of DIAPH1 causes SCBMS, combined immunodeficiency, and mitochondrial dysfunction. Journal of Allergy and Clinical Immunology. ISSN 0091-6749. 148(2), s. 599–611. doi: 10.1016/j.jaci.2020.12.656. Fulltekst i vitenarkiv
• Harjama, Liisa; Karvonen, V; Elomaa, O.; Einarsdottir, E; Heikkilä, H & Kivirikko, Sirpa [Vis alle 11 forfattere av denne artikkelen] (2021). Hereditary palmoplantar keratoderma – phenotypes and mutations in 64 patients. Journal of the European Academy of Dermatology and Venereology. ISSN 0926-9959. doi: 10.1111/jdv.17314.
• Cotsapas, Chris; Saarela, Janna Saija; Farmer, Jocelyn R.; Scaria, Vinod & Abraham, Roshini S. (2021). Do monogenic inborn errors of immunity cause susceptibility to severe COVID-19? Journal of Clinical Investigation. ISSN 0021-9738. doi: 10.1172/JCI149459.
• Savola, Paula; Martelius, Timi; Kankainen, Matti; Huuhtanen, Jani; Lundgren, Sofie & Koski, Yrjö [Vis alle 16 forfattere av denne artikkelen] (2021). Somatic mutations and T-cell clonality in patients with immunodeficiency. Haematologica. ISSN 0390-6078. doi: 10.3324/haematol.2019.220889. Fulltekst i vitenarkiv
• Gawel, Kinga Aurelia; Kukula-Koch, Wirginia; Banono, Nancy Saana; Nieoczym, Dorota; Targowska-Duda, Katarzyna M & Czernicka, Lidia [Vis alle 8 forfattere av denne artikkelen] (2021). 6-Gingerol, a Major Constituent of Zingiber officinale Rhizoma, Exerts Anticonvulsant Activity in the Pentylenetetrazole-Induced Seizure Model in Larval Zebrafish . International Journal of Molecular Sciences. ISSN 1661-6596. 22(14), s. 1–22. doi: 10.3390/ijms22147745. Fulltekst i vitenarkiv
• Kalinichenko, Artem; Perinetti Casoni, Giovanna; Dupré, Loïc; Trotta, Luca; Huemer, Jakob & Galgano, Donatella [Vis alle 24 forfattere av denne artikkelen] (2021). RhoG deficiency abrogates cytotoxicity of human lymphocytes and causes hemophagocytic lymphohistiocytosis. Blood. ISSN 0006-4971. 137(15), s. 2033–2045. doi: 10.1182/blood.2020008738.
• Malani, Disha; Adish Kumar, Kumar; Brück, Oscar; Kontro, Mika; Yadav, Bhagwan & Hellesøy, Monica [Vis alle 27 forfattere av denne artikkelen] (2021). Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia. Cancer Discovery. ISSN 2159-8274. doi: 10.1158/2159-8290.CD-21-0410. Fulltekst i vitenarkiv
• Reint, Ganna; Li, Zhuokun; Labun, Kornel; Keskitalo, Salla; Soppa, Inkeri & Mamia, Katariina Aino Inkeri [Vis alle 19 forfattere av denne artikkelen] (2021). Rapid genome editing by CRISPR-Cas9-POLD3 fusion. eLIFE. ISSN 2050-084X. 11. doi: 10.7554/eLife.75415. Fulltekst i vitenarkiv
• Hetemäki, Iivo; Kaustio, Meri; Kinnunen, Matias; Heikkilä, Nelli; Keskitalo, Salla & Nowlan, Kirsten [Vis alle 26 forfattere av denne artikkelen] (2021). Loss-of-function mutation in IKZF2 leads to immunodeficiency with dysregulated germinal center reactions and reduction of MAIT cells. Science immunology. ISSN 2470-9468. 6(65). doi: 10.1126/sciimmunol.abe3454.
• Stewart, Lorna M.; Gerner, Lisa; Rettel, Mandy; Stein, Frank; Burrows, James F. & Mills, Ian [Vis alle 7 forfattere av denne artikkelen] (2021). CaMKK2 facilitates Golgi-associated vesicle trafficking to sustain cancer cell proliferation. Cell Death & Disease. ISSN 2041-4889. 12(11), s. 1–12. doi: 10.1038/s41419-021-04335-x.
• Gillman, Aaron Nicholas; Mahmutovic, Anel; Abel zur Wiesch, Pia & Abel, Sören (2021). The Infectious Dose Shapes Vibrio Cholerae Within-Host Dynamics. mSystems. ISSN 2379-5077. 6(6), s. 1–19. doi: 10.1128/mSystems.00659-21. Fulltekst i vitenarkiv
• Gillman, Aaron Nicholas; Helleux, Alexandra & Abel, Sören (2021). A single step three-strain in vivo Gateway reaction. Plasmid. ISSN 0147-619X. 118. doi: 10.1016/j.plasmid.2021.102608. Fulltekst i vitenarkiv
• Klionsky, Daniel J.; Abdel-Aziz, Amal Kamal; Abdelfatah, Sara; Abdellatif, Mahmoud Khaled; Abdoli, Asghar & Abudu, Yakubu Princely [Vis alle 50 forfattere av denne artikkelen] (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) . Autophagy. ISSN 1554-8627. 17(1), s. 1–382. doi: 10.1080/15548627.2020.1797280.
