Papers – Weigelworld

Featured Publications

Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana

Exposito-Alonso M., Vasseur F., Ding W., Wang G., Burbano H. A. and Weigel D.
Nat Ecol Evol (2018), 2(2) 352-358.

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

Swarts K., Gutaker R. M., Benz B., Blake M., Bukowski R., Holland J., Kruse-Peeples M., Lepak N., Prim L., Romay M. C., Ross-Ibarra J., Sanchez-Gonzalez J. J., Schmidt C., Schuenemann V. J., Krause J., Matson R. G., Weigel D., Buckler E. S. and Burbano H. A.
Science (2017), 357(6350) 512-515.

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

1001 Genomes Consortium
Cell (2016), 166(2) 481-91.

Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis

Chae E., Bomblies K., Kim S. T., Karelina D., Zaidem M., Ossowski S., Martin-Pizarro C., Laitinen R. A., Rowan B. A., Tenenboim H., Lechner S., Demar M., Habring-Muller A., Lanz C., Ratsch G. and Weigel D.
Cell (2014), 159(6) 1341-51.

2023

Cycles of satellite and evolution in Arabidopsis centromeres

Wlodzimierz, P.*, Rabanal, F. A.*, Burns, R.*, Naish, M., Primetis, E., Scott, A., Mandáková, T., Gorringe, N., Tock, A. J., Holland, D., Fritschi, K., Habring, A., Lanz, C., Patel, C., Schlegel, T., Collenberg, M., Mielke, M., Nordborg, M., Roux, F., Shirsekar, G., Alonso-Blanco, C., Lysak, M. A., Novikova, P., Bousios, A., Weigel, D., and Henderson, I. R.
Nature (2023), 618, 557-565

Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1b in promoting posttranscriptional transgene silencing

Bazin, J., Elvira-Matelot, E., Blein, T., Jauvion, V., Bouteiller, N., Cao, J., Crespi, M. D., Vaucheret, H.
The Plant Cell (2023), 35(6), 1917-1935

Transposon dynamics in the emerging oilseed crop Thlaspi arvense

Contreras-Garrido, A., Galanti, D., Movilli, A., Becker, C., Bossdorf, O., Drost, H.-G., Weigel, D.
bioRxiv (2023), 542068

Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis

Fernandes, J. B. Naish, M., Lian, Q., Burns, R., Tock, A. J., Rabanal, F. A., Wlodzimierz, P., Habring, A., Nicholas, R. E., Weigel, D., Mercier, R., and Henderson, I. R.
bioRxiv (2023), 544545

Building pangenome graphs

Garrison, E., Guarracino, A., Heumos, S., Villani, F., Bao, Z., Tattini, L., Hagmann, J., Vorbrugg, S., Marco-Sola, S., Kubica, C., Ashbrook, D. G., Thorell, K., Rusholme-Pilcher, R. L., Liti, G., Rudbeck, E., Nahnsen, S., Yang, Z., Moses, M. N., Nobrega, F. L., Wu, Y., Chen, H., de Ligt, J., Sudmant, P. H., Soranzo, N., Colonna, V., Williams, R. W., and Prins, P.
bioRxiv (2023), 535718

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Kersten, S., Chang, J., Huber, C. D., Voichek, Y., Lanz, C., Hagmaier, T., Lang, P., Lutz, U., Hirschberg, I., Lerchl, J., Porri, A., Van de Peer, Y., Schmid, K., Weigel, D., and Rabanal, F. A.
Proc. Natl. Acad. Sci. USA (2023), 120(16):e2206808120

The genetic and physiological basis of Arabidopsis thaliana tolerance to Pseudomonas viridiflava

Duque-Jaramillo, A., Ulmer, U., Alseekh, S., Bezrukov, I., Fernie, A., Skirycz, A., Karasov, T., Weigel, D.
bioRxiv (2023), 533268

Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra

Barrera-Redondo, J., Lotharukpong, J. S., Drost, H. G., and Coelho, S. M.
Genome Biol (2023), Vol. 24(1), 54

PICLN modulates alternative splicing and light/temperature responses in plants

Mateos, J., Sanchez, S., Legris, M., Esteve-Bruna, D., Torchio, J., Petrillo, E., Goretti, D., Blanco-Touriñán, N., Seymour, D., Schmid, M., Weigel, D., Alabadí, D., & Yanofsky, M.
Plant Physiol. (2023), 191(2), 1036-1051

The immune receptor SNC1 monitors helper NLRs targeted by a bacterial effector

Wang, M., Chen, J., Wu, R., Guo, H., Chen, Y., Li, Z., Wei, L., Liu, C., He, S., Du, M., Guo, Y., Peng, Y.-L., Jones, J. D. G., Weigel, D., Huang, J., and Zhu, W.
bioRxiv (2023), 533910

Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust

Buchfink, B., Ashkenazy, H., Reuter, K., Kennedy, J. A., Drost, H.-D.
bioRxiv (2023), 520048

PlantACT! – how to tackle the climate crisis

Arce, A. L., Mencia, R., Cambiagno, D.A., Lang, P. L., Liu, C., Burbano, H. A., Weigel, D., Manavella, P. A.
Trends Plant Sci (2023),

Polymorphic Inverted Repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana

Hirt, H., Al-Babili, S., Almeida-Trapp, M., Antoine, M., Aranda, M., Bartels, D., …, Weigel, D. et al
Cell Rep (2023), 42(1) 112029.

Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD

Grigorjew, A., Gynter, A., Dias, F., Buchfink, B., Drost, H.-G., Tomescu, A. I.
bioRxiv (2023), 520048

2022

miR472 deficiency enhances Arabidopsis thaliana defence without reducing seed production

Vasseur, F., Baldrich, P., Jiménez-Góngora,T. Villar-Martin, L., Weigel, D., and Rubio-Somoza, I.
bioRxiv (2022), 520224

Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere

Lundberg, D., Jove, de Pedro Jové, Roger, Pramoj Na Ayutthaya, P., Karasov, T. L., Shalev, O., Poersch, K., Ding, W., Bollmann-Giolai, A., Bezrukov, I., Weigel, D.
Proc Natl Acad Sci USA (2022), 119(52) e2211881119

Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation

Srikant, T., Yuan, W., Berendzen, K. W., Contreras-Garrido, A., Drost, H.-G., Schwab, R., Weigel, D.
Genome Biol (2022), 23(1) 263

The Arabidopsis TIR–NBS-LRR protein CSA1 guards BAK1-BIR3 homeostasis and mediates convergence of pattern- and effector-induced immune responses

Schulze, S., Yu, L, Hua, C., Zhang, L, Kolb, D., Weber, H, Ehinger, A., Saile, S. C., Stahl, M., Franz-Wachtel, M., Li, L., El Kasmi, F., Nürnberger, T., Cevik, V., Kemmerling, B.
Cell Host Microbe (2022), 30(12) 1717-1731

Conservation of antiviral systems across domains of life reveals novel immune mechanisms in humans

Cury, J., Mordret, E., Hernandez Trejo, V., Tesson, F., Ofir, G., Poirier, E. Z., Bernheim, A.
bioRxiv (2022), 520048

Rapid weed adaptation and range expansion in response to agriculture over the past two centuries

Kreiner, J. M., Latorre, S. M., Burbano, H. M., Stinchcombe, J. R., Otto, S. P., Weigel, D., Wright, S. I.
Science (2022), 378 (6624) 1079-1085

Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

Rabanal, F. A., Graff M., Lanz, C., Fritschi, K., Llaca, V., Lang, M., Carbonell-Bejerano, P., Henderson, I., Weigel, D.
Nucleic Acids Res (2022), 50(1) 12309-12327

Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor

Wibowo, A. T., Antunez-Sanchez, J., Dawson, A., Price, J., Meehan, C., Wrightsman, T., Collenberg, M., Bezrukov, I., Becker, C., Benhamed, M., Weigel, D., Gutierrez-Marcos, J.
PLoS Genet (2022), 18(11) e1010479

MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data

Hüther, P., Hagmann, J., Nunn, A., Kakoulidou, I., Pisupati, R., Langenberger, D., Weigel, D., Johannes, F., Schultheiss, S. J., and Becker, C.
Quant Plant Biol (2022), 3 e19.

Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism

Yoshihara T., Miller N. D., Rabanal F. A., Myles H., Kwak I. Y., Broman K. W., Sadkhin B., Baxter I., Dilkes B. P., Hudson M. E. and Spalding E. P.
Proc Natl Acad Sci U S A (2022), 119(40) e2212199119.

The improved genome of the nematode Parapristionchus giblindavisi provides insights into lineage-specific gene family evolution

Roseler W., Collenberg M., Yoshida K., Lanz C., Sommer R. J. and Rodelsperger C.
G3 (Bethesda) (2022), 12(10).

Rapid weed adaptation and range expansion in response to agriculture over the last two centuries

Kreiner Julia, Latorre Sergio M., Burbano Hernán A., Stinchcombe John R., Otto Sarah P., Weigel Detlef and Wright Stephen
bioRxiv (2022), 2022.02.25.482047.

Report of mutation biases mirroring selection in Arabidopsis thaliana unlikely to be entirely due to variant calling errors

Monroe J. Grey, Murray Kevin D., Xian Wenfei, Carbonell-Bejerano Pablo, Fenster Charles B. and Weigel Detlef
bioRxiv (2022), 2022.08.21.504682.

Plant genetic effects on microbial hubs impact host fitness in repeated field trials

Brachi B., Filiault D., Whitehurst H., Darme P., Le Gars P., Le Mentec M., Morton T. C., Kerdaffrec E., Rabanal F., Anastasio A., Box M. S., Duncan S., Huang F., Leff R., Novikova P., Perisin M., Tsuchimatsu T., Woolley R., Dean C., Nordborg M., Holm S. and Bergelson J.
Proc Natl Acad Sci U S A (2022), 119(30) e2201285119.

Spatially resolved host-bacteria-fungi interactomes via spatial metatranscriptomics

Saarenpää Sami, Shalev Or, Ashkenazy Haim, de Oliveira-Carlos Vanessa, Lundberg Derek Severi, Weigel Detlef and Giacomello Stefania
bioRxiv (2022), 2022.07.18.496977.

Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation

Srikant Thanvi, Yuan Wei, Berendzen Kenneth Wayne, Garrido Adrián Contreras, Drost Hajk-Georg, Schwab Rebecca and Weigel Detlef
bioRxiv (2022), 2022.07.14.500095.

Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra

Barrera-Redondo Josué, Lotharukpong Jaruwatana Sodai, Drost Hajk-Georg and Coelho Susana M.
bioRxiv (2022), 2022.07.07.498977.

Polymorphic Inverted Repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana

Arce Agustín L., Mencia Regina, Cambiagno Damian A., Lang Patricia L., Liu Chang, Burbano Hernán A., Weigel Detlef and Manavella Pablo A.
bioRxiv (2022), 2022.07.05.498814.

Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Nunn A., Rodriguez-Arevalo I., Tandukar Z., Frels K., Contreras-Garrido A., Carbonell-Bejerano P., Zhang P., Ramos-Cruz D., Jandrasits K., Lanz C., Brusa A., Mirouze M., Dorn K., Galbraith D., Jarvis B. A., Sedbrook J. C., Wyse D. L., Otto C., Langenberger D., Stadler P. F., Weigel D., Marks M. D., Anderson J. A., Becker C. and Chopra R.
Plant Biotechnol J (2022), 20(5) 944-963.

Deep haplotype analyses of target-site resistance locus ACCase in blackgrass enabled by pool-based amplicon sequencing

Kersten Sonja, Rabanal Fernando A., Herrmann Johannes, Hess Martin, Kronenberg Zev N., Schmid Karl and Weigel Detlef
bioRxiv (2022), 2022.06.22.496946.

PICLN modulates alternative splicing and ensures adaptation to light and temperature changes in plants

Mateos Julieta L., Sanchez Sabrina E, Legris Martina, Esteve-Bruna David, Torchio Jeanette C., Petrillo Ezequiel, Goretti Daniela, Blanco-Touriñán Noel, Seymour Danelle K., Schmid Markus, Weigel Detlef, Alabadí David and Yanovsky Marcelo J.
bioRxiv (2022), 2022.06.14.496170.

Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms

Shalev O., Ashkenazy H., Neumann M. and Weigel D.
ISME J (2022), 16(5) 1235-1244.

Characterization of the Different Levels of Variation in 45S rRNA Genes

Rabanal F. A.
Methods Mol Biol (2022), 2484 363-379.

Drought selection on Arabidopsis populations and their microbiomes

Karasov Talia L., Neumann Manuela, Shirsekar Gautam, Monroe Grey, Team PATHODOPSIS, Weigel Detlef and Schwab Rebecca
bioRxiv (2022), 2022.04.08.487684.

Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant

Shalev O., Karasov T. L., Lundberg D. S., Ashkenazy H., Pramoj Na Ayutthaya P. and Weigel D.
Nat Ecol Evol (2022), 6(4) 383-396.

Predictable and stable epimutations induced during clonal propagation with embryonic transcription factors

Wibowo Anjar, Antunez-Sanchez Javier, Dawson Alexander, Price Jonathan, Meehan Cathal, Wrightsman Travis, Collenberg Maximillian, Berzukov Ilja, Becker Claude, Benhamed Moussa, Weigel Detlef and Gutierrez-Marcos Jose
bioRxiv (2022), 2022.03.15.484412.

Rapid phenotypic differentiation and local adaptation in Japanese knotweed s.l. (Reynoutria japonica and R. x bohemica, Polygonaceae) invading novel habitats

Yuan Wei, Pigliucci Massimo and Richards Christina L.
bioRxiv (2022), 2022.03.07.483296.

Pervasive Under-Dominance in Gene Expression as Unifying Principle of Biomass Heterosis in Arabidopsis

Yuan Wei, Beitel Fiona, Srikant Thanvi, Bezrukov Ilja, Schäfer Sabine, Kraft Robin and Weigel Detlef
bioRxiv (2022), 2022.03.03.482808.

Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

Rabanal Fernando A., Gräff Maike, Lanz Christa, Fritschi Katrin, Llaca Victor, Lang Michelle, Carbonell-Bejerano Pablo, Henderson Ian and Weigel Detlef
bioRxiv (2022), 2022.02.15.480579.

Monitoring rapid evolution of plant populations at scale with Pool-Sequencing

Czech Lucas, Peng Yunru, Spence Jeffrey P., Lang Patricia L.M., Bellagio Tatiana, Hildebrandt Julia, Fritschi Katrin, Schwab Rebecca, Rowan Beth A., consortium GrENE-net, Weigel Detlef, Scheepens J.F., Vasseur François and Exposito-Alonso Moises
bioRxiv (2022), 2022.02.02.477408.

Mutation bias reflects natural selection in Arabidopsis thaliana

Monroe J. G., Srikant T., Carbonell-Bejerano P., Becker C., Lensink M., Exposito-Alonso M., Klein M., Hildebrandt J., Neumann M., Kliebenstein D., Weng M. L., Imbert E., Agren J., Rutter M. T., Fenster C. B. and Weigel D.
Nature (2022), 602(7895) 101-105.

Petabase-scale sequence alignment catalyses viral discovery

Edgar R. C., Taylor J., Lin V., Altman T., Barbera P., Meleshko D., Lohr D., Novakovsky G., Buchfink B., Al-Shayeb B., Banfield J. F., de la Pena M., Korobeynikov A., Chikhi R. and Babaian A.
Nature (2022), 602(7895) 142-147.

Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata)

van der Zee M. J., Whiting J. R., Paris J. R., Bassar R. D., Travis J., Weigel D., Reznick D. N. and Fraser B. A.
Evol Lett (2022), 6(2) 149-161.

Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations

Kreiner J. M., Sandler G., Stern A. J., Tranel P. J., Weigel D., Stinchcombe J. and Wright S. I.
Elife (2022), 11.

2021

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Kersten Sonja, Chang Jiyang, Huber Christian D., Voichek Yoav, Lanz Christa, Hagmaier Timo, Lang Patricia, Lutz Ulrich, Hirschberg Insa, Lerchl Jens, Porri Aimone, Van de Peer Yves, Schmid Karl, Weigel Detlef and Rabanal Fernando A.
bioRxiv (2021), 2021.12.14.472587.

Reduced gamete viability associated to somatic genome rearrangements increases fruit set sensitivity to the environment in Tempranillo Blanco grapevine cultivar

Tello J., Royo C., Baroja E., García-Escudero E., Martínez-Zapater J. M. and Carbonell-Bejerano P.
Sci Hort. (2021), 290(110497).

