Timothy Hughes

  • Project leader
  • +47 991 61 818

Challenges
The advent of High Through-put sequencing has revolutionized both practice and research within the field of Medical Genetics. In order to exploit the power that lies within the huge datasets generated by this technology, one needs the computational and bioinformatics skills to generate, store and analyse these data. The projects in which we participate (either as lead or as a collaborative partner) usually involve a large component of bioinformatics analysis of HTS data.

Projects

  • Sequencing of repetitive regions using single molecule sequencing technologies.
  • GenAP (with Dag Undlien): development of a national hardware and software infrastructure for the storage, analysis and communication of patient genomic data, with the goal of facilitating personalised medicine in Norway.
  • Causes of mendelian disorders in particular in progressive encephalopathies (with Eirik Frengen).
  • ChIPseq scale-down to low cell numbers (with Gregor Gilfillan).
  • Addisons disease (with Dag Undlien)
  • Role of ANK3 in the etiology of bipolar disorder (with Srdjan Djurovic)

Publication list available from Google Scholar 

 

Publications 2024

Holmgren A, Akkouh I, O'Connell KS, Osete JR, Bjørnstad PM, Djurovic S, Hughes T (2024)
Bipolar patients display stoichiometric imbalance of gene expression in post-mortem brain samples
Mol Psychiatry, 29 (4), 1128-1138
DOI 10.1038/s41380-023-02398-0, PubMed 38351171

Szabo A, Akkouh I, Osete JR, de Assis DR, Kondratskaya E, Hughes T, Ueland T, Andreassen OA, Djurovic S (2024)
NLRP3 inflammasome mediates astroglial dysregulation of innate and adaptive immune responses in schizophrenia
Brain Behav Immun, 124, 144-156
DOI 10.1016/j.bbi.2024.11.030, PubMed 39617069

Publications 2023

Akkouh IA, Ueland T, Szabo A, Hughes T, Smeland OB, Andreassen OA, Osete JR, Djurovic S (2023)
Longitudinal Transcriptomic Analysis of Human Cortical Spheroids Identifies Axonal Dysregulation in the Prenatal Brain as a Mediator of Genetic Risk for Schizophrenia
Biol Psychiatry, 95 (7), 687-698
DOI 10.1016/j.biopsych.2023.08.017, PubMed 37661009

Osete JR, Akkouh IA, Ievglevskyi O, Vandenberghe M, de Assis DR, Ueland T, Kondratskaya E, Holen B, Szabo A, Hughes T, Smeland OB, Steen VM, Andreassen OA, Djurovic S (2023)
Transcriptional and functional effects of lithium in bipolar disorder iPSC-derived cortical spheroids
Mol Psychiatry, 28 (7), 3033-3043
DOI 10.1038/s41380-023-01944-0, PubMed 36653674

Torsvik A, Brattbakk HR, Trentani A, Holdhus R, Stansberg C, Bartz-Johannessen CA, Hughes T, Steen NE, Melle I, Djurovic S, Andreassen OA, Steen VM (2023)
Patients with schizophrenia and bipolar disorder display a similar global gene expression signature in whole blood that reflects elevated proportion of immature neutrophil cells with association to lipid changes
Transl Psychiatry, 13 (1), 147
DOI 10.1038/s41398-023-02442-1, PubMed 37147304

Publications 2022

Holmgren A, Hansson L, Bjerkaas-Kjeldal K, Impellizzeri AAR, Gilfillan GD, Djurovic S, Hughes T (2022)
Mapping the expression of an ANK3 isoform associated with bipolar disorder in the human brain
Transl Psychiatry, 12 (1), 45
DOI 10.1038/s41398-022-01784-6, PubMed 35091539

Publications 2021

Akkouh IA, Hughes T, Steen VM, Glover JC, Andreassen OA, Djurovic S, Szabo A (2021)
Transcriptome analysis reveals disparate expression of inflammation-related miRNAs and their gene targets in iPSC-astrocytes from people with schizophrenia
Brain Behav Immun, 94, 235-244
DOI 10.1016/j.bbi.2021.01.037, PubMed 33571628

Krull F, Akkouh I, Hughes T, Bettella F, Athanasiu L, Smeland OB, O'Connell KS, Brattbakk HR, Steen VM, Steen NE, Djurovic S, Andreassen OA (2021)
Dose-dependent transcriptional effects of lithium and adverse effect burden in a psychiatric cohort
Prog Neuropsychopharmacol Biol Psychiatry, 112, 110408
DOI 10.1016/j.pnpbp.2021.110408, PubMed 34320404

O'Connell KS, Sønderby IE, Frei O, van der Meer D, Athanasiu L, Smeland OB, Alnæs D, Kaufmann T, Westlye LT, Steen VM, Andreassen OA, Hughes T, Djurovic S (2021)
Association between complement component 4A expression, cognitive performance and brain imaging measures in UK Biobank
Psychol Med, 52 (15), 1-11 (in press)
DOI 10.1017/S0033291721000179, PubMed 33653435

