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Publicaties

A1 publications

2017

De Tender C, Devriese L, Haegeman A, Maes S, Vangeyte J, Cattrijsse A, Dawyndt P and Ruttink T. (2017). The temporal dynamics of microbial colonisation on plastic debris in the North Sea. Environmental Science and Technology. DOI: 10.1021/acs.est.7b00697.

Fraiture M-A, Herman Ph, Papazova N, De Loose M, Deforce D. Ruttink T and Roosens NH (2017). An integrated strategy combining DNA walking and NGS to detect GMO. Food Chemistry. DOI: dx.doi.org/10.1016/j.foodchem.2017.03.067

2016

Calliauw F, De Mulder T, Broekaert K, Vlaemynck G, Michiels C, Heyndrickx M. (2016). Assessment throughout a whole fishing year of the dominant microbiota of peeled brown shrimp (Crangon crangon) stored for 7days under modified atmosphere packaging at 4 degrees C without preservatives. Food Microbiology. 54, 60-71.

Daeseleire E, De Graef E, Rasschaert G, De Mulder T, Van den Meersche T, Van Coillie E, Dewulf J, Heyndrickx M. (2016). Antibiotic use and resistance in animals: Belgian initiatives. Drug Testing and Analysis 8, 549-555.

De Mulder T, Goossen K, Peiren N, Vandaele L, Haegeman A, De Tender C, Ruttink T, Van de Wiele T, De Campeneere S. (2016). Exploring the methanogen and bacterial communities of rumen micro environments. FEBS microbiology ecology. DOI: dx.doi.org/10.1093/femsec/fiw251

De Tender CA, Haegeman A, Vandecasteele B, Clement L, Cremelie P, Dawyndt P, Maes M, Debode J (2016). Dynamics in the strawberry rhizosphere microbiome in response to biochar and Botrytis cinerea leaf infection. In Frontiers in Microbiology, 7, 2062.

De Tender CA, Debode J, Vandecasteele B, D’Hose T, Cremelie P, Haegeman A, Ruttink T, Dawyndt P and Maes M. (2016). Responses assayed in lettuce and strawberry grown in soil or peat amended with biochar. Applied Soil Ecology 107 1–12. dx.doi.org/10.1016/j.apsoil.2016.05.001

Debode J, De Tender C, Soltaninejad S, Van Malderghem C, Haegeman A, Van der Linden I, Cottyn B, Heyndrickx M and Maes M. (2016). Chitin mixed in potting soil alters lettuce growth, the survival of zoonotic bacteria on the leaves and associated rhizosphere microbiology. Frontiers in Microbiology. 7: 565, dx.doi.org/10.3389/fmicb.2016.00565

Rombouts S, Van Vaerenbergh J, Volckaert A, Baeyen S, De Langhe T, Declercq B, Lavigne R and Maes M. (2016). Isolation and characterization of Pseudomonas syringae pv. porri from leek in Flanders. European Journal of Plant Pathology, 144(1), 185-198. DOI: 10.1007/s10658-015-0761-1

Stočes S, Ruttink T, Bartoš J, Studer B, Yates S, Zwierzykowski Z, Abrouk M, Roldán-Ruiz I, Książczyk T, Rey E, Doležel J and Kopecký D. (2016). Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue for single nucleotide polymorphisms discovery. The Plant Genome. doi: 10.3835/plantgenome2016.02.0017

Veeckman E, Ruttink T, and Vandepoele K. (2016). Are we there yet? Reliably estimating the completeness of plant genome sequences. The Plant Cell 28 1759-1768. dx.doi.org/10.1105/tpc.16.00349

2015

Fraiture M-A, Herman P, Taverniers I, De Loose M, Deforce D and Roosens N. (2015). Current and new approaches in GMO detection: challenges and solutions. biomed Research International. dx.doi.org/10.1155/2015/392872

Constantin EC, Cleenwerck I, Maes M, Baeyen S, Van Malderghem C, De Vos P and Cottyn B. (2015). Genetic characterization of strains named as Xanthomonas axonopodis pv. dieffenbachiae leads to a taxonomic revision of the X. axonopodis species complex. Plant Pathology. DOI: 10.1111/ppa.12461

