Publications by Gregor D. Gilfillan

54 publications found

  1. Cobb L, de Muinck E, Kollias S, Skage M, Gilfillan GD, Sydenham MAK, Qiao SW, Star B (2024)
    High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method
    PLoS One, 19 (3), e0300865
    DOI 10.1371/journal.pone.0300865, PubMed 38517905
  2. Bjørnstad PM, Aaløkken R, Åsheim J, Sundaram AYM, Felde CN, Østby GH, Dalland M, Sjursen W, Carrizosa C, Vigeland MD, Sorte HS, Sheng Y, Ariansen SL, Grindedal EM, Gilfillan GD (2024)
    Publisher Correction: A 39 kb structural variant causing Lynch syndrome detected by optical genome mapping and nanopore sequencing
    Eur J Hum Genet, 32 (5), 601-602
    DOI 10.1038/s41431-023-01519-1, PubMed 38172175
  3. Bjørnstad PM, Aaløkken R, Åsheim J, Sundaram AYM, Felde CN, Østby GH, Dalland M, Sjursen W, Carrizosa C, Vigeland MD, Sorte HS, Sheng Y, Ariansen SL, Grindedal EM, Gilfillan GD (2023)
    A 39 kb structural variant causing Lynch Syndrome detected by optical genome mapping and nanopore sequencing
    Eur J Hum Genet, 32 (5), 513-520
    DOI 10.1038/s41431-023-01494-7, PubMed 38030917
  4. Lekva T, Sundaram AYF, Roland MCP, Åsheim J, Michelsen AE, Norwitz ER, Aukrust P, Gilfillan GD, Ueland T (2023)
    Platelet and mitochondrial RNA is decreased in plasma-derived extracellular vesicles in women with preeclampsia-an exploratory study
    BMC Med, 21 (1), 458
    DOI 10.1186/s12916-023-03178-x, PubMed 37996819
  5. Diaz-Lundahl S, Nørstebø SF, Klem TB, Gilfillan GD, Dalland M, Gillund P, Krogenæs A (2023)
    The microbiota of uterine biopsies, cytobrush and vaginal swabs at artificial insemination in Norwegian red cows
    Theriogenology, 209, 115-125
    DOI 10.1016/j.theriogenology.2023.06.024, PubMed 37390751
  6. Soares JZ, Valeur J, Šaltytė Benth J, Knapskog AB, Selbæk G, Arefi G, Gilfillan GD, Tollisen A, Bogdanovic N, Pettersen R (2022)
    Vitamin D in Alzheimer's Disease: Low Levels in Cerebrospinal Fluid Despite Normal Amounts in Serum
    J Alzheimers Dis, 86 (3), 1301-1314
    DOI 10.3233/JAD-215536, PubMed 35180126
  7. Ribarska T, Bjørnstad PM, Sundaram AYM, Gilfillan GD (2022)
    Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing
    BMC Genomics, 23 (1), 92
    DOI 10.1186/s12864-022-08316-y, PubMed 35105301
  8. Diaz-Lundahl S, Sundaram AYM, Gillund P, Gilfillan GD, Olsaker I, Krogenæs A (2022)
    Gene Expression in Embryos From Norwegian Red Bulls With High or Low Non Return Rate: An RNA-Seq Study of in vivo-Produced Single Embryos
    Front Genet, 12, 780113
    DOI 10.3389/fgene.2021.780113, PubMed 35096004
  9. 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
  10. Tønne E, Due-Tønnessen BJ, Vigeland MD, Amundsen SS, Ribarska T, Åsten PM, Sheng Y, Helseth E, Gilfillan GD, Mero IL, Heimdal KR (2022)
    Whole-exome sequencing in syndromic craniosynostosis increases diagnostic yield and identifies candidate genes in osteogenic signaling pathways
    Am J Med Genet A, 188 (5), 1464-1475
    DOI 10.1002/ajmg.a.62663, PubMed 35080095
  11. Kaitetzidou E, Gilfillan GD, Antonopoulou E, Sarropoulou E (2021)
    Sex-biased dynamics of three-spined stickleback (Gasterosteus aculeatus) gene expression patterns
    Genomics, 114 (1), 266-277
    DOI 10.1016/j.ygeno.2021.12.010, PubMed 34933072
  12. Lind A, Barlinn R, Landaas ET, Andresen LL, Jakobsen K, Fladeby C, Nilsen M, Bjørnstad PM, Sundaram AYM, Ribarska T, Müller F, Gilfillan GD, Holberg-Petersen M (2021)
    Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory
    J Clin Virol, 141, 104906
    DOI 10.1016/j.jcv.2021.104906, PubMed 34273860
