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Items: 41

1.

An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.

Yang C, Ambayo H, Baets B, Kolsteren P, Thanintorn N, Hawwash D, Bouwman J, Bronselaer A, Pattyn F, Lachat C.

Nutrients. 2019 Jun 8;11(6). pii: E1300. doi: 10.3390/nu11061300.

2.

Cost-effective and robust genotyping using double-mismatch allele-specific quantitative PCR.

Lefever S, Rihani A, Van der Meulen J, Pattyn F, Van Maerken T, Van Dorpe J, Hellemans J, Vandesompele J.

Sci Rep. 2019 Feb 15;9(1):2150. doi: 10.1038/s41598-019-38581-z.

3.

The paradigm shift in Antarctic ice sheet modelling.

Pattyn F.

Nat Commun. 2018 Jul 16;9(1):2728. doi: 10.1038/s41467-018-05003-z.

4.

High-throughput PCR assay design for targeted resequencing using primerXL.

Lefever S, Pattyn F, De Wilde B, Coppieters F, De Keulenaer S, Hellemans J, Vandesompele J.

BMC Bioinformatics. 2017 Sep 6;18(1):400. doi: 10.1186/s12859-017-1809-3.

5.

Actively evolving subglacial conduits and eskers initiate ice shelf channels at an Antarctic grounding line.

Drews R, Pattyn F, Hewitt IJ, Ng FSL, Berger S, Matsuoka K, Helm V, Bergeot N, Favier L, Neckel N.

Nat Commun. 2017 May 9;8:15228. doi: 10.1038/ncomms15228.

6.

State dependence of climatic instability over the past 720,000 years from Antarctic ice cores and climate modeling.

Dome Fuji Ice Core Project Members:, Kawamura K, Abe-Ouchi A, Motoyama H, Ageta Y, Aoki S, Azuma N, Fujii Y, Fujita K, Fujita S, Fukui K, Furukawa T, Furusaki A, Goto-Azuma K, Greve R, Hirabayashi M, Hondoh T, Hori A, Horikawa S, Horiuchi K, Igarashi M, Iizuka Y, Kameda T, Kanda H, Kohno M, Kuramoto T, Matsushi Y, Miyahara M, Miyake T, Miyamoto A, Nagashima Y, Nakayama Y, Nakazawa T, Nakazawa F, Nishio F, Obinata I, Ohgaito R, Oka A, Okuno J, Okuyama J, Oyabu I, Parrenin F, Pattyn F, Saito F, Saito T, Saito T, Sakurai T, Sasa K, Seddik H, Shibata Y, Shinbori K, Suzuki K, Suzuki T, Takahashi A, Takahashi K, Takahashi S, Takata M, Tanaka Y, Uemura R, Watanabe G, Watanabe O, Yamasaki T, Yokoyama K, Yoshimori M, Yoshimoto T.

Sci Adv. 2017 Feb 8;3(2):e1600446. doi: 10.1126/sciadv.1600446. eCollection 2017 Feb.

7.

Advances in modelling subglacial lakes and their interaction with the Antarctic ice sheet.

Pattyn F, Carter SP, Thoma M.

Philos Trans A Math Phys Eng Sci. 2016 Jan 28;374(2059). pii: 20140296. doi: 10.1098/rsta.2014.0296. Review.

PMID:
26667909
8.

Single-nucleotide polymorphisms and other mismatches reduce performance of quantitative PCR assays.

Lefever S, Pattyn F, Hellemans J, Vandesompele J.

Clin Chem. 2013 Oct;59(10):1470-80. doi: 10.1373/clinchem.2013.203653. Epub 2013 Sep 6.

9.

Effective Alu repeat based RT-Qpcr normalization in cancer cell perturbation experiments.

Rihani A, Van Maerken T, Pattyn F, Van Peer G, Beckers A, De Brouwer S, Kumps C, Mets E, Van der Meulen J, Rondou P, Leonelli C, Mestdagh P, Speleman F, Vandesompele J.

PLoS One. 2013 Aug 14;8(8):e71776. doi: 10.1371/journal.pone.0071776. eCollection 2013.

10.

Ice-sheet mass balance and climate change.

