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Items: 40

1.

Systematic assessment of commercially available low-input miRNA library preparation kits.

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.

RNA Biol. 2019 Sep 27:1-12. doi: 10.1080/15476286.2019.1667741. [Epub ahead of print]

PMID:
31559901
2.

Going low to reach high: Small-scale ChIP-seq maps new terrain.

Fosslie M, Manaf A, Lerdrup M, Hansen K, Gilfillan GD, Dahl JA.

Wiley Interdiscip Rev Syst Biol Med. 2019 Sep 3:e1465. doi: 10.1002/wsbm.1465. [Epub ahead of print] Review.

PMID:
31478357
3.

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2.

Cernilogar FM, Hasenöder S, Wang Z, Scheibner K, Burtscher I, Sterr M, Smialowski P, Groh S, Evenroed IM, Gilfillan GD, Lickert H, Schotta G.

Nucleic Acids Res. 2019 Sep 26;47(17):9069-9086. doi: 10.1093/nar/gkz627.

4.

Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host.

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.

J Bacteriol. 2019 Sep 6;201(19). pii: e00370-19. doi: 10.1128/JB.00370-19. Print 2019 Oct 1.

5.

Monocytes accumulate in the airways of children with fatal asthma.

Eguíluz-Gracia I, Malmstrom K, Dheyauldeen SA, Lohi J, Sajantila A, Aaløkken R, Sundaram AYM, Gilfillan GD, Makela M, Baekkevold ES, Jahnsen FL.

Clin Exp Allergy. 2018 Dec;48(12):1631-1639. doi: 10.1111/cea.13265. Epub 2018 Oct 16.

PMID:
30184280
6.

Transcriptomics of the Vaccine Immune Response: Priming With Adjuvant Modulates Recall Innate Responses After Boosting.

Santoro F, Pettini E, Kazmin D, Ciabattini A, Fiorino F, Gilfillan GD, Evenroed IM, Andersen P, Pozzi G, Medaglini D.

Front Immunol. 2018 Jun 5;9:1248. doi: 10.3389/fimmu.2018.01248. eCollection 2018.

7.

Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms.

Wilkinson D, Váchová L, Hlaváček O, Maršíková J, Gilfillan GD, Palková Z.

Oxid Med Cell Longev. 2018 Mar 25;2018:4950591. doi: 10.1155/2018/4950591. eCollection 2018. Review.

8.

An optimized FAIRE procedure for low cell numbers in yeast.

Segorbe D, Wilkinson D, Mizeranschi A, Hughes T, Aaløkken R, Váchová L, Palková Z, Gilfillan GD.

Yeast. 2018 Aug;35(8):507-512. doi: 10.1002/yea.3316. Epub 2018 May 28.

9.

Transcriptome Remodeling of Differentiated Cells during Chronological Ageing of Yeast Colonies: New Insights into Metabolic Differentiation.

Wilkinson D, Maršíková J, Hlaváček O, Gilfillan GD, Ježková E, Aaløkken R, Váchová L, Palková Z.

Oxid Med Cell Longev. 2018 Jan 11;2018:4932905. doi: 10.1155/2018/4932905. eCollection 2018.

10.

Microbial Community Composition of Tap Water and Biofilms Treated with or without Copper-Silver Ionization.

Stüken A, Haverkamp THA, Dirven HAAM, Gilfillan GD, Leithaug M, Lund V.

Environ Sci Technol. 2018 Mar 20;52(6):3354-3364. doi: 10.1021/acs.est.7b05963. Epub 2018 Feb 28.

PMID:
29461810
11.

Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili.

Sarropoulou E, Sundaram AYM, Kaitetzidou E, Kotoulas G, Gilfillan GD, Papandroulakis N, Mylonas CC, Magoulas A.

Gigascience. 2017 Dec 1;6(12):1-13. doi: 10.1093/gigascience/gix108.

12.

How low can you go? Pushing the limits of low-input ChIP-seq.

Dahl JA, Gilfillan GD.

Brief Funct Genomics. 2018 Mar 1;17(2):89-95. doi: 10.1093/bfgp/elx037. Review.

PMID:
29087438
13.

Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling.