Multiple Sources of Introduction of North American Arabidopsis thaliana From Across Eurasia

Shirsekar G., Devos J., Latorre S. M., Blaha A., Queiroz Dias M., Gonzalez Hernando A., Lundberg D. S., Burbano H. A., Fenster C. B. and Weigel D.
Mol Biol Evol (2021), 38(12) 5328-5344.

It Is Just a Matter of Time: Balancing Homologous Recombination and Non-homologous End Joining at the rDNA Locus During Meiosis

Sims J., Rabanal F. A., Elgert C., von Haeseler A. and Schlogelhofer P.
Front Plant Sci (2021), 12 773052.

Extensive gene duplication in Arabidopsis revealed by pseudo-heterozygosity

Jaegle Benjamin, Soto-Jimenez Luz Mayela, Burns Robin, Rabanal Fernando A. and Nordborg Magnus
bioRxiv (2021), 2021.11.15.468652.

Grafting vigour is associated with DNA de-methylation in eggplant

Cerruti E., Gisbert C., Drost H. G., Valentino D., Portis E., Barchi L., Prohens J., Lanteri S., Comino C. and Catoni M.
Hortic Res (2021), 8(1) 241.

vcf2gwas-python API for comprehensive GWAS analysis using GEMMA

Vogt F., Shirsekar G. and Weigel D.
Bioinformatics (2021), 38(3) 839-840.

The EDS1-PAD4-ADR1 node mediates Arabidopsis pattern-triggered immunity

Pruitt R. N., Locci F., Wanke F., Zhang L., Saile S. C., Joe A., Karelina D., Hua C., Frohlich K., Wan W. L., Hu M., Rao S., Stolze S. C., Harzen A., Gust A. A., Harter K., Joosten Mhaj, Thomma Bphj, Zhou J. M., Dangl J. L., Weigel D., Nakagami H., Oecking C., Kasmi F. E., Parker J. E. and Nurnberger T.
Nature (2021), 598(7881) 495-499.

noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise

Moutsopoulos I., Maischak L., Lauzikaite E., Vasquez Urbina S. A., Williams E. C., Drost H. G. and Mohorianu II
Nucleic Acids Res (2021), 49(14) e83.

The Underlying Nature of Epigenetic Variation: Origin Establishment, and Regulatory Function of Plant Epialleles

Srikant T. and Tri Wibowo A.
Int Journal of Mol Sciences (IJMS) (2021), 22(16) 8618.

Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition

Lundberg D. S., Pramoj Na Ayutthaya P., Strauss A., Shirsekar G., Lo W. S., Lahaye T. and Weigel D.
Elife (2021), 10 e66186.

eLife and medicine: Rigorous review and editorial oversight of clinical preprints

Zaidi M., Harper D. M., Akhmanova A., Weigel D., Behrens T. and Eisen M.
eLife (2021), 10 e67528.

Is aromatic terpenoid composition of grapes in Northwestern Iberian wine cultivars related to variation in VviDXS1 gene?

Royo C., Carbonell-Bejerano P., Torres-Pérez R., Freire L., Ibáñez J., Martínez-Zapater J. M. and Vilanova M.
J. Berry Res (2021), 11(2) 187-200.

vcf2gwas – Python API for comprehensive GWAS analysis using GEMMA

Vogt Frank, Shirsekar Gautam and Weigel Detlef
bioRxiv (2021), 2021.06.01.446586.

Population structure and evolution of resistance to acetolactate synthase (ALS)-inhibitors in Amaranthus tuberculatus in Italy

Milani A., Lutz U., Galla G., Scarabel L., Weigel D. and Sattin M.
Pest Manag Sci (2021), 77(6) 2971-2980.

Plant NLR diversity: the known unknowns of pan-NLRomes

Barragan A. C. and Weigel D.
Plant Cell (2021), 33(4) 814-831.

Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies

Whiting J. R., Paris J. R., van der Zee M. J., Parsons P. J., Weigel D. and Fraser B. A.
PLoS Genet (2021), 17(5) e1009566.

Repeated origins, gene flow, and allelic interactions of herbicide resistance mutations in a widespread agricultural weed

Kreiner J.M., Sandler G., Stern A.J., Tranel P.J., Weigel D, Stinchcombe J.R. and Wright S.I.
bioRxiv (2021), 2021.05.10.443516.

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Katz E., Li J. J., Jaegle B., Ashkenazy H., Abrahams S. R., Bagaza C., Holden S., Pires C. J., Angelovici R. and Kliebenstein D. J.
Elife (2021), 10.

Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine

Zinelabidine L. H., Torres-Perez R., Grimplet J., Baroja E., Ibanez S., Carbonell-Bejerano P., Martinez-Zapater J. M., Ibanez J. and Tello J.
Plant Sci (2021), 306 110875.

A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants

Benoit M. and Drost H. G.
Methods Mol Biol (2021), 2250 1-14.

The genetic architecture and genome-wide signatures of glyphosate resistance in Amaranthus tuberculatus

Kreiner J. M., Tranel P. J., Weigel D., Stinchcombe J. R. and Wright S. I.
Mol Ecol (2021), 30(21) 5373-5389.

Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere

Lundberg Derek S., de Pedro Jové Roger, Na Ayutthaya Pratchaya Pramoj, Karasov Talia L., Shalev Or, Poersch Karin, Ding Wei, Bollmann-Giolai Anita, Bezrukov Ilja and Weigel Detlef
bioRxiv (2021), 2021.04.06.438366.

Protective host-dependent antagonism among Pseudomonas in the Arabidopsis phyllosphere

Skriptchak Or Shalev, Karasov Talia L., Lundberg Derek S., Ashkenazy Haim and Weigel Detlef
bioRxiv (2021), 2021.04.08.438928.

Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

Calderon L., Mauri N., Munoz C., Carbonell-Bejerano P., Bree L., Bergamin D., Sola C., Gomez-Talquenca S., Royo C., Ibanez J., Martinez-Zapater J. M. and Lijavetzky D.
Sci Rep (2021), 11(1) 7775.

Sensitive protein alignments at tree-of-life scale using DIAMOND

Buchfink B., Reuter K. and Drost H. G.
Nat Methods (2021), 18(4) 366-368.

Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Ignacio J. C. I., Zaidem M., Casal C., Jr., Dixit S., Kretzschmar T., Samaniego J. M., Mendioro M. S., Weigel D. and Septiningsih E. M.
Plants (Basel) (2021), 10(4).

Genotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1

Fan Li, Fröhlich Katja, Melzer Eric, Albert Isabell, Pruitt Rory N., Zhang Lisha, Albert Markus, Kim Sang-Tae, Chae Eunyoung, Weigel Detlef, Gust Andrea A. and Nürnberger Thorsten
bioRxiv (2021), 2021.03.04.433884.

HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing

Cambiagno D. A., Giudicatti A. J., Arce A. L., Gagliardi D., Li L., Yuan W., Lundberg D. S., Weigel D. and Manavella P. A.
Mol Plant (2021), 14(3) 426-439.

Male-specific Y-chromosomal regions in waterhemp (Amaranthus tuberculatus) and Palmer amaranth (Amaranthus palmeri)

Montgomery J. S., Giacomini D. A., Weigel D. and Tranel P. J.
New Phytol (2021), 229(6) 3522-3533.

Challenges of viticulture adaptation to global change: tackling the issue from the roots

Marín D., Armengol J., Carbonell-Bejerano P., Escalona J. M., Gramaje D., Hernández-Montes E., Intrigliolo D. S., Martínez-Zapater M., Medrano H., Mirás-Avalos J. M., Palomares-Rius J. E., Romero-Azorín P., Savé R., Santesteban L. G. and de Herralde F.
Aus. J. of Grape Wine Res (2021), 27 8-25.

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus

Langner T., Harant A., Gomez-Luciano L. B., Shrestha R. K., Malmgren A., Latorre S. M., Burbano H. A., Win J. and Kamoun S.
PLoS Genet (2021), 17(2) e1009386.

Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata)

van der Zee Mijke J., Whiting James R., Paris Josephine R., Bassar Ron D., Travis Joseph, Weigel Detlef, Reznick David N. and Fraser Bonnie A.
bioRxiv (2021), 2021.02.10.430609.

The population genomics of adaptive loss of function

Monroe J. G., McKay J. K., Weigel D. and Flood P. J.
Heredity (Edinb) (2021), 126(3) 383-395.

How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity

Srikant T. and Drost H. G.
Front Plant Sci (2021), 11 606800.

Small peptides modulate the immune function of the ion channel-like protein ACD6 in Arabidopsis thaliana

Zhu Wangsheng, Li Lei, Neuhaeuser Benjamin, Thelen Michael, Wang Mingyu, Chen Junbin, Wei Luyang, Venkataramani Kavita, Exposito-Alonso Moises, Liu Chang, Keck Jakob, Barragan A. Cristina, Schwab Rebecca, Lutz Ulrich, Ludewig Uwe and Weigel Detlef
bioRxiv (2021), 2021.01.25.428077.

Homozygosity at its Limit: Inbreeding Depression in Wild Arabidopsis arenosa Populations

Barragan A. Cristina, Collenberg Maximilian, Schwab Rebecca, Kerstens Merijn, Bezrukov Ilja, Bemm Felix, Požárová Doubravka, Kolá? Filip and Weigel Detlef
bioRxiv (2021), 2021.01.24.427284.

A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana

Barragan A. C., Collenberg M., Wang J., Lee R. R. Q., Cher W. Y., Rabanal F. A., Ashkenazy H., Weigel D. and Chae E.
Mol Biol Evol (2021), 38(2) 557-574.

Fine-scale Population Structure of North American Arabidopsis thaliana Reveals Multiple Sources of Introduction from Across Eurasia

Shirsekar Gautam, Devos Jane, Latorre Sergio M., Blaha Andreas, Dias Maique Queiroz, González Hernando Alba, Lundberg Derek S., Burbano Hernán A., Fenster Charles B. and Weigel Detlef
bioRxiv (2021), 2021.01.22.427575.

noisyR: Enhancing biological signal in sequencing datasets by characterising random technical noise

Moutsopoulos Ilias, Maischak Lukas, Lauzikaite Elze, Vasquez Urbina Sergio Alberto, Williams Eleanor C, Drost Hajk Georg and Mohorianu Irina I
bioRxiv (2021), 2021.01.17.427026.

CRISPR-finder: A high throughput and cost-effective method to identify successfully edited Arabidopsis thaliana individuals

Symeonidi E., Regalado J., Schwab R. and Weigel D.
Quant. Plant Biol (2021), 2:e1 1-7.

2020

A gibberellin methyltransferase modulates the timing of floral transition at the Arabidopsis shoot meristem

Lee J. E., Goretti D., Neumann M., Schmid M. and You Y.
Physiol Plant (2020), 170(4) 474-487.

Implementing a “publish, then review” model of publishing

Eisen M. B., Akhmanova A., Behrens T. E., Harper D. M., Weigel D. and Zaidi M.
Elife (2020), 9.

Draft genomes of Amaranthus tuberculatus, Amaranthus hybridus and Amaranthus palmeri

Montgomery J. S., Giacomini D., Waithaka B., Lanz C., Murphy B. P., Campe R., Lerchl J., Landes A., Gatzmann F., Janssen A., Antonise R., Patterson E., Weigel D. and Tranel P. J.
Genome Biol Evol (2020), 12(11) 1988-1993.

The trehalose 6-phosphate pathway impacts vegetative phase change in Arabidopsis thaliana

Ponnu J., Schlereth A., Zacharaki V., Dzialo M. A., Abel C., Feil R., Schmid M. and Wahl V.
Plant J (2020), 104(3) 768-780.

A new role for histone demethylases in the maintenance of plant genome integrity

Antunez-Sanchez J., Naish M., Ramirez-Prado J. S., Ohno S., Huang Y., Dawson A., Opassathian K., Manza-Mianza D., Ariel F., Raynaud C., Wibowo A., Daron J., Ueda M., Latrasse D., Slotkin R. K., Weigel D., Benhamed M. and Gutierrez-Marcos J.
Elife (2020), 9.

Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies

Whiting James R., Paris Josephine R., van der Zee Mijke J., Parsons Paul J., Weigel Detlef and Fraser Bonnie A.
bioRxiv (2020), 2020.10.14.339333.

ARADEEPOPSIS, an Automated Workflow for Top-View Plant Phenomics using Semantic Segmentation of Leaf States

Huther P., Schandry N., Jandrasits K., Bezrukov I. and Becker C.
Plant Cell (2020), 32(12) 3674-3688.

Improved reference genome uncovers novel sex-linked regions in the guppy (Poecilia reticulata)

Fraser B. A., Whiting J. R., Paris J. R., Weadick C. J., Parsons P. J., Charlesworth D., Bergero R., Bemm F., Hoffmann M., Kottler V. A., Liu C., Dreyer C. and Weigel D.
Genome Biol Evol (2020), 12(10) 1789-1805.

Hybridization ddRAD-sequencing for population genomics of non-model plants using highly degraded historical specimen DNA

Lang P. L. M., Weiss C. L., Kersten S., Latorre S. M., Nagel S., Nickel B., Meyer M. and Burbano H. A.
Mol Ecol Resour (2020), 20(5) 1228-1247.

Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus

Latorre S. M., Reyes-Avila C. S., Malmgren A., Win J., Kamoun S. and Burbano H. A.
BMC Biol (2020), 18(1) 88.

Non-additive polygenic models improve predictions of fitness traits in three eukaryote model species

Exposito-Alonso Moises, Wilton Peter and Nielsen Rasmus
bioRxiv (2020), 2020.07.14.194407.

CRISPR-finder: A high throughput and cost effective method for identifying successfully edited A. thaliana individuals

Symeonidi Efthymia, Regalado Julian, Schwab Rebecca and Weigel Detlef
bioRxiv (2020), 2020.06.25.171538.

LTRpred: de novo annotation of intact retrotransposons

Drost, H. G.
Journal of Open Source Software (2020), 5(50) 2170.

Mutation bias shapes gene evolution in Arabidopsis thaliana

Monroe J. Grey, Srikant Thanvi, Carbonell-Bejerano Pablo, Exposito-Alonso Moises, Weng Mao-Lun, Rutter Matthew T., Fenster Charles B. and Weigel Detlef
bioRxiv (2020), 2020.06.17.156752.

What natural variation can teach us about resistance durability

Karasov T. L., Shirsekar G., Schwab R. and Weigel D.
Curr Opin Plant Biol (2020), 56 89-98.

Measuring both microbial load and diversity with a single amplicon sequencing library

Lundberg Derek S., Ayutthaya Pratchaya Pramoj Na, Strauß Annett, Shirsekar Gautam, Lo Wen-Sui, Lahaye Thomas and Weigel Detlef
bioRxiv (2020), 2020.05.19.103937.

Convergent Loss of an EDS1/PAD4 Signaling Pathway in Several Plant Lineages Reveals Co-evolved Components of Plant Immunity and Drought Response

Baggs E., Monroe J. G., Thanki A. S., O’Grady R., Schudoma C., Haerty W. and Krasileva K. V.
Plant Cell (2020), 32(7) 2158-2177.

Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

Regalado J., Lundberg D. S., Deusch O., Kersten S., Karasov T., Poersch K., Shirsekar G. and Weigel D.
ISME J (2020), 14 2116-2130.

Identifying genetic variants underlying phenotypic variation in plants without complete genomes

Voichek Y. and Weigel D.
Nat Genet (2020), 52(5) 534-540.

An Algorithm to Build a Multi-genome Reference

Rabbani Leily, Müller Jonas and Weigel Detlef
bioRxiv (2020), 2020.04.11.036871.

Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for the Analysis of Protein Oligomers in Plants

Na Ayutthaya P. P., Lundberg D., Weigel D. and Li L.
Curr Protoc Plant Biol (2020), 5(2) e20107.

The Earth BioGenome project: Opportunities and Challenges for Plant Genomics and Conservation

Exposito-Alonso M., Drost H. G., Burbano H. A. and Weigel D.
Plant J (2020), 102(2) 222-229.

Tropical Trees as Time Capsules of Anthropogenic Activity

Caetano-Andrade V. L., Clement C. R., Weigel D., Trumbore S., Boivin N., Schongart J. and Roberts P.
Trends Plant Sci (2020), 25(4) 369-380.

Publishing in the time of COVID-19

Eisen M. B., Akhmanova A., Behrens T. E. and Weigel D.
Elife (2020), 9.

Atypical Resistance Protein RPW8/HR Triggers Oligomerization of the NLR Immune Receptor RPP7 and Autoimmunity

Li L., Habring A., Wang K. and Weigel D.
Cell Host Microbe (2020), 27(3) 405-417.

Museum phylogenomics of extinct Oryctes beetles from the Mascarene Islands

Latorre Sergio M., Herrmann Matthias, Paulsen M.J., Rödelsperger Christian, Dréau Andreea, Röseler Waltraud, Sommer Ralf J. and Burbano Hernán A.
bioRxiv (2020), 2020.02.19.954339.