Willems S, Fraiture M-A, Deforce D, De Keersmaecker SCJ, De Loose M, Ruttink T, Herman P, Van Nieuwerburgh F and Roosens N. (2015). Statistical framework for detection of Genetically Modified Organisms based on Next Generation Sequencing. Food Chemistry, DOI: 10.1016/j.foodchem.2015.07.074

De Tender CA, Devriese LI, Haegeman A, Maes S, Ruttink T and Dawyndt P. (2015). Bacterial community profiling of plastic litter in the Belgian part of the North Sea. Environmental Science and Technology, DOI: 10.1021/acs.est.5b01093

Ruttink T, Haegeman A, Van Parijs F, van Glabeke S, Muylle H, Byrne S, Asp T, Roldan-Ruiz I. (2015). Genetic diversity in candidate genes for developmental traits and cell wall characteristics in perennial ryegrass (Lolium perenne). in: H. Budak, G. Spangenberg (eds.), Molecular Breeding of Forage and Turf, DOI: 10.1007/978-3-319-08714-6_9

Van Parijs F, Ruttink T, Boerjan W, Haesaert G, Byrne S, Asp T, Roldan-Ruiz I, Muylle H. (2015). Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne. Plant Biology, DOI: 10.1111/plb.12316

2014

Yates A, Swain MT, Hegarty MJ, Chernukin I, Lowe M, Allison GG, Ruttink T, Abberton MT, Jenkins G, Skøt L. (2014). De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. BMC Genomics, 15, 453. DOI:10.1186/1471-2164-15-453

Vandepitte K, de Meyer T, Helsen K, van Acker K, Roldán-Ruiz I, Mergeay J and Honnay O (2014). Rapid genetic adaptation precedes the spread of an exotic plant species. Molecular Ecology, 23(9), 2157-2164. DOI:10.1111/mec.12683

Zaluga J, Stragier P, Baeyen S, Haegeman A, Van Vaerenbergh J, Maes M, De Vos P. (2014). Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle. BMC Genomics, 15, 392. DOI:10.1186/1471-2164-15-392

Cornille A, Giraud T, Smulders M, Roldan-Ruiz I, Gladieux P. (2014). The domestication and evolutionary ecology of apples. Trends in genetics, 30(2), 57-65. DOI: 10.1016/j.tig.2013.10.002

2013

Ruttink T, Sterck L, Rohde A, Bendixen C, Rouzé P, Asp T, Van de Peer Y, Roldan-Ruiz I. (2013). Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne. Plant Biotechnology Journal, 11(5), 605-617. DOI: 10.1111/pbi.12051

Pritchard L, Humphris S, Baeyen S, Maes M, Van Vaerenbergh J, Elphinstone J, Saddler G, Toth I. (2013). Draft genome sequences of four Dickeya dianthicola and four Dickeya solani strains. Genome Announcements, 1 (4), e00087-12. DOI: 10.1128/genomeA.00087-12

Vandroemme J, Cottyn B, Baeyen S, De Vos P, Maes, M. (2013). Draft genome sequence of Xanthomonas fragariae reveals reductive evolution and distinct virulence-related gene content. BMC Genomics, 14 (1), 829. DOI: 10.1186/1471-2164-14-829.

Meeting presentations, abstracts, posters,....

2017

Haegeman A, De Keyser E, De Riek J, Heungens K, Kirov I, Leus L, Maes M, Muylle H, Roldán-Ruiz I, Van Glabeke S, Van Huylenbroeck J, Van Laere K, Van Poucke K, Verwimp C, and Ruttink T. (2017). The next generation of molecular markers in plant sciences. Revolutionizing Next Generation Sequencing (2nd edition) - Antwerpen - 21-22/03/17

Stočes S, Yates S, Ruttink T, Studer B, Zwierzykowski Z, Roldán-Ruiz I, Książczyk T, Doležel J, Kopecký D and Bartoš J. (2017). Gene Expression Changes in First Generations of Reciprocal Interspecific Grass Hybrids. Plant and Animal Genome Conference XXV, San Diego, USA. 14/01/17 - 18/01/17

Ruttink T, Kirov I, De Keyser E, De Riek J, Leus L, Haegeman A, Bendahmane M, Liu C, and Van Laere K. (2017). Building bridges: integrating in situ Hi-C and molecular cytogenetics to reconstruct Rosa wichurana pseudochromosomes. Plant and Animal Genome Conference XXV, San Diego, USA. 14/01/17 - 18/01/17