Hanna E, Navarro FJ, Pattyn F, Domingues CM, Fettweis X, Ivins ER, Nicholls RJ, Ritz C, Smith B, Tulaczyk S, Whitehouse PL, Zwally HJ.

Nature. 2013 Jun 6;498(7452):51-9. doi: 10.1038/nature12238. Review.

PMID:
23739423
11.

Future sea-level rise from Greenland's main outlet glaciers in a warming climate.

Nick FM, Vieli A, Andersen ML, Joughin I, Payne A, Edwards TL, Pattyn F, van de Wal RS.

Nature. 2013 May 9;497(7448):235-8. doi: 10.1038/nature12068.

PMID:
23657350
12.

MYCN and HDAC2 cooperate to repress miR-183 signaling in neuroblastoma.

Lodrini M, Oehme I, Schroeder C, Milde T, Schier MC, Kopp-Schneider A, Schulte JH, Fischer M, De Preter K, Pattyn F, Castoldi M, Muckenthaler MU, Kulozik AE, Westermann F, Witt O, Deubzer HE.

Nucleic Acids Res. 2013 Jul;41(12):6018-33. doi: 10.1093/nar/gkt346. Epub 2013 Apr 26.

13.

Focal DNA copy number changes in neuroblastoma target MYCN regulated genes.

Kumps C, Fieuw A, Mestdagh P, Menten B, Lefever S, Pattyn F, De Brouwer S, Sante T, Schulte JH, Schramm A, Van Roy N, Van Maerken T, Noguera R, Combaret V, Devalck C, Westermann F, Laureys G, Eggert A, Vandesompele J, De Preter K, Speleman F.

PLoS One. 2013;8(1):e52321. doi: 10.1371/journal.pone.0052321. Epub 2013 Jan 4.

14.

Targeted expression of mutated ALK induces neuroblastoma in transgenic mice.

Heukamp LC, Thor T, Schramm A, De Preter K, Kumps C, De Wilde B, Odersky A, Peifer M, Lindner S, Spruessel A, Pattyn F, Mestdagh P, Menten B, Kuhfittig-Kulle S, Künkele A, König K, Meder L, Chatterjee S, Ullrich RT, Schulte S, Vandesompele J, Speleman F, Büttner R, Eggert A, Schulte JH.

Sci Transl Med. 2012 Jul 4;4(141):141ra91. doi: 10.1126/scitranslmed.3003967.

15.

Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform.

De Keulenaer S, Hellemans J, Lefever S, Renard JP, De Schrijver J, Van de Voorde H, Tabatabaiefar MA, Van Nieuwerburgh F, Flamez D, Pattyn F, Scharlaken B, Deforce D, Bekaert S, Van Criekinge W, Vandesompele J, Van Camp G, Coucke P.

BMC Med Genomics. 2012 May 18;5:17. doi: 10.1186/1755-8794-5-17.

16.

Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis.

Coppieters F, De Wilde B, Lefever S, De Meester E, De Rocker N, Van Cauwenbergh C, Pattyn F, Meire F, Leroy BP, Hellemans J, Vandesompele J, De Baere E.

Genet Med. 2012 Jun;14(6):576-85. doi: 10.1038/gim.2011.51. Epub 2012 Jan 26.

PMID:
22261762
17.

Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics.

De Leeneer K, De Schrijver J, Clement L, Baetens M, Lefever S, De Keulenaer S, Van Criekinge W, Deforce D, Van Nieuwerburgh F, Bekaert S, Pattyn F, De Wilde B, Coucke P, Vandesompele J, Claes K, Hellemans J.

PLoS One. 2011;6(9):e25531. doi: 10.1371/journal.pone.0025531. Epub 2011 Sep 30.

18.

The microRNA body map: dissecting microRNA function through integrative genomics.

Mestdagh P, Lefever S, Pattyn F, Ridzon D, Fredlund E, Fieuw A, Ongenaert M, Vermeulen J, De Paepe A, Wong L, Speleman F, Chen C, Vandesompele J.

Nucleic Acids Res. 2011 Nov 1;39(20):e136. doi: 10.1093/nar/gkr646. Epub 2011 Aug 10.

19.

Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas.