• Arjmandi, Hamidreza; Rudsari, Hamid Khoshfekr; Santos, Joao; Zoofaghari, Mohammad; Ievglevskyi, Oleksandr & Kanada, Masamitsu [Vis alle 9 forfattere av denne artikkelen] (2021). Extracellular Vesicle-Mediated Communication Nanonetworks: Opportunities and Challenges. IEEE Communications Magazine. ISSN 0163-6804. 59(5), s. 68–73. doi: 10.1109/MCOM.001.2000994.
• Riudavets, Rafael; Boddie, Paul; Khan, Aziz; Castro Mondragon, Jaime Abraham & Mathelier, Anthony (2021). UniBind: maps of high-confidence direct TF-DNA interactions across nine species. BMC Genomics. ISSN 1471-2164. 22(482), s. 1–17. doi: 10.1186/s12864-021-07760-6. Fulltekst i vitenarkiv
• Lemma, Roza Berhanu; Ledsaak, Marit; Fuglerud, Bettina Maria; Sandve, Geir Kjetil; Eskeland, Ragnhild & Gabrielsen, Odd Stokke (2021). Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB. Scientific Reports. ISSN 2045-2322. 11(9008). doi: 10.1038/s41598-021-88516-w. Fulltekst i vitenarkiv Vis sammendrag

  The transcription factor MYB is a master regulator in haematopoietic progenitor cells and a pioneer factor affecting differentiation and proliferation of these cells. Leukaemic transformation may be promoted by high MYB levels. Despite much accumulated molecular knowledge of MYB, we still lack a comprehensive understanding of its target genes and its chromatin action. In the present work, we performed a ChIP-seq analysis of MYB in K562 cells accompanied by detailed bioinformatics analyses. We found that MYB occupies both promoters and enhancers. Five clusters (C1–C5) were found when we classified MYB peaks according to epigenetic profiles. C1 was enriched for promoters and C2 dominated by enhancers. C2-linked genes were connected to hematopoietic specific functions and had GATA factor motifs as second in frequency. C1 had in addition to MYB-motifs a significant frequency of ETS-related motifs. Combining ChIP-seq data with RNA-seq data allowed us to identify direct MYB target genes. We also compared ChIP-seq data with digital genomic footprinting. MYB is occupying nearly a third of the super-enhancers in K562. Finally, we concluded that MYB cooperates with a subset of the other highly expressed TFs in this cell line, as expected for a master regulator

• Taboada-Castro, Hermenegildo; Castro Mondragón, Jaime Abraham; Aguilar-Vera, Alejandro; Hernández-Álvarez, Alfredo José; van Helden, Jacques & Encarnación-Guevara, Sergio (2020). RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach. Frontiers in Microbiology. ISSN 1664-302X. 11, s. 1–11. doi: 10.3389/fmicb.2020.567471. Fulltekst i vitenarkiv
• Wang, Shixiong; Somisetty, Venkata Satheesh; Bai, Baoyan; Chernukhin, Igor; Niskanen, Henri & Kaikkonen, Minna [Vis alle 9 forfattere av denne artikkelen] (2020). The proapoptotic gene interferon regulatory factor-1 mediates the antiproliferative outcome of paired box 2 gene and tamoxifen. Oncogene. ISSN 0950-9232. 39, s. 6300–6312. doi: 10.1038/s41388-020-01435-4. Fulltekst i vitenarkiv
• Hannula-Jouppi, Katariina; Harjama, Liisa; Einarsdottir, Elisabet; Elomaa, Outi; Kettunen, Kaisa & Saarela, Janna [Vis alle 14 forfattere av denne artikkelen] (2020). Nagashima-type palmoplantar keratosis in Finland caused by a SERPINB7 founder mutation. Journal of American Academy of Dermatology. ISSN 0190-9622. 83(2), s. 643–645. doi: 10.1016/j.jaad.2019.11.004. Fulltekst i vitenarkiv
• Harjama, Liisa; Kettunen, Kaisa; Elomaa, Outi; Einarsdottir, Elisabet; Heikkilä, Hannele & Kivirikko, Sirpa [Vis alle 13 forfattere av denne artikkelen] (2020). Phenotypic Variability with SLURP1 Mutations and Diffuse Palmoplantar Keratoderma. Acta Dermato-Venereologica. ISSN 0001-5555. 100(4). doi: 10.2340/00015555-3404. Fulltekst i vitenarkiv
• Hakonen, Anna H; Lehtonen, Johanna; Kivirikko, Sirpa; Keski‐Filppula, Riikka; Moilanen, Jukka & Kivisaari, Reetta [Vis alle 11 forfattere av denne artikkelen] (2020). Recessive MYH3 variants cause “Contractures, pterygia, and variable skeletal fusions syndrome 1B” mimicking Escobar variant multiple pterygium syndrome. American Journal of Medical Genetics. Part A. ISSN 1552-4825. 182(11), s. 2605–2610. doi: 10.1002/ajmg.a.61836.
