Timothy Hughes

• Akkouh, Ibrahim; Ueland, Thor; Hansson, Lars; Inderhaug, Elin; Hughes, Timothy; Steen, Nils Eiel; Aukrust, Pål; Andreassen, Ole Andreas; Szabo, Attila & Djurovic, Srdjan (2020). Decreased IL-1β-induced CCL20 response in human iPSC-astrocytes in schizophrenia: Potential attenuating effects on recruitment of regulatory T cells. Brain, behavior, and immunity.  ISSN 0889-1591.  87, s 634- 644 . doi: 10.1016/j.bbi.2020.02.008 Fulltekst i vitenarkiv.
• Akkouh, Ibrahim; Skrede, Silje; Holmgren, Asbjørn; Ersland, Kari Merete; Hansson, Lars Johan Axel; Bahrami, Shahram; Andreassen, Ole Andreas; Steen, Vidar Martin; Djurovic, Srdjan & Hughes, Timothy (2019). Exploring lithium's transcriptional mechanisms of action in bipolar disorder: a multi-step study. Neuropsychopharmacology.  ISSN 0893-133X.  s 1- 9 . doi: 10.1038/s41386-019-0556-8 Fulltekst i vitenarkiv.
• Akkouh, Ibrahim; Ueland, Torill; Andreassen, Ole Andreas; Brattbakk, Hans-Richard; Steen, Vidar Martin; Hughes, Timothy & Djurovic, Srdjan (2018). Expression of TCN1 in Blood is Negatively Associated with Verbal Declarative Memory Performance. Scientific Reports.  ISSN 2045-2322.  8:12654, s 1- 11 . doi: 10.1038/s41598-018-30898-5 Fulltekst i vitenarkiv.
• Hughes, Timothy; Sønderby, Ida Elken; Polushina, Tatiana; Hansson, Lars Johan Axel; Holmgren, Asbjørn; Athanasiu, Lavinia; Melbø-Jørgensen, Christian; Hassani, Sahar; Hoeffding, Louise K.; Herms, Stefan; Bergen, Sarah E.; Karlsson, Robert; Song, Jie; Rietschel, Marcella; Nöthen, Markus M.; Forstner, Andreas J.; Hoffmann, Per; Hultman, Christina M.; Landén, Mikael; Cichon, Sven; Werge, Thomas; Andreassen, Ole Andreas; Le Hellard, Stephanie & Djurovic, Srdjan (2018). Elevated expression of a minor isoform of ANK3 is a risk factor for bipolar disorder. Translational Psychiatry.  ISSN 2158-3188.  8(210), s 1- 10 . doi: 10.1038/s41398-018-0175-x Fulltekst i vitenarkiv.
• Segorbe, David; Wilkinson, Derek; Mizeranschi, Alexandru; Hughes, Timothy; Aaløkken, Ragnhild; Váchová, Libuše; Palková, Zdena & Gilfillan, Gregor Duncan (2018). An optimized FAIRE procedure for low cell numbers in yeast. Yeast.  ISSN 0749-503X.  35(8), s 507- 512 . doi: 10.1002/yea.3316 Fulltekst i vitenarkiv. Vis sammendrag

  We report an optimized low‐input FAIRE‐seq (Formaldehyde‐Assisted Isolation of Regulatory Elements‐sequencing) procedure to assay chromatin accessibility from limited amounts of yeast cells. We demonstrate that the method performs well on as little as 4 mg of cells scraped directly from a few colonies. Sensitivity, specificity and reproducibility of the scaled‐down method are comparable with those of regular, higher input amounts, and allow the use of 100‐fold fewer cells than existing procedures. The method enables epigenetic analysis of chromatin structure without the need for cell multiplication of exponentially growing cells in liquid culture, thus opening the possibility of studying colony cell subpopulations, or those that can be isolated directly from environmental samples.