Veeckman E, Asp T, Roldan-Ruiz I, Vandepoele K and Tom Ruttink. (2017). Perennial ryegrass: unaveling the structure and content of a many faced genome. Plant and Animal Genome Conference XXV, San Diego, USA. 14/01/17 - 18/01/17

Roldan Ruiz I, van Parijs F, Van Waes G, Haesaert G, Ruttink T and Muylle H. (2017). Genetic dissection of cell wall digestibility in perennial ryegrass. Plant and Animal Genome Conference XXV, San Diego, USA. 14/01/17 - 18/01/17

2016

Waeyenberge L, Haegeman A, De Sutter N, Debode J, Viaene N, Maes M. (2016). Karakteriseren van nematodengemeenschappen via DNA metabarcoding ter bepaling van de bodemgezondheid. In L. De Cock (editor), De Biologische landbouw in Vlaanderen : Onderzoek 2015-2016. Merelbeke: NOBL-Netwerk Onderzoek Biologische Landbouw & Voeding.

Waeyenberge L, Haegeman A, De Sutter N, Demey A, De Schrijver A, Schelfhout S, Viaene N, Verheyen K, and Maes M (2016). Bepaling van nematodengemeenschappen in halfnatuurlijke graslanden in verschillende fasen van natuurherstel. in Starters in het natuur- en bosonderzoek .

Waeyenberge L, Haegeman A, De Sutter N, Viaene N, and Maes M. (2016). DNA metabarcoding to characterize soil nematode communities. In 32nd symposium of the European Society of Nematologists. (blz. 311)

Devriese L, Haegeman A, Maes S, Ruttink T, De Backer A, Van Hoey G, Wittoeck J, Hillewaert H, De Tender C, Hostens K. (2016). A DNA (meta)barcoding approach to tackle marine benthic biodiversity. nov-2016 North Sea Open Science Conference. Abstract booklet: Interdisciplinary Science in support of Marine Management. Ostend, Belgium, 7-10/11/2016.

De Tender C, Devriese L, Haegeman A, Maes S, Ruttink T, Dawyndt P. (2016). The dynamic bacterial colonization on plastic: an exposure experiment at sea nov-2016. North Sea Open Science Conference. Abstract booklet: Interdisciplinary Science in support of Marine Management. Ostend, Belgium, 7-10/11/2016.

De Tender C, Devriese L, Haegeman A, Cattrijsse A, Vangeyte J, Maes S, Ruttink T, Dawyndt P.(2016). Temporal dynamics of bacterial colonization of plastic debris in the North Sea. Setac/iEOS Joint Focused Topic Meeting: Environmtal and (eco)toxicological omics and epigenetics: science, technology and regulatory applications. 12/09/2016

De Tender C, Devriese L, Haegeman A, Maes S, Ruttink T, Robbens J, Dawyndt, P. (2016). Living in the anthropocene: plastic debris as a new bacterial habitat. ISME 16 Montreal, 21/08/2016

De Mulder T, Goossens K, Van De Wiele T and De Campeneere S. (2016). Exploring the methanogen and bacterial communities of rumen environments. Proceedings 10th Joint Symposium INRA-ROWETT 2016: Gut Microbiology: 20 years and counting. 21/06/2016

De Mulder T, Goossens K, Peiren N, Vandaele L, Van de Wiele T and De Campeneere S. (2016). Influence of host dependent factors on the methanogen community and methane production. Proceedings 6th Greenhouse Gas and Animal Agriculture Conference (GGAA2016). 14/02/2016

Veeckman E, Vandepoele K, Asp T, Roldán-Ruiz I and Ruttink T. (2016) The perennial ryegrass genome and its alter egos. BIG N2N annual symposium. Gent, Belgium. 19/05/16

Devriese L, Hostens K, Maes S, Haegeman A, De Backer A, Wittoeck J, Vansteenbrugge L and Ruttink T. (2016) A DNA metabarcoding approach to profile macrobenthos and zooplankton biodiversity. ICES/PICES 6th Zooplankton Production Symposium. Bergen, Noorwegen. 9/05/16 - 13/05/16

Ruttink T, Lamour K, Barre P, Van Glabeke S, Muylle H, Roschanski A, Dehmer K, Sampoux J-P. and Roldán-Ruiz I. (2016). Allele frequency profiling of candidate adaptive genes for landscape genomics in perennial ryegrass. Applied Bioinformatics for Life Sciences. Leuven, Belgium. 17/03/16 - 18/03/16