• Partanen, Terhi; Chen, Jie; Lehtonen, Johanna; Kuismin, Outi; Rusanen, Harri & Vapalahti, Olli [Vis alle 21 forfattere av denne artikkelen] (2020). Heterozygous TLR3 Mutation in Patients with Hantavirus Encephalitis. Journal of Clinical Immunology. ISSN 0271-9142. 40(8). doi: 10.1007/s10875-020-00834-2. Fulltekst i vitenarkiv
• Hautala, Timo; Chen, Jie; Tervonen, Laura; Partanen, Terhi; Winqvist, Satu & Lehtonen, Johanna [Vis alle 17 forfattere av denne artikkelen] (2020). Herpes simplex virus 2 encephalitis in a patient heterozygous for a TLR3 mutation. Neurology: Genetics. ISSN 2376-7839. 6(6). doi: 10.1212/NXG.0000000000000532. Fulltekst i vitenarkiv
• Caglayan, Safak; Hashim, Adnan; Cieslar-Pobuda, Artur; Jensen, Vidar; Behringer, Sidney & Talug, Burcu [Vis alle 16 forfattere av denne artikkelen] (2020). Optic Atrophy 1 Controls Human Neuronal Development by Preventing Aberrant Nuclear DNA Methylation. iScience. ISSN 2589-0042. 23(6). doi: 10.1016/j.isci.2020.101154. Fulltekst i vitenarkiv Vis sammendrag

  Optic atrophy 1 (OPA1), a GTPase at the inner mitochondrial membrane involved in regulating mitochondrial fusion, stability, and energy output, is known to be crucial for neural development: Opa1 heterozygous mice show abnormal brain development, and inactivating mutations in OPA1 are linked to human neurological disorders. Here, we used genetically modified human embryonic and patient-derived induced pluripotent stem cells and reveal that OPA1 haploinsufficiency leads to aberrant nuclear DNA methylation and significantly alters the transcriptional circuitry in neural progenitor cells (NPCs). For instance, expression of the forkhead box G1 transcription factor, which is needed for GABAergic neuronal development, is repressed in OPA1+/− NPCs. Supporting this finding, OPA1+/− NPCs cannot give rise to GABAergic interneurons, whereas formation of glutamatergic neurons is not affected. Taken together, our data reveal that OPA1 controls nuclear DNA methylation and expression of key transcription factors needed for proper neural cell specification.

• Cieslar-Pobuda, Artur; Ahrens, Theresa Dorothee; Caglayan, Safak; Behringer, Sidney; Hannibal, Luciana & Staerk, Judith (2020). DNMT3B deficiency alters mitochondrial biogenesis and α‐ketoglutarate levels in human embryonic stem cells. Stem Cells. ISSN 1066-5099. 38(11), s. 1409–1422. doi: 10.1002/stem.3256. Fulltekst i vitenarkiv Vis sammendrag

  Embryonic stem cell renewal and differentiation is regulated by metabolites that serve as cofactors for epigenetic enzymes. An increase of α‐ketoglutarate (α‐KG), a cofactor for histone and DNA demethylases, triggers multilineage differentiation in human embryonic stem cells (hESCs). To gain further insight into how the metabolic fluxes in pluripotent stem cells can be influenced by inactivating mutations in epigenetic enzymes, we generated hESCs deficient for de novo DNA methyltransferases (DNMTs) 3A and 3B. Our data reveal a bidirectional dependence between DNMT3B and α‐KG levels: a‐KG is significantly upregulated in cells deficient for DNMT3B, while DNMT3B expression is downregulated in hESCs treated with α‐KG. In addition, DNMT3B null hESCs exhibit a disturbed mitochondrial fission and fusion balance and a switch from glycolysis to oxidative phosphorylation. Taken together, our data reveal a novel link between DNMT3B and the metabolic flux of hESCs.

• Köksal, Elif; Liese, Susanne; Xue, Lin; Ryskulov, Ruslan; Viitala, Lauri & Carlson, Andreas [Vis alle 7 forfattere av denne artikkelen] (2020). Rapid Growth and Fusion of Protocells in Surface‐Adhered Membrane Networks. Small. ISSN 1613-6810. 16(38). doi: 10.1002/smll.202002529.
• Gözen, Irep & Dommersnes, Paul Gunnar (2020). Biological lipid nanotubes and their potential role in evolution. The European Physical Journal Special Topics. ISSN 1951-6355. 229(17-18), s. 2843–2862. doi: 10.1140/epjst/e2020-000130-7. Fulltekst i vitenarkiv
• Spustová, Karolina; Köksal, Elif; Ainla, Alar & Gözen, Irep (2020). Subcompartmentalization and Pseudo‐Division of Model Protocells. Small. ISSN 1613-6810. 17(2). doi: 10.1002/smll.202005320.
• Guldvik, Ingrid Jenny; Zuber, Verena; Braadland, Peder Rustøen; Grytli, Helene Hartvedt; Ramberg, Håkon Andre & Lilleby, Wolfgang [Vis alle 18 forfattere av denne artikkelen] (2020). Identification and Validation of Leucine-rich alpha-2-glycoprotein 1 as a Noninvasive Biomarker for Improved Precision in Prostate Cancer Risk Stratification. European Urology Open Science. ISSN 2666-1691. 21, s. 51–61. doi: 10.1016/j.euros.2020.08.007. Fulltekst i vitenarkiv
• Weikum, Julia; Kulakova, Alina; Tesei, Giulio; Yoshimoto, Shogo; Vejby Jægerum, Line & Schütz, Monika [Vis alle 11 forfattere av denne artikkelen] (2020). The extracellular juncture domains in the intimin passenger adopt a constitutively extended conformation inducing restraints to its sphere of action. Scientific Reports. ISSN 2045-2322. 10(1). doi: 10.1038/s41598-020-77706-7. Fulltekst i vitenarkiv
• Perdreau-Dahl, Harmonie; Progida, Cinzia; Barfeld, Stefan Jörg; Guldsten, Hanne; Thiede, Bernd & Arntzen, Magnus Øverlie [Vis alle 10 forfattere av denne artikkelen] (2020). Sjögren syndrome/scleroderma autoantigen 1 is a direct Tankyrase binding partner in cancer cells. Communications Biology. ISSN 2399-3642. 3(1). doi: 10.1038/s42003-020-0851-2.