Trait plasticity and covariance along a continuous soil moisture gradient

Monroe J. Grey, Cai Haoran and Des Marais David L.
bioRxiv (2020), 2020.02.17.952853.

Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes

Latorre Sergio M., Reyes-Avila C. Sarai, Malmgren Angus, Win Joe, Kamoun Sophien and Burbano Hernán A.
bioRxiv (2020), 2020.01.09.900308.

Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes

Latorre Sergio M., Reyes-Avila C. Sarai, Malmgren Angus, Win Joe, Kamoun Sophien and Burbano Hernán A.
bioRxiv (2020), 2020.01.09.900308.

AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana

Togninalli M., Seren U., Freudenthal J. A., Monroe J. G., Meng D., Nordborg M., Weigel D., Borgwardt K., Korte A. and Grimm D. G.
Nucleic Acids Res (2020), 48(D1) D1063-D1068.

A singleton NLR of recent origin causes hybrid necrosis in Arabidopsis thaliana

Barragan A. Cristina, Collenberg Maximilian, Wang Jinge, Lee Rachelle R.Q., Cher Wei Yuan, Rabanal Fernando A., Ashkenazy Haim, Weigel Detlef and Chae Eunyoung
bioRxiv (2020), 2020.05.18.101451.

TERMINAL FLOWER1 Functions as a Mobile Transcriptional Cofactor in the Shoot Apical Meristem

Goretti D., Silvestre M., Collani S., Langenecker T., Mendez C., Madueno F. and Schmid M.
Plant Physiol (2020), 182(4) 2081-2095.

2019

An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features

Rowan B. A., Heavens D., Feuerborn T. R., Tock A. J., Henderson I. R. and Weigel D.
Genetics (2019), 213(3) 771-787.

The relationship between microbial biomass and disease in the Arabidopsis thaliana phyllosphere

Karasov Talia L., Neumann Manuela, Duque-Jaramillo Alejandra, Kersten Sonja, Bezrukov Ilja, Schröppel Birgit, Symeonidi Efthymia, Lundberg Derek S., Regalado Julian, Shirsekar Gautam, Bergelson Joy and Weigel Detlef
bioRxiv (2019), 828814.

Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

Regalado Julian, Lundberg Derek S., Deusch Oliver, Kersten Sonja, Karasov Talia, Poersch Karin, Shirsekar Gautam and Weigel Detlef
bioRxiv (2019), 823492.

Finding genetic variants in plants without complete genomes

Voichek Yoav and Weigel Detlef
bioRxiv (2019), 818096.

The BIR2/BIR3-interacting Phospholipase D gamma 1 negatively regulates immunity in Arabidopsis

Schlöffel Maria A., Salzer Andrea, Wan Wei-Lin, van Wijk Ringo, Šemanjski Maja, Symeonidi Efthymia, Slaby Peter, Kilian Joachim, Ma?ek Boris, Munnik Teun and Gust Andrea A.
bioRxiv (2019), 815282.

Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus

Kreiner J. M., Giacomini D. A., Bemm F., Waithaka B., Regalado J., Lanz C., Hildebrandt J., Sikkema P. H., Tranel P. J., Weigel D., Stinchcombe J. R. and Wright S. I.
Proc Natl Acad Sci U S A (2019), 116(42) 21076-21084.

CRISPR-based tools for targeted transcriptional and epigenetic regulation in plants

Lee J. E., Neumann M., Duro D. I. and Schmid M.
PLoS One (2019), 14(9) e0222778.

Position-dependent effects of cytosine methylation on FWA expression in Arabidopsis thaliana

Srikant Thanvi, Wibowo Anjar, Schwab Rebecca and Weigel Detlef
bioRxiv (2019), 774281.

Natural selection on the Arabidopsis thaliana genome in present and future climates

Exposito-Alonso M., Genomes Field Experiment Team, Burbano H. A., Bossdorf O., Nielsen R. and Weigel D.
Nature (2019), 573(7772) 126-129.

RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis

Lange H., Ndecky S. Y. A., Gomez-Diaz C., Pflieger D., Butel N., Zumsteg J., Kuhn L., Piermaria C., Chicher J., Christie M., Karaaslan E. S., Lang P. L. M., Weigel D., Vaucheret H., Hammann P. and Gagliardi D.
Nat Commun (2019), 10(1) 3871.

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

Van de Weyer A. L., Monteiro F., Furzer O. J., Nishimura M. T., Cevik V., Witek K., Jones J. D. G., Dangl J. L., Weigel D. and Bemm F.
Cell (2019), 178(5) 1260-1272 e14.

RPW8/HR repeats control NLR activation in Arabidopsis thaliana

Barragan C. A., Wu R., Kim S. T., Xi W., Habring A., Hagmann J., Van de Weyer A. L., Zaidem M., Ho W. W. H., Wang G., Bezrukov I., Weigel D. and Chae E.
PLoS Genet (2019), 15(7) e1008313.

The origins and adaptation of European potatoes reconstructed from historical genomes

Gutaker R. M., Weiss C. L., Ellis D., Anglin N. L., Knapp S., Luis Fernandez-Alonso J., Prat S. and Burbano H. A.
Nat Ecol Evol (2019), 3(7) 1093-1101.

Oligomerization of NLR immune receptor RPP7 triggered by atypical resistance protein RPW8/HR as ligand

Li Lei, Habring Anette, Wang Kai and Weigel Detlef
bioRxiv (2019), 682807.

NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches

Yang E. J., Yoo C. Y., Liu J., Wang H., Cao J., Li F. W., Pryer K. M., Sun T. P., Weigel D., Zhou P. and Chen M.
Nat Commun (2019), 10(1) 2630.

Phytochrome activates the plastid-encoded RNA polymerase for chloroplast biogenesis via nucleus-to-plastid signaling

Yoo C. Y., Pasoreck E. K., Wang H., Cao J., Blaha G. M., Weigel D. and Chen M.
Nat Commun (2019), 10(1) 2629.

All in the Family: The First Whole-genome Survey of NLR Genes

Weigel D.
Plant Cell (2019), 31(6) 1212-1213.

Arabidopsis FLL2 promotes liquid-liquid phase separation of polyadenylation complexes

Fang X., Wang L., Ishikawa R., Li Y., Fiedler M., Liu F., Calder G., Rowan B., Weigel D., Li P. and Dean C.
Nature (2019), 569(7755) 265-269.

Chemical genetic identification of a lectin receptor kinase that transduces immune responses and interferes with abscisic acid signaling

Park J., Kim T. H., Takahashi Y., Schwab R., Dressano K., Stephan A. B., Ceciliato P. H. O., Ramirez E., Garin V., Huffaker A. and Schroeder J. I.
Plant Journal (2019), 98(3) 492-510.

FT Modulates Genome-Wide DNA-Binding of the bZIP Transcription Factor FD

Collani S., Neumann M., Yant L. and Schmid M.
Plant Physiol (2019), 180(1) 367-380.

RPW8/HR Repeats Control NLR Activation in A. thaliana

Barragan Cristina A., Wu Rui, Kim Sang-Tae, Xi Wanyan, Habring Anette, Hagmann Jörg, Van de Weyer Anna-Lena, Zaidem Maricris, Ho William Wing Ho, Wang George, Bezrukov Ilja, Weigel Detlef and Chae Eunyoung
bioRxiv (2019), 559864.

Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana

Vasseur F., Fouqueau L., de Vienne D., Nidelet T., Violle C. and Weigel D.
PLoS Biol (2019), 17(4) e3000214.

Alternative use of miRNA-biogenesis co-factors in plants at low temperatures

Re D. A., Lang P. L. M., Yones C., Arce A. L., Stegmayer G., Milone D. and Manavella P. A.
Development (2019), 146(5).

Transmission ratio distortion is frequent in Arabidopsis thaliana controlled crosses

Seymour D. K., Chae E., Arioz B. I., Koenig D. and Weigel D.
Heredity (Edinb) (2019), 122(3) 294-304.

Comparing Arabidopsis receptor kinase and receptor protein-mediated immune signaling reveals BIK1-dependent differences

Wan W. L., Zhang L., Pruitt R., Zaidem M., Brugman R., Ma X., Krol E., Perraki A., Kilian J., Grossmann G., Stahl M., Shan L., Zipfel C., van Kan J. A. L., Hedrich R., Weigel D., Gust A. A. and Nurnberger T.
New Phytol (2019), 221(4) 2080-2095.

Long-term balancing selection drives evolution of immunity genes in Capsella

Koenig D., Hagmann J., Li R., Bemm F., Slotte T., Nueffer B., Wright S. I. and Weigel D.
Elife (2019), 8.

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana

Weng M. L., Becker C., Hildebrandt J., Rutter M. T., Shaw R. G., Weigel D. and Fenster C. B.
Genetics (2019), 211(2) 703-714.

The Arabidopsis thaliana pan-NLRome

Van de Weyer Anna-Lena, Monteiro Freddy, Furzer Oliver J., Nishimura Marc T., Cevik Volkan, Witek Kamil, Jones Jonathan D.G., Dangl Jeffery L., Weigel Detlef and Bemm Felix
bioRxiv (2019), 537001.

Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production

Gutaker R. M., Zaidem M., Fu Y. B., Diederichsen A., Smith O., Ware R. and Allaby R. G.
Sci Rep (2019), 9(1) 976.

Phloem companion cell-specific transcriptomic and epigenomic analyses identify MRF1, a novel regulator of flowering

You Y., Sawikowska A., Lee J. E., Benstein R. M., Neumann M., Krajewski P. and Schmid M.
Plant Cell (2019), 31(2) 325-345.

EFFECTOR OF TRANSCRIPTION factors are novel plant-specific regulators associated with genomic DNA methylation in Arabidopsis

Tedeschi F., Rizzo P., Huong B. T. M., Czihal A., Rutten T., Altschmied L., Scharfenberg S., Grosse I., Becker C., Weigel D., Baumlein H. and Kuhlmann M.
New Phytol (2019), 221(1) 261-278.

Using herbaria to study global environmental change

Lang P. L. M., Willems F. M., Scheepens J. F., Burbano H. A. and Bossdorf O.
New Phytol (2019), 221(1) 110-122.

2018

Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation

Wibowo A., Becker C., Durr J., Price J., Spaepen S., Hilton S., Putra H., Papareddy R., Saintain Q., Harvey S., Bending G. D., Schulze-Lefert P., Weigel D. and Gutierrez-Marcos J.
Proc Natl Acad Sci U S A (2018), 115(39) E9145-E9152.

Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene

Zhu W., Zaidem M., Van de Weyer A. L., Gutaker R. M., Chae E., Kim S. T., Bemm F., Li L., Todesco M., Schwab R., Unger F., Beha M. J., Demar M. and Weigel D.
PLoS Genet (2018), 14(9) e1007628.

An efficient CRISPR vector toolbox for engineering large deletions in Arabidopsis thaliana

Wu R., Lucke M., Jang Y. T., Zhu W., Symeonidi E., Wang C., Fitz J., Xi W., Schwab R. and Weigel D.
Plant Methods (2018), 14 65.

Genome-wide signatures of flowering adaptation to climate temperature: regional analyses in a highly diverse native range of Arabidopsis thaliana

Tabas-Madrid D., Mendez-Vigo B., Arteaga N., Marcer A., Pascual-Montano A., Weigel D., Xavier Pico F. and Alonso-Blanco C.
Plant Cell Environ (2018), 41(8) 1806-1820.

Image-based methods for phenotyping growth dynamics and fitness components in Arabidopsis thaliana

Vasseur F., Bresson J., Wang G., Schwab R. and Weigel D.
Plant Methods (2018), 14 63.

Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales

Karasov T. L., Almario J., Friedemann C., Ding W., Giolai M., Heavens D., Kersten S., Lundberg D. S., Neumann M., Regalado J., Neher R. A., Kemen E. and Weigel D.
Cell Host Microbe (2018), 24(1) 168-179 e4.

PORCUPINE regulates development in response to temperature through alternative splicing

Capovilla G., Delhomme N., Collani S., Shutava I., Bezrukov I., Symeonidi E., de Francisco Amorim M., Laubinger S. and Schmid M.
Nat Plants (2018), 4(8) 534-539.

Spatio-temporal variation in fitness responses to contrasting environments in Arabidopsis thaliana

Exposito-Alonso M., Brennan A. C., Alonso-Blanco C. and Pico F. X.
Evolution (2018), 72(8) 1570-1586.

Linking Genomic and Metabolomic Natural Variation Uncovers Nematode Pheromone Biosynthesis

Falcke J. M., Bose N., Artyukhin A. B., Rodelsperger C., Markov G. V., Yim J. J., Grimm D., Claassen M. H., Panda O., Baccile J. A., Zhang Y. K., Le H. H., Jolic D., Schroeder F. C. and Sommer R. J.
Cell Chem Biol (2018), 25(6) 787-796 e12.

Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays

Bilinski P., Albert P. S., Berg J. J., Birchler J. A., Grote M. N., Lorant A., Quezada J., Swarts K., Yang J. and Ross-Ibarra J.
PLoS Genet (2018), 14(5) e1007162.

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

Huson D. H., Albrecht B., Bagci C., Bessarab I., Gorska A., Jolic D. and Williams R. B. H.
Biol Direct (2018), 13(1) 6.

nQuire: a statistical framework for ploidy estimation using next generation sequencing

Weiss C. L., Pais M., Cano L. M., Kamoun S. and Burbano H. A.
BMC Bioinformatics (2018), 19(1) 122.

Complex relationships between chromatin accessibility, sequence divergence, and gene expression in A. thaliana

Alexandre C. M., Urton J. R., Jean-Baptiste K., Huddleston J. L., Dorrity M. W., Cuperus J. T., Sullivan A. M., Bemm F., Jolic D., Arsovski A. A., Thompson A., Nemhauser J. L., Fields S., Weigel D., Bubb K. L. and Queitsch C.
Mol Biol Evol (2018), 35(4) 837-854.

Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

Vasseur F., Exposito-Alonso M., Ayala-Garay O. J., Wang G., Enquist B. J., Vile D., Violle C. and Weigel D.
Proc Natl Acad Sci U S A (2018), 115(13) 3416-3421.

An artificial miRNA system reveals that relative contribution of translational inhibition to miRNA-mediated regulation depends on environmental and developmental factors in Arabidopsis thaliana

von Born P., Bernardo-Faura M. and Rubio-Somoza I.
PLoS One (2018), 13(2) e0192984.

The rate and potential relevance of new mutations in a colonizing plant lineage

Exposito-Alonso M., Becker C., Schuenemann V. J., Reiter E., Setzer C., Slovak R., Brachi B., Hagmann J., Grimm D. G., Chen J., Busch W., Bergelson J., Ness R. W., Krause J., Burbano H. A. and Weigel D.
PLoS Genet (2018), 14(2) e1007155.

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

Michael T. P., Jupe F., Bemm F., Motley S. T., Sandoval J. P., Lanz C., Loudet O., Weigel D. and Ecker J. R.
Nat Commun (2018), 9(1) 541.

Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana

Exposito-Alonso M., Vasseur F., Ding W., Wang G., Burbano H. A. and Weigel D.
Nat Ecol Evol (2018), 2(2) 352-358.

The microRNA miR773 is involved in the Arabidopsis immune response to fungal pathogens

Salvador-Guirao R., Baldrich P., Weigel D., Rubio-Somoza I. and San Segundo B.
Mol Plant Microbe Interact (2018), 31(2) 249-259.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Stein J. C., Yu Y., Copetti D., Zwickl D. J., Zhang L., Zhang C., Chougule K., Gao D., Iwata A., Goicoechea J. L., Wei S., Wang J., Liao Y., Wang M., Jacquemin J., Becker C., Kudrna D., Zhang J., Londono C. E. M., Song X., Lee S., Sanchez P., Zuccolo A., Ammiraju J. S. S., Talag J., Danowitz A., Rivera L. F., Gschwend A. R., Noutsos C., Wu C. C., Kao S. M., Zeng J. W., Wei F. J., Zhao Q., Feng Q., El Baidouri M., Carpentier M. C., Lasserre E., Cooke R., Rosa Farias D. D., da Maia L. C., Dos Santos R. S., Nyberg K. G., McNally K. L., Mauleon R., Alexandrov N., Schmutz J., Flowers D., Fan C., Weigel D., Jena K. K., Wicker T., Chen M., Han B., Henry R., Hsing Y. C., Kurata N., de Oliveira A. C., Panaud O., Jackson S. A., Machado C. A., Sanderson M. J., Long M., Ware D. and Wing R. A.
Nat Genet (2018), 50(2) 285-296.

