Timothy Hughes

Researcher - NORMENT part UiO
Image of Timothy Hughes
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Visiting address Department of Medical Genetics Oslo University Hospital (Ullevål)
Postal address OUS, Postboks 4956 Nydalen 0424 OSLO

Goals and research environment

My primary scientific goal is to contribute to the understanding of human pathology through the statistical and bioinformatic analysis of genetic data and particularly high throughput sequencing data. I also have a particular interest in identifying the molecular mechanisms causing neuropsychiatric disorders.

 

Teaching

I teach on several courses at the MSc and PhD level:

  • INF-BIO9121 - High Throughput Sequencing technologies and bioinformatics analysis
  • MBV-INF9410 - Bioinformatics for Molecular Biology
  • MF9195 – OMICs in medical research
  • Special PhD course - Genome-Wide Associations Studies: Why, How and then What?

Supervision

  • Main supervisor for PhD student Asbjørn Holmgren (UiO - 2018-2021) - Molecular mechanisms of myelin maturation in the CNS and its disruption in bipolar disorder
  • Co-supervisor for PhD student Ibrahim Akkouh (UiO - 2016-2020): Transcriptomics Modelling of Neuropsychiatric Disorders
  • Completed: co-supervisor for PhD student Niladri Banerjee (UiB - 2014-2018) - The Role of Differentially Methylated Regions (DMR) in the Susceptibility to Schizophrenia and Bipolar Disorder

On-going projects

Neuropsychiatric genetics with a particular focus on the role of ANK3 in bipolar disorder and schizophrenia (with Srdjan Djurovic - UiO) since 2014: 5 publications

Pharmaco-genetics - Genotyping of homologous genes

  • Individualization of treatments with drugs metabolized by CES1 (with Henrik Berg Rasmussen, Institute of Biological Psychiatry, Roskilde, Denmark) 2014-2018: 2 publications
  • Genetics of Immunosuppression - Individualisation of immunosuppression treatment of transplant patients (Stein Bergan, Sara Bremer, Helge Rootwelt Rikshospitalet / UiO)

 

Completed projects

3D yeast colony genomics (with Gregor Gilfillan, Libuse Vachova, Zdena Palkova Charles University Prague) 2013-2017. 2 publications

Low cell number ChIPseq methods (with Gregor Gilfillan - UiO) 2012-2016. 2 publications

Genetics of Progressive Encephalopathy (with Eirik Frengen - UiO) 2013-2016:  2 publications

GenAP (with Dag Undlien - UiO) 2012-2015: contributed to creation of UiOs TSD solution

 

Professional background

  • 2013-present: Senior Researcher at the Department of Medical Genetics (Oslo University Hospital)
  • 2013-present: Senior Researcher at the Norwegian Centre for Mental Disorders Research (University of Oslo)
  • 2009-2013: PostDoc/Bioinformatician at the Norwegian Sequencing Center (Oslo University Hospital)
  • 2007-2008: PostDoc at the department of Molecular Biology (University of Bergen)
  • 2003-2007: PhD University of Bergen
  • 2000-2003 Consultant Cap Gemini Ernst & Young
  • 1999-2000 MSc Imperial College London
  • 1996-1998 MPhil University of Oxford (Merton College)
  • 1992-1995 BSc London School of Economics

Publications

  • 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
  • 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 Full text in Research Archive.
  • 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 Full text in Research Archive.
  • 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 Full text in Research Archive.
  • 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 Full text in Research Archive. Show summary
  • 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 Full text in Research Archive.
  • 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 Full text in Research Archive.
  • 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 Full text in Research Archive.
  • 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. Show summary
  • 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. Show summary
  • Hughes, Timothy (2008). Computational analysis of the evolutionary dynamics of proteins on a genomic scale.

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Published Jan. 15, 2015 12:03 PM - Last modified Feb. 18, 2020 3:10 PM