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Items: 27

1.

Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: Neisseria meningitidis as a Proof-of-Concept.

Bogaerts B, Winand R, Fu Q, Van Braekel J, Ceyssens PJ, Mattheus W, Bertrand S, De Keersmaecker SCJ, Roosens NHC, Vanneste K.

Front Microbiol. 2019 Mar 6;10:362. doi: 10.3389/fmicb.2019.00362. eCollection 2019.

2.

Isolation of Burkholderia pseudomallei from a Pet Green Iguana, Belgium.

Hellebuyck T, Wattiau P, Boyen F, Moeremans I, Roosens NH, Vanneste K, Garmyn A, Saey V, Pasmans F, Haesebrouck F.

Emerg Infect Dis. 2018 Dec;24(12):2331-2333. doi: 10.3201/eid2412.171661.

3.

Application of whole genome data for in silico evaluation of primers and probes routinely employed for the detection of viral species by RT-qPCR using dengue virus as a case study.

Vanneste K, Garlant L, Broeders S, Van Gucht S, Roosens NH.

BMC Bioinformatics. 2018 Sep 4;19(1):312. doi: 10.1186/s12859-018-2313-0.

4.

Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO.

Fraiture MA, Saltykova A, Hoffman S, Winand R, Deforce D, Vanneste K, De Keersmaecker SCJ, Roosens NHC.

Sci Rep. 2018 May 21;8(1):7903. doi: 10.1038/s41598-018-26259-x.

5.

Insights into earthquake hazard map performance from shaking history simulations.

Vanneste K, Stein S, Camelbeeck T, Vleminckx B.

Sci Rep. 2018 Jan 30;8(1):1855. doi: 10.1038/s41598-018-20214-6.

6.

Detection of Plasmid-Mediated Colistin Resistance, mcr-1 and mcr-2 Genes, in Salmonella spp. Isolated from Food at Retail in Belgium from 2012 to 2015.

Garcia-Graells C, De Keersmaecker SCJ, Vanneste K, Pochet B, Vermeersch K, Roosens N, Dierick K, Botteldoorn N.

Foodborne Pathog Dis. 2018 Feb;15(2):114-117. doi: 10.1089/fpd.2017.2329. Epub 2017 Nov 28.

PMID:
29182477
7.

Revisiting ancestral polyploidy in plants.

Ruprecht C, Lohaus R, Vanneste K, Mutwil M, Nikoloski Z, Van de Peer Y, Persson S.

Sci Adv. 2017 Jul 5;3(7):e1603195. doi: 10.1126/sciadv.1603195. eCollection 2017 Jul.

8.

Two-stage opening of the Dover Strait and the origin of island Britain.

Gupta S, Collier JS, Garcia-Moreno D, Oggioni F, Trentesaux A, Vanneste K, De Batist M, Camelbeeck T, Potter G, Van Vliet-Lanoë B, Arthur JC.

Nat Commun. 2017 Apr 4;8:15101. doi: 10.1038/ncomms15101.

9.

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.

Olsen JL, Rouzé P, Verhelst B, Lin YC, Bayer T, Collen J, Dattolo E, De Paoli E, Dittami S, Maumus F, Michel G, Kersting A, Lauritano C, Lohaus R, Töpel M, Tonon T, Vanneste K, Amirebrahimi M, Brakel J, Boström C, Chovatia M, Grimwood J, Jenkins JW, Jueterbock A, Mraz A, Stam WT, Tice H, Bornberg-Bauer E, Green PJ, Pearson GA, Procaccini G, Duarte CM, Schmutz J, Reusch TB, Van de Peer Y.

Nature. 2016 Feb 18;530(7590):331-5. doi: 10.1038/nature16548. Epub 2016 Jan 27.

PMID:
26814964
10.

Technology for Large-Scale Translation of Clinical Practice Guidelines: A Pilot Study of the Performance of a Hybrid Human and Computer-Assisted Approach.

Van de Velde S, Macken L, Vanneste K, Goossens M, Vanschoenbeek J, Aertgeerts B, Vanopstal K, Vander Stichele R, Buysschaert J.

JMIR Med Inform. 2015 Oct 9;3(4):e33. doi: 10.2196/medinform.4450.

11.

Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum.

Vanneste K, Sterck L, Myburg AA, Van de Peer Y, Mizrachi E.

Plant Cell. 2015 Jun;27(6):1567-78. doi: 10.1105/tpc.15.00157. Epub 2015 May 22.

12.

Corrigendum: The genome sequence of the orchid Phalaenopsis equestris.

Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, Dievart A, Dufayard JF, Xu X, Wang JY, Wang J, Xiao XJ, Zhao XM, Du R, Zhang GQ, Wang M, Su YY, Xie GC, Liu GH, Li LQ, Huang LQ, Luo YB, Chen HH, Van de Peer Y, Liu ZJ.