A role for the F-box protein HAWAIIAN SKIRT in plant microRNA function

Lang P. L. M., Christie M. D., Dogan E. S., Schwab R., Hagmann J., Van de Weyer A. L., Weigel D. and Scacchi E.
Plant Physiol (2018), 176(1) 730-741.

The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog

Togninalli M., Seren U., Meng D., Fitz J., Nordborg M., Weigel D., Borgwardt K., Korte A. and Grimm D. G.
Nucleic Acids Res (2018), 46(D1) D1150-D1156.

Dose-dependent interactions between two loci trigger altered shoot growth in BG-5 x Krotzenburg-0 (Kro-0) hybrids of Arabidopsis thaliana

Alhajturki D., Muralidharan S., Nurmi M., Rowan B. A., Lunn J. E., Boldt H., Salem M. A., Alseekh S., Jorzig C., Feil R., Giavalisco P., Fernie A. R., Weigel D. and Laitinen R. A. E.
New Phytol (2018), 217(1) 392-406.

2017

Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana

Capovilla G., Symeonidi E., Wu R. and Schmid M.
J Exp Bot (2017), 68(18) 5117-5127.

Arabidopsis BTB/POZ protein-dependent PENETRATION3 trafficking and disease susceptibility

Mao H., Aryal B., Langenecker T., Hagmann J., Geisler M. and Grebe M.
Nat Plants (2017), 3(11) 854-858.

Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus

Rodelsperger C., Meyer J. M., Prabh N., Lanz C., Bemm F. and Sommer R. J.
Cell Rep (2017), 21(3) 834-844.

Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis

Liu C., Cheng Y. J., Wang J. W. and Weigel D.
Nat Plants (2017), 3 742-748.

Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid

Zhu W., Hu B., Becker C., Dogan E. S., Berendzen K. W., Weigel D. and Liu C.
Genome Biol (2017), 18(1) 157.

Different but overlapping populations of Strongyloides stercoralis in dogs and humans-Dogs as a possible source for zoonotic strongyloidiasis

Jaleta T. G., Zhou S., Bemm F. M., Schar F., Khieu V., Muth S., Odermatt P., Lok J. B. and Streit A.
PLoS Negl Trop Dis (2017), 11(8) e0005752.

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

SPF45-related splicing factor for phytochrome signaling promotes photomorphogenesis by regulating pre-mRNA splicing in Arabidopsis

Xin R., Zhu L., Salome P. A., Mancini E., Marshall C. M., Harmon F. G., Yanovsky M. J., Weigel D. and Huq E.
Proc Natl Acad Sci U S A (2017), 114(33) E7018-E7027.

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Daccord N., Celton J. M., Linsmith G., Becker C., Choisne N., Schijlen E., van de Geest H., Bianco L., Micheletti D., Velasco R., Di Pierro E. A., Gouzy J., Rees D. J. G., Guerif P., Muranty H., Durel C. E., Laurens F., Lespinasse Y., Gaillard S., Aubourg S., Quesneville H., Weigel D., van de Weg E., Troggio M. and Bucher E.
Nat Genet (2017), 49(7) 1099-1106.

Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering

You Y., Sawikowska A., Neumann M., Pose D., Capovilla G., Langenecker T., Neher R. A., Krajewski P. and Schmid M.
Nat Commun (2017), 8 15120.

African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana

Durvasula A., Fulgione A., Gutaker R. M., Alacakaptan S. I., Flood P. J., Neto C., Tsuchimatsu T., Burbano H. A., Pico F. X., Alonso-Blanco C. and Hancock A. M.
Proc Natl Acad Sci U S A (2017), 114(20) 5213-5218.

Neandertal and Denisovan DNA from Pleistocene sediments

Slon V., Hopfe C., Weiss C. L., Mafessoni F., de la Rasilla M., Lalueza-Fox C., Rosas A., Soressi M., Knul M. V., Miller R., Stewart J. R., Derevianko A. P., Jacobs Z., Li B., Roberts R. G., Shunkov M. V., de Lumley H., Perrenoud C., Gusic I., Kucan Z., Rudan P., Aximu-Petri A., Essel E., Nagel S., Nickel B., Schmidt A., Prufer K., Kelso J., Burbano H. A., Paabo S. and Meyer M.
Science (2017), 356(6338) 605-608.

Arabidopsis proteins with a transposon-related domain act in gene silencing

Ikeda Y., Pelissier T., Bourguet P., Becker C., Pouch-Pelissier M. N., Pogorelcnik R., Weingartner M., Weigel D., Deragon J. M. and Mathieu O.
Nat Commun (2017), 8 15122.

A Robust Framework for Microbial Archaeology

Warinner C., Herbig A., Mann A., Fellows Yates J. A., Weiss C. L., Burbano H. A., Orlando L. and Krause J.
Annu Rev Genomics Hum Genet (2017), 18 321-356.

Assessing Distribution and Variation of Genome-Wide DNA Methylation Using Short-Read Sequencing

Hagmann J. and Becker C.
Methods Mol Biol (2017), 1610 61-72.

A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation

Conn V. M., Hugouvieux V., Nayak A., Conos S. A., Capovilla G., Cildir G., Jourdain A., Tergaonkar V., Schmid M., Zubieta C. and Conn S. J.
Nat Plants (2017), 3 17053.

Activation of a Plant NLR Complex through Heteromeric Association with an Autoimmune Risk Variant of Another NLR

Tran D. T. N., Chung E. H., Habring-Muller A., Demar M., Schwab R., Dangl J. L., Weigel D. and Chae E.
Curr Biol (2017), 27(8) 1148-60.

Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana

Plotner B., Nurmi M., Fischer A., Watanabe M., Schneeberger K., Holm S., Vaid N., Schottler M. A., Walther D., Hoefgen R., Weigel D. and Laitinen R. A.
Plant J (2017), 91(2) 251-262.

Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion

Nekrasov V., Wang C., Win J., Lanz C., Weigel D. and Kamoun S.
Sci Rep (2017), 7(1) 482.

The Arabidopsis miR396 mediates pathogen-associated molecular pattern-triggered immune responses against fungal pathogens

Soto-Suarez M., Baldrich P., Weigel D., Rubio-Somoza I. and San Segundo B.
Sci Rep (2017), 7 44898.

Mechanisms to Mitigate the Tradeoff between Growth and Defense

Karasov T., Chae E., Herman J. and Bergelson J.
Plant Cell (2017), 29(4) 666-680.

A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina

Kasulin L., Rowan B., Leon R. J., Schuenemann V. J., Weigel D. and Botto J. F.
Mol Ecol (2017), 26(13) 3389-3404.

The causes and consequences of DNA methylome variation in plants

Seymour D. K. and Becker C.
Curr Opin Plant Biol (2017), 36 56-63.

Extraction of ultrashort DNA molecules from herbarium specimens

Gutaker R. M., Reiter E., Furtwangler A., Schuenemann V. J. and Burbano H. A.
Biotechniques (2017), 62(2) 76-79.

On the post-glacial spread of human commensal Arabidopsis thaliana

Lee C. R., Svardal H., Farlow A., Exposito-Alonso M., Ding W., Novikova P., Alonso-Blanco C., Weigel D. and Nordborg M.
Nat Commun (2017), 8 14458.

Forever Young: The Role of Ubiquitin Receptor DA1 and E3 Ligase BIG BROTHER in Controlling Leaf Growth and Development

Vanhaeren H., Nam Y. J., De Milde L., Chae E., Storme V., Weigel D., Gonzalez N. and Inze D.
Plant Physiol (2017), 173(2) 1269-1282.

Reinforcing plant evolutionary genomics using ancient DNA

Gutaker R. M. and Burbano H. A.
Curr Opin Plant Biol (2017), 36 38-45.

Characterization Of Phytochrome Interacting Factors From The Moss Physcomitrella Patens Illustrates Conservation Of Phytochrome Signaling Modules In Land Plants

Possart A., Xu T., Paik I., Hanke S., Keim S., Hermann H. M., Wolf L., Hiss M., Becker C., Huq E., Rensing S. A. and Hiltbrunner A.
Plant Cell (2017), 29(2) 310-330.

easyGWAS: A Cloud-based Platform for Comparing the Results of Genome-wide Association Studies

Grimm D. G., Roqueiro D., Salome P., Kleeberger S., Greshake B., Zhu W., Liu C., Lippert C., Stegle O., Scholkopf B., Weigel D. and Borgwardt K.
Plant Cell (2017), 29(1) 5-19.

Methods for Genotyping-by-Sequencing

Rowan B. A., Seymour D. K., Chae E., Lundberg D. S. and Weigel D.
Methods Mol Biol (2017), 1492 221-242.

What causes mating system shifts in plants? Arabidopsis lyrata as a case study

Mable B. K., Hagmann J., Kim S. T., Adam A., Kilbride E., Weigel D. and Stift M.
Heredity (Edinb) (2017), 118(1) 52-63.

DNA sequence properties that predict susceptibility to epiallelic switching

Catoni M., Griffiths J., Becker C., Zabet N. R., Bayon C., Dapp M., Lieberman-Lazarovich M., Weigel D. and Paszkowski J.
EMBO J (2017), 36(5) 617-628.

AraPheno: a public database for Arabidopsis thaliana phenotypes

Seren U., Grimm D., Fitz J., Weigel D., Nordborg M., Borgwardt K. and Korte A.
Nucleic Acids Res (2017), 45(D1) D1054-D1059.

Natural Variation of Molecular and Morphological Gibberellin Responses

Nam Y. J., Herman D., Blomme J., Chae E., Kojima M., Coppens F., Storme V., Van Daele T., Dhondt S., Sakakibara H., Weigel D., Inze D. and Gonzalez N.
Plant Physiol (2017), 173(1) 703-714.

Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana

Swiadek M., Proost S., Sieh D., Yu J., Todesco M., Jorzig C., Rodriguez Cubillos A. E., Plotner B., Nikoloski Z., Chae E., Giavalisco P., Fischer A., Schroder F., Kim S. T., Weigel D. and Laitinen R. A.
New Phytol (2017), 213(2) 900-915.

2016

The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population

Kunstner A., Hoffmann M., Fraser B. A., Kottler V. A., Sharma E., Weigel D. and Dreyer C.
PLoS One (2016), 11(12) e0169087.

TBro: visualization and management of de novo transcriptomes

Ankenbrand M. J., Weber L., Becker D., Forster F. and Bemm F.
Database (Oxford) (2016), 2016.

Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids

Seymour D. K., Chae E., Grimm D. G., Martin Pizarro C., Habring-Muller A., Vasseur F., Rakitsch B., Borgwardt K. M., Koenig D. and Weigel D.
Proc Natl Acad Sci U S A (2016), 113(46) E7317-E7326.

Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants

Dueck A., Evers M., Henz S. R., Unger K., Eichner N., Merkl R., Berezikov E., Engelmann J. C., Weigel D., Wenzl S. and Meister G.
BMC Genomics (2016), 17(1) 853.

Regulation of MIR165/166 by class II and class III homeodomain leucine zipper proteins establishes leaf polarity

Merelo P., Ram H., Pia Caggiano M., Ohno C., Ott F., Straub D., Graeff M., Cho S. K., Yang S. W., Wenkel S. and Heisler M. G.
Proc Natl Acad Sci U S A (2016), 113(42) 11973-11978.

Effector-Triggered Immune Response in Arabidopsis thaliana Is a Quantitative Trait

Iakovidis M., Teixeira P. J., Exposito-Alonso M., Cowper M. G., Law T. F., Liu Q., Vu M. C., Dang T. M., Corwin J. A., Weigel D., Dangl J. L. and Grant S. R.
Genetics (2016), 204(1) 337-53.

Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution

Liu C., Wang C., Wang G., Becker C., Zaidem M. and Weigel D.
Genome Res (2016), 26(8) 1057-68.

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

Novikova P. Y., Hohmann N., Nizhynska V., Tsuchimatsu T., Ali J., Muir G., Guggisberg A., Paape T., Schmid K., Fedorenko O. M., Holm S., Sall T., Schlotterer C., Marhold K., Widmer A., Sese J., Shimizu K. K., Weigel D., Kramer U., Koch M. A. and Nordborg M.
Nat Genet (2016), 48(9) 1077-82.

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

1001 Genomes Consortium
Cell (2016), 166(2) 481-91.

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Kawakatsu T., Huang S. S., Jupe F., Sasaki E., Schmitz R. J., Urich M. A., Castanon R., Nery J. R., Barragan C., He Y., Chen H., Dubin M., Lee C. R., Wang C., Bemm F., Becker C., O’Neil R., O’Malley R. C., Quarless D. X., Genomes Consortium, Schork N. J., Weigel D., Nordborg M. and Ecker J. R.
Cell (2016), 166(2) 492-505.

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens

Weiss C. L., Schuenemann V. J., Devos J., Shirsekar G., Reiter E., Gould B. A., Stinchcombe J. R., Krause J. and Burbano H. A.
R Soc Open Sci (2016), 3(6) 160239.

Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity

Wibowo A., Becker C., Marconi G., Durr J., Price J., Hagmann J., Papareddy R., Putra H., Kageyama J., Becker J., Weigel D. and Gutierrez-Marcos J.
Elife (2016), 5.

Allelochemicals of the phenoxazinone class act at physiologically relevant concentrations

Venturelli S., Petersen S., Langenecker T., Weigel D., Lauer U. M. and Becker C.
Plant Signal Behav (2016), 11(5) e1176818.

Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids

Rigal M., Becker C., Pelissier T., Pogorelcnik R., Devos J., Ikeda Y., Weigel D. and Mathieu O.
Proc Natl Acad Sci U S A (2016), 113(14) 2083-92.

Cooperation and Conflict in the Plant Immune System

Chae E., Tran D. T. and Weigel D.
PLoS Pathog (2016), 12(3) e1005452.

Ancient gene flow from early modern humans into Eastern Neanderthals

Kuhlwilm M., Gronau I., Hubisz M. J., de Filippo C., Prado-Martinez J., Kircher M., Fu Q., Burbano H. A., Lalueza-Fox C., de la Rasilla M., Rosas A., Rudan P., Brajkovic D., Kucan Z., Gusic I., Marques-Bonet T., Andres A. M., Viola B., Paabo S., Meyer M., Siepel A. and Castellano S.
Nature (2016), 530(7591) 429-33.

A proposed regulatory framework for genome-edited crops

Huang S., Weigel D., Beachy R. N. and Li J.
Nat Genet (2016), 48(2) 109-11.

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

Agler M. T., Ruhe J., Kroll S., Morhenn C., Kim S. T., Weigel D. and Kemen E. M.
PLoS Biol (2016), 14(1) e1002352.

A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants

Bergelson J., Buckler E. S., Ecker J. R., Nordborg M. and Weigel D.
Plant Cell (2016), 28(3) 606-9.

2015

Population Genomics for Understanding Adaptation in Wild Plant Species

Weigel D. and Nordborg M.
Annu Rev Genet (2015), 49 315-38.

Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data

Weiß C. L., Dannemann M., Prüfer K. and Burbano H. A.
eLife (2015), 4.

Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors

Venturelli S., Belz R. G., Kamper A., Berger A., von Horn K., Wegner A., Bocker A., Zabulon G., Langenecker T., Kohlbacher O., Barneche F., Weigel D., Lauer U. M., Bitzer M. and Becker C.
Plant Cell (2015), 27(11) 3175-89.

KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1

Karlsson P., Christie M. D., Seymour D. K., Wang H., Wang X., Hagmann J., Kulcheski F. and Manavella P. A.
Proc Natl Acad Sci U S A (2015), 112(45) 14096-101.

Ubiquitin facilitates a quality-control pathway that removes damaged chloroplasts

Woodson J. D., Joens M. S., Sinson A. B., Gilkerson J., Salome P. A., Weigel D., Fitzpatrick J. A. and Chory J.
Science (2015), 350(6259) 450-4.

Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M

Lutz U., Pose D., Pfeifer M., Gundlach H., Hagmann J., Wang C., Weigel D., Mayer K. F., Schmid M. and Schwechheimer C.
PLoS Genet (2015), 11(10) e1005588.

Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana

Galvao V. C., Collani S., Horrer D. and Schmid M.
Plant J (2015), 84(5) 949-62.

Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella

Steige K. A., Reimegard J., Koenig D., Scofield D. G. and Slotte T.
Mol Biol Evol (2015), 32(10) 2501-14.

Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

Rawat V., Abdelsamad A., Pietzenuk B., Seymour D. K., Koenig D., Weigel D., Pecinka A. and Schneeberger K.
PLoS One (2015), 10(9) e0137391.

Chromatin in 3D: progress and prospects for plants

Liu C. and Weigel D.
Genome Biol (2015), 16(1) 170.