Fieuw A, Kumps C, Schramm A, Pattyn F, Menten B, Antonacci F, Sudmant P, Schulte JH, Van Roy N, Vergult S, Buckley PG, De Paepe A, Noguera R, Versteeg R, Stallings R, Eggert A, Vandesompele J, De Preter K, Speleman F.

Int J Cancer. 2012 Jun 1;130(11):2599-606. doi: 10.1002/ijc.26317. Epub 2011 Aug 29.

20.

Dickkopf-3 is regulated by the MYCN-induced miR-17-92 cluster in neuroblastoma.

De Brouwer S, Mestdagh P, Lambertz I, Pattyn F, De Paepe A, Westermann F, Schroeder C, Schulte JH, Schramm A, De Preter K, Vandesompele J, Speleman F.

Int J Cancer. 2012 Jun 1;130(11):2591-8. doi: 10.1002/ijc.26295. Epub 2011 Aug 30.

21.

Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline.

De Schrijver JM, De Leeneer K, Lefever S, Sabbe N, Pattyn F, Van Nieuwerburgh F, Coucke P, Deforce D, Vandesompele J, Bekaert S, Hellemans J, Van Criekinge W.

BMC Bioinformatics. 2010 May 20;11:269. doi: 10.1186/1471-2105-11-269.

22.

An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours.

Mestdagh P, Fredlund E, Pattyn F, Rihani A, Van Maerken T, Vermeulen J, Kumps C, Menten B, De Preter K, Schramm A, Schulte J, Noguera R, Schleiermacher G, Janoueix-Lerosey I, Laureys G, Powel R, Nittner D, Marine JC, Ringnér M, Speleman F, Vandesompele J.

Oncogene. 2010 Jun 17;29(24):3583-92. doi: 10.1038/onc.2010.106. Epub 2010 Apr 12.

PMID:
20383195
23.

methGraph: a genome visualization tool for PCR-based methylation assays.

Lefever S, Hoebeeck J, Pattyn F, Tusnády G, De Paepe A, Speleman F, Arányi T, Vandesompele J.

Epigenetics. 2010 Feb 16;5(2):159-63. Epub 2010 Feb 11.

PMID:
20160504
24.

MYCN/c-MYC-induced microRNAs repress coding gene networks associated with poor outcome in MYCN/c-MYC-activated tumors.

Mestdagh P, Fredlund E, Pattyn F, Schulte JH, Muth D, Vermeulen J, Kumps C, Schlierf S, De Preter K, Van Roy N, Noguera R, Laureys G, Schramm A, Eggert A, Westermann F, Speleman F, Vandesompele J.

Oncogene. 2010 Mar 4;29(9):1394-404. doi: 10.1038/onc.2009.429. Epub 2009 Nov 30.

PMID:
19946337
25.

RNA pre-amplification enables large-scale RT-qPCR gene-expression studies on limiting sample amounts.

Vermeulen J, Derveaux S, Lefever S, De Smet E, De Preter K, Yigit N, De Paepe A, Pattyn F, Speleman F, Vandesompele J.

BMC Res Notes. 2009 Nov 25;2:235. doi: 10.1186/1756-0500-2-235.

26.

External oligonucleotide standards enable cross laboratory comparison and exchange of real-time quantitative PCR data.

Vermeulen J, Pattyn F, De Preter K, Vercruysse L, Derveaux S, Mestdagh P, Lefever S, Hellemans J, Speleman F, Vandesompele J.

Nucleic Acids Res. 2009 Nov;37(21):e138. doi: 10.1093/nar/gkp721.

27.

The emerging molecular pathogenesis of neuroblastoma: implications for improved risk assessment and targeted therapy.

Van Roy N, De Preter K, Hoebeeck J, Van Maerken T, Pattyn F, Mestdagh P, Vermeulen J, Vandesompele J, Speleman F.

Genome Med. 2009 Jul 27;1(7):74. doi: 10.1186/gm74.

28.

Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening.

D'haene B, Attanasio C, Beysen D, Dostie J, Lemire E, Bouchard P, Field M, Jones K, Lorenz B, Menten B, Buysse K, Pattyn F, Friedli M, Ucla C, Rossier C, Wyss C, Speleman F, De Paepe A, Dekker J, Antonarakis SE, De Baere E.

PLoS Genet. 2009 Jun;5(6):e1000522. doi: 10.1371/journal.pgen.1000522. Epub 2009 Jun 19.