  13. Heinicke F, Zhong X, Zucknick M, Breidenbach J, Sundaram AYM, T Flåm S, Leithaug M, Dalland M, Rayner S, Lie BA, Gilfillan GD (2020)
    An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits
    RNA Biol, 17 (9), 1284-1292
    DOI 10.1080/15476286.2020.1761081, PubMed 32436772
  14. Heinicke F, Zhong X, Zucknick M, Breidenbach J, Sundaram AYM, T Flåm S, Leithaug M, Dalland M, Farmer A, Henderson JM, Hussong MA, Moll P, Nguyen L, McNulty A, Shaffer JM, Shore S, Yip HK, Vitkovska J, Rayner S, Lie BA, Gilfillan GD (2019)
    Systematic assessment of commercially available low-input miRNA library preparation kits
    RNA Biol, 17 (1), 75-86
    DOI 10.1080/15476286.2019.1667741, PubMed 31559901
  15. Fosslie M, Manaf A, Lerdrup M, Hansen K, Gilfillan GD, Dahl JA (2019)
    Going low to reach high: Small-scale ChIP-seq maps new terrain
    Wiley Interdiscip Rev Syst Biol Med, 12 (1), e1465
    DOI 10.1002/wsbm.1465, PubMed 31478357
  16. Cernilogar FM, Hasenöder S, Wang Z, Scheibner K, Burtscher I, Sterr M, Smialowski P, Groh S, Evenroed IM, Gilfillan GD, Lickert H, Schotta G (2019)
    Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2
    Nucleic Acids Res, 47 (17), 9069-9086
    DOI 10.1093/nar/gkz627, PubMed 31350899
  17. Furi L, Crawford LA, Rangel-Pineros G, Manso AS, De Ste Croix M, Haigh RD, Kwun MJ, Engelsen Fjelland K, Gilfillan GD, Bentley SD, Croucher NJ, Clokie MR, Oggioni MR (2019)
    Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host
    J Bacteriol, 201 (19)
    DOI 10.1128/JB.00370-19, PubMed 31285240
  18. Eguíluz-Gracia I, Malmstrom K, Dheyauldeen SA, Lohi J, Sajantila A, Aaløkken R, Sundaram AYM, Gilfillan GD, Makela M, Baekkevold ES, Jahnsen FL (2018)
    Monocytes accumulate in the airways of children with fatal asthma
    Clin Exp Allergy, 48 (12), 1631-1639
    DOI 10.1111/cea.13265, PubMed 30184280
  19. Santoro F, Pettini E, Kazmin D, Ciabattini A, Fiorino F, Gilfillan GD, Evenroed IM, Andersen P, Pozzi G, Medaglini D (2018)
    Transcriptomics of the Vaccine Immune Response: Priming With Adjuvant Modulates Recall Innate Responses After Boosting
    Front Immunol, 9, 1248
    DOI 10.3389/fimmu.2018.01248, PubMed 29922291
  20. Wilkinson D, Váchová L, Hlaváček O, Maršíková J, Gilfillan GD, Palková Z (2018)
    Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms
    Oxid Med Cell Longev, 2018, 4950591
    DOI 10.1155/2018/4950591, PubMed 29765496
  21. 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
  22. Wilkinson D, Maršíková J, Hlaváček O, Gilfillan GD, Ježková E, Aaløkken R, Váchová L, Palková Z (2018)
    Transcriptome Remodeling of Differentiated Cells during Chronological Ageing of Yeast Colonies: New Insights into Metabolic Differentiation
    Oxid Med Cell Longev, 2018, 4932905
    DOI 10.1155/2018/4932905, PubMed 29576850
  23. Stüken A, Haverkamp THA, Dirven HAAM, Gilfillan GD, Leithaug M, Lund V (2018)
    Microbial Community Composition of Tap Water and Biofilms Treated with or without Copper-Silver Ionization
    Environ Sci Technol, 52 (6), 3354-3364
    DOI 10.1021/acs.est.7b05963, PubMed 29461810
  24. Sarropoulou E, Sundaram AYM, Kaitetzidou E, Kotoulas G, Gilfillan GD, Papandroulakis N, Mylonas CC, Magoulas A (2017)
    Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili
    Gigascience, 6 (12), 1-13
    DOI 10.1093/gigascience/gix108, PubMed 29126158
  25. Dahl JA, Gilfillan GD (2018)
    How low can you go? Pushing the limits of low-input ChIP-seq
    Brief Funct Genomics, 17 (2), 89-95
    DOI 10.1093/bfgp/elx037, PubMed 29087438
  26. 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
  27. Ribarska T, Gilfillan GD (2018)