Role of alternative pre-mRNA splicing in temperature signaling

Capovilla G., Pajoro A., Immink R. G. and Schmid M.
Curr Opin Plant Biol (2015), 27 97-103.

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

Warren R. L., Keeling C. I., Yuen M. M., Raymond A., Taylor G. A., Vandervalk B. P., Mohamadi H., Paulino D., Chiu R., Jackman S. D., Robertson G., Yang C., Boyle B., Hoffmann M., Weigel D., Nelson D. R., Ritland C., Isabel N., Jaquish B., Yanchuk A., Bousquet J., Jones S. J., MacKay J., Birol I. and Bohlmann J.
Plant J (2015), 83(2) 189-212.

Mutant Allele-Specific Uncoupling of PENETRATION3 Functions Reveals Engagement of the ATP-Binding Cassette Transporter in Distinct Tryptophan Metabolic Pathways

Lu X., Dittgen J., Pislewska-Bednarek M., Molina A., Schneider B., Svatos A., Doubsky J., Schneeberger K., Weigel D., Bednarek P. and Schulze-Lefert P.
Plant Physiol (2015), 168(3) 814-27.

Adenylate cyclase 5 is required for melanophore and male pattern development in the guppy (Poecilia reticulata)

Kottler V. A., Kunstner A., Koch I., Flotenmeyer M., Langenecker T., Hoffmann M., Sharma E., Weigel D. and Dreyer C.
Pigment Cell Melanoma Res (2015), 28(5) 545-558.

Genome-wide detection of intervals of genetic heterogeneity associated with complex traits

Llinares-Lopez F., Grimm D. G., Bodenham D. A., Gieraths U., Sugiyama M., Rowan B. and Borgwardt K.
Bioinformatics (2015), 31(12) i240-i249.

Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana

Slane D., Kong J., Schmid M., Jurgens G. and Bayer M.
Genom Data (2015), 4 96-8.

Single Geographic Origin of a Widespread Autotetraploid Arabidopsis arenosa Lineage Followed by Interploidy Admixture

Arnold B., Kim S. T. and Bomblies K.
Mol Biol Evol (2015), 32(6) 1382-95.

THO2, a core member of the THO/TREX complex, is required for microRNA production in Arabidopsis

Francisco-Mangilet A. G., Karlsson P., Kim M. H., Eo H. J., Oh S. A., Kim J. H., Kulcheski F. R., Park S. K. and Manavella P. A.
Plant J (2015), 82(6) 1018-29.

Salinity is an agent of divergent selection driving local adaptation of Arabidopsis thaliana to coastal habitats

Busoms S., Teres J., Huang X., Bomblies K., Danku J., Douglas A., Weigel D., Poschenrieder C. and Salt D. E.
Plant Physiol (2015), 168(3) 915-929.

FYVE1 is essential for vacuole biogenesis and intracellular trafficking in Arabidopsis

Kolb C., Nagel M. K., Kalinowska K., Hagmann J., Ichikawa M., Anzenberger F., Alkofer A., Sato M. H., Braun P. and Isono E.
Plant Physiol (2015), 167(4) 1361-73.

Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping

Rowan B. A., Patel V., Weigel D. and Schneeberger K.
G3 (Bethesda) (2015), 5(3) 385-398.

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

Willing Eva-Maria, Rawat Vimal, Mandáková Terezie, Maumus Florian, James Geo Velikkakam, Nordström Karl J. V., Becker Claude, Warthmann Norman, Chica Claudia, Szarzynska Bogna, Zytnicki Matthias, Albani Maria C., Kiefer Christiane, Bergonzi Sara, Castaings Loren, Mateos Julieta L., Berns Markus C., Bujdoso Nora, Piofczyk Thomas, de Lorenzo Laura, Barrero-Sicilia Cristina, Mateos Isabel, Piednoël Mathieu, Hagmann Jörg, Chen-Min-Tao Romy, Iglesias-Fernández Raquel, Schuster Stephan C., Alonso-Blanco Carlos, Roudier François, Carbonero Pilar, Paz-Ares Javier, Davis Seth J., Pecinka Ales, Quesneville Hadi, Colot Vincent, Lysak Martin A., Weigel Detlef, Coupland George and Schneeberger Korbinian
Nature Plants (2015), 1 14023.

A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network

Leal Valentim F., Mourik Sv, Pose D., Kim M. C., Schmid M., van Ham R. C., Busscher M., Sanchez-Perez G. F., Molenaar J., Angenent G. C., Immink R. G. and van Dijk A. D.
PLoS One (2015), 10(2) e0116973.

Beyond the thale: comparative genomics and genetics of Arabidopsis relatives

Koenig D. and Weigel D.
Nat Rev Genet (2015), 16(5) 285-98.

Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage

Hagmann J., Becker C., Muller J., Stegle O., Meyer R. C., Wang G., Schneeberger K., Fitz J., Altmann T., Bergelson J., Borgwardt K. and Weigel D.
PLoS Genet (2015), 11(1) e1004920.

Control of flowering by ambient temperature

Capovilla G., Schmid M. and Pose D.
J Exp Bot (2015), 66(1) 59-69.

Dissection of miRNA pathways using arabidopsis mesophyll protoplasts

Martinho C., Confraria A., Elias C. A., Crozet P., Rubio-Somoza I., Weigel D. and Baena-Gonzalez E.
Mol Plant (2015), 8(2) 261-75.

Evolution. Response to Comment on “A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity”

Brockington S. F., Moyroud E., Sayou C., Monniaux M., Nanao M. H., Thevenon E., Chahtane H., Warthmann N., Melkonian M., Zhang Y., Wong G. K., Weigel D., Dumas R. and Parcy F.
Science (2015), 347(6222) 621.

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana

Wang C., Liu C., Roqueiro D., Grimm D., Schwab R., Becker C., Lanz C. and Weigel D.
Genome Res (2015), 25(2) 246-56.

Lack of symmetric CG methylation and long-lasting retrotransposon activity have shaped the genome of Arabis alpina

Schneeberger K., Willing E. M., Rawat V., Mandáková T., Maumus F., Velikkakam James G., Nordström K., Becker C., Warthmann N., Chica C., Szarzynska B., Zytnicki M., Albani M., Kiefer C., Bergonzi S., Castaings L., Mateos J., Berns M., Bujdoso N., Piofczyk T., de Lorenzo L., Barrero-Sicilia C., Mateos I., Piednoël M., Hagmann J., Chen-Min-Tao R., Iglesias-Fernández R., Schuster S., Alonso-Blanco C., Roudier F., Carbonero P., Paz-Ares J., Davis S., Pecinka A., Quesneville H., Colot V., Lysak M., Weigel D. and Coupland G.
Nat Plants (2015), , accepted for publication.

Mutations in the EDR1 Gene Alter the Response of Arabidopsis thaliana to Phytophthora infestans and the Bacterial PAMPs flg22 and elf18

Geissler K., Eschen-Lippold L., Naumann K., Schneeberger K., Weigel D., Scheel D., Rosahl S. and Westphal L.
Mol Plant Microbe Interact (2015), 28(2) 122-33.

Pheomelanin in fish?

Kottler V. A., Kunstner A. and Schartl M.
Pigment Cell Melanoma Res (2015), 28(3) 355-6.

Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

Fraser B. A., Kunstner A., Reznick D. N., Dreyer C. and Weigel D.
Mol Ecol (2015), 24(2) 389-408.

Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae

Smith L. M., Burbano H. A., Wang X., Fitz J., Wang G., Ural-Blimke Y. and Weigel D.
Plant J (2015), 81(4) 597-610.

Recognizing the importance of new tools and resources for research

Schekman R., Weigel D. and Watt F. M.
Elife (2015), 4.

2014

Plant Genetic Archaeology: Whole-Genome Sequencing Reveals the Pedigree of a Classical Trisomic Line

Salome P. A. and Weigel D.
G3 (Bethesda) (2014), 5(2) 253-9.

Recent geographic convergence in diurnal and annual temperature cycling flattens global thermal profiles

Wang G. and Dillon M. E.
Nature Clim. Change (2014), 4(11) 988-992.

A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana

Heyndrickx K. S., Van de Velde J., Wang C., Weigel D. and Vandepoele K.
Plant Cell (2014), 26(10) 3894-910.

A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity

Sayou C., Monniaux M., Nanao M. H., Moyroud E., Brockington S. F., Thevenon E., Chahtane H., Warthmann N., Melkonian M., Zhang Y., Wong G. K., Weigel D., Parcy F. and Dumas R.
Science (2014), 343(6171) 645-8.

A regulatory framework for shoot stem cell control integrating metabolic, transcriptional, and phytohormone signals

Schuster C., Gaillochet C., Medzihradszky A., Busch W., Daum G., Krebs M., Kehle A. and Lohmann J. U.
Dev Cell (2014), 28(4) 438-49.

Activation of the Arabidopsis thaliana immune system by combinations of common ACD6 alleles

Todesco M., Kim S. T., Chae E., Bomblies K., Zaidem M., Smith L. M., Weigel D. and Laitinen R. A.
PLoS Genet (2014), 10(7) e1004459.

Advancing research

Patterson M., Schekman R., Watt F. M. and Weigel D.
Elife (2014), 3 e03980.

Analysis of a plant complex resistance gene locus underlying immune-related hybrid incompatibility and its occurrence in nature

Alcazar R., von Reth M., Bautor J., Chae E., Weigel D., Koornneef M. and Parker J. E.
PLoS Genet (2014), 10(12) e1004848.

Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo

Slane D., Kong J., Berendzen K. W., Kilian J., Henschen A., Kolb M., Schmid M., Harter K., Mayer U., De Smet I., Bayer M. and Jurgens G.
Development (2014), 141(24) 4831-40.

CHOLINE TRANSPORTER-LIKE1 is required for sieve plate development to mediate long-distance cell-to-cell communication

Dettmer J., Ursache R., Campilho A., Miyashima S., Belevich I., O’Regan S., Mullendore D. L., Yadav S. R., Lanz C., Beverina L., Papagni A., Schneeberger K., Weigel D., Stierhof Y. D., Moritz T., Knoblauch M., Jokitalo E. and Helariutta Y.
Nat Commun (2014), 5 4276.

Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life

Wessling R., Epple P., Altmann S., He Y., Yang L., Henz S. R., McDonald N., Wiley K., Bader K. C., Glasser C., Mukhtar M. S., Haigis S., Ghamsari L., Stephens A. E., Ecker J. R., Vidal M., Jones J. D., Mayer K. F., Ver Loren van Themaat E., Weigel D., Schulze-Lefert P., Dangl J. L., Panstruga R. and Braun P.
Cell Host Microbe (2014), 16(3) 364-75.

Different mechanisms for Arabidopsis thaliana hybrid necrosis cases inferred from temperature responses

Muralidharan S., Box M. S., Sedivy E. L., Wigge P. A., Weigel D. and Rowan B. A.
Plant Biol (Stuttg) (2014), 16(6) 1033-41.

DNA topoisomerase 1alpha promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis

Dinh T. T., Gao L., Liu X., Li D., Li S., Zhao Y., O’Leary M., Le B., Schmitz R. J., Manavella P., Li S., Weigel D., Pontes O., Ecker J. R. and Chen X.
PLoS Genet (2014), 10(7) e1004446.

Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization

Seymour D. K., Koenig D., Hagmann J., Becker C. and Weigel D.
PLoS Genet (2014), 10(11) e1004785.

Mating system shifts and transposable element evolution in the plant genus Capsella

Agren J. A., Wang W., Koenig D., Neuffer B., Weigel D. and Wright S. I.
BMC Genomics (2014), 15 602.

Mining herbaria for plant pathogen genomes: back to the future

Yoshida K., Burbano H. A., Krause J., Thines M., Weigel D. and Kamoun S.
PLoS Pathog (2014), 10(4) e1004028.

Multiple pigment cell types contribute to the black, blue, and orange ornaments of male guppies (Poecilia reticulata)

Kottler V. A., Koch I., Flotenmeyer M., Hashimoto H., Weigel D. and Dreyer C.
PLoS One (2014), 9(1) e85647.

New Arabidopsis advanced intercross recombinant inbred lines reveal female control of nonrandom mating

Fitz Gerald J. N., Carlson A. L., Smith E., Maloof J. N., Weigel D., Chory J., Borevitz J. O. and Swanson R. J.
Plant Physiol (2014), 165(1) 175-85.

Reciprocal responses in the interaction between Arabidopsis and the cell-content-feeding chelicerate herbivore spider mite

Zhurov V., Navarro M., Bruinsma K. A., Arbona V., Santamaria M. E., Cazaux M., Wybouw N., Osborne E. J., Ens C., Rioja C., Vermeirssen V., Rubio-Somoza I., Krishna P., Diaz I., Schmid M., Gomez-Cadenas A., Van de Peer Y., Grbic M., Clark R. M., Van Leeuwen T. and Grbic V.
Plant Physiol (2014), 164(1) 384-99.

Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis

Koster T., Meyer K., Weinholdt C., Smith L. M., Lummer M., Speth C., Grosse I., Weigel D. and Staiger D.
Nucleic Acids Res (2014), 42(15) 9925-36.

Sex chromosome polymorphism in guppies

Nanda I., Schories S., Tripathi N., Dreyer C., Haaf T., Schmid M. and Schartl M.
Chromosoma (2014), 123(4) 373-83.

Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis

Structural features determining flower-promoting activity of Arabidopsis FLOWERING LOCUS T

Ho W. W. and Weigel D.
Plant Cell (2014), 26(2) 552-64.

Temporal Control of Leaf Complexity by miRNA-Regulated Licensing of Protein Complexes

Rubio-Somoza I., Zhou C. M., Confraria A., Martinho C., von Born P., Baena-Gonzalez E., Wang J. W. and Weigel D.
Curr Biol (2014), 24(22) 2714-9.

The genome of the stress-tolerant wild tomato species Solanum pennellii

Bolger A., Scossa F., Bolger M. E., Lanz C., Maumus F., Tohge T., Quesneville H., Alseekh S., Sorensen I., Lichtenstein G., Fich E. A., Conte M., Keller H., Schneeberger K., Schwacke R., Ofner I., Vrebalov J., Xu Y., Osorio S., Aflitos S. A., Schijlen E., Jimenez-Gomez J. M., Ryngajllo M., Kimura S., Kumar R., Koenig D., Headland L. R., Maloof J. N., Sinha N., van Ham R. C., Lankhorst R. K., Mao L., Vogel A., Arsova B., Panstruga R., Fei Z., Rose J. K., Zamir D., Carrari F., Giovannoni J. J., Weigel D., Usadel B. and Fernie A. R.
Nat Genet (2014), 46(9) 1034-8.

Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata

Sharma E., Kunstner A., Fraser B. A., Zipprich G., Kottler V. A., Henz S. R., Weigel D. and Dreyer C.
BMC Genomics (2014), 15 400.

Trowel: a fast and accurate error correction module for Illumina sequencing reads

Lim E. C., Muller J., Hagmann J., Henz S. R., Kim S. T. and Weigel D.
Bioinformatics (2014), 30(22) 3264-5.

2013

A genomic-scale artificial microRNA library as a tool to investigate the functionally redundant gene space in Arabidopsis

Hauser F., Chen W., Deinlein U., Chang K., Ossowski S., Fitz J., Hannon G. J. and Schroeder J. I.
Plant Cell (2013), 25(8) 2848-63.

A Lasso multi-marker mixed model for association mapping with population structure correction

Rakitsch B., Lippert C., Stegle O. and Borgwardt K.
Bioinformatics (2013), 29(2) 206-14.

A year in the life of eLife

Schekman R., Watt F. M. and Weigel D.
Elife (2013), 2 e01516.

Accurate indel prediction using paired-end short reads

Grimm D., Hagmann J., Koenig D., Weigel D. and Borgwardt K.
BMC Genomics (2013), 14 132.

Artificial microRNAs for specific gene silencing in rice

Warthmann N., Ossowski S., Schwab R. and Weigel D.
Methods Mol Biol (2013), 956 131-49.

Circadian clock adjustment to plant iron status depends on chloroplast and phytochrome function

Salome P. A., Oliva M., Weigel D. and Kramer U.
EMBO J (2013), 32(4) 511-23.

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

Koenig D., Jimenez-Gomez J. M., Kimura S., Fulop D., Chitwood D. H., Headland L. R., Kumar R., Covington M. F., Devisetty U. K., Tat A. V., Tohge T., Bolger A., Schneeberger K., Ossowski S., Lanz C., Xiong G., Taylor-Teeples M., Brady S. M., Pauly M., Weigel D., Usadel B., Fernie A. R., Peng J., Sinha N. R. and Maloof J. N.
Proc Natl Acad Sci U S A (2013), 110(28) E2655-62.