Osete JR, Akkouh IA, de Assis DR, Szabo A, Frei E, Hughes T, Smeland OB, Steen NE, Andreassen OA, Djurovic S (2021)
Lithium increases mitochondrial respiration in iPSC-derived neural precursor cells from lithium responders
Mol Psychiatry, 26 (11), 6789-6805
DOI 10.1038/s41380-021-01164-4, PubMed 34075196

Reis de Assis D, Szabo A, Requena Osete J, Puppo F, O'Connell KS, A Akkouh I, Hughes T, Frei E, A Andreassen O, Djurovic S (2021)
Using iPSC Models to Understand the Role of Estrogen in Neuron-Glia Interactions in Schizophrenia and Bipolar Disorder
Cells, 10 (2)
DOI 10.3390/cells10020209, PubMed 33494281

Szabo A, Akkouh IA, Vandenberghe M, Osete JR, Hughes T, Heine V, Smeland OB, Glover JC, Andreassen OA, Djurovic S (2021)
A human iPSC-astroglia neurodevelopmental model reveals divergent transcriptomic patterns in schizophrenia
Transl Psychiatry, 11 (1), 554
DOI 10.1038/s41398-021-01681-4, PubMed 34716291

Publications 2020

Akkouh IA, Ueland T, Hansson L, Inderhaug E, Hughes T, Steen NE, Aukrust P, Andreassen OA, Szabo A, Djurovic S (2020)
Decreased IL-1β-induced CCL20 response in human iPSC-astrocytes in schizophrenia: Potential attenuating effects on recruitment of regulatory T cells
Brain Behav Immun, 87, 634-644
DOI 10.1016/j.bbi.2020.02.008, PubMed 32109548

Hughes T, Hansson L, Akkouh I, Hajdarevic R, Bringsli JS, Torsvik A, Inderhaug E, Steen VM, Djurovic S (2020)
Runaway multi-allelic copy number variation at the α-defensin locus in African and Asian populations
Sci Rep, 10 (1), 9101
DOI 10.1038/s41598-020-65675-w, PubMed 32499510

Publications 2019

Akkouh IA, Skrede S, Holmgren A, Ersland KM, Hansson L, Bahrami S, Andreassen OA, Steen VM, Djurovic S, Hughes T (2019)
Exploring lithium's transcriptional mechanisms of action in bipolar disorder: a multi-step study
Neuropsychopharmacology, 45 (6), 947-955
DOI 10.1038/s41386-019-0556-8, PubMed 31652432

Publications 2018

Akkouh IA, Ueland T, Andreassen OA, Brattbakk HR, Steen VM, Hughes T, Djurovic S (2018)
Expression of TCN1 in Blood is Negatively Associated with Verbal Declarative Memory Performance
Sci Rep, 8 (1), 12654
DOI 10.1038/s41598-018-30898-5, PubMed 30139959

Hughes T, Sønderby IE, Polushina T, Hansson L, Holmgren A, Athanasiu L, Melbø-Jørgensen C, Hassani S, Hoeffding LK, Herms S, Bergen SE, Karlsson R, Song J, Rietschel M, Nöthen MM, Forstner AJ, Hoffmann P, Hultman CM, Landén M, Cichon S, Werge T, Andreassen OA, Le Hellard S, Djurovic S (2018)
Elevated expression of a minor isoform of ANK3 is a risk factor for bipolar disorder
Transl Psychiatry, 8 (1), 210
DOI 10.1038/s41398-018-0175-x, PubMed 30297702

Segorbe D, Wilkinson D, Mizeranschi A, Hughes T, Aaløkken R, Váchová L, Palková Z, Gilfillan GD (2018)
An optimized FAIRE procedure for low cell numbers in yeast
Yeast, 35 (8), 507-512
DOI 10.1002/yea.3316, PubMed 29577419

Witoelar A, Rongve A, Almdahl IS, Ulstein ID, Engvig A, White LR, Selbæk G, Stordal E, Andersen F, Brækhus A, Saltvedt I, Engedal K, Hughes T, Bergh S, Bråthen G, Bogdanovic N, Bettella F, Wang Y, Athanasiu L, Bahrami S, Le Hellard S, Giddaluru S, Dale AM, Sando SB, Steinberg S et al. (2018)
Meta-analysis of Alzheimer's disease on 9,751 samples from Norway and IGAP study identifies four risk loci
Sci Rep, 8 (1), 18088
DOI 10.1038/s41598-018-36429-6, PubMed 30591712

Publications 2017

Maršíková J, Wilkinson D, Hlaváček O, Gilfillan GD, Mizeranschi A, Hughes T, Begany M, Rešetárová S, Váchová L, Palková Z (2017)
Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling
BMC Genomics, 18 (1), 814
DOI 10.1186/s12864-017-4214-4, PubMed 29061122