Veeckman E, Vandepoele K, Asp T, Roldán-Ruiz I and Ruttink T. (2016). Revealing genomic variation in perennial ryegrass (Lolium perenne). Applied Bioinformatics for Life Sciences. Leuven, Belgium 17/03/16 - 18/03/16

Haegeman A, De Tender C, Debode J, Waeyenberge L, De Sutter N, Viaene N and Maes M. (2016). Metabarcoding as a tool to uncover soil biodiversity (bacteria, fungi and nematodes). Applied Bioinformatics for Life Sciences. Leuven, Belgium. 17/03/16 - 18/03/16

De Tender C, Devriese L, Maes S, Vanhalst K, De Bock T, Vangeyte J, Cattrijsse A, Robbens J and Dawyndt P. (2016). Food for bacteria: a plastic exposure trial at sea. VLIZ Marine Scientist's Day 2016. 12/02/2016.

Verwimp C, Vansteenbrugge L, Hostens K, Muylle H, Honnay O, Roldan-Ruiz I, Robbens J, Ruttink T. (2016) Exploring population structure of Mnemiopsis leidyi in north-western European waters. VLIZ Marine Scientist Day 2016. 12/02/16

Veeckman E, Vandepoele K, Asp T, Roldán-Ruiz I, Ruttink T. (2016). Genomic variation in the FT gene family of perennial ryegrass (Lolium perenne). In Baert, Reheul and Roldan-ruiz (eds.) Breeding for scarcity. Ghent (Belgium).

van Parijs FRD, Ruttink T, Haesaert G, Roldán-Ruiz I and Muylle H. (2016). Association mapping ofLpCCR1 with lignin content and cell wall digestibility of perennial ryegrass. In Baert, Reheul and Roldan-ruiz (eds.) Breeding for scarcity. Ghent (Belgium).

Ruttink T, Muylle H and Barre Ph. (2016). Association mapping and Genomics selection. In Baert, Reheul and Roldan-ruiz (eds.) Breeding for scarcity. Ghent (Belgium).

De Mulder T, Rasschaert G, Van Coillie E, Van de Wiele T and Heyndrickx M. (2016). Effect of three concentrations of doxycycline on the microbial community and resistance development in the ex vivo simulated pigs gut. Oral presentation and Abstract in Proceedings of 21st Conference on Food Microbiology, p. 109, September 15-16, 2016 Brussels, Belgium

2015

Veeckman E, Haegeman A, Muylle H, Vandepoele K, Asp T and Ruttink T. (2015) Identification of genomic variation in perennial ryegrass (Lolium perenne). BIG N2N annual symposium. Gent, Belgium. 21/05/15

De Tender C, Debode J, Haegeman A, Ruttink T, Baeyen S, Cremelie P, Vandecasteele B, Dawyndt P and Maes M. (2015). Effects of biochar addition on bacterial populations of the lettuce and strawberry rhizosphere. BIG N2N annual symposium, Gent, Belgium, 21/05/15.

De Tender C, Devriese L, Haegeman A, Maes S, Ruttink T, Dawyndt P and Robbens, J (2015). Plastic debris: a distinct niche in the marine environment. BIG N2N annual symposium, Gent, Belgium, 21/05/15, 

De Keyser E, Van Poucke C, Ruttink T and De Riek J. (2015). Fifty shades of red: flavonoid analysis inRhododendron simsii hybrids. IN: 25th International EUCARPIA Symposium Section Ornamentals: Crossing Borders: Book of abstracts. Van Huylenbroeck, J. & Dhooghe, E. (eds.). Melle, België

Foucher F, Hibrand-Saint Oyant L, Hamama L, Sakr S, Baudino S, Caissard JP, Smulders JMS, Debener T, De Riek J, Torres A, Millan T, Amaya I, Zamir D, Sargent D, Nybom H, Hokanson SC, Byrne DM, Desnoyé B, Bruneau A, Matsumoto S, Yamada K, Wincker P, Gouzy J, Bendahmane M, Raymond O, Vergne P, Dubois A and Just J. (2015). Towards the rose genome sequence and its use in research and breeding. Proceedings of the VI International Symposium on Rose Research and Cultivation. Debener, T. & Linde, M. (eds.). Acta Horticulturae; nr. 1064, blz. 167-175