• Arain, Fizza Kanwal; Abraityte, Judita Aurelija; Bogdanova, Mariia; Solberg, Ole Geir; Michelsen, Annika & Lekva, Tove [Vis alle 19 forfattere av denne artikkelen] (2020). YKL-40 (Chitinase-3-Like Protein 1) Serum Levels in Aortic Stenosis. Circulation: Heart Failure. ISSN 1941-3289. 13(10). doi: 10.1161/CIRCHEARTFAILURE.119.006643. Fulltekst i vitenarkiv
• Tuovinen, Elina A.; Grönholm, Juha; Ohman, Tiina; Pöysti, Sakari; Toivonen, Raine & Kreutzman, Anna [Vis alle 17 forfattere av denne artikkelen] (2020). Novel Hemizygous IL2RG p.(Pro58Ser) Mutation Impairs IL-2 Receptor Complex Expression on Lymphocytes Causing X-Linked Combined Immunodeficiency. Journal of Clinical Immunology. ISSN 0271-9142. 40(3), s. 503–514. doi: 10.1007/s10875-020-00745-2. Fulltekst i vitenarkiv
• Gawel, Kinga Aurelia; Kukula-Koch, Wirginia; Nieoczym, Dorota; Stępnik, Katarzyna; van der Ent, Wietske & Banono, Nancy Saana [Vis alle 9 forfattere av denne artikkelen] (2020). The Influence of Palmatine Isolated from Berberis sibirica Radix on Pentylenetetrazole-Induced Seizures in Zebrafish. Cells. ISSN 2073-4409. 9(5). doi: 10.3390/cells9051233. Fulltekst i vitenarkiv
• Mahmutovic, Anel; Abel zur Wiesch, Pia & Abel, Sören (2020). Selection or drift: the population biology underlying transposon insertion sequencing experiments. Computational and Structural Biotechnology Journal. ISSN 2001-0370. 18, s. 791–804. doi: 10.1016/j.csbj.2020.03.021. Fulltekst i vitenarkiv
• Clarelli, Fabrizio; Palmer, Adam; Singh, Bhupender; Storflor, Merete; Lauksund, Silje & Cohen, Ted [Vis alle 8 forfattere av denne artikkelen] (2020). Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones. PLoS Computational Biology. ISSN 1553-734X. 16(8). doi: 10.1371/journal.pcbi.1008106. Fulltekst i vitenarkiv
• Villatoro, Alicia; Konieczny, Joanna; Cuminetti, Vincent & Arranz, Lorena (2020). Leukemia Stem Cell Release From the Stem Cell Niche to Treat Acute Myeloid Leukemia. Frontiers in Cell and Developmental Biology. ISSN 2296-634X. 8. doi: 10.3389/fcell.2020.00607. Fulltekst i vitenarkiv
• Mohammadzadeh, Naiyereh; Melleby, Arne Olav; Palmero, Sheryl; Sjaastad, Ivar; Chakravarti, Shukti & Engebretsen, Kristin V Thunheim [Vis alle 9 forfattere av denne artikkelen] (2020). Moderate Loss of the Extracellular Matrix Proteoglycan Lumican Attenuates Cardiac Fibrosis in Mice Subjected to Pressure Overload. Cardiology. ISSN 0008-6312. 145(3), s. 187–198. doi: 10.1159/000505318.
• Pladsen, Arne Valebjørg; Nilsen, Gro; Rueda, Oscar M.; Aure, Miriam Ragle; Borgan, Ørnulf & Liestøl, Knut [Vis alle 18 forfattere av denne artikkelen] (2020). DNA copy number motifs are strong and independent predictors of survival in breast cancer. Communications Biology. ISSN 2399-3642. 3. doi: 10.1038/s42003-020-0884-6. Fulltekst i vitenarkiv
• Khalid, Khalisanni; Tan, Xuefei; Mohd Zaid, Hayyiratul Fatimah; Tao, Yang; Lye Chew, Chien & Chu, Dinh Toi [Vis alle 10 forfattere av denne artikkelen] (2020). Advanced in developmental organic and inorganic nanomaterial: a review. Bioengineered. ISSN 2165-5979. 11(1), s. 328–355. doi: 10.1080/21655979.2020.1736240. Fulltekst i vitenarkiv
• Chu, Dinh Toi; Phuong, Thuy Nguyen Thi; Tien, Nguyen Le Bao; Tran, Dang Khoa; Thanh, Vo Van & Quang, Thuy Luu [Vis alle 11 forfattere av denne artikkelen] (2020). An update on the progress of isolation, culture, storage, and clinical application of human bone marrow mesenchymal stem/stromal cells. International Journal of Molecular Sciences. ISSN 1661-6596. 21:708(3), s. 1–27. doi: 10.3390/ijms21030708. Fulltekst i vitenarkiv
• Lindner, Paula Maria; Christensen, Søren Brøgger; Nissen, Poul; Møller, Jesper Vuust & Engedal, Nikolai (2020). Cell death induced by the ER stressor thapsigargin involves death receptor 5, a non-autophagic function of MAP1LC3B, and distinct contributions from unfolded protein response components. Cell Communication and Signaling. ISSN 1478-811X. 18(1), s. 1–23. doi: 10.1186/s12964-019-0499-z. Fulltekst i vitenarkiv
• Connell, Shea P; Yazbek-Hanna, Marcelino; McCarthy, Frank; Hurst, Rachel; Webb, Martyn & Curley, Helen [Vis alle 24 forfattere av denne artikkelen] (2019). A four‐group urine risk classifier for predicting outcomes in patients with prostate cancer. BJU International. ISSN 1464-4096. 124(4), s. 609–620. doi: 10.1111/bju.14811. Fulltekst i vitenarkiv
• Keskitalo, Salla; Haapaniemi, Emma M.; Glumoff, Virpi; Liu, Xiaonan; Lehtinen, Ville & Fogarty, Christopher [Vis alle 16 forfattere av denne artikkelen] (2019). Dominant TOM1 mutation associated with combined immunodeficiency and autoimmune disease. NPJ GENOMIC MEDICINE. ISSN 2056-7944. 4:14, s. 1–7. doi: 10.1038/s41525-019-0088-5. Fulltekst i vitenarkiv
• Joemetsa, Silver; Spustová, Karolina; Kustanovich, Kiryl; Ainla, Alar; Schindler, Severin & Eigler, Siegfried [Vis alle 10 forfattere av denne artikkelen] (2019). Molecular Lipid Films on Microengineering Materials. Langmuir. ISSN 0743-7463. 35(32), s. 10286–10298. doi: 10.1021/acs.langmuir.9b01120.