Maršíková J, Wilkinson D, Hlaváček O, Gilfillan GD, Mizeranschi A, Hughes T, Begany M, Rešetárová S, Váchová L, Palková Z.

BMC Genomics. 2017 Oct 23;18(1):814. doi: 10.1186/s12864-017-4214-4.

14.

Native Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) from Low Cell Numbers.

Ribarska T, Gilfillan GD.

Methods Mol Biol. 2018;1689:157-166. doi: 10.1007/978-1-4939-7380-4_14.

PMID:
29027173
15.

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform.

de Muinck EJ, Trosvik P, Gilfillan GD, Hov JR, Sundaram AYM.

Microbiome. 2017 Jul 6;5(1):68. doi: 10.1186/s40168-017-0279-1.

16.

Interaction between plasma fetuin-A and free fatty acids predicts changes in insulin sensitivity in response to long-term exercise.

Lee S, Norheim F, Gulseth HL, Langleite TM, Kolnes KJ, Tangen DS, Stadheim HK, Gilfillan GD, Holen T, Birkeland KI, Jensen J, Drevon CA.

Physiol Rep. 2017 Mar;5(5). pii: e13183. doi: 10.14814/phy2.13183.

17.

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.

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.

Physiol Rep. 2016 Nov;4(21). pii: e13019.

18.

A comparative study of ChIP-seq sequencing library preparation methods.

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.

BMC Genomics. 2016 Oct 21;17(1):816.

19.

Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure.

Beulig F, Urich T, Nowak M, Trumbore SE, Gleixner G, Gilfillan GD, Fjelland KE, Küsel K.

Nat Microbiol. 2016 Jan 27;1:15025. doi: 10.1038/nmicrobiol.2015.25.

PMID:
27571979
20.

Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata).

Sarropoulou E, Tsalafouta A, Sundaram AY, Gilfillan GD, Kotoulas G, Papandroulakis N, Pavlidis M.

BMC Genomics. 2016 Jul 26;17:506. doi: 10.1186/s12864-016-2874-0.

21.

BsRADseq: screening DNA methylation in natural populations of non-model species.

Trucchi E, Mazzarella AB, Gilfillan GD, Lorenzo MT, Schönswetter P, Paun O.

Mol Ecol. 2016 Apr;25(8):1697-713. doi: 10.1111/mec.13550. Epub 2016 Mar 28.

22.

Genome-wide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans.

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.

Curr Biol. 2014 Nov 3;24(21):2518-25. doi: 10.1016/j.cub.2014.09.057. Epub 2014 Oct 23.

23.

Endogenous RNAs modulate microRNA sorting to exosomes and transfer to acceptor cells.

Squadrito ML, Baer C, Burdet F, Maderna C, Gilfillan GD, Lyle R, Ibberson M, De Palma M.

Cell Rep. 2014 Sep 11;8(5):1432-46. doi: 10.1016/j.celrep.2014.07.035. Epub 2014 Aug 21.

24.

Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA.

Star B, Nederbragt AJ, Hansen MH, Skage M, Gilfillan GD, Bradbury IR, Pampoulie C, Stenseth NC, Jakobsen KS, Jentoft S.

PLoS One. 2014 Mar 7;9(3):e89676. doi: 10.1371/journal.pone.0089676. eCollection 2014. Erratum in: PLoS One. 2014;9(7):e103170.

25.

Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication.

Peña-Diaz J, Hegre SA, Anderssen E, Aas PA, Mjelle R, Gilfillan GD, Lyle R, Drabløs F, Krokan HE, Sætrom P.

Nucleic Acids Res. 2013 Mar 1;41(5):2846-56. doi: 10.1093/nar/gks1336. Epub 2013 Jan 15.

26.

Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq.

Straub T, Zabel A, Gilfillan GD, Feller C, Becker PB.

Genome Res. 2013 Mar;23(3):473-85. doi: 10.1101/gr.146407.112. Epub 2012 Dec 11.

27.

Limitations and possibilities of low cell number ChIP-seq.

Gilfillan GD, Hughes T, Sheng Y, Hjorthaug HS, Straub T, Gervin K, Harris JR, Undlien DE, Lyle R.