De Tender C, Devriese L, Maes S, Haegeman A, Ruttink T, Robbens J, Dawyndt P. Metagenomics @ Sea: a floating house in a marine environment. VLIZ Young marine scientist day. VIVEZ, Brugge, België. 20/02/2015

Verwimp C, Vansteenbrugge L, Devriese L, Hostens K, Muylle H, Honnay O, Roldan-Ruiz I, Ruttink T, Robbens J. Population genomics of Mnemiopsis Leidyi, a notorious marine invader in the North Sea. VLIZ Young marine scientist day. VIVEZ, Brugge, België. 20/02/2015, 

Ruttink T. Probing genome diversity in natural and breeding populations of Lolium perenne. (2015). Plant and Animal Genome Conference XXIII, San Diego, USA. 10/01/15 - 14/01/15

Stoces S, Ruttink T, Kopecky D, Abrouk M, Bartos J, Dolezel J. Gene expression changes in interspecific Festuca x Lolium hybrids. (2015). Plant and Animal Genome Conference XXIII, San Diego, USA. 10/01/15 - 14/01/15

Muylle M. An association mapping approach on cell wall digestibility and plant architecture gives insight in yield, persistency and forage quality in perennial ryegrass. (2015). Plant and Animal Genome Conference XXIII, San Diego, USA. 10/01/15 - 14/01/15

Heyndrickx M, Calliauw F, Broekaert K, Vlaemynck G, De Mulder T and Michiels C. (2015). Microbiota of peeled brown shrimp (Crangon crangon) stored under modified atmosphere packaging at 4°C without preservatives. 6th Congress of European Microbiologists (FEMS 2015 Congress), Maastricht, The Netherlands, June 7 – 11, 2015. Reference no. 1865

De Tender C, Baeyen S, Haegeman A, De Mulder T, Devriese L, Debode J, Maes M, Roldan-Ruiz I, Heyndrickx M, Robbens J and Ruttink T. (2015). Towards population genomics and metagenomics in agriculture and marine environments (poster). Big N2N meeting, Gent, May 21, 2015.

Calliauw F, De Mulder T, Broekaert K, Vlaemynck G, Michiels C and Heyndrickx M. (2015). Polyphasic identification of the dominant microbiota of peeled brown shrimp (Crangon crangon) stored under modified atmosphere packaging at 4 °C without preservatives. Poster with abstract in Proceedings of the 20th Conference on Food Microbiology, Brussels, Belgium, 8 & 9 October 2015, Part Poster Presentation Abstracts, p 98.

2014

Ruttink T. Towards population genomics and metagenomics in agriculture and marine environments. In: MRP-N2N 'from Nucleotides to Networks' seminar series, 17/12/2014 - VIB, Zwijnaarde, België.

De Tender C, Debode J, Devriese L, Haegeman A, Ruttink T, Baeyen S, Cremelie P, Maes S, Dawyndt P, Maes M, Robbens J. Metagenome analyses of a soil and marine environment. In: Fourth MRP-N2N Bioinformatics symposium. Zwijnaarde, België. 21/05/14

Devriese L. The role of microplastics as a vector for bacteria. ICES Working Group (WGBEC), Kopenhagen, Denemarken. 06/03/2014

Haegeman A, Ruttink T, Muylle H, Verwimp C, van Parijs F, Van Glabeke S, Roldán-Ruiz I, Debode J, Baeyen S, De Tender C, Maes M. Population genomics @ ILVO - Plant Sciences Unit. In : Agricultural -Omics course (European Bioinformatics Institute). Hinxton, Engeland. 17/02/14 - 21/02/14

Van Glabeke S, Boonefaes T, Ruttink T, Montoye T. A new approach using spectral content profiling for in-depth plant DNA QC during NGS library preparation. In: Plant and Animal Genome Conference XXII, Plant and Animal Genome Conference, San Diego, USA. 10/01/14 - 15/01/14

Ruttink T, van Parijs F, Van Glabeke S, Muylle H, Haegeman A, Byrne S, Asp T, Roldan-Ruiz I. Exploring genetic diversity in perennial ryegrass (L. perenne) populations by targeted resequencing. In: Plant and Animal Genome Conference XXII, San Diego, USA. 10/01/14 - 15/01/14

 

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