Nat Genet. 2015 Mar;47(3):304. doi: 10.1038/ng0315-304a. No abstract available.

PMID:
25711871
13.

The genome sequence of the orchid Phalaenopsis equestris.

Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, Dievart A, Dufayard JF, Xu X, Wang JY, Wang J, Xiao XJ, Zhao XM, Du R, Zhang GQ, Wang M, Su YY, Xie GC, Liu GH, Li LQ, Huang LQ, Luo YB, Chen HH, Van de Peer Y, Liu ZJ.

Nat Genet. 2015 Jan;47(1):65-72. doi: 10.1038/ng.3149. Epub 2014 Nov 24. Erratum in: Nat Genet. 2015 Mar;47(3):304.

PMID:
25420146
14.

Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution.

Vanneste K, Maere S, Van de Peer Y.

Philos Trans R Soc Lond B Biol Sci. 2014 Aug 5;369(1648). pii: 20130353. doi: 10.1098/rstb.2013.0353. Review.

15.

The genome of Eucalyptus grandis.

Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Külheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J.

Nature. 2014 Jun 19;510(7505):356-62. doi: 10.1038/nature13308. Epub 2014 Jun 11.

PMID:
24919147
16.

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary.

Vanneste K, Baele G, Maere S, Van de Peer Y.

Genome Res. 2014 Aug;24(8):1334-47. doi: 10.1101/gr.168997.113. Epub 2014 May 16.

17.

The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants.

Gadeyne A, Sánchez-Rodríguez C, Vanneste S, Di Rubbo S, Zauber H, Vanneste K, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Mayers JR, Adamowski M, Kania U, Ehrlich M, Schweighofer A, Ketelaar T, Maere S, Bednarek SY, Friml J, Gevaert K, Witters E, Russinova E, Persson S, De Jaeger G, Van Damme D.

Cell. 2014 Feb 13;156(4):691-704. doi: 10.1016/j.cell.2014.01.039.

18.

The Norway spruce genome sequence and conifer genome evolution.

Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S.

Nature. 2013 May 30;497(7451):579-84. doi: 10.1038/nature12211. Epub 2013 May 22.

PMID:
23698360
19.

Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication.

Voordeckers K, Brown CA, Vanneste K, van der Zande E, Voet A, Maere S, Verstrepen KJ.

PLoS Biol. 2012;10(12):e1001446. doi: 10.1371/journal.pbio.1001446. Epub 2012 Dec 11.

20.

Recombinant antibody production in Arabidopsis seeds triggers an unfolded protein response.

De Wilde K, De Buck S, Vanneste K, Depicker A.

Plant Physiol. 2013 Feb;161(2):1021-33. doi: 10.1104/pp.112.209718. Epub 2012 Nov 27.

21.

Inference of genome duplications from age distributions revisited.

Vanneste K, Van de Peer Y, Maere S.

Mol Biol Evol. 2013 Jan;30(1):177-90. doi: 10.1093/molbev/mss214. Epub 2012 Aug 30.

PMID:
22936721
22.

Expansive evolution of the trehalose-6-phosphate phosphatase gene family in Arabidopsis.

Vandesteene L, López-Galvis L, Vanneste K, Feil R, Maere S, Lammens W, Rolland F, Lunn JE, Avonce N, Beeckman T, Van Dijck P.

Plant Physiol. 2012 Oct;160(2):884-96. doi: 10.1104/pp.112.201400. Epub 2012 Aug 1.

23.

Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification.

Vekemans D, Proost S, Vanneste K, Coenen H, Viaene T, Ruelens P, Maere S, Van de Peer Y, Geuten K.

Mol Biol Evol. 2012 Dec;29(12):3793-806. doi: 10.1093/molbev/mss183. Epub 2012 Jul 20.

PMID:
22821009
24.

Interaction between developing spinal locomotor networks in the neonatal mouse.

Gordon IT, Dunbar MJ, Vanneste KJ, Whelan PJ.

J Neurophysiol. 2008 Jul;100(1):117-28. doi: 10.1152/jn.00829.2007. Epub 2008 Apr 24.

25.

Guiding adult Mammalian sensory axons during regeneration.

Webber CA, Xu Y, Vanneste KJ, Martinez JA, Verge VM, Zochodne DW.

J Neuropathol Exp Neurol. 2008 Mar;67(3):212-22. doi: 10.1097/NEN.0b013e3181654972.

PMID:
18344912
26.

Unilateral bloody nipple discharge in a two-month-old male.

De Praeter C, De Coen K, Vanneste K, Vanhaesebrouck P.

Eur J Pediatr. 2008 Apr;167(4):457-9. Epub 2007 Apr 19.

PMID:
17443348
27.

Tight nuchal cord and neonatal hypovolaemic shock.

Vanhaesebrouck P, Vanneste K, de Praeter C, Van Trappen Y, Thiery M.

Arch Dis Child. 1987 Dec;62(12):1276-7.

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