29.

Meta-mining of neuroblastoma and neuroblast gene expression profiles reveals candidate therapeutic compounds.

De Preter K, De Brouwer S, Van Maerken T, Pattyn F, Schramm A, Eggert A, Vandesompele J, Speleman F.

Clin Cancer Res. 2009 Jun 1;15(11):3690-6. doi: 10.1158/1078-0432.CCR-08-2699. Epub 2009 May 12.

30.

RDML: structured language and reporting guidelines for real-time quantitative PCR data.

Lefever S, Hellemans J, Pattyn F, Przybylski DR, Taylor C, Geurts R, Untergasser A, Vandesompele J; RDML consortium.

Nucleic Acids Res. 2009 Apr;37(7):2065-9. doi: 10.1093/nar/gkp056. Epub 2009 Feb 17.

31.

RTPrimerDB: the portal for real-time PCR primers and probes.

Lefever S, Vandesompele J, Speleman F, Pattyn F.

Nucleic Acids Res. 2009 Jan;37(Database issue):D942-5. doi: 10.1093/nar/gkn777. Epub 2008 Oct 23.

32.

Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas.

Westermann F, Muth D, Benner A, Bauer T, Henrich KO, Oberthuer A, Brors B, Beissbarth T, Vandesompele J, Pattyn F, Hero B, König R, Fischer M, Schwab M.

Genome Biol. 2008 Oct 13;9(10):R150. doi: 10.1186/gb-2008-9-10-r150.

33.

Aberrant methylation of candidate tumor suppressor genes in neuroblastoma.

Hoebeeck J, Michels E, Pattyn F, Combaret V, Vermeulen J, Yigit N, Hoyoux C, Laureys G, De Paepe A, Speleman F, Vandesompele J.

Cancer Lett. 2009 Jan 18;273(2):336-46. doi: 10.1016/j.canlet.2008.08.019. Epub 2008 Sep 25.

PMID:
18819746
34.

Mapping of 5q35 chromosomal rearrangements within a genomically unstable region.

Buysse K, Crepel A, Menten B, Pattyn F, Antonacci F, Veltman JA, Larsen LA, Tümer Z, de Klein A, van de Laar I, Devriendt K, Mortier G, Speleman F.

J Med Genet. 2008 Oct;45(10):672-8. doi: 10.1136/jmg.2008.058883. Epub 2008 Jul 15. Erratum in: J Med Genet. 2009 Dec;46(12):861.

PMID:
18628311
35.

methBLAST and methPrimerDB: web-tools for PCR based methylation analysis.

Pattyn F, Hoebeeck J, Robbrecht P, Michels E, De Paepe A, Bottu G, Coornaert D, Herzog R, Speleman F, Vandesompele J.

BMC Bioinformatics. 2006 Nov 9;7:496.

36.

RTPrimerDB: the real-time PCR primer and probe database, major update 2006.

Pattyn F, Robbrecht P, De Paepe A, Speleman F, Vandesompele J.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D684-8.

37.

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays.

Menten B, Pattyn F, De Preter K, Robbrecht P, Michels E, Buysse K, Mortier G, De Paepe A, van Vooren S, Vermeesch J, Moreau Y, De Moor B, Vermeulen S, Speleman F, Vandesompele J.

BMC Bioinformatics. 2005 May 23;6:124.

38.

Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

De Preter K, Pattyn F, Berx G, Strumane K, Menten B, Van Roy F, De Paepe A, Speleman F, Vandesompele J.

BMC Genomics. 2004 Feb 3;5(1):11.

39.

Neuroblastoma cells with overexpressed MYCN retain their capacity to undergo neuronal differentiation.

Edsjö A, Nilsson H, Vandesompele J, Karlsson J, Pattyn F, Culp LA, Speleman F, Påhlman S.

Lab Invest. 2004 Apr;84(4):406-17.

40.

RTPrimerDB: the real-time PCR primer and probe database.

Pattyn F, Speleman F, De Paepe A, Vandesompele J.

Nucleic Acids Res. 2003 Jan 1;31(1):122-3.

41.

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes.

Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F.

Genome Biol. 2002 Jun 18;3(7):RESEARCH0034. Epub 2002 Jun 18.

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