Publications 2016

Barøy T, Pedurupillay CR, Bliksrud YT, Rasmussen M, Holmgren A, Vigeland MD, Hughes T, Brink M, Rodenburg R, Nedregaard B, Strømme P, Frengen E, Misceo D (2016)
A novel mutation in FBXL4 in a Norwegian child with encephalomyopathic mitochondrial DNA depletion syndrome 13
Eur J Med Genet, 59 (6-7), 342-6
DOI 10.1016/j.ejmg.2016.05.005, PubMed 27182039

Sundaram AY, Hughes T, Biondi S, Bolduc N, Bowman SK, Camilli A, Chew YC, Couture C, Farmer A, Jerome JP, Lazinski DW, McUsic A, Peng X, Shazand K, Xu F, Lyle R, Gilfillan GD (2016)
A comparative study of ChIP-seq sequencing library preparation methods
BMC Genomics, 17 (1), 816
DOI 10.1186/s12864-016-3135-y, PubMed 27769162

Tesli M, Wirgenes KV, Hughes T, Bettella F, Athanasiu L, Hoseth ES, Nerhus M, Lagerberg TV, Steen NE, Agartz I, Melle I, Dieset I, Djurovic S, Andreassen OA (2016)
VRK2 gene expression in schizophrenia, bipolar disorder and healthy controls
Br J Psychiatry, 209 (2), 114-20
DOI 10.1192/bjp.bp.115.161950, PubMed 26941264

Publications 2015

Barøy T, Koster J, Strømme P, Ebberink MS, Misceo D, Ferdinandusse S, Holmgren A, Hughes T, Merckoll E, Westvik J, Woldseth B, Walter J, Wood N, Tvedt B, Stadskleiv K, Wanders RJ, Waterham HR, Frengen E (2015)
A novel type of rhizomelic chondrodysplasia punctata, RCDP5, is caused by loss of the PEX5 long isoform
Hum Mol Genet, 24 (20), 5845-54
DOI 10.1093/hmg/ddv305, PubMed 26220973

Hughes T, Hansson L, Sønderby IE, Athanasiu L, Zuber V, Tesli M, Song J, Hultman CM, Bergen SE, Landén M, Melle I, Andreassen OA, Djurovic S (2015)
A Loss-of-Function Variant in a Minor Isoform of ANK3 Protects Against Bipolar Disorder and Schizophrenia
Biol Psychiatry, 80 (4), 323-330
DOI 10.1016/j.biopsych.2015.09.021, PubMed 26682468

Publications 2014

Wirgenes KV, Tesli M, Inderhaug E, Athanasiu L, Agartz I, Melle I, Hughes T, Andreassen OA, Djurovic S (2014)
ANK3 gene expression in bipolar disorder and schizophrenia
Br J Psychiatry, 205 (3), 244-5
DOI 10.1192/bjp.bp.114.145433, PubMed 24809399

Publications 2012

Gilfillan GD, Hughes T, Sheng Y, Hjorthaug HS, Straub T, Gervin K, Harris JR, Undlien DE, Lyle R (2012)
Limitations and possibilities of low cell number ChIP-seq
BMC Genomics, 13, 645
DOI 10.1186/1471-2164-13-645, PubMed 23171294

Hamfjord J, Stangeland AM, Hughes T, Skrede ML, Tveit KM, Ikdahl T, Kure EH (2012)
Differential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing
PLoS One, 7 (4), e34150
DOI 10.1371/journal.pone.0034150, PubMed 22529906

Publications 2011

Selmer KK, Gilfillan GD, Strømme P, Lyle R, Hughes T, Hjorthaug HS, Brandal K, Nakken S, Misceo D, Egeland T, Munthe LA, Braekken SK, Undlien DE (2011)
A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions
Eur J Hum Genet, 20 (1), 58-63
DOI 10.1038/ejhg.2011.126, PubMed 21712855

Publications 2008

Hughes T, Liberles DA (2008)
The power-law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families
Gene, 414 (1-2), 85-94
DOI 10.1016/j.gene.2008.02.014, PubMed 18378100

Hughes T, Liberles DA (2008)
Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species
J Mol Evol, 67 (4), 343-57
DOI 10.1007/s00239-008-9145-x, PubMed 18815825

Publications 2007

Hughes T, Ekman D, Ardawatia H, Elofsson A, Liberles DA (2007)
Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia
Genome Biol, 8 (5), 213
DOI 10.1186/gb-2007-8-5-213, PubMed 17521457

Hughes T, Liberles DA (2007)
The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation
J Mol Evol, 65 (5), 574-88
DOI 10.1007/s00239-007-9041-9, PubMed 17957399

Hughes T, Rusten TE (2007)
Origin and evolution of self-consumption: autophagy
Adv Exp Med Biol, 607, 111-8
DOI 10.1007/978-0-387-74021-8_9, PubMed 17977463

Publications 2004

Hughes T, Hyun Y, Liberles DA (2004)
Visualising very large phylogenetic trees in three dimensional hyperbolic space
BMC Bioinformatics, 5, 48
DOI 10.1186/1471-2105-5-48, PubMed 15117420

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