Coordination of flower maturation by a regulatory circuit of three microRNAs

Rubio-Somoza I. and Weigel D.
PLoS Genet (2013), 9(3) e1003374.

Efficient network-guided multi-locus association mapping with graph cuts

Azencott C. A., Grimm D., Sugiyama M., Kawahara Y. and Borgwardt K. M.
Bioinformatics (2013), 29(13) i171-9.

eLife and early career researchers

Schekman R., Watt F. M. and Weigel D.
Elife (2013), 2 e01633.

Functional analysis of splice variant expression of MADS AFFECTING FLOWERING 2 of Arabidopsis thaliana

Rosloski S. M., Singh A., Jali S. S., Balasubramanian S., Weigel D. and Grbic V.
Plant Mol Biol (2013), 81(1-2) 57-69.

Genome-wide identification of KANADI1 target genes

Merelo P., Xie Y., Brand L., Ott F., Weigel D., Bowman J. L., Heisler M. G. and Wenkel S.
PLoS One (2013), 8(10) e77341.

Geometric tree kernels: classification of COPD from airway tree geometry

Feragen A., Petersen J., Grimm D., Dirksen A., Pedersen J. H., Borgwardt K. and de Bruijne M.
Inf Process Med Imaging (2013), 23 171-83.

Impaired sterol ester synthesis alters the response of Arabidopsis thaliana to Phytophthora infestans

Kopischke M., Westphal L., Schneeberger K., Clark R., Ossowski S., Wewer V., Fuchs R., Landtag J., Hause G., Dormann P., Lipka V., Weigel D., Schulze-Lefert P., Scheel D. and Rosahl S.
Plant J (2013), 73(3) 456-68.

LNK genes integrate light and clock signaling networks at the core of the Arabidopsis oscillator

Rugnone M. L., Faigon Soverna A., Sanchez S. E., Schlaen R. G., Hernando C. E., Seymour D. K., Mancini E., Chernomoretz A., Weigel D., Mas P. and Yanovsky M. J.
Proc Natl Acad Sci U S A (2013), 110(29) 12120-5.

Measuring Statistical Dependence via the Mutual Information Dimension

Sugiyama M and Borgwardt K.
International Joint Conferences on Artificial Intelligence (2013), .

Pigment pattern formation in the guppy, Poecilia reticulata, involves the Kita and Csf1ra receptor tyrosine kinases

Kottler V. A., Fadeev A., Weigel D. and Dreyer C.
Genetics (2013), 194(3) 631-46.

QnAs with Detlef Weigel. Interview by Sandeep Ravindran

Weigel D.
Proc Natl Acad Sci U S A (2013), 110(28) 11216.

Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana

Wahl V., Ponnu J., Schlereth A., Arrivault S., Langenecker T., Franke A., Feil R., Lunn J. E., Stitt M. and Schmid M.
Science (2013), 339(6120) 704-7.

Regulation of temperature-responsive flowering by MADS-box transcription factor repressors

Lee J. H., Ryu H. S., Chung K. S., Pose D., Kim S., Schmid M. and Ahn J. H.
Science (2013), 342(6158) 628-32.

Sixty years of genome biology

Doolittle W. F., Fraser P., Gerstein M. B., Graveley B. R., Henikoff S., Huttenhower C., Oshlack A., Ponting C. P., Rinn J. L., Schatz M. C., Ule J., Weigel D. and Weinstock G. M.
Genome Biol (2013), 14(4) 113.

Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease

Nekrasov V., Staskawicz B., Weigel D., Jones J. D. and Kamoun S.
Nat Biotechnol (2013), 31(8) 691-3.

Temperature-dependent regulation of flowering by antagonistic FLM variants

Pose D., Verhage L., Ott F., Yant L., Mathieu J., Angenent G. C., Immink R. G. and Schmid M.
Nature (2013), 503(7476) 414-7.

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

Slotte T., Hazzouri K. M., Agren J. A., Koenig D., Maumus F., Guo Y. L., Steige K., Platts A. E., Escobar J. S., Newman L. K., Wang W., Mandáková T., Vello E., Smith L. M., Henz S. R., Steffen J., Takuno S., Brandvain Y., Coop G., Andolfatto P., Hu T. T., Blanchette M., Clark R. M., Quesneville H., Nordborg M., Gaut B. S., Lysak M. A., Jenkins J., Grimwood J., Chapman J., Prochnik S., Shu S., Rokhsar D., Schmutz J., Weigel D. and Wright S. I.
Nat Genet (2013), 45(7) 831-5.

The eLife approach to peer review

Schekman R., Watt F. and Weigel D.
Elife (2013), 2 e00799.

The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana

Wijnker E., Velikkakam James G., Ding J., Becker F., Klasen J. R., Rawat V., Rowan B. A., de Jong D. F., de Snoo C. B., Zapata L., Huettel B., de Jong H., Ossowski S., Weigel D., Koornneef M., Keurentjes J. J. and Schneeberger K.
Elife (2013), 2 e01426.

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

Yoshida K., Schuenemann V. J., Cano L. M., Pais M., Mishra B., Sharma R., Lanz C., Martin F. N., Kamoun S., Krause J., Thines M., Weigel D. and Burbano H. A.
Elife (2013), 2 e00731.

Tissue-specific silencing of Arabidopsis SU(VAR)3-9 HOMOLOG8 by miR171a

Manavella P. A., Koenig D., Rubio-Somoza I., Burbano H. A., Becker C. and Weigel D.
Plant Physiol (2013), 161(2) 805-12.

Transposon variants and their effects on gene expression in Arabidopsis

Wang X., Weigel D. and Smith L. M.
PLoS Genet (2013), 9(2) e1003255.

User guide for mapping-by-sequencing in Arabidopsis

James G. V., Patel V., Nordstrom K. J., Klasen J. R., Salome P. A., Weigel D. and Schneeberger K.
Genome Biol (2013), 14(6) R61.

2012

1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions

Joshi H. J., Christiansen K. M., Fitz J., Cao J., Lipzen A., Martin J., Smith-Moritz A. M., Pennacchio L. A., Schackwitz W. S., Weigel D. and Heazlewood J. L.
Bioinformatics (2012), 28(10) 1303-6.

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis

Windram O., Madhou P., McHattie S., Hill C., Hickman R., Cooke E., Jenkins D. J., Penfold C. A., Baxter L., Breeze E., Kiddle S. J., Rhodes J., Atwell S., Kliebenstein D. J., Kim Y. S., Stegle O., Borgwardt K., Zhang C., Tabrett A., Legaie R., Moore J., Finkenstadt B., Wild D. L., Mead A., Rand D., Beynon J., Ott S., Buchanan-Wollaston V. and Denby K. J.
Plant Cell (2012), 24(9) 3530-57.

Characterization of SOC1’s central role in flowering by the identification of its upstream and downstream regulators

Immink R. G., Pose D., Ferrario S., Ott F., Kaufmann K., Valentim F. L., de Folter S., van der Wal F., van Dijk A. D., Schmid M. and Angenent. C.
Plant Physiol (2012), 160(1) 433-49.

Epialleles in plant evolution

Weigel D. and Colot V.
Genome Biol (2012), 13(10) 249.

Epigenetic variation: origin and transgenerational inheritance

Becker C. and Weigel D.
Curr Opin Plant Biol (2012), 15(5) 562-7.

Estimates of genetic differentiation measured by F(ST) do not necessarily require large sample sizes when using many SNP markers

Willing E. M., Dreyer C. and van Oosterhout C.
PLoS One (2012), 7(8) e42649.

Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1

Manavella P. A., Hagmann J., Ott F., Laubinger S., Franz M., Macek B. and Weigel D.
Cell (2012), 151(4) 859-70.

Fitness of Arabidopsis thaliana mutation accumulation lines whose spontaneous mutations are known

Rutter M. T., Roles A., Conner J. K., Shaw R. G., Shaw F. H., Schneeberger K., Ossowski S., Weigel D. and Fenster C. B.
Evolution (2012), 66(7) 2335-9.

Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses

Brandt R., Salla-Martret M., Bou-Torrent J., Musielak T., Stahl M., Lanz C., Ott F., Schmid M., Greb T., Schwarz M., Choi S. B., Barton M. K., Reinhart B. J., Liu T., Quint M., Palauqui J. C., Martinez-Garcia J. F. and Wenkel S.
Plant J (2012), 72(1) 31-42.

Gibberellin regulates the Arabidopsis floral transition through miR156-targeted SQUAMOSA promoter binding-like transcription factors

Yu S., Galvao V. C., Zhang Y. C., Horrer D., Zhang T. Q., Hao Y. H., Feng Y. Q., Wang S., Schmid M. and Wang J. W.
Plant Cell (2012), 24(8) 3320-32.

GLIDE: GPU-based linear regression for detection of epistasis

Kam-Thong T., Azencott C. A., Cayton L., Putz B., Altmann A., Karbalai N., Samann P. G., Scholkopf B., Muller-Myhsok B. and Borgwardt K. M.
Hum Hered (2012), 73(4) 220-36.

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis

Breakfield N. W., Corcoran D. L., Petricka J. J., Shen J., Sae-Seaw J., Rubio-Somoza I., Weigel D., Ohler U. and Benfey P. N.
Genome Res (2012), 22(1) 163-76.

Independent FLC mutations as causes of flowering-time variation in Arabidopsis thaliana and Capsella rubella

Guo Y. L., Todesco M., Hagmann J., Das S. and Weigel D.
Genetics (2012), 192(2) 729-39.

Launching eLife, Part 1

Schekman R., Patterson M., Watt F. and Weigel D.
Elife (2012), 1 e00270.

Launching eLife, Part 2

Schekman R., Watt F. and Weigel D.
Elife (2012), 1 e00365.

MIGS: miRNA-induced gene silencing

Felippes F. F., Wang J. W. and Weigel D.
Plant J (2012), 70(3) 541-7.

Natural variation in Arabidopsis: from molecular genetics to ecological genomics

Weigel D.
Plant Physiol (2012), 158(1) 2-22.

Natural variation in biogenesis efficiency of individual Arabidopsis thaliana microRNAs

Todesco M., Balasubramanian S., Cao J., Ott F., Sureshkumar S., Schneeberger K., Meyer R. C., Altmann T. and Weigel D.
Curr Biol (2012), 22(2) 166-70.

On epigenetics and epistasis: hybrids and their non-additive interactions

Smith L. M. and Weigel D.
EMBO J (2012), 31(2) 249-50.

Plant secondary siRNA production determined by microRNA-duplex structure

Manavella P. A., Koenig D. and Weigel D.
Proc Natl Acad Sci U S A (2012), 109(7) 2461-6.

Reasons for the invasive success of a guppy (Poecilia reticulata) population in Trinidad

Sievers C., Willing E. M., Hoffmann M., Dreyer C., Ramnarine I. and Magurran A.
PLoS One (2012), 7(5) e38404.

Role of recently evolved miRNA regulation of sunflower HaWRKY6 in response to temperature damage

Giacomelli J. I., Weigel D., Chan R. L. and Manavella P. A.
New Phytol (2012), 195(4) 766-73.

ShapePheno: unsupervised extraction of shape phenotypes from biological image collections

Karaletsos T., Stegle O., Dreyer C., Winn J. and Borgwardt K. M.
Bioinformatics (2012), 28(7) 1001-8.

Spatial control of flowering by DELLA proteins in Arabidopsis thaliana

Galvao V. C., Horrer D., Kuttner F. and Schmid M.
Development (2012), 139(21) 4072-82.

Synteny-based mapping-by-sequencing enabled by targeted enrichment

Galvao V. C., Nordstrom K. J., Lanz C., Sulz P., Mathieu J., Pose D., Schmid M., Weigel D. and Schneeberger K.
Plant J (2012), 71(3) 517-26.

The end of innocence: flowering networks explode in complexity

Pose D., Yant L. and Schmid M.
Curr Opin Plant Biol (2012), 15(1) 45-50.

The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element

Dinh T. T., Girke T., Liu X., Yant L., Schmid M. and Chen X.
Development (2012), 139(11) 1978-86.

The recombination landscape in Arabidopsis thaliana F2 populations

Salome P. A., Bomblies K., Fitz J., Laitinen R. A., Warthmann N., Yant L. and Weigel D.
Heredity (Edinb) (2012), 108(4) 447-55.

2011

A major QTL controls susceptibility to spinal curvature in the curveback guppy

Gorman K. F., Christians J. K., Parent J., Ahmadi R., Weigel D., Dreyer C. and Breden F.
BMC Genet (2011), 12 16.

Argonaute10 as a miRNA locker

Manavella P. A., Weigel D. and Wu L.
Cell (2011), 145(2) 173-4.

ccSVM: correcting Support Vector Machines for confounding factors in biological data classification

Li L., Rakitsch B. and Borgwardt K.
Bioinformatics (2011), 27(13) i342-8.

ceRNAs: miRNA target mimic mimics

Rubio-Somoza I., Weigel D., Franco-Zorilla J. M., Garcia J. A. and Paz-Ares J.
Cell (2011), 147(7) 1431-2.

Comparative analysis of non-autonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana

de Felippes F. F., Ott F. and Weigel D.
Nucleic Acids Res (2011), 39(7) 2880-9.

Complex evolutionary events at a tandem cluster of Arabidopsis thaliana genes resulting in a single-locus genetic incompatibility

Smith L. M., Bomblies K. and Weigel D.
PLoS Genet (2011), 7(7) e1002164.

Developmental genetics and new sequencing technologies: the rise of nonmodel organisms

Rowan B. A., Weigel D. and Koenig D.
Dev Cell (2011), 21(1) 65-76.

Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis

Davila J. I., Arrieta-Montiel M. P., Wamboldt Y., Cao J., Hagmann J., Shedge V., Xu Y. Z., Weigel D. and Mackenzie S. A.
BMC Biol (2011), 9 64.

EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units

Kam-Thong T., Czamara D., Tsuda K., Borgwardt K., Lewis C. M., Erhardt-Lehmann A., Hemmer B., Rieckmann P., Daake M., Weber F., Wolf C., Ziegler A., Putz B., Holsboer F., Scholkopf B. and Muller-Myhsok B.
Eur J Hum Genet (2011), 19(4) 465-71.

Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs

Kam-Thong T., Putz B., Karbalai N., Muller-Myhsok B. and Borgwardt K.
Bioinformatics (2011), 27(13) i214-21.

Evolution of the S-locus region in Arabidopsis relatives

Guo Y. L., Zhao X., Lanz C. and Weigel D.
Plant Physiol (2011), 157(2) 937-46.

Fast-forward genetics enabled by new sequencing technologies

Schneeberger K. and Weigel D.
Trends Plant Sci (2011), 16(5) 282-8.

Gene duplication and divergence of long wavelength-sensitive opsin genes in the guppy, Poecilia reticulata

Watson C. T., Gray S. M., Hoffmann M., Lubieniecki K. P., Joy J. B., Sandkam B. A., Weigel D., Loew E., Dreyer C., Davidson W. S. and Breden F.
J Mol Evol (2011), 72(2) 240-52.

Genetic architecture of flowering-time variation in Arabidopsis thaliana

Salome P. A., Bomblies K., Laitinen R. A., Yant L., Mott R. and Weigel D.
Genetics (2011), 188(2) 421-33.

Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis

Guo Y. L., Fitz J., Schneeberger K., Ossowski S., Cao J. and Weigel D.
Plant Physiol (2011), 157(2) 757-69.

LOCAS–a low coverage assembly tool for resequencing projects

Klein J. D., Ossowski S., Schneeberger K., Weigel D. and Huson D. H.
PLoS One (2011), 6(8) e23455.

MicroRNA networks and developmental plasticity in plants

Rubio-Somoza I. and Weigel D.
Trends Plant Sci (2011), 16(5) 258-64.

miRNA control of vegetative phase change in trees

Wang J. W., Park M. Y., Wang L. J., Koo Y., Chen X. Y., Weigel D. and Poethig R. S.
PLoS Genet (2011), 7(2) e1002012.

Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor

Gou J. Y., Felippes F. F., Liu C. J., Weigel D. and Wang J. W.
Plant Cell (2011), 23(4) 1512-22.

Paired-end RAD-seq for de novo assembly and marker design without available reference

Willing E. M., Hoffmann M., Klein J. D., Weigel D. and Dreyer C.
Bioinformatics (2011), 27(16) 2187-93.

Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor

Moyroud E., Minguet E. G., Ott F., Yant L., Pose D., Monniaux M., Blanchet S., Bastien O., Thevenon E., Weigel D., Schmid M. and Parcy F.
Plant Cell (2011), 23(4) 1293-306.