    Native Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) from Low Cell Numbers
    Methods Mol Biol, 1689, 157-166
    DOI 10.1007/978-1-4939-7380-4_14, PubMed 29027173
  28. de Muinck EJ, Trosvik P, Gilfillan GD, Hov JR, Sundaram AYM (2017)
    A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform
    Microbiome, 5 (1), 68
    DOI 10.1186/s40168-017-0279-1, PubMed 28683838
  29. Lee S, Norheim F, Gulseth HL, Langleite TM, Kolnes KJ, Tangen DS, Stadheim HK, Gilfillan GD, Holen T, Birkeland KI, Jensen J, Drevon CA (2017)
    Interaction between plasma fetuin-A and free fatty acids predicts changes in insulin sensitivity in response to long-term exercise
    Physiol Rep, 5 (5)
    DOI 10.14814/phy2.13183, PubMed 28270597
  30. Lee S, Norheim F, Langleite TM, Noreng HJ, Storås TH, Afman LA, Frost G, Bell JD, Thomas EL, Kolnes KJ, Tangen DS, Stadheim HK, Gilfillan GD, Gulseth HL, Birkeland KI, Jensen J, Drevon CA, Holen T, NutriTech Consortium (2016)
    Effect of energy restriction and physical exercise intervention on phenotypic flexibility as examined by transcriptomics analyses of mRNA from adipose tissue and whole body magnetic resonance imaging
    Physiol Rep, 4 (21)
    DOI 10.14814/phy2.13019, PubMed 27821717
  31. 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
  32. Beulig F, Urich T, Nowak M, Trumbore SE, Gleixner G, Gilfillan GD, Fjelland KE, Küsel K (2016)
    Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure
    Nat Microbiol, 1, 15025
    DOI 10.1038/nmicrobiol.2015.25, PubMed 27571979
  33. Sarropoulou E, Tsalafouta A, Sundaram AY, Gilfillan GD, Kotoulas G, Papandroulakis N, Pavlidis M (2016)
    Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata)
    BMC Genomics, 17, 506
    DOI 10.1186/s12864-016-2874-0, PubMed 27461489
  34. Trucchi E, Mazzarella AB, Gilfillan GD, Lorenzo MT, Schönswetter P, Paun O (2016)
    BsRADseq: screening DNA methylation in natural populations of non-model species
    Mol Ecol, 25 (8), 1697-713
    DOI 10.1111/mec.13550, PubMed 26818626
  35. Moreno-Mayar JV, Rasmussen S, Seguin-Orlando A, Rasmussen M, Liang M, Flåm ST, Lie BA, Gilfillan GD, Nielsen R, Thorsby E, Willerslev E, Malaspinas AS (2014)
    Genome-wide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans
    Curr Biol, 24 (21), 2518-25
    DOI 10.1016/j.cub.2014.09.057, PubMed 25447991
  36. Squadrito ML, Baer C, Burdet F, Maderna C, Gilfillan GD, Lyle R, Ibberson M, De Palma M (2014)
    Endogenous RNAs modulate microRNA sorting to exosomes and transfer to acceptor cells
    Cell Rep, 8 (5), 1432-46
    DOI 10.1016/j.celrep.2014.07.035, PubMed 25159140
  37. Star B, Nederbragt AJ, Hansen MH, Skage M, Gilfillan GD, Bradbury IR, Pampoulie C, Stenseth NC, Jakobsen KS, Jentoft S (2014)
    Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA
    PLoS One, 9 (3), e89676
    DOI 10.1371/journal.pone.0089676, PubMed 24608104
  38. Peña-Diaz J, Hegre SA, Anderssen E, Aas PA, Mjelle R, Gilfillan GD, Lyle R, Drabløs F, Krokan HE, Sætrom P (2013)
    Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication
    Nucleic Acids Res, 41 (5), 2846-56
    DOI 10.1093/nar/gks1336, PubMed 23325852
  39. Straub T, Zabel A, Gilfillan GD, Feller C, Becker PB (2012)
    Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq
    Genome Res, 23 (3), 473-85
    DOI 10.1101/gr.146407.112, PubMed 23233545
  40. 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
  41. Squadrito ML, Pucci F, Magri L, Moi D, Gilfillan GD, Ranghetti A, Casazza A, Mazzone M, Lyle R, Naldini L, De Palma M (2012)
    miR-511-3p modulates genetic programs of tumor-associated macrophages
    Cell Rep, 1 (2), 141-54
    DOI 10.1016/j.celrep.2011.12.005, PubMed 22832163
  42. Leidenroth A, Sorte HS, Gilfillan G, Ehrlich M, Lyle R, Hewitt JE (2012)
    Diagnosis by sequencing: correction of misdiagnosis from FSHD2 to LGMD2A by whole-exome analysis
    Eur J Hum Genet, 20 (9), 999-1003
    DOI 10.1038/ejhg.2012.42, PubMed 22378277
  43. 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
  44. Skinningsrud B, Husebye ES, Gilfillan GD, Frengen E, Erichsen A, Gervin K, Ormerod E, Egeland T, Undlien DE (2009)
    X-linked congenital adrenal hypoplasia with hypogonadotropic hypogonadism caused by an inversion disrupting a conserved noncoding element upstream of the NR0B1 (DAX1) gene
    J Clin Endocrinol Metab, 94 (10), 4086-93
    DOI 10.1210/jc.2009-0923, PubMed 19773398
  45. Roxrud I, Raiborg C, Gilfillan GD, Strømme P, Stenmark H (2009)
    Dual degradation mechanisms ensure disposal of NHE6 mutant protein associated with neurological disease
    Exp Cell Res, 315 (17), 3014-27
    DOI 10.1016/j.yexcr.2009.07.012, PubMed 19619532
  46. Bartkuhn M, Straub T, Herold M, Herrmann M, Rathke C, Saumweber H, Gilfillan GD, Becker PB, Renkawitz R (2009)
    Active promoters and insulators are marked by the centrosomal protein 190
    EMBO J, 28 (7), 877-88
    DOI 10.1038/emboj.2009.34, PubMed 19229299
  47. Straub T, Grimaud C, Gilfillan GD, Mitterweger A, Becker PB (2008)
    The chromosomal high-affinity binding sites for the Drosophila dosage compensation complex
    PLoS Genet, 4 (12), e1000302
    DOI 10.1371/journal.pgen.1000302, PubMed 19079572
  48. Gilfillan GD, Selmer KK, Roxrud I, Smith R, Kyllerman M, Eiklid K, Kroken M, Mattingsdal M, Egeland T, Stenmark H, Sjøholm H, Server A, Samuelsson L, Christianson A, Tarpey P, Whibley A, Stratton MR, Futreal PA, Teague J, Edkins S, Gecz J, Turner G, Raymond FL, Schwartz C, Stevenson RE et al. (2008)
    SLC9A6 mutations cause X-linked mental retardation, microcephaly, epilepsy, and ataxia, a phenotype mimicking Angelman syndrome
    Am J Hum Genet, 82 (4), 1003-10
    DOI 10.1016/j.ajhg.2008.01.013, PubMed 18342287
  49. Gilfillan GD, König C, Dahlsveen IK, Prakoura N, Straub T, Lamm R, Fauth T, Becker PB (2007)
    Cumulative contributions of weak DNA determinants to targeting the Drosophila dosage compensation complex
    Nucleic Acids Res, 35 (11), 3561-72
    DOI 10.1093/nar/gkm282, PubMed 17483514
  50. Gilfillan GD, Straub T, de Wit E, Greil F, Lamm R, van Steensel B, Becker PB (2006)
    Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex
    Genes Dev, 20 (7), 858-70
    DOI 10.1101/gad.1399406, PubMed 16547172
  51. Dahlsveen IK, Gilfillan GD, Shelest VI, Lamm R, Becker PB (2006)
    Targeting determinants of dosage compensation in Drosophila
    PLoS Genet, 2 (2), e5
    DOI 10.1371/journal.pgen.0020005, PubMed 16462942
  52. Straub T, Gilfillan GD, Maier VK, Becker PB (2005)
    The Drosophila MSL complex activates the transcription of target genes
    Genes Dev, 19 (19), 2284-8
    DOI 10.1101/gad.1343105, PubMed 16204179
  53. Gilfillan GD, Dahlsveen IK, Becker PB (2004)
    Lifting a chromosome: dosage compensation in Drosophila melanogaster
    FEBS Lett, 567 (1), 8-14
    DOI 10.1016/j.febslet.2004.03.110, PubMed 15165886
  54. Kageyama Y, Mengus G, Gilfillan G, Kennedy HG, Stuckenholz C, Kelley RL, Becker PB, Kuroda MI (2001)
    Association and spreading of the Drosophila dosage compensation complex from a discrete roX1 chromatin entry site
    EMBO J, 20 (9), 2236-45
    DOI 10.1093/emboj/20.9.2236, PubMed 11331589

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