• Kustanovich, Kiryl; Yantchev, Ventsislav; Doosti, Baharan Ali; Gözen, Irep & Jesorka, Aldo (2019). A microfluidics-integrated impedance/surface acoustic resonance tandem sensor. Sensing and Bio-Sensing Research. 25. doi: 10.1016/j.sbsr.2019.100291.
• Kamiński, Krzysztof; Socała, Katarzyna; Zagaja, Mirosław; Andres-Mach, Marta; Abram, Michał & Jakubiec, Marcin [Vis alle 17 forfattere av denne artikkelen] (2019). N-Benzyl-(2,5-dioxopyrrolidin-1-yl)propanamide (AS-1) with Hybrid Structure as a Candidate for a Broad-Spectrum Antiepileptic Drug. Neurotherapeutics. ISSN 1933-7213. doi: 10.1007/s13311-019-00773-w. Fulltekst i vitenarkiv
• Salvatore, Stefania; Rand, Knut Dagestad; Grytten, Ivar; Ferkingstad, Egil; Domanska, Diana & Holden, Lars [Vis alle 10 forfattere av denne artikkelen] (2019). Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings in Bioinformatics. ISSN 1467-5463. s. 1–8. doi: 10.1093/bib/bbz083.
• Vu, Le Nguyen; Nghia, Nguyen Quang; Thanh, Do Truong; Giang, Tran Binh; Nga, Vu Thi & Bui, Le Minh [Vis alle 7 forfattere av denne artikkelen] (2019). Laparoscopic living donor right nephrectomy: Assessment of outcome and association of BMI to length of right renal vein. Actas Urológicas Españolas. ISSN 0210-4806. 43(10), s. 536–542. doi: 10.1016/j.acuro.2019.05.005.
• Copmans, Daniëlle; Kildgaard, Sara; Rasmussen, Silas A.; Ślęzak, Monika; Dirkx, Nina & Partoens, Michèle [Vis alle 10 forfattere av denne artikkelen] (2019). Zebrafish-based discovery of antiseizure compounds from the north sea: Isoquinoline alkaloids TMC-120A and TMC-120B. Marine Drugs. ISSN 1660-3397. 17:607(11), s. 1–20. doi: 10.3390/md17110607. Fulltekst i vitenarkiv
• Nielsen, Nis Valentin; Roedel, Elfie; Manna, Dipankar; Etscheid, Michael; Morth, Jens Preben & Kanse, Sandip (2019). Characterization of the enzymatic activity of the serine protease domain of Factor VII activating protease (FSAP). Scientific Reports. ISSN 2045-2322. 9(1). doi: 10.1038/s41598-019-55531-x. Fulltekst i vitenarkiv
• Braadland, Peder Rustøen; Ramberg, Håkon Andre; Grytli, Helene Hartvedt; Urbanucci, Alfonso; Nielsen, Heidi Kristin & Guldvik, Ingrid Jenny [Vis alle 13 forfattere av denne artikkelen] (2019). The β2-adrenergic receptor is a molecular switch for neuroendocrine transdifferentiation of prostate cancer cells. Molecular Cancer Research. ISSN 1541-7786. 17(11), s. 2154–2168. doi: 10.1158/1541-7786.MCR-18-0605.
• Tepekule, Burcu; Abel zur Wiesch, Pia; Kouyos, Roger D. & Bonhoeffer, Sebastian (2019). Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 116(46), s. 23106–23116. doi: 10.1073/pnas.1912188116. Fulltekst i vitenarkiv
• Skånland, Sigrid Strand; Cremaschi, Andrea; Bendiksen, Henrik; Hermansen, Johanne Uthus; Thimiri Govinda Raj, Deepak Balaji & Munthe, Ludvig Andre [Vis alle 8 forfattere av denne artikkelen] (2019). An in vitro assay for biomarker discovery and dose prediction applied to ibrutinib plus venetoclax treatment of CLL. Leukemia. ISSN 0887-6924. doi: 10.1038/s41375-019-0569-7.