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

Schneeberger K., Ossowski S., Ott F., Klein J. D., Wang X., Lanz C., Smith L. M., Cao J., Fitz J., Warthmann N., Henz S. R., Huson D. H. and Weigel D.
Proc Natl Acad Sci U S A (2011), 108(25) 10249-54.

Regulation of flowering time: all roads lead to Rome

Srikanth A. and Schmid M.
Cell Mol Life Sci (2011), 68(12) 2013-37.

RNA 3′ processing functions of Arabidopsis FCA and FPA limit intergenic transcription

Sonmez C., Baurle I., Magusin A., Dreos R., Laubinger S., Weigel D. and Dean C.
Proc Natl Acad Sci U S A (2011), 108(20) 8508-13.

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Becker C., Hagmann J., Muller J., Koenig D., Stegle O., Borgwardt K. and Weigel D.
Nature (2011), 480(7376) 245-9.

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

Hu T. T., Pattyn P., Bakker E. G., Cao J., Cheng J. F., Clark R. M., Fahlgren N., Fawcett J. A., Grimwood J., Gundlach H., Haberer G., Hollister J. D., Ossowski S., Ottilar R. P., Salamov A. A., Schneeberger K., Spannagl M., Wang X., Yang L., Nasrallah M. E., Bergelson J., Carrington J. C., Gaut B. S., Schmutz J., Mayer K. F., Van de Peer Y., Grigoriev I. V., Nordborg M., Weigel D. and Guo Y. L.
Nat Genet (2011), 43(5) 476-81.

The bZIP Transcription Factor PERIANTHIA: A Multifunctional Hub for Meristem Control

Maier A. T., Stehling-Sun S., Offenburger S. L. and Lohmann J. U.
Front Plant Sci (2011), 2 79.

The control of developmental phase transitions in plants

Huijser P. and Schmid M.
Development (2011), 138(19) 4117-29.

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

Hollister J. D., Smith L. M., Guo Y. L., Ott F., Weigel D. and Gaut B. S.
Proc Natl Acad Sci U S A (2011), 108(6) 2322-7.

Trehalose-6-phosphate: connecting plant metabolism and development

Ponnu J., Wahl V. and Schmid M.
Front Plant Sci (2011), 2 70.

Weisfeiler-Lehman graph kernels

Shervashidze N., Schweitzer P., van Leeuwen E. J., Mehlhorn K. and Borgwardt K.
Journal of Machine Learning Research (2011), .

What developmental biologists can learn from plant pathogens

Weigel D.
Dev Cell (2011), 20(2) e2.

Whole-genome sequencing of multiple Arabidopsis thaliana populations

Cao J., Schneeberger K., Ossowski S., Gunther T., Bender S., Fitz J., Koenig D., Lanz C., Stegle O., Lippert C., Wang X., Ott F., Muller J., Alonso-Blanco C., Borgwardt K., Schmid K. J. and Weigel D.
Nat Genet (2011), 43(10) 956-63.

2010

A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana

Todesco M., Rubio-Somoza I., Paz-Ares J. and Weigel D.
PLoS Genet (2010), 6(7) e1001031.

AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling

Rehrauer H., Aquino C., Gruissem W., Henz S. R., Hilson P., Laubinger S., Naouar N., Patrignani A., Rombauts S., Shu H., Van de Peer Y., Vuylsteke M., Weigel D., Zeller G. and Hennig L.
Plant Physiol (2010), 152(2) 487-99.

Arabidopsis and relatives as models for the study of genetic and genomic incompatibilities

Bomblies K. and Weigel D.

Philos Trans R Soc Lond B Biol Sci (2010), 365(1547) 1815-23.

Climate change and the integrity of science

Gleick P. H., Adams R. M., Amasino R. M., Anders E., Anderson D. J., Anderson W. W., Anselin L. E., Arroyo M. K., Asfaw B., Ayala F. J., Bax A., Bebbington A. J., Bell G., Bennett M. V., Bennetzen J. L., Berenbaum M. R., Berlin O. B., Bjorkman P. J., Blackburn E., Blamont J. E., Botchan M. R., Boyer J. S., Boyle E. A., Branton D., Briggs S. P., Briggs W. R., Brill W. J., Britten R. J., Broecker W. S., Brown J. H., Brown P. O., Brunger A. T., Cairns J., Jr., Canfield D. E., Carpenter S. R., Carrington J. C., Cashmore A. R., Castilla J. C., Cazenave A., Chapin F. S., 3rd, Ciechanover A. J., Clapham D. E., Clark W. C., Clayton R. N., Coe M. D., Conwell E. M., Cowling E. B., Cowling R. M., Cox C. S., Croteau R. B., Crothers D. M., Crutzen P. J., Daily G. C., Dalrymple G. B., Dangl J. L., Darst S. A., Davies D. R., Davis M. B., De Camilli P. V., Dean C., DeFries R. S., Deisenhofer J., Delmer D. P., DeLong E. F., DeRosier D. J., Diener T. O., Dirzo R., Dixon J. E., Donoghue M. J., Doolittle R. F., Dunne T., Ehrlich P. R., Eisenstadt S. N., Eisner T., Emanuel K. A., Englander S. W., Ernst W. G., Falkowski P. G., Feher G., Ferejohn J. A., Fersht A., Fischer E. H., Fischer R., Flannery K. V., Frank J., Frey P. A., Fridovich I., Frieden C., Futuyma D. J., Gardner W. R., Garrett C. J., Gilbert W., Goldberg R. B., Goodenough W. H., Goodman C. S., Goodman M., Greengard P., Hake S., Hammel G., Hanson S. and others
Science (2010), 328(5979) 689-90.

Control of cell proliferation in Arabidopsis thaliana by microRNA miR396

Rodriguez R. E., Mecchia M. A., Debernardi J. M., Schommer C., Weigel D. and Palatnik J. F.
Development (2010), 137(1) 103-12.

Control of lateral organ development and flowering time by the Arabidopsis thaliana MADS-box Gene AGAMOUS-LIKE6

Koo S. C., Bracko O., Park M. S., Schwab R., Chun H. J., Park K. M., Seo J. S., Grbic V., Balasubramanian S., Schmid M., Godard F., Yun D. J., Lee S. Y., Cho M. J., Weigel D. and Kim M. C.
Plant J (2010), 62(5) 807-16.

Directed gene silencing with artificial microRNAs

Schwab R., Ossowski S., Warthmann N. and Weigel D.
Methods Mol Biol (2010), 592 71-88.

Gene function prediction from synthetic lethality networks via ranking on demand

Lippert C., Ghahramani Z. and Borgwardt K. M.
Bioinformatics (2010), 26(7) 912-8.

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

Atwell S., Huang Y. S., Vilhjalmsson B. J., Willems G., Horton M., Li Y., Meng D., Platt A., Tarone A. M., Hu T. T., Jiang R., Muliyati N. W., Zhang X., Amer M. A., Baxter I., Brachi B., Chory J., Dean C., Debieu M., de Meaux J., Ecker J. R., Faure N., Kniskern J. M., Jones J. D., Michael T., Nemri A., Roux F., Salt D. E., Tang C., Todesco M., Traw M. B., Weigel D., Marjoram P., Borevitz J. O., Bergelson J. and Nordborg M.
Nature (2010), 465(7298) 627-31.

Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies

Willing E. M., Bentzen P., van Oosterhout C., Hoffmann M., Cable J., Breden F., Weigel D. and Dreyer C.
Mol Ecol (2010), 19(5) 968-84.

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome

Laubinger S., Zeller G., Henz S. R., Buechel S., Sachsenberg T., Wang J. W., Ratsch G. and Weigel D.
Proc Natl Acad Sci U S A (2010), 107(41) 17466-73.

Hormonal control of the shoot stem-cell niche

Zhao Z., Andersen S. U., Ljung K., Dolezal K., Miotk A., Schultheiss S. J. and Lohmann J. U.
Nature (2010), 465(7301) 1089-92.

Identification of a spontaneous frame shift mutation in a nonreference Arabidopsis accession using whole genome sequencing

Laitinen R. A., Schneeberger K., Jelly N. S., Ossowski S. and Weigel D.
Plant Physiol (2010), 153(2) 652-4.

Increased leaf size: different means to an end

Gonzalez N., De Bodt S., Sulpice R., Jikumaru Y., Chae E., Dhondt S., Van Daele T., De Milde L., Weigel D., Kamiya Y., Stitt M., Beemster G. T. and Inze D.
Plant Physiol (2010), 153(3) 1261-79.

Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana

Bomblies K., Yant L., Laitinen R. A., Kim S. T., Hollister J. D., Warthmann N., Fitz J. and Weigel D.
PLoS Genet (2010), 6(3) e1000890.

MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana

Fahlgren N., Jogdeo S., Kasschau K. D., Sullivan C. M., Chapman E. J., Laubinger S., Smith L. M., Dasenko M., Givan S. A., Weigel D. and Carrington J. C.
Plant Cell (2010), 22(4) 1074-89.

MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor

Schlereth A., Moller B., Liu W., Kientz M., Flipse J., Rademacher E. H., Schmid M., Jurgens G. and Weijers D.
Nature (2010), 464(7290) 913-6.

Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana

Todesco M., Balasubramanian S., Hu T. T., Traw M. B., Horton M., Epple P., Kuhns C., Sureshkumar S., Schwartz C., Lanz C., Laitinen R. A., Huang Y., Chory J., Lipka V., Borevitz J. O., Dangl J. L., Bergelson J., Nordborg M. and Weigel D.
Nature (2010), 465(7298) 632-6.

Natural diversity in flowering responses of Arabidopsis thaliana caused by variation in a tandem gene array

Rosloski S. M., Jali S. S., Balasubramanian S., Weigel D. and Grbic V.
Genetics (2010), 186(1) 263-76.

Next generation molecular ecology

Tautz D., Ellegren H. and Weigel D.
Mol Ecol (2010), 19 Suppl 1 1-3.

On reconciling the interactions between APETALA2, miR172 and AGAMOUS with the ABC model of flower development

Wollmann H., Mica E., Todesco M., Long J. A. and Weigel D.
Development (2010), 137(21) 3633-42.

Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2

Yant L., Mathieu J., Dinh T. T., Ott F., Lanz C., Wollmann H., Chen X. and Schmid M.
Plant Cell (2010), 22(7) 2156-70.

Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories

Massonnet C., Vile D., Fabre J., Hannah M. A., Caldana C., Lisec J., Beemster G. T., Meyer R. C., Messerli G., Gronlund J. T., Perkovic J., Wigmore E., May S., Bevan M. W., Meyer C., Rubio-Diaz S., Weigel D., Micol J. L., Buchanan-Wollaston V., Fiorani F., Walsh S., Rinn B., Gruissem W., Hilson P., Hennig L., Willmitzer L. and Granier C.
Plant Physiol (2010), 152(4) 2142-57.

Role of A-type ARABIDOPSIS RESPONSE REGULATORS in meristem maintenance and regeneration

Buechel S., Leibfried A., To J. P., Zhao Z., Andersen S. U., Kieber J. J. and Lohmann J. U.
Eur J Cell Biol (2010), 89(2-3) 279-84.

Small RNAs in flower development

Wollmann H. and Weigel D.
Eur J Cell Biol (2010), 89(2-3) 250-7.

STIMPY mediates cytokinin signaling during shoot meristem establishment in Arabidopsis seedlings

Skylar A., Hong F., Chory J., Weigel D. and Wu X.
Development (2010), 137(4) 541-9.

Structure determinants for accurate processing of miR172a in Arabidopsis thaliana

Werner S., Wollmann H., Schneeberger K. and Weigel D.
Curr Biol (2010), 20(1) 42-8.

Ten years of genetics and genomics: what have we achieved and where are we heading?

Heard E., Tishkoff S., Todd J. A., Vidal M., Wagner G. P., Wang J., Weigel D. and Young R.
Nat Rev Genet (2010), 11(10) 723-33.

The FANTASTIC FOUR proteins influence shoot meristem size in Arabidopsis thaliana

Wahl V., Brand L. H., Guo Y. L. and Schmid M.
BMC Plant Biol (2010), 10 285.

The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana

Ossowski S., Schneeberger K., Lucas-Lledo J. I., Warthmann N., Clark R. M., Shaw R. G., Weigel D. and Lynch M.
Science (2010), 327(5961) 92-4.

The role of the Arabidopsis morning loop components CCA1, LHY, PRR7, and PRR9 in temperature compensation

Salome P. A., Weigel D. and McClung C. R.
Plant Cell (2010), 22(11) 3650-61.

The scale of population structure in Arabidopsis thaliana

Platt A., Horton M., Huang Y. S., Li Y., Anastasio A. E., Mulyati N. W., Agren J., Bossdorf O., Byers D., Donohue K., Dunning M., Holub E. B., Hudson A., Le Corre V., Loudet O., Roux F., Warthmann N., Weigel D., Rivero L., Scholl R., Nordborg M., Bergelson J. and Borevitz J. O.
PLoS Genet (2010), 6(2) e1000843.

Transcriptional control of a plant stem cell niche

Busch W., Miotk A., Ariel F. D., Zhao Z., Forner J., Daum G., Suzaki T., Schuster C., Schultheiss S. J., Leibfried A., Haubeiss S., Ha N., Chan R. L. and Lohmann J. U.
Dev Cell (2010), 18(5) 849-61.

Transcriptional control of gene expression by microRNAs

Khraiwesh B., Arif M. A., Seumel G. I., Ossowski S., Weigel D., Reski R. and Frank W.
Cell (2010), 140(1) 111-22.

Transient assays for the analysis of miRNA processing and function

de Felippes F. F. and Weigel D.
Methods Mol Biol (2010), 592 255-64.

Transmission electron microscopy (TEM) freeze substitution of plant tissues

Weigel D. and Glazebrook J.
Cold Spring Harb Protoc (2010), 2010(7) pdb prot4959.

2009

A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana

Sureshkumar S., Todesco M., Schneeberger K., Harilal R., Balasubramanian S. and Weigel D.
Science (2009), 323(5917) 1060-3.

Cis-regulatory changes at FLOWERING LOCUS T mediate natural variation in flowering responses of Arabidopsis thaliana

Schwartz C., Balasubramanian S., Warthmann N., Michael T. P., Lempe J., Sureshkumar S., Kobayashi Y., Maloof J. N., Borevitz J. O., Chory J. and Weigel D.
Genetics (2009), 183(2) 723-32, 1SI-7SI.

Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance

Plantegenet S., Weber J., Goldstein D. R., Zeller G., Nussbaumer C., Thomas J., Weigel D., Harshman K. and Hardtke C. S.
Mol Syst Biol (2009), 5 242.

Deep sequencing to reveal new variants in pooled DNA samples

Out A. A., van Minderhout I. J., Goeman J. J., Ariyurek Y., Ossowski S., Schneeberger K., Weigel D., van Galen M., Taschner P. E., Tops C. M., Breuning M. H., van Ommen G. J., den Dunnen J. T., Devilee P. and Hes F. J.
Hum Mutat (2009), 30(12) 1703-12.

Dellaporta miniprep for plant DNA isolation

Weigel D. and Glazebrook J.
Cold Spring Harb Protoc (2009), 2009(3) pdb prot5178.

DETORQUEO, QUIRKY, and ZERZAUST represent novel components involved in organ development mediated by the receptor-like kinase STRUBBELIG in Arabidopsis thaliana

Fulton L., Batoux M., Vaddepalli P., Yadav R. K., Busch W., Andersen S. U., Jeong S., Lohmann J. U. and Schneitz K.
PLoS Genet (2009), 5(1) e1000355.

Dual roles of the bZIP transcription factor PERIANTHIA in the control of floral architecture and homeotic gene expression

Maier A. T., Stehling-Sun S., Wollmann H., Demar M., Hong R. L., Haubeiss S., Weigel D. and Lohmann J. U.
Development (2009), 136(10) 1613-20.

Genetic linkage map of the guppy, Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation

Tripathi N., Hoffmann M., Willing E. M., Lanz C., Weigel D. and Dreyer C.
Proc Biol Sci (2009), 276(1665) 2195-208.

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

McNally K. L., Childs K. L., Bohnert R., Davidson R. M., Zhao K., Ulat V. J., Zeller G., Clark R. M., Hoen D. R., Bureau T. E., Stokowski R., Ballinger D. G., Frazer K. A., Cox D. R., Padhukasahasram B., Bustamante C. D., Weigel D., Mackill D. J., Bruskiewich R. M., Ratsch G., Buell C. R., Leung H. and Leach J. E.
Proc Natl Acad Sci U S A (2009), 106(30) 12273-8.

Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii

Molnar A., Bassett A., Thuenemann E., Schwach F., Karkare S., Ossowski S., Weigel D. and Baulcombe D.
Plant J (2009), 58(1) 165-74.

Just say no: floral repressors help Arabidopsis bide the time

Yant L., Mathieu J. and Schmid M.
Curr Opin Plant Biol (2009), 12(5) 580-6.

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences

Schultheiss S. J., Busch W., Lohmann J. U., Kohlbacher O. and Ratsch G.
Bioinformatics (2009), 25(16) 2126-33.

Linkage analysis reveals the independent origin of Poeciliid sex chromosomes and a case of atypical sex inheritance in the guppy (Poecilia reticulata)

Tripathi N., Hoffmann M., Weigel D. and Dreyer C.
Genetics (2009), 182(1) 365-74.

miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana

Wang J. W., Czech B. and Weigel D.
Cell (2009), 138(4) 738-49.

Phenotypic analysis of Arabidopsis mutants: bacterial pathogens

Weigel D. and Glazebrook J.
Cold Spring Harb Protoc (2009), 2009(7) pdb prot4983.

QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines

Balasubramanian S., Schwartz C., Singh A., Warthmann N., Kim M. C., Maloof J. N., Loudet O., Trainer G. T., Dabi T., Borevitz J. O., Chory J. and Weigel D.
PLoS One (2009), 4(2) e4318.

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., Ratsch G., Inze D., Kuiper M., De Veylder L. and Vuylsteke M.
Plant J (2009), 57(1) 184-94.

Quick miniprep for plant DNA isolation

Weigel D. and Glazebrook J.
Cold Spring Harb Protoc (2009), 2009(3) pdb prot5179.

Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck

Guo Y. L., Bechsgaard J. S., Slotte T., Neuffer B., Lascoux M., Weigel D. and Schierup M. H.
Proc Natl Acad Sci U S A (2009), 106(13) 5246-51.

Regulation and functional specialization of small RNA-target nodes during plant development

Rubio-Somoza I., Cuperus J. T., Weigel D. and Carrington J. C.
Curr Opin Plant Biol (2009), 12(5) 622-7.

Repression of flowering by the miR172 target SMZ

Mathieu J., Yant L. J., Murdter F., Kuttner F. and Schmid M.
PLoS Biol (2009), 7(7) e1000148.

Selective epigenetic control of retrotransposition in Arabidopsis

Mirouze M., Reinders J., Bucher E., Nishimura T., Schneeberger K., Ossowski S., Cao J., Weigel D., Paszkowski J. and Mathieu O.
Nature (2009), 461(7262) 427-30.

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

Schneeberger K., Ossowski S., Lanz C., Juul T., Petersen A. H., Nielsen K. L., Jorgensen J. E., Weigel D. and Andersen S. U.
Nat Methods (2009), 6(8) 550-1.

Simultaneous alignment of short reads against multiple genomes

Schneeberger K., Hagmann J., Ossowski S., Warthmann N., Gesing S., Kohlbacher O. and Weigel D.
Genome Biol (2009), 10(9) R98.

Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays

Zeller G., Henz S. R., Widmer C. K., Sachsenberg T., Ratsch G., Weigel D. and Laubinger S.
Plant J (2009), 58(6) 1068-82.

The 1001 genomes project for Arabidopsis thaliana

Weigel D. and Mott R.
Genome Biol (2009), 10(5) 107.

The NGATHA genes direct style development in the Arabidopsis gynoecium

Trigueros M., Navarrete-Gomez M., Sato S., Christensen S. K., Pelaz S., Weigel D., Yanofsky M. F. and Ferrandiz C.
Plant Cell (2009), 21(5) 1394-409.

The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis

Wu G., Park M. Y., Conway S. R., Wang J. W., Weigel D. and Poethig R. S.
Cell (2009), 138(4) 750-9.

Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173

Felippes F. F. and Weigel D.
EMBO Rep (2009), 10(3) 264-70.

2008

A quantitative and dynamic model for plant stem cell regulation

Geier F., Lohmann J. U., Gerstung M., Maier A. T., Timmer J. and Fleck C.
PLoS One (2008), 3(10) e3553.

A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana

Loudet O., Michael T. P., Burger B. T., Le Mette C., Mockler T. C., Weigel D. and Chory J.
Proc Natl Acad Sci U S A (2008), 105(44) 17193-8.

Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light

Filiault D. L., Wessinger C. A., Dinneny J. R., Lutes J., Borevitz J. O., Weigel D., Chory J. and Maloof J. N.
Proc Natl Acad Sci U S A (2008), 105(8) 3157-62.

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana

Laubinger S., Zeller G., Henz S. R., Sachsenberg T., Widmer C. K., Naouar N., Vuylsteke M., Scholkopf B., Ratsch G. and Weigel D.
Genome Biol (2008), 9(7) R112.

Auxin responses in mutants of the Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC9 signalosome

Dohmann E. M., Levesque M. P., Isono E., Schmid M. and Schwechheimer C.
Plant Physiol (2008), 147(3) 1369-79.

Comparative analysis of the MIR319a microRNA locus in Arabidopsis and related Brassicaceae

Warthmann N., Das S., Lanz C. and Weigel D.
Mol Biol Evol (2008), 25(5) 892-902.

Control of jasmonate biosynthesis and senescence by miR319 targets

Schommer C., Palatnik J. F., Aggarwal P., Chetelat A., Cubas P., Farmer E. E., Nath U. and Weigel D.
PLoS Biol (2008), 6(9) e230.

Criteria for annotation of plant MicroRNAs

Meyers B. C., Axtell M. J., Bartel B., Bartel D. P., Baulcombe D., Bowman J. L., Cao X., Carrington J. C., Chen X., Green P. J., Griffiths-Jones S., Jacobsen S. E., Mallory A. C., Martienssen R. A., Poethig R. S., Qi Y., Vaucheret H., Voinnet O., Watanabe Y., Weigel D. and Zhu J. K.
Plant Cell (2008), 20(12) 3186-90.

Crystal families and systems in higher dimensions, and geometrical symbols of their point groups. II. Cubic families in five- and n-dimensional spaces

Weigel D., Phan T. and Veysseyre R.
Acta Crystallogr A (2008), 64(Pt 6) 687-97.

Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays

Zeller G., Clark R. M., Schneeberger K., Bohlen A., Weigel D. and Ratsch G.
Genome Res (2008), 18(6) 918-29.

Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana

Wang J. W., Schwab R., Czech B., Mica E. and Weigel D.
Plant Cell (2008), 20(5) 1231-43.

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

Laubinger S., Sachsenberg T., Zeller G., Busch W., Lohmann J. U., Ratsch G. and Weigel D.
Proc Natl Acad Sci U S A (2008), 105(25) 8795-800.

Evolution of Arabidopsis thaliana microRNAs from random sequences

Felippes F. F., Schneeberger K., Dezulian T., Huson D. H. and Weigel D.
RNA (2008), 14(12) 2455-9.

Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4

Hanikenne M., Talke I. N., Haydon M. J., Lanz C., Nolte A., Motte P., Kroymann J., Weigel D. and Kramer U.
Nature (2008), 453(7193) 391-5.

Fixation, embedding, and sectioning of plant tissues

Weigel D. and Glazebrook J.
CSH Protoc (2008), 2008 pdb prot4941.

Gene silencing in plants using artificial microRNAs and other small RNAs

Ossowski S., Schwab R. and Weigel D.
Plant J (2008), 53(4) 674-90.

Genetic analysis of Arabidopsis mutants

Weigel D. and Glazebrook J.
CSH Protoc (2008), 2008 pdb top35.

Highly specific gene silencing by artificial miRNAs in rice

Warthmann N., Chen H., Ossowski S., Weigel D. and Herve P.
PLoS One (2008), 3(3) e1829.

Immunohistochemistry on sections of plant tissues using enzyme-coupled avidin-biotin complex

Weigel D. and Glazebrook J.
CSH Protoc (2008), 2008 pdb prot4945.

Next-generation genetics in plants

Nordborg M. and Weigel D.
Nature (2008), 456(7223) 720-3.

Reduced V-ATPase activity in the trans-Golgi network causes oxylipin-dependent hypocotyl growth Inhibition in Arabidopsis

Brux A., Liu T. Y., Krebs M., Stierhof Y. D., Lohmann J. U., Miersch O., Wasternack C. and Schumacher K.
Plant Cell (2008), 20(4) 1088-100.

Requirement of B2-type cyclin-dependent kinases for meristem integrity in Arabidopsis thaliana

Andersen S. U., Buechel S., Zhao Z., Ljung K., Novak O., Busch W., Schuster C. and Lohmann J. U.
Plant Cell (2008), 20(1) 88-100.

Sequencing of natural strains of Arabidopsis thaliana with short reads

Ossowski S., Schneeberger K., Clark R. M., Lanz C., Warthmann N. and Weigel D.
Genome Res (2008), 18(12) 2024-33.

Specific gene silencing by artificial MicroRNAs in Physcomitrella patens: an alternative to targeted gene knockouts

Khraiwesh B., Ossowski S., Weigel D., Reski R. and Frank W.
Plant Physiol (2008), 148(2) 684-93.

The Arabidopsis COP9 signalosome is essential for G2 phase progression and genomic stability

Dohmann E. M., Levesque M. P., De Veylder L., Reichardt I., Jurgens G., Schmid M. and Schwechheimer C.
Development (2008), 135(11) 2013-22.

The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana

Skirycz A., Radziejwoski A., Busch W., Hannah M. A., Czeszejko J., Kwasniewski M., Zanor M. I., Lohmann J. U., De Veylder L., Witt I. and Mueller-Roeber B.
Plant J (2008), 56(5) 779-92.

The impact of Arabidopsis on human health: diversifying our portfolio

Jones A. M., Chory J., Dangl J. L., Estelle M., Jacobsen S. E., Meyerowitz E. M., Nordborg M. and Weigel D.
Cell (2008), 133(6) 939-43.

The impact of shared ancestral variation on hybrid male lethality–a 16 codon indel in the Drosophila simulans Lhr gene

Nolte V., Weigel D. and Schlotterer C.
J Evol Biol (2008), 21(2) 551-5.

Transcript normalization and segmentation of tiling array data

Zeller G., Henz S. R., Laubinger S., Weigel D. and Ratsch G.
Pac Symp Biocomput (2008), 527-38.

2007

10 years of Current Opinion in Plant Biology 1997-2007

Weigel D. and Dangl J. L.
Curr Opin Plant Biol (2007), 10(6) 543-5.

Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux

Michniewicz M., Zago M. K., Abas L., Weijers D., Schweighofer A., Meskiene I., Heisler M. G., Ohno C., Zhang J., Huang F., Schwab R., Weigel D., Meyerowitz E. M., Luschnig C., Offringa R. and Friml J.
Cell (2007), 130(6) 1044-56.

Arabidopsis: a model genus for speciation

Bomblies K. and Weigel D.
Curr Opin Genet Dev (2007), 17(6) 500-4.

Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants

Bomblies K., Lempe J., Epple P., Warthmann N., Lanz C., Dangl J. L. and Weigel D.
PLoS Biol (2007), 5(9) e236.

Combinations of WOX activities regulate tissue proliferation during Arabidopsis embryonic development

Wu X., Chory J. and Weigel D.
Dev Biol (2007), 309(2) 306-16.

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

Clark R. M., Schweikert G., Toomajian C., Ossowski S., Zeller G., Shinn P., Warthmann N., Hu T. T., Fu G., Hinds D. A., Chen H., Frazer K. A., Huson D. H., Scholkopf B., Nordborg M., Ratsch G., Ecker J. R. and Weigel D.
Science (2007), 317(5836) 338-42.

Distinct expression patterns of natural antisense transcripts in Arabidopsis

Henz S. R., Cumbie J. S., Kasschau K. D., Lohmann J. U., Carrington J. C., Weigel D. and Schmid M.
Plant Physiol (2007), 144(3) 1247-55.

ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata

Dreyer C., Hoffmann M., Lanz C., Willing E. M., Riester M., Warthmann N., Sprecher A., Tripathi N., Henz S. R. and Weigel D.
BMC Genomics (2007), 8 269.

Export of FT protein from phloem companion cells is sufficient for floral induction in Arabidopsis

Mathieu J., Warthmann N., Kuttner F. and Schmid M.
Curr Biol (2007), 17(12) 1055-60.

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Borevitz J. O., Hazen S. P., Michael T. P., Morris G. P., Baxter I. R., Hu T. T., Chen H., Werner J. D., Nordborg M., Salt D. E., Kay S. A., Chory J., Weigel D., Jones J. D. and Ecker J. R.
Proc Natl Acad Sci U S A (2007), 104(29) 12057-62.

HUA2 caused natural variation in shoot morphology of A. thaliana

Wang Q., Sajja U., Rosloski S., Humphrey T., Kim M. C., Bomblies K., Weigel D. and Grbic V.
Curr Biol (2007), 17(17) 1513-9.

Hybrid necrosis: autoimmunity as a potential gene-flow barrier in plant species

Bomblies K. and Weigel D.
Nat Rev Genet (2007), 8(5) 382-93.

Move on up, it’s time for change–mobile signals controlling photoperiod-dependent flowering

Kobayashi Y. and Weigel D.
Genes Dev (2007), 21(19) 2371-84.

MSQT for choosing SNP assays from multiple DNA alignments

Warthmann N., Fitz J. and Weigel D.
Bioinformatics (2007), 23(20) 2784-7.

Opsin gene duplication and diversification in the guppy, a model for sexual selection

Hoffmann M., Tripathi N., Henz S. R., Lindholm A. K., Weigel D., Breden F. and Dreyer C.
Proc Biol Sci (2007), 274(1606) 33-42.

Profiling a plant: expression analysis in Arabidopsis

Busch W. and Lohmann J. U.
Curr Opin Plant Biol (2007), 10(2) 136-41.

Recombination and linkage disequilibrium in Arabidopsis thaliana

Kim S., Plagnol V., Hu T. T., Toomajian C., Clark R. M., Ossowski S., Ecker J. R., Weigel D. and Nordborg M.
Nat Genet (2007), 39(9) 1151-5.

Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319

Palatnik J. F., Wollmann H., Schommer C., Schwab R., Boisbouvier J., Rodriguez R., Warthmann N., Allen E., Dezulian T., Huson D., Carrington J. C. and Weigel D.
Dev Cell (2007), 13(1) 115-25.

Target mimicry provides a new mechanism for regulation of microRNA activity

Franco-Zorrilla J. M., Valli A., Todesco M., Mateos I., Puga M. I., Rubio-Somoza I., Leyva A., Weigel D., Garcia J. A. and Paz-Ares J.
Nat Genet (2007), 39(8) 1033-7.

The evolution of selfing in Arabidopsis thaliana

Tang C., Toomajian C., Sherman-Broyles S., Plagnol V., Guo Y. L., Hu T. T., Clark R. M., Nasrallah J. B., Weigel D. and Nordborg M.
Science (2007), 317(5841) 1070-2.

2006

A divergent external loop confers antagonistic activity on floral regulators FT and TFL1

Ahn J. H., Miller D., Winter V. J., Banfield M. J., Lee J. H., Yoo S. Y., Henz S. R., Brady R. L. and Weigel D.
EMBO J (2006), 25(3) 605-14.

A tiny helper lightens the maternal load

Weigel D. and Izaurralde E.
Cell (2006), 124(6) 1117-8.

CrossLink: visualization and exploration of sequence relationships between (micro) RNAs

Dezulian T., Schaefer M., Wiese R., Weigel D. and Huson D. H.
Nucleic Acids Res (2006), 34(Web Server issue) W400-4.

EMS Mutagenesis of Arabidopsis Seed

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(5).

Evolutionary divergence of LFY function in the mustards Arabidopsis thaliana and Leavenworthia crassa

Sliwinski M. K., White M. A., Maizel A., Weigel D. and Baum D. A.
Plant Mol Biol (2006), 62(1-2) 279-89.

Forward Genetics in Arabidopsis: Finding Mutations that Cause Particular Phenotypes

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(5).

Glufosinate ammonium selection of transformed Arabidopsis

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(7).

Highly specific gene silencing by artificial microRNAs in Arabidopsis

Schwab R., Ossowski S., Riester M., Warthmann N. and Weigel D.
Plant Cell (2006), 18(5) 1121-33.

Identification of plant microRNA homologs

Dezulian T., Remmert M., Palatnik J. F., Weigel D. and Huson D. H.
Bioinformatics (2006), 22(3) 359-60.

In planta transformation of Arabidopsis

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(7).

In vitro culture of embryos of the guppy, Poecilia reticulata

Martyn U., Weigel D. and Dreyer C.
Dev Dyn (2006), 235(3) 617-22.

Kanamycin selection of transformed Arabