Publications

615. Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development

VERMEIRSSEN, V, JOSHI, A, MICHOEL, T, BONNET, E, CASNEUF, T, VAN DE PEER, Y

(2009) - MOLECULAR BIOSYSTEMS

DOI
614. Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus

PIGANEAU, G, VANDEPOELE, K, GOURBIERE, S, VAN DE PEER, Y, MOREAU, H

(2009) - JOURNAL OF MOLECULAR EVOLUTION

DOI
613. Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

VANDEPOELE, K, QUIMBAYA, M, CASNEUF, T, DE VEYLDER, L, VAN DE PEER, Y

(2009) - PLANT PHYSIOLOGY

DOI
612. Toward a gold standard for promoter prediction evaluation

ABEEL, T, VAN DE PEER, Y, SAEYS, Y

(2009) - BIOINFORMATICS

DOI
611. The flowering world: a tale of duplications

VAN DE PEER, Y, FAWCETT, JA, PROOST, S, STERCK, L, VANDEPOELE, K

(2009) - TRENDS IN PLANT SCIENCE

DOI
610. Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress

DITTAMI, SM, SCORNET, D, PETIT, JL, SEGURENS, B, DA SILVA, C, CORRE, E, DONDRUP, M, GLATTING, KH, KONIG, R, STERCK, L, ROUZE, P, VAN DE PEER, Y, COCK, JM, BOYEN, C, TONON, T

(2009) - GENOME BIOLOGY

DOI
609. Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

DE BODT, S, PROOST, S, VANDEPOELE, K, ROUZE, P, VAN DE PEER, Y

(2009) - BMC GENOMICS

DOI
608. Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences

BAELE, G, VAN DE PEER, Y, VANSTEELANDT, S

(2009) - BMC EVOLUTIONARY BIOLOGY

DOI
607. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

FAWCETT, JA, MAERE, S, VAN DE PEER, Y

(2009) - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DOI
606. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

WORDEN, AZ, LEE, JH, MOCK, T, ROUZE, P, SIMMONS, MP, AERTS, AL, ALLEN, AE, CUVELIER, ML, DERELLE, E, EVERETT, MV, FOULON, E, GRIMWOOD, J, GUNDLACH, H, HENRISSAT, B, NAPOLI, C, MCDONALD, SM, PARKER, MS, ROMBAUTS, S, SALAMOV, A, VON DASSOW, P, BADGER, JH, COUTINHO, PM, DEMIR, E, DUBCHAK, I, GENTEMANN, C, EIKREM, W, GREADY, JE, JOHN, U, LANIER, W, LINDQUIST, EA, LUCAS, S, MAYER, KFX, MOREAU, H, NOT, F, OTILLAR, R, PANAUD, O, PANGILINAN, J, PAULSEN, I, PIEGU, B, POLIAKOV, A, ROBBENS, S, SCHMUTZ, J, TOULZA, E, WYSS, T, ZELENSKY, A, ZHOU, K, ARMBRUST, EV, BHATTACHARYA, D, GOODENOUGH, UW, VAN DE PEER, Y, GRIGORIEV, IV

(2009) - SCIENCE

DOI
605. Module networks revisited: computational assessment and prioritization of model predictions

JOSHI, A, DE SMET, R, MARCHAL, K, VAN DE PEER, Y, MICHOEL, T

(2009) - BIOINFORMATICS

DOI
604. PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

PROOST, S, VAN BEL, M, STERCK, L, BILLIAU, K, VAN PARYS, T, VAN DE PEER, Y, VANDEPOELE, K

(2009) - Plant Cell

DOI
603. Reverse-Engineering Transcriptional Modules from Gene Expression Data

MICHOEL, T, DE SMET, R, JOSHI, A, MARCHAL, K, VAN DE PEER, Y

(2009) - CHALLENGES OF SYSTEMS BIOLOGY: COMMUNITY EFFORTS TO HARNESS BIOLOGICAL COMPLEXITY

DOI
602. The evolutionary significance of ancient genome duplications

Van De Peer, Y., Maere, S., Meyer, A.