BMC Genomics. 2012 Nov 21;13:645. doi: 10.1186/1471-2164-13-645.

28.

miR-511-3p modulates genetic programs of tumor-associated macrophages.

Squadrito ML, Pucci F, Magri L, Moi D, Gilfillan GD, Ranghetti A, Casazza A, Mazzone M, Lyle R, Naldini L, De Palma M.

Cell Rep. 2012 Feb 23;1(2):141-54. doi: 10.1016/j.celrep.2011.12.005. Epub 2012 Feb 9.

29.

A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions.

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.

Eur J Hum Genet. 2012 Jan;20(1):58-63. doi: 10.1038/ejhg.2011.126. Epub 2011 Jun 29.

30.

X-linked congenital adrenal hypoplasia with hypogonadotropic hypogonadism caused by an inversion disrupting a conserved noncoding element upstream of the NR0B1 (DAX1) gene.

Skinningsrud B, Husebye ES, Gilfillan GD, Frengen E, Erichsen A, Gervin K, Ormerod E, Egeland T, Undlien DE.

J Clin Endocrinol Metab. 2009 Oct;94(10):4086-93. doi: 10.1210/jc.2009-0923. Epub 2009 Sep 22.

PMID:
19773398
31.

Dual degradation mechanisms ensure disposal of NHE6 mutant protein associated with neurological disease.

Roxrud I, Raiborg C, Gilfillan GD, Strømme P, Stenmark H.

Exp Cell Res. 2009 Oct 15;315(17):3014-27. doi: 10.1016/j.yexcr.2009.07.012. Epub 2009 Jul 17.

PMID:
19619532
32.

Active promoters and insulators are marked by the centrosomal protein 190.

Bartkuhn M, Straub T, Herold M, Herrmann M, Rathke C, Saumweber H, Gilfillan GD, Becker PB, Renkawitz R.

EMBO J. 2009 Apr 8;28(7):877-88. doi: 10.1038/emboj.2009.34. Epub 2009 Feb 19.

33.

The chromosomal high-affinity binding sites for the Drosophila dosage compensation complex.

Straub T, Grimaud C, Gilfillan GD, Mitterweger A, Becker PB.

PLoS Genet. 2008 Dec;4(12):e1000302. doi: 10.1371/journal.pgen.1000302. Epub 2008 Dec 12.

34.

SLC9A6 mutations cause X-linked mental retardation, microcephaly, epilepsy, and ataxia, a phenotype mimicking Angelman syndrome.

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, Undlien DE, Strømme P.

Am J Hum Genet. 2008 Apr;82(4):1003-10. doi: 10.1016/j.ajhg.2008.01.013. Epub 2008 Mar 13.

35.

Cumulative contributions of weak DNA determinants to targeting the Drosophila dosage compensation complex.

Gilfillan GD, König C, Dahlsveen IK, Prakoura N, Straub T, Lamm R, Fauth T, Becker PB.

Nucleic Acids Res. 2007;35(11):3561-72. Epub 2007 May 5.

36.

Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex.

Gilfillan GD, Straub T, de Wit E, Greil F, Lamm R, van Steensel B, Becker PB.

Genes Dev. 2006 Apr 1;20(7):858-70. Epub 2006 Mar 17.

37.

Targeting determinants of dosage compensation in Drosophila.

Dahlsveen IK, Gilfillan GD, Shelest VI, Lamm R, Becker PB.

PLoS Genet. 2006 Feb;2(2):e5. Epub 2006 Feb 3.

38.

The Drosophila MSL complex activates the transcription of target genes.

Straub T, Gilfillan GD, Maier VK, Becker PB.

Genes Dev. 2005 Oct 1;19(19):2284-8.

39.

Lifting a chromosome: dosage compensation in Drosophila melanogaster.

Gilfillan GD, Dahlsveen IK, Becker PB.

FEBS Lett. 2004 Jun 1;567(1):8-14. Review.

40.

Candida dubliniensis: phylogeny and putative virulence factors.

Gilfillan GD, Sullivan DJ, Haynes K, Parkinson T, Coleman DC, Gow NA.

Microbiology. 1998 Apr;144 ( Pt 4):829-38.

PMID:
9579058

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