• Korecki, Andrea J; Hickmott, Jack W; Lam, Siu Ling; Dreolini, Lisa; Mathelier, Anthony & Baker, Oliver [Vis alle 17 forfattere av denne artikkelen] (2019). Twenty-seven tamoxifen-inducible icre-driver mouse strains for eye and brain, including seventeen carrying a new inducible-first constitutive-ready allele. Genetics. ISSN 0016-6731. 211(4), s. 1155–1177. doi: 10.1534/genetics.119.301984.
• Halnes, Geir; Pettersen, Klas Henning; Øyehaug, Leiv; Rognes, Marie Elisabeth & Einevoll, Gaute (2019). Astrocytic Ion Dynamics: Implications for Potassium Buffering and Liquid Flow. I Berry, Hugues & De Pittà, Maurizio (Red.), Computational Glioscience. Springer Nature. ISSN 978-3-030-00817-8. s. 363–391. doi: 10.1007/978-3-030-00817-8_14. Fulltekst i vitenarkiv
• Mayer, Alexander E.; Löffler, Mona C; Valdés, Angel E Loza; Schmitz, Werner; El-Merahbi, Rabih & Viera, Jonathan Trujillo [Vis alle 13 forfattere av denne artikkelen] (2019). The kinase PKD3 provides negative feedback on cholesterol and triglyceride synthesis by suppressing insulin signaling. Science Signaling. ISSN 1945-0877. 12(593). doi: 10.1126/scisignal.aav9150.
• Sisodiya, Sanjay M.; Fowler, Hayley J.; Lake, Iain; Nanji, Rosemary Ogwen; Gawel, Kinga Aurelia & Esguerra, Camila Vicencio [Vis alle 8 forfattere av denne artikkelen] (2019). Climate change and epilepsy: Time to take action. Epilepsia Open. ISSN 2470-9239. 4(4), s. 524–536. doi: 10.1002/epi4.12359. Fulltekst i vitenarkiv
• Rydmark, Marcella Orwick; Christensen, Mikkel; Köksal, Elif; Kantarci, Ilayda; Kustanovich, Kiryl & Yantchev, Ventsislav [Vis alle 8 forfattere av denne artikkelen] (2019). Styrene maleic acid copolymer induces pores in biomembranes . Soft Matter. ISSN 1744-683X. 15(39), s. 7934–7944. doi: 10.1039/C9SM01407A. Fulltekst i vitenarkiv
• Gözen, Irep (2019). A Hypothesis for Protocell Division on the Early Earth. ACS Nano. ISSN 1936-0851. 13(10), s. 10869–10871. doi: 10.1021/acsnano.9b06584.
• Post, Joakim Iver; Leergaard, Trygve B.; Ratz, Veronika; Walaas, S. Ivar; von Hörsten, Stephan & Nissen-Meyer, Lise Sofie Haug (2019). Differential Levels and Phosphorylation of Type 1 Inositol 1,4,5-Trisphosphate Receptor in Four Different Murine Models of Huntington Disease . Journal of Huntington's Disease. ISSN 1879-6397. 8(3), s. 271–289. doi: 10.3233/JHD-180301.
• Köksal, Elif; Belletati, Patrícia Fernandes; Reint, Ganna; Olsson, Ragni; Leitl, Kira & Kantarci, Ilayda [Vis alle 7 forfattere av denne artikkelen] (2019). Spontaneous Formation and Rearrangement of Artificial Lipid Nanotube Networks as a Bottom-Up Model for Endoplasmic Reticulum. Journal of Visualized Experiments. ISSN 1940-087X. 2019(143), s. 1–9. doi: 10.3791/58923. Fulltekst i vitenarkiv
• Bösl, Korbinian; Ianevski, Aleksandr; Than, Thoa T.; Anderssen, Petter Inge; Kuivanen, Suvi & Teppor, Mona [Vis alle 25 forfattere av denne artikkelen] (2019). Common nodes of virus-host interaction revealed through an integrated network analysis. Frontiers in Immunology. ISSN 1664-3224. 10. doi: 10.3389/fimmu.2019.02186. Fulltekst i vitenarkiv
• Ali Ahmad, Ahmad; Bilokapic, Silvija; Schafer, Ingmar B; Halic, Mario & Sekulic, Nikolina (2019). CENP‐C unwraps the human CENP‐A nucleosome through the H2A C‐terminal tail. EMBO Reports. ISSN 1469-221X. doi: 10.15252/embr.201948913. Fulltekst i vitenarkiv
• Köksal, Elif; Liese, Susanne; Kantarci, Ilayda; Olsson, Ragni; Carlson, Andreas & Gözen, Irep (2019). Nanotube-Mediated Path to Protocell Formation. ACS Nano. ISSN 1936-0851. 13(6), s. 6867–6878. doi: 10.1021/acsnano.9b01646. Fulltekst i vitenarkiv
• Horowitz, Viva R; Chambers, Zachary C; Gözen, Irep; Dimiduk, Thomas G & Manoharan, Vinothan N (2019). Active colloidal particles in emulsion droplets: a model system for the cytoplasm. The European Physical Journal Special Topics. ISSN 1951-6355. 227(17), s. 2413–2424. doi: 10.1140/epjst/e2019-800026-y.