(2009) - Nature Reviews Genetics

DOI
601. Phylogenetic inference based on distance methods: Theory

Yves Van de Peer

(2009) - Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing

DOI
600. Java-ML: A machine learning library

Abeel, T., Van De Peer, Y., Saeys, Y.

(2009) - Journal of Machine Learning Research

DOI
599. The Arabidopsis thaliana F-box protein FBL17 is essential for progression through the second mitosis during pollen development.

Gusti A, Baumberger N, Nowack M, Pusch S, Eisler H, Potuschak T, De Veylder L, Schnittger A, Genschik P

(2009) -

DOI
598. Translational control of eukaryotic gene expression.

Van Der Kelen K, Beyaert R, Inzé D, De Veylder L

(2009) -

DOI
597. The Arabidopsis thaliana F-box protein FBL17 is essential for progression through the second mitosis during pollen development.

Gusti A, Baumberger N, Nowack M, Pusch S, Eisler H, Potuschak T, De Veylder L, Schnittger A, Genschik P

(2009) -

DOI
596. Hydrogen Peroxide-Responsive Genes in Stress Acclimation and Cell Death

Sandy Vanderauwera, Frank A. Hoeberichts, Frank Van Breusegem

(2009) - Reactive Oxygen Species in Plant Signaling

DOI
595. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

Fawcett, Jeffrey A., Maere, Steven, Van de Peer, Yves

(2009) - Proceedings of the National Academy of Sciences of the United States of America

DOI
594. OPINION The evolutionary significance of ancient genome duplications

Van de Peer, Yves, Maere, Steven, Meyer, Axel

(2009) - Nature Reviews Genetics

DOI
593. Open-ended On-board Evolutionary Robotics for Robot Swarms

Baele, Guy, Bredeche, Nicolas, Haasdijk, Evert, Maere, Steven, Michiels, Nico, Van de Peer, Yves, Schmickl, Thomas, Schwarzer, Christopher, Thenius, Ronald, IEEE

(2009) - 2009 Ieee Congress on Evolutionary Computation, Vols 1-5

DOI
592. Cryopreservation of hairy root cultures of Maesa lanceolata and Medicago truncatula.

Lambert E, Goossens A, Panis B, Van Labeke MC, Geelen D

(2009) - Plant Cell, Tissue and Organ Culture

DOI
591. Auxin signaling in algal lineages: fact or myth?

Lau, S., Shao, N., Bock, R., Jurgens, G., De Smet, I.

(2009) - Trends in Plant Science

DOI
590. Receptor-like kinases shape the plant

De Smet, I., Voss, U., Jurgens, G., Beeckman, T.

(2009) - Nature Cell Biology

DOI
589. Extensive expression regulation and lack of heterologous enzymatic activity of the Class II trehalose metabolism proteins from Arabidopsis thaliana

Ramon, M., De Smet, I., Vandesteene, L., Naudts, M., Leyman, B., Van Dijck, P., Rolland, F., Beeckman, T., Thevelein, J. M.

(2009) - Plant Cell and Environment

DOI
588. Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen Marchal

(2009) - BMC Systems Biology

DOI
587. The past, present, and future of chemical biology in auxin research.

De Rybel B, Audenaert D, Beeckman T, Kepinski S

(2009) -

DOI
586. Receptor endocytosis and signaling in plants.

Irani NG, Russinova E

(2009) -

DOI
585. Systematic localization of the Arabidopsis core cell cycle proteins reveals novel cell division complexes.

Boruc J, Mylle E, Duda M, De Clercq R, Rombauts S, Geelen D, Hilson P, Inzé D, Van Damme D, Russinova E

(2009) - Plant physiology

DOI
584. Gene silencing induced by hairpin or inverted repeated sense transgenes varies among promoters and cell types

Gordana Marjanac, Mansour Karimi, Mirande Naudts, Tom Beeckman, Anna Depicker, Sylvie De Buck

(2009) - New Phytologist

DOI
583. The Past, Present, and Future of Chemical Biology in Auxin Research

Bert De Rybel, Dominique Audenaert, Tom Beeckman, Stefan Kepinski

(2009) - ACS Chemical Biology

DOI
582. Control of cell proliferation, organ growth, and DNA damage response operate independently of dephosphorylation of the Arabidopsis Cdk1 homolog CDKA;1.

