Ghent University Academic Bibliography

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Whole-genome deep sequencing reveals host-driven in-planta evolution of Columnea Latent Viroid (CLVd) quasi-species populations

Parichate Tangkanchanapas (UGent) , Annelies Haegeman, Tom Ruttink, Monica Höfte (UGent) and Kris De Jonghe

(2020) INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 21(9).
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Establishment of CRISPR/Cas9 Genome Editing in Witloof (Cichorium intybus var. foliosum)

Charlotte De Bruyn (UGent) , Tom Ruttink, Tom Eeckhaut, Thomas Jacobs (UGent) , Ellen De Keyser (UGent) , Alain Goossens (UGent) and Katrijn Van Laere (UGent)

(2020) Frontiers in Genome Editing. 2.
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Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea

Christophe Verwimp, Lies Vansteenbrugge, Sofie Derycke (UGent) , Thomas Kerkhove (UGent) , Hilde Muylle, Olivier Honnay, Tom Ruttink, Isabel Roldàn-Ruiz (UGent) and Kris Hostens

(2020) ECOLOGY AND EVOLUTION. 10(1). p.11-25
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Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

José Luis Blanco‐Pastor, Philippe Barre, Thomas Keep, Thomas Ledauphin, Abraham Escobar‐Gutiérrez, Anna Maria Roschanski, Evelyn Willner, Klaus J. Dehmer, Matthew Hegarty, Hilde Muylle, et al.

(2020) MOLECULAR ECOLOGY RESOURCES.
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Cichorium intybus L. × Cicerbita alpina Walbr. : doubled haploid chicory induction and CENH3 characterization

Jeroen Van der Veken (UGent) , Tom Eeckhaut, Joost Baert, Tom Ruttink, Olivier Maudoux, Stefaan Werbrouck (UGent) and Johan Van Huylenbroeck

(2019) EUPHYTICA. 215(7).
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Single nucleotide polymorphisms and biochemical markers as complementary tools to characterize hops (Humulus lupulus L.) in brewing practice

Ann Van Holle (UGent) , Hilde Muylle, Tom Ruttink, Anita Van Landschoot (UGent) , Geert Haesaert (UGent) , Dirk Naudts, Denis De Keukeleire (UGent) and Isabel Roldàn-Ruiz (UGent)

(2019) JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY. 67(13). p.3761-3771
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Impact of cross-contamination concentrations of doxycycline hyclate on the microbial ecosystem in an ex vivo model of the pig's cecum

Thijs De Mulder, Geertrui Rasschaert, Els Van Coillie, Tina Van den Meersche (UGent) , Annelies Haegeman, Tom Ruttink, Tom Van de Wiele (UGent) and Marc Heyndrickx (UGent)

(2019) MICROBIAL DRUG RESISTANCE. 25(2). p.304-315
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Overcoming challenges in variant calling : exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)

Elisabeth Veeckman (UGent) , Sabine Van Glabeke, Annelies Haegeman, Hilde Muylle, Frederik RD van Parijs, Stephen L Byrne, Torben Asp, Bruno Studer, Antje Rohde, Isabel Roldàn-Ruiz (UGent) , et al.

(2019) DNA RESEARCH. 26(1). p.1-12
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Impact of breed on the rumen microbial community composition and methane emission of Holstein Friesian and Belgian Blue heifers

Thijs De Mulder, Nico Peiren, Leen Vandaele, Tom Ruttink, Sam De Campeneere, Tom Van de Wiele (UGent) and Karen Goossens

(2018) LIVESTOCK SCIENCE. 207. p.38-44
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Temporal dynamics of bacterial and fungal colonization on plastic debris in the North Sea

Caroline De Tender (UGent) , Lisa I Devriese, Annelies Haegeman, Sara Maes, Jürgen Vangeyte, André Cattrijsse, Peter Dawyndt (UGent) and Tom Ruttink

(2017) ENVIRONMENTAL SCIENCE & TECHNOLOGY. 51(13). p.7350-7360
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Exploring the methanogen and bacterial communities of rumen environments : solid adherent, fluid and epimural

Thijs De Mulder (UGent) , Karen Goossens, Nico Peiren, Leen Vandaele, Annelies Haegeman, Caroline De Tender (UGent) , Tom Ruttink, Tom Van de Wiele (UGent) and Sam De Campeneere

(2017) FEMS MICROBIOLOGY ECOLOGY. 93(3).
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Are we there yet? : reliably estimating the completeness of plant genome sequences

Elisabeth Veeckman (UGent) , Tom Ruttink and Klaas Vandepoele (UGent)

(2016) PLANT CELL. 28(8). p.1759-1768
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- C1
Genomic variation in the FT gene family of perennial ryegrass (Lolium perenne)

Elisabeth Veeckman (UGent) , Klaas Vandepoele (UGent) , T Asp, Isabel Roldàn-Ruiz (UGent) and Tom Ruttink

(2016) Breeding in a world of scarcity : proceedings of the 2015 meeting of the section 'Forage Crops and Amenity Grasses' of Eucarpia. p.121-126
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High-throughput phenotyping of lateral expansion and regrowth of spaced Lolium perenne plants using on-field image analysis

Peter Lootens, Tom Ruttink, Antje Rohde, Didier Combes, Philippe Barre and Isabel Roldàn-Ruiz (UGent)

(2016) PLANT METHODS. 12.
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Biological, physicochemical and plant health responses in lettuce and strawberry in soil or peat amended with biochar

Caroline De Tender (UGent) , Jane Debode, Bart Vandecasteele, Tommy D’Hose, Pieter Cremelie, Annelies Haegeman, Tom Ruttink, Peter Dawyndt (UGent) and Martine Maes (UGent)

(2016) APPLIED SOIL ECOLOGY. 107. p.1-12
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Statistical framework for detection of genetically modified organisms based on Next Generation Sequencing

Sander Willems (UGent) , Marie-Alice Fraiture (UGent) , Dieter Deforce (UGent) , Sigrid De Keersmaecker, Philippe Herman, Marc De Loose (UGent) , Tom Ruttink, Filip Van Nieuwerburgh (UGent) and Nancy Roosens

(2016) FOOD CHEMISTRY. 192. p.788-798
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Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue for single-nucleotide polymorphism discovery

Štěpán Stočes, Tom Ruttink, Jan Bartoš, Bruno Studer, Steven Yates, Zbigniew Zwierzykowski, Michael Abrouk, Isabel Roldàn-Ruiz (UGent) , Tomasz Książczyk, Elodie Rey, et al.