• Martinecz, Antal; Clarelli, Fabrizio; Abel, Sören & Abel zur Wiesch, Pia (2019). Reaction Kinetic Models of Antibiotic Heteroresistance. International Journal of Molecular Sciences. ISSN 1661-6596. 20(16). doi: 10.3390/ijms20163965. Fulltekst i vitenarkiv
• Luhr, Morten; Torgersen, Maria Lyngaas; Szalai, Paula; Hashim, Adnan; Brech, Andreas & Stärk, Judith [Vis alle 7 forfattere av denne artikkelen] (2019). The kinase PERK and the transcription factor ATF4 play distinct and essential roles in autophagy resulting from tunicamycin-induced ER stress. Journal of Biological Chemistry. ISSN 0021-9258. 294(20), s. 8197–8217. doi: 10.1074/jbc.RA118.002829. Fulltekst i vitenarkiv
• Stiksrud, Birgitte; Aass, Hans Christian Dalsbotten; Lorvik, Kristina Berg; Ueland, Thor; Trøseid, Marius & Dyrhol-Riise, Anne Ma (2019). Activated dendritic cells and monocytes in HIV immunological nonresponders: HIV-induced interferon-inducible protein-10 correlates with low future CD4+ recovery. AIDS (London). ISSN 0269-9370. 33(7), s. 1117–1129. doi: 10.1097/QAD.0000000000002173. Fulltekst i vitenarkiv
• Gupta, Abhay; Gözen, Irep & Taylor, Michael (2019). A cellular automaton for modeling non-trivial biomembrane ruptures. Soft Matter. ISSN 1744-683X. 15(20), s. 4178–4186. doi: 10.1039/c8sm02032a. Fulltekst i vitenarkiv
• Itkonen, Harri; Poulose, Ninu; Walker, Suzanne & Mills, Ian Geoffrey (2019). CDK9 Inhibition Induces a Metabolic Switch that Renders Prostate Cancer Cells Dependent on Fatty Acid Oxidation. Neoplasia. ISSN 1522-8002. 21(7), s. 713–720. doi: 10.1016/j.neo.2019.05.001. Fulltekst i vitenarkiv
• Chellappa, Stalin ; Kushekhar, Kushi; Munthe, Ludvig Andre; Tjønnfjord, Geir Erland; Aandahl, Einar Martin & Okkenhaug, Klaus [Vis alle 7 forfattere av denne artikkelen] (2019). The PI3K p110δ isoform inhibitor idelalisib preferentially inhibits human regulatory T cell function. Journal of Immunology. ISSN 0022-1767. 202(5), s. 1397–1405. doi: 10.4049/jimmunol.1701703.
• Cuminetti, Vincent & Arranz, Lorena (2019). Bone marrow adipocytes: The enigmatic components of the hematopoietic stem cell niche. Journal of Clinical Medicine. ISSN 2077-0383. 8(5). doi: 10.3390/jcm8050707. Fulltekst i vitenarkiv
• Goodridge, Jodie; Jacobs, Benedikt Marcel; Sætersmoen, Michelle Lu; Clement, Dennis; Hammer, Quirin & Clancy, Trevor [Vis alle 24 forfattere av denne artikkelen] (2019). Remodeling of secretory lysosomes during education tunes functional potential in NK cells. Nature Communications. ISSN 2041-1723. 10:14, s. 1–15. doi: 10.1038/s41467-019-08384-x. Fulltekst i vitenarkiv
• Nieoczym, Dorota; Socala, Katarzyna; Gawel, Kinga Aurelia; Esguerra, Camila Vicencio; Wyska, Elzbieta & Wlaz, Piotr (2019). Anticonvulsant Activity of Pterostilbene in Zebrafish and Mouse Acute Seizure Tests. Neurochemical Research. ISSN 0364-3190. 44(5), s. 1043–1055. doi: 10.1007/s11064-019-02735-2. Fulltekst i vitenarkiv
• Subbannayya, Yashwanth; Pinto, Sneha; Bösl, Korbinian; Prasad, T. S. Keshava & Kandasamy, Richard Kumaran (2019). Dynamics of Dual Specificity Phosphatases and Their Interplay with Protein Kinases in Immune Signaling. International Journal of Molecular Sciences. ISSN 1661-6596. 20(9), s. 1–22. doi: 10.3390/ijms20092086. Fulltekst i vitenarkiv
• Itkonen, Harri; Urbanucci, Alfonso; Sara ES, Martin; Khan, Aziz; Mathelier, Anthony & Thiede, Bernd [Vis alle 8 forfattere av denne artikkelen] (2019). High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics. ISSN 1838-7640. 9(8), s. 2183–2197. doi: 10.7150/thno.30834. Fulltekst i vitenarkiv
• Engedal, Nikolai; Luhr, Morten; Szalai, Paula & Seglen, Per O. (2019). Measurement of Bulk Autophagy by a Cargo Sequestration Assay. Methods in molecular biology. ISSN 1064-3745. 1880, s. 307–313. doi: 10.1007/978-1-4939-8873-0_20.
• Abudu, Yakubu Princely; Pankiv, Serhiy; Mathai, Benan John; Lystad, Alf Håkon; Bindesbøll, Christian & Brenne, Hanne Britt [Vis alle 14 forfattere av denne artikkelen] (2019). NIPSNAP1 and NIPSNAP2 act as “eat-me signal” for mitophagy. Developmental Cell. ISSN 1534-5807. 49(4), s. 509–525.e12. doi: 10.1016/j.devcel.2019.03.013. Fulltekst i vitenarkiv
• Brennecke, Philip; Rasina, Dace; Aubi Catevilla, Oscar; Herzog, Katja; Landskron, Johannes & Cautain, Bastien [Vis alle 42 forfattere av denne artikkelen] (2019). EU-OPENSCREEN: A novel collaborative approach to facilitate chemical biology. SLAS Discovery. ISSN 2472-5552. 24(3), s. 398–413. doi: 10.1177/2472555218816276. Fulltekst i vitenarkiv
• Wang, Shixiong; Singh, Sachin Kumar; Katika, MR; Lopez Aviles, Sandra & Hurtado, Antoni (2018). High Throughput Chemical Screening Reveals Multiple Regulatory Proteins on FOXA1 in Breast Cancer Cell Lines. International Journal of Molecular Sciences. ISSN 1661-6596. 19(12). doi: 10.3390/ijms19124123.