• Witoelar, Aree; Rongve, Arvid; Almdahl, Ina Selseth; Ulstein, Ingun; Engvig, Andreas; White, Linda Rosemary; Selbæk, Geir; Stordal, Eystein; Andersen, Fred; Brækhus, Anne; Saltvedt, Ingvild; Engedal, Knut; Hughes, Timothy; Bergh, Sverre; Bråthen, Geir; Bogdanovic, Nenad; Bettella, Francesco; Wang, Yunpeng; Athanasiu, Lavinia; Bahrami, Shahram; Le Hellard, Stephanie; Giddaluru, Sudheer; Dale, Anders M; Sando, Sigrid Botne; Steinberg, Stacy; Stefansson, Hreinn; Snaedal, Jon; Desikan, Rahul S; Stefansson, Kari; Aarsland, Dag; Djurovic, Srdjan; Fladby, Tormod & Andreassen, Ole Andreas (2018). Meta-analysis of Alzheimer’s disease on 9,751 samples from Norway and IGAP study identifies four risk loci. Scientific Reports.  ISSN 2045-2322.  8 . doi: 10.1038/s41598-018-36429-6 Fulltekst i vitenarkiv.
• Maršíková, Jana; Wilkinson, Derek; Hlaváček, Otakar; Gilfillan, Gregor Duncan; Mizeranschi, Alexandru; Hughes, Timothy; Begany, Markéta; Rešetárová, Stanislava; Váchová, Libuše & Palková, Zdena (2017). Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling. BMC Genomics.  ISSN 1471-2164.  18:814, s 1- 16 . doi: 10.1186/s12864-017-4214-4 Fulltekst i vitenarkiv.
• Rasmussen, Henrik Berg; Madsen, Majbritt Busk; Lyauk, Yassine Kamal; Hansen, Peter Riis & Hughes, Timothy (2017). Carboxylesterase 1A2 encoding gene with increased transcription and potential rapid drug metabolism in Asian populations. Drug Metabolism and Personalized Therapy.  ISSN 2363-8907.  32(3), s 163- 168 . doi: 10.1515/dmpt-2017-0012
• Barøy, Tuva; Pedurupillay Jesuthasan, Christeen Ramane; Bliksrud, Yngve Thomas; Rasmussen, Magnhild; Holmgren, Asbjørn; Vigeland, Magnus Dehli; Hughes, Timothy; Brink, Maaike; Rodenburg, Richard J.; Nedregaard, Bård; Strømme, Petter; Frengen, Eirik & Misceo, Doriana (2016). A novel mutation in FBXL4 in a Norwegian child with encephalomyopathic mitochondrial DNA depletion syndrome 13. European Journal of Medical Genetics.  ISSN 1769-7212.  59(6-7), s 342- 346 . doi: 10.1016/j.ejmg.2016.05.005
• Sundaram, Arvind; Hughes, Timothy; Biondi, Shea; Bolduc, Nathalie; Bowman, Sarah K; Camilli, Andrew; Chew, Yap C; Couture, Catherine; Farmer, Andrew; Jerome, John P; Lazinski, David W; McUsic, Andrew; Peng, Xu; Shazand, Kamran; Xu, Feng; Lyle, Robert & Gilfillan, Gregor Duncan (2016). A comparative study of ChIP-seq sequencing library preparation methods. BMC Genomics.  ISSN 1471-2164.  17(1) . doi: 10.1186/s12864-016-3135-y
• Tesli, Martin Steen; Wirgenes, Katrine Verena; Hughes, Timothy; Bettella, Francesco; Athanasiu, Lavinia; Hoseth, Eva Zsuzsanna; Nerhus, Mari; Lagerberg, Trine Vik; Steen, Nils Eiel; Agartz, Ingrid; Melle, Ingrid; Dieset, Ingrid; Djurovic, Srdjan & Andreassen, Ole Andreas (2016). VRK2 gene expression in schizophrenia, bipolar disorder and healthy controls. British Journal of Psychiatry.  ISSN 0007-1250.  209(2), s 114- 120 . doi: 10.1192/bjp.bp.115.161950
• Barøy, Tuva; Koster, Janet; Strømme, Petter; Ebberink, Merel S.; Misceo, Doriana; Ferdinandusse, Sacha; Holmgren, Asbjørn; Hughes, Timothy; Merckoll, Else; Westvik, Jostein; Woldseth, Berit; Walter, John; Wood, Nick; Tvedt, Bjørn; Stadskleiv, Kristine; Wanders, Ronald J.A.; Waterham, Hans R. & Frengen, Eirik (2015). A novel type of rhizomelic chondrodysplasia punctata, RCDP5, is caused by loss of the PEX5 long isoform. Human Molecular Genetics.  ISSN 0964-6906.  24(20), s 5845- 5854 . doi: 10.1093/hmg/ddv305
• Hughes, Timothy; Hansson, Lars Johan Axel; Sønderby, Ida Elken; Athanasiu, Lavinia; Zuber, Verena; Tesli, Martin Steen; Song, J; Hultman, Christina M.; Bergen, SE; Landen, M.; Melle, Ingrid; Andreassen, Ole Andreas & Djurovic, Srdjan (2015). A Loss-of-Function Variant in a Minor Isoform of ANK3 Protects Against Bipolar Disorder and Schizophrenia. Biological Psychiatry.  ISSN 0006-3223. . doi: 10.1016/j.biopsych.2015.09.021