Dissmeyer N, Weimer AK, Pusch S, De Schutter K, Alvim Kamei CL, Nowack MK, Novak B, Duan GL, Zhu YG, De Veylder L, Schnittger A

(2009) -

DOI
581. Control of cell proliferation, organ growth, and DNA damage response operate independently of dephosphorylation of the Arabidopsis Cdk1 homolog CDKA;1.

Dissmeyer N, Weimer AK, Pusch S, De Schutter K, Alvim Kamei CL, Nowack MK, Novak B, Duan GL, Zhu YG, De Veylder L, Schnittger A

(2009) -

DOI
580. Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield.

Hauben M, Haesendonckx B, Standaert E, Van Der Kelen K, Azmi A, Akpo H, Van Breusegem F, Guisez Y, Bots M, Lambert B, Laga B, De Block M

(2009) -

DOI
579. Joint GC–MS and LC–MS platforms for comprehensive plant metabolomics: Repeatability and sample pre-treatment

Ruben t’Kindt, Kris Morreel, Dieter Deforce, Wout Boerjan, Jan Van Bocxlaer

(2009) - Journal of Chromatography B

DOI
578. (Homo)glutathione depletion modulates host gene expression during the symbiotic interaction between Medicago truncatula and Sinorhizobium meliloti.

Pucciariello C, Innocenti G, Van de Velde W, Lambert A, Hopkins J, Clément M, Ponchet M, Pauly N, Goormachtig S, Holsters M, Puppo A, Frendo P

(2009) -

DOI
577. Developmental stage specificity and the role of mitochondrial metabolism in the response of Arabidopsis leaves to prolonged mild osmotic stress.

Skirycz A, De Bodt S, Obata T, De Clercq I, Claeys H, De Rycke R, Andriankaja M, Van Aken O, Van Breusegem F, Fernie AR, Inzé D

(2009) - Plant Physiology

DOI
576. Transcriptional control of the cell cycle.

Berckmans B, De Veylder L

(2009) -

DOI
575. Division plane determination during plant somatic cytokinesis.

Van Damme D

(2009) - Current opinion in plant biology

DOI
574. Receptor-like kinases shape the plant

Ive De Smet, Ute Voß, Gerd Jürgens, Tom Beeckman

(2009) - Nature Cell Biology

DOI
573. Manipulation of auxin transport in plant roots during Rhizobium symbiosis and nematode parasitism.

Grunewald W, van Noorden G, Gert Van Isterdael, Tom Beeckman, Gheysen G, Ulrike Mathesius

(2009) - The Plant Cell

DOI
572. Systematic analysis of cell-cycle gene expression during Arabidopsis development.

de Almeida Engler J, De Veylder L, De Groodt R, Rombauts S, Boudolf V, De Meyer B, Hemerly A, Ferreira P, Beeckman T, Karimi M, Hilson P, Inzé D, Engler G

(2009) -

DOI
571. Expression of the Arabidopsis jasmonate signalling repressor JAZ1/TIFY10A is stimulated by auxin

Wim Grunewald, Bartel Vanholme, Laurens Pauwels, Eva Plovie, Dirk Inzé, Godelieve Gheysen, Alain Goossens

(2009) - EMBO reports

DOI
570. Extensive expression regulation and lack of heterologous enzymatic activity of the Class II trehalose metabolism proteins from Arabidopsis thaliana

MATTHEW RAMON, IVE DE SMET, LIES VANDESTEENE, MIRANDE NAUDTS, BARBARA LEYMAN, PATRICK VAN DIJCK, FILIP ROLLAND, TOM BEECKMAN, JOHAN M. THEVELEIN

(2009) - Plant, Cell & Environment

DOI
569. CDKB1;1 forms a functional complex with CYCA2;3 to suppress endocycle onset.

Boudolf V, Lammens T, Boruc J, Van Leene J, Van Den Daele H, Maes S, Van Isterdael G, Russinova E, Kondorosi E, Witters E, De Jaeger G, Inzé D, De Veylder L

(2009) -

DOI
568. APC/C-CCS52A complexes control meristem maintenance in the Arabidopsis root.

Vanstraelen M, Baloban M, Da Ines O, Cultrone A, Lammens T, Boudolf V, Brown SC, De Veylder L, Mergaert P, Kondorosi E

(2009) -

DOI
567. Arabidopsis lateral root development: an emerging story.

Péret B, De Rybel B, Casimiro I, Benková E, Swarup R, Laplaze L, Beeckman T, Bennett MJ

(2009) -

DOI
566. CDKB1;1 forms a functional complex with CYCA2;3 to suppress endocycle onset.

Boudolf V, Lammens T, Boruc J, Van Leene J, Van Den Daele H, Maes S, Van Isterdael G, Russinova E, Kondorosi E, Witters E, De Jaeger G, Inzé D, De Veylder L

(2009) -

DOI
565. Arabidopsis lateral root development: an emerging story

Benjamin Péret, Bert De Rybel, Ilda Casimiro, Eva Benková, Ranjan Swarup, Laurent Laplaze, Tom Beeckman, Malcolm J. Bennett

(2009) - Trends in Plant Science

DOI
564. Genome sequence of the recombinant protein production host Pichia pastoris

Kristof De Schutter, Yao-Cheng Lin, Petra Tiels, Annelies Van Hecke, Sascha Glinka, Jacqueline Weber-Lehmann, Pierre Rouzé, Yves Van de Peer, Nico Callewaert

(2009) - Nature Biotechnology

DOI
563. Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks.

Vandepoele K, Quimbaya M, Casneuf T, De Veylder L, Van de Peer Y

(2009) -

DOI
562. Chemical inhibition of a subset of Arabidopsis thaliana GSK3-like kinases activates brassinosteroid signaling.

De Rybel B, Audenaert D, Vert G, Rozhon W, Mayerhofer J, Peelman F, Coutuer S, Denayer T, Jansen L, Nguyen L, Vanhoutte I, Beemster GT, Vleminckx K, Jonak C, Chory J, Inzé D, Russinova E, Beeckman T

(2009) -

DOI
561. Strangled at birth? Forest biotech and the Convention on Biological Diversity

Steven H. Strauss, Huimin Tan, Wout Boerjan, Roger Sedjo

(2009) - Nature Biotechnology

DOI
560. Chemical inhibition of a subset of Arabidopsis thaliana GSK3-like kinases activates brassinosteroid signaling.

De Rybel B, Audenaert D, Vert G, Rozhon W, Mayerhofer J, Peelman F, Coutuer S, Denayer T, Jansen L, Nguyen L, Vanhoutte I, Beemster GT, Vleminckx K, Jonak C, Chory J, Inzé D, Russinova E, Beeckman T

(2009) -

DOI
559. Chemical inhibition of a subset of Arabidopsis thaliana GSK3-like kinases activates brassinosteroid signaling.

Bert De Rybel, Audenaert D, Greg Vert, Wilfried Rozhon, Mayerhofer J, Peelman F, Coutuer S, Denayer T, Jansen L, Nguyen L, Vanhoutte I, Gerrit Beemster, Vleminckx K, Claudia Jonak, Chory J, Dirk Inzé, Eugenia Russinova, Tom Beeckman

(2009) - Chemistry & biology

DOI
558. Calcium spiking patterns and the role of the calcium/calmodulin-dependent kinase CCaMK in lateral root base nodulation of Sesbania rostrata.