• Tsui, Carlson; Martínez-Martín, Nuria; Gaya, Mauro; Maldonado, Paula; Llorian, Miriam & Legrave, Nathalie M. [Vis alle 13 forfattere av denne artikkelen] (2018). Protein kinase C-β dictates B cell fate by regulating mitochondrial remodeling, metabolic reprogramming, and heme biosynthesis. Immunity. ISSN 1074-7613. 48(6), s. 1144–1159.e5. doi: 10.1016/j.immuni.2018.04.031. Fulltekst i vitenarkiv

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• Ben Guebila, Marouen; Weighill, Deborah; Lopes-Ramos, Camila M.; Burkholz, Rebekka; Pop, Romana-Tabita & Palepu, Kalyan [Vis alle 14 forfattere av denne artikkelen] (2022). An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nature Methods. ISSN 1548-7091. 19, s. 511–513. doi: 10.1038/s41592-022-01479-2.
• Bjørgo, Elisa; Solheim, Silje Anette; Abrahamsen, Hilde; Baillie, George S.; Brown, Kim M. & Berge, Torunn [Vis alle 9 forfattere av denne artikkelen] (2022). Erratum: Cross Talk between Phosphatidylinositol 3-Kinase and Cyclic AMP (cAMP)-Protein Kinase A Signaling Pathways at the Level of a Protein Kinase B/b-Arrestin/cAMP Phosphodiesterase 4 Complex (Molecular and Cellular Biology (2010) 30:7 (1660–1672) DOI: 10.1128/MCB.00696-09). Molecular and Cellular Biology. ISSN 0270-7306. 42(2). doi: 10.1128/mcb.00556-21.
• Fromm, Bastian; Domanska, Diana; Høye, Eirik; Ovchinnikov, Vladimir; Kang, Wenjing & Aparicio-Puerta, Ernesto [Vis alle 13 forfattere av denne artikkelen] (2020). Erratum: MirGeneDB 2.0: The metazoan microRNA complement (Nucleic Acids Research (2019) DOI: 10.1093/nar/gkz885). Nucleic Acids Research (NAR). ISSN 0305-1048. 48(1). doi: 10.1093/nar/gkz1016.
• Tran, Vi Ngoc-Nha; Shams, Alireza; Ascioglu, Sinan; Martinecz, Antal; Liang, Jingyi & Clarelli, Fabrizio [Vis alle 9 forfattere av denne artikkelen] (2020). vCOMBAT: a novel tool to create and visualize a computational model of bacterial antibiotic target-binding. Vis sammendrag

  Background As antibiotic resistance creates a significant global health threat, we need not only to accelerate the development of novel antibiotics but also to develop better treatment strategies using existing drugs to improve their efficacy and prevent the selection of further resistance. We require new tools to rationally design dosing regimens from data collected in early phases of antibiotic and dosing development. Mathematical models such as mechanistic pharmacodynamic drug-target binding explain mechanistic details of how the given drug concentration affects its targeted bacteria. However, there are no available tools in the literature that allow non-quantitative scientists to develop computational models to simulate antibiotic-target binding and its effects on bacteria. Results In this work, we have devised an extension of a mechanistic binding-kinetic model to incorporate clinical drug concentration data. Based on the extended model, we develop a novel and interactive web-based tool that allows non-quantitative scientists to create and visualize their own computational models of bacterial antibiotic target-binding based on their considered drugs and bacteria. We also demonstrate how Rifampicin affects bacterial populations of Tuberculosis bacteria using our vCOMBAT tool. Conclusions The vCOMBAT online tool is publicly available at https://combat-bacteria.org/.

• Gheorghe, Marius; Sandve, Geir Kjetil Ferkingstad; Khan, Aziz; Chèneby, Jeanne; Ballester, Benoit & Mathelier, Anthony (2019). Erratum: A map of direct TF-DNA interactions in the human genome (Nucleic acids research (2019) 47 4 (e21)). Nucleic Acids Research (NAR). ISSN 0305-1048. 47(14). doi: 10.1093/nar/gkz582.
• Sharapova, Svetlana O.; Haapaniemi, Emma; Sakovich, Inga S.; Kostyuchenko, Larysa V.; Donkó, Agnes & Dulau-Florea, Alina [Vis alle 15 forfattere av denne artikkelen] (2019). Heterozygous activating mutation in RAC2 causes infantile-onset combined immunodeficiency with susceptibility to viral infections. Clinical Immunology. ISSN 1521-6616. 205, s. 1–5. doi: 10.1016/j.clim.2019.05.003.
• Bösl, Korbinian; Ianevski, Aleksandr; Than, Thoa T.; Andersen, Petter I.; Teppor, Mona & Zusinaite, Eva [Vis alle 23 forfattere av denne artikkelen] (2019). Critical Nodes of Viral Modulation Revealed Through an Integrated Network Analysis of Host-Virus Interaction Landscape.

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