• Rasmussen, Henrik Berg; Bjerre, Ditte; Linnet, Kristian; Jürgens, Gesche; Dalhoff, Kim; Stefansson, Hreinn; Hankemeier, Thomas; Kaddurah-Daouk, Rima; Taboureau, Olivier; Brunak, Søren; Houmann, Tine; Jeppesen, Pia; Pagsberg, Anne Katrine; Plessen, Kerstin J.; Dyrborg, Jørgen; Hansen, Peter Riis; Hansen, Poul Erik; Hughes, Timothy & Werge, Thomas (2015). Individualization of treatments with drugs metabolized by CES1: Combining genetics and metabolomics. Pharmacogenomics (London).  ISSN 1462-2416.  16(6), s 649- 665 . doi: 10.2217/pgs.15.7
• Wirgenes, Katrine Verena; Tesli, Martin Steen; Inderhaug, Elin; Athanasiu, Lavinia; Agartz, Ingrid; Melle, Ingrid; Hughes, Timothy; Andreassen, Ole Andreas & Djurovic, Srdjan (2014). ANK3 gene expression in bipolar disorder and schizophrenia. British Journal of Psychiatry.  ISSN 0007-1250.  205(3), s 244- 245 . doi: 10.1192/bjp.bp.114.145433
• Baccarani, Michele; Deininger, MW; Rosti, Gianantonio; Hochhaus, Andreas; Soverini, Simona; Apperley, J.F.; Cervantes, Francisco Javier; Clark, RE; Cortes, JE; Guilhot, F; Hjort-Hansen, Henrik; Hughes, Timothy; Kantarjian, HM; Kim, DW; Larson, RA; Lipton, JH; Mahon, François-Xavier; Martinelli, Giovanni; Mayer, Jiri; Müller, Martin C.; Niederwieser, Dietger; Pane, Fabrizio; Radich, JP; Rousselot, P; Saglio, Giuseppe; Saussele, S; Schiffer, C; Silver, R; Simonsson, Bengt; Steegmann, JL; Goldman, JM & Hehlmann, R (2013). European LeukemiaNet recommendations for the management of chronic myeloid leukemia: 2013. Blood.  ISSN 0006-4971.  122(6), s 872- 884 . doi: 10.1182/blood-2013-05-501569
• Gilfillan, Gregor Duncan; Hughes, Timothy; Sheng, Ying; Hjorthaug, Hanne Sagsveen; Straub, Tobias; Gervin, Kristina; Harris, Jennifer; Undlien, Dag Erik & Lyle, Robert (2012). Limitations and possibilities of low cell number ChIP-seq. BMC Genomics.  ISSN 1471-2164.  13 . doi: 10.1186/1471-2164-13-645
• Hamfjord, Julian; Stangeland, Astrid Marie; Hughes, Timothy; Skrede, Martina; Tveit, Magne Kjell; Andersen, Tone Ikdahl & Kure, Elin H. (2012). Differential Expression of miRNAs in Colorectal Cancer: Comparison of Paired Tumor Tissue and Adjacent Normal Mucosa Using High-Throughput Sequencing. PLOS ONE.  ISSN 1932-6203.  7(4) . doi: 10.1371/journal.pone.0034150
• Selmer, Kaja Kristine; Gilfillan, Gregor Duncan; Strømme, Petter; Lyle, Robert; Hughes, Timothy; Hjorthaug, Hanne Sagsveen; Brandal, Kristin; Nakken, Sigve; Misceo, Doriana; Egeland, Thore; Munthe, Ludvig Andre; Brækken, Sigrun Kierulf & Undlien, Dag Erik (2012). A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions. European Journal of Human Genetics.  ISSN 1018-4813.  20(1), s 58- 63 . doi: 10.1038/ejhg.2011.126
• Gould, Cathryn M.; Diella, Francesca; Via, Allegra; Puntervoll, Pål; Gemünd, Christine; Chabanis-Davidson, Sophie; Michael, Sushama; Sayadi, Ahmed; Bryne, Jan Christian; Chica, Claudia; Seiler, Markus; Davey, Norman E.; Haslam, Neill; Weatheritt, Robert J.; Budd, Aidan; Hughes, Timothy; Pas, Jakub; Rychlewski, Leszek; Trave, Gilles Michel; Aasland, Rein; Helmer-Citterich, Manuela; Linding, Rune & Gibson, Toby J. (2010). ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Research.  ISSN 0305-1048.  38, s D167- D180 . doi: 10.1093/nar/gkp1016 Fulltekst i vitenarkiv.
• Hughes, Timothy & Liberles, David A (2008). The power-law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families. Gene.  ISSN 0378-1119.  414(1-2), s 85- 94 . doi: 10.1016/j.gene.2008.02.014
• Hughes, Timothy & Liberles, David A (2008). Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species. Journal of Molecular Evolution.  ISSN 0022-2844.  67(4), s 343- 357 . doi: 10.1007/s00239-008-9145-x
• Hughes, Timothy; Ekman, Daniel; Ardawatia, Himanshu; Elofsson, Arne & Liberles, David A (2007). Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biology.  ISSN 1465-6906.  8(8) . doi: 10.1186/gb-2007-8-5-213
• Hughes, Timothy & Liberles, David A (2007). The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo-than subfunctionalisation. Journal of Molecular Evolution.  ISSN 0022-2844.  65(5), s 574- 588 . doi: 10.1007/s00239-007-9041-9
• Hughes, Timothy; Hyun, Y & Liberles, David A (2004). Visualising very large phylogenetic trees in three dimensional hyperbolic space. BMC Bioinformatics.  ISSN 1471-2105.  5, s art. no.- 48