Capoen W, Den Herder J, Sun J, Verplancke C, De Keyser A, De Rycke R, Goormachtig S, Oldroyd G, Holsters M

(2009) -

DOI
557. Systematic analysis of cell-cycle gene expression during Arabidopsis development.

de Almeida Engler J, Lieven De Veylder, De Groodt R, Stephane Rombauts, Veronique Boudolf, De Meyer B, Adriana Hemerly, Ferreira P, Tom Beeckman, Karimi M, Hilson P, Dirk Inzé, Engler G

(2009) - The Plant journ

DOI
556. A Snapshot of the Emerging Tomato Genome Sequence

Lukas A. Mueller, René Klein Lankhorst, Steven D. Tanksley, James J. Giovannoni, Ruth White, Julia Vrebalov, Zhangjun Fei, Joyce van Eck, Robert Buels, Adri A. Mills, Naama Menda, Isaak Y. Tecle, Aureliano Bombarely, Stephen Stack, Suzanne M. Royer, Song‐Bin Chang, Lindsay A. Shearer, Byung Dong Kim, Sung‐Hwan Jo, Cheol‐Goo Hur, Doil Choi, Chang‐Bao Li, Jiuhai Zhao, Hongling Jiang, Yu Geng, Yuanyuan Dai, Huajie Fan, Jinfeng Chen, Fei Lu, Jinfeng Shi, Shouhong Sun, Jianjun Chen, Xiaohua Yang, Chen Lu, Mingsheng Chen, Zhukuan Cheng, Chuanyou Li, Hongqing Ling, Yongbiao Xue, Ying Wang, Graham B. Seymour, Gerard J. Bishop, Glenn Bryan, Jane Rogers, Sarah Sims, Sarah Butcher, Daniel Buchan, James Abbott, Helen Beasley, Christine Nicholson, Clare Riddle

(2009) - The Plant Genome

DOI
555. Eternal youth, the fate of developing Arabidopsis leaves upon Rhodococcus fascians infection.

Depuydt S, De Veylder L, Holsters M, Vereecke D

(2009) -

DOI
554. Atypical E2Fs: new players in the E2F transcription factor family.

Lammens T, Li J, Leone G, De Veylder L

(2009) -

DOI
553. How relevant are flavonoids as antioxidants in plants?

Hernández I, Alegre L, Van Breusegem F, Munné-Bosch S

(2009) -

DOI
552. Cryopreservation of hairy root cultures of Maesa lanceolata and Medicago truncatula

E. Lambert, A. Goossens, B. Panis, M. C. Van Labeke, D. Geelen

(2009) - Plant Cell, Tissue and Organ Culture

DOI
551. DNA stress checkpoint control and plant development.

Cools T, De Veylder L

(2009) -

DOI
550. Integrative genetical genomics in Arabidopsis

Wout Boerjan, Marnik Vuylsteke

(2009) - Nature Genetics

DOI
549. Vacuolar transport of nicotine is mediated by a multidrug and toxic compound extrusion (MATE) transporter in Nicotiana tabacum

Masahiko Morita, Nobukazu Shitan, Keisuke Sawada, Marc C. E. Van Montagu, Dirk Inzé, Heiko Rischer, Alain Goossens, Kirsi-Marja Oksman-Caldentey, Yoshinori Moriyama, Kazufumi Yazaki

(2009) - Proceedings of the National Academy of Sciences

DOI
548. Jasmonate-inducible gene: what does it mean?

Laurens Pauwels, Dirk Inzé, Alain Goossens

(2009) - Trends in Plant Science

DOI
547. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes.

Naouar N, Vandepoele K, Lammens T, Casneuf T, Zeller G, van Hummelen P, Weigel D, Rätsch G, Inzé D, Kuiper M, De Veylder L, Vuylsteke M

(2009) -

DOI
546. Genomic regions involved in productivity of two interspecific poplar families in Europe. 1. Stem height, circumference and volume

Dillen SY, Storme V, Marron N, Bastien C, Neyrinck S, Steenackers M, Ceulemans R, Boerjan W

(2009) - Tree Genetics & Genomes

DOI