(2016) PLANT GENOME. 9(3).
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Bacterial community profiling of plastic litter in the Belgian part of the North Sea

Caroline De Tender (UGent) , Lisa I Devriese, Annelies Haegeman, Sara Maes, Tom Ruttink and Peter Dawyndt (UGent)

(2015) ENVIRONMENTAL SCIENCE & TECHNOLOGY. 49(16). p.9629-9638
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Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne

Frederik van Parijs, Tom Ruttink, Wout Boerjan (UGent) , Geert Haesaert (UGent) , SL Byrne, T Asp, Isabel Roldàn-Ruiz (UGent) and H Muylle

(2015) PLANT BIOLOGY. 17(4). p.877-892
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Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne

Tom Ruttink, Lieven Sterck (UGent) , Antje Rohde (UGent) , Christian Bendixen, Pierre Rouzé (UGent) , Torben Asp, Yves Van de Peer (UGent) and Isabel Roldàn-Ruiz (UGent)

(2013) PLANT BIOTECHNOLOGY JOURNAL. 11(5). p.605-617
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Bud set in poplar: genetic dissection of a complex trait in natural and hybrid populations

Antje Rohde (UGent) , Veronique Storme (UGent) , Véronique Jorge, Muriel Gaudet, Nicola Vitacolonna, Francesco Fabbrini, Tom Ruttink, Giusi Zaina, Nicolas Marron, Sophie Dillen, et al.

(2011) NEW PHYTOLOGIST. 189(1). p.106-121
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Molecular toolbox for the identification of unknown genetically modified organisms

Tom Ruttink, Rolinde Demeyer, Elke Van Gulck, Bart Van Droogenbroeck, Maddalena Querci, Isabel Taverniers and Marc De Loose (UGent)

(2010) ANALYTICAL AND BIOANALYTICAL CHEMISTRY. 396(6). p.2073-2089
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Assessment of primer/template mismatch effects on real-time PCR amplification of target taxa for GMO quantification

Rim Ghedira (UGent) , Nina Papazova, Marnik Vuylsteke (UGent) , Tom Ruttink, Isabel Taverniers and Marc De Loose (UGent)

(2009) JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY. 57(20). p.9370-9377
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Gene expression during the induction, maintenance, and release of dormancy in apical buds of poplar

Antje Rohde (UGent) , Tom Ruttink, Vanessa Hostyn, Lieven Sterck (UGent) , Klara Van Driessche and Wout Boerjan (UGent)

(2007) JOURNAL OF EXPERIMENTAL BOTANY. 58(15-16). p.4047-4060
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A molecular timetable for apical bud formation and dormancy induction in poplar

Tom Ruttink, Matthias Arend, Kris Morreel (UGent) , Veronique Storme (UGent) , Stephane Rombauts (UGent) , Jörg Fromm, Rishikesh P Bhalerao, Wout Boerjan (UGent) and Antje Rohde (UGent)

(2007) PLANT CELL. 19(8). p.2370-2390

Academic Bibliography

Whole-genome deep sequencing reveals host-driven in-planta evolution of Columnea Latent Viroid (CLVd) quasi-species populations

Establishment of CRISPR/Cas9 Genome Editing in Witloof (Cichorium intybus var. foliosum)

Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea

Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

Cichorium intybus L. × Cicerbita alpina Walbr. : doubled haploid chicory induction and CENH3 characterization

Single nucleotide polymorphisms and biochemical markers as complementary tools to characterize hops (Humulus lupulus L.) in brewing practice

Impact of cross-contamination concentrations of doxycycline hyclate on the microbial ecosystem in an ex vivo model of the pig's cecum

Overcoming challenges in variant calling : exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)

Impact of breed on the rumen microbial community composition and methane emission of Holstein Friesian and Belgian Blue heifers

Temporal dynamics of bacterial and fungal colonization on plastic debris in the North Sea

Exploring the methanogen and bacterial communities of rumen environments : solid adherent, fluid and epimural

Are we there yet? : reliably estimating the completeness of plant genome sequences

Genomic variation in the FT gene family of perennial ryegrass (Lolium perenne)

High-throughput phenotyping of lateral expansion and regrowth of spaced Lolium perenne plants using on-field image analysis

Biological, physicochemical and plant health responses in lettuce and strawberry in soil or peat amended with biochar

Statistical framework for detection of genetically modified organisms based on Next Generation Sequencing

Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue for single-nucleotide polymorphism discovery

Bacterial community profiling of plastic litter in the Belgian part of the North Sea

Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne

Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne

Bud set in poplar: genetic dissection of a complex trait in natural and hybrid populations

Molecular toolbox for the identification of unknown genetically modified organisms

Assessment of primer/template mismatch effects on real-time PCR amplification of target taxa for GMO quantification

Gene expression during the induction, maintenance, and release of dormancy in apical buds of poplar

A molecular timetable for apical bud formation and dormancy induction in poplar

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