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• Hughes, Timothy (2007). Eukaryotic membranes and cytoskeleton. Springer Science+Business Media B.V..  ISBN 978-0-387-74020-1.  145 s.

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• Eike, Morten Christoph; Lærum, Hallvard; Hughes, Timothy; Bremer, Sara; Bergan, Stein; Thomassen, Gard O Sundby; Aanestad, Margunn; Grünfeld, Thomas & Undlien, Dag Erik (2012). A national platform for clinical genetic analysis of high-throughput sequencing data in Norway. Vis sammendrag

  The introduction of high-throughput sequencing (HTS) into clinical practice poses great challenges in terms of analytic resources, integration and data security. The project Norwegian clinical genetic Analysis Platform (genAP) was initiated as a response to these challenges, aiming to establish a centralised infrastructure for secure storage and analysis of human sequencing data that allows for disseminated clinical use. GenAP is a collaborative project between Oslo University Hospital and the University of Oslo, with implementation of the system in an established high-performance computing environment. As part of this project, we are in the process of establishing pilot HTS pipelines for a set of clinical packages, each with a defined set of targeted genes. The pilots cover diagnostic, prognostic and pharmacogenetic areas, including cardiomyopathies, breast cancer and tacrolimus dosage, respectively. Initially, the pipelines involve targeted capture and resequencing, but the system will be scalable to exome and genome data for a large number of patients. To reduce the workload associated with manual analysis, we have sought to achieve a high degree of automation, including variant annotation and quality control, filtering based on public resources, identification of previously classified variants, and standardization of report information structure for integration with existing patient journal systems. The pilot phase includes comparing the performance of HTS to conventional methods, building a database of genetic variants adapted to our patient populations and real-world testing using collaborating clinicians. The experiences gained will be used to expand to other clinical packages, and the ultimate goal is to introduce the pipelines for widespread use in the clinic. Complementing the genetic, bioinformatic and clinical issues, the project also addresses legal, ethical and organizational issues encountered when HTS is deployed in large scale clinical decision making. This presentation will demonstrate the overall architecture of our system and present initial experiences with the pilot systems.

• Eike, Morten Christoph; Lærum, Hallvard; Hughes, Timothy; Håndstad, Tony; Bremer, Sara; Bergan, Stein; Thomassen, Gard O Sundby; Aanestad, Margunn; Grünfeld, Thomas & Undlien, Dag Erik (2012). GenAP: a platform for clinical genetic analysis of high-throughput sequencing data. Vis sammendrag

  The introduction of high-throughput sequencing (HTS) into clinical practice poses great challenges in terms of analytic resources, integration and data security. The project Norwegian clinical genetic Analysis Platform (genAP) was initiated as a response to these challenges, aiming to establish a centralised infrastructure for secure storage and analysis of human sequencing data, with possibilities for disseminated clinical use. GenAP is a collaborative project between Oslo University Hospital and the University of Oslo, with implementation of the system in a high-performance computing environment. As part of this project, we are in the process of establishing pilot HTS pipelines for a set of clinical packages, each with a defined set of targeted genes. The pilots cover diagnostic, prognostic and pharmacogenetic areas, including cardiomyopathies, breast cancer and tacrolimus dosage, respectively. Initially, the pipelines involve data for a limited set of candidate genes, but the system will be scalable to exome and whole-genome data for a large number of patients. To reduce the workload associated with manual analysis, we have sought to achieve a high degree of automation, including variant annotation and quality control, filtering and prioritisation based on public resources, identification of previously classified variants, and standardisation of report information structure for integration with existing medical journal systems. The pilot phase includes comparing the performance of HTS to conventional methods, building a database of genetic variants adapted to our patient populations and real-world testing using collaborating clinicians. The experiences gained will be used to expand to other clinical packages, and the ultimate goal is to introduce the system in the clinic. Complementing the genetic, bioinformatic and clinical issues, the project also addresses legal, ethical and organizational issues encountered when HTS is deployed in large scale clinical decision making. This presentation will demonstrate the overall architecture of our system and present initial experiences with the pilot systems.

• Hughes, Timothy (2008). Computational analysis of the evolutionary dynamics of proteins on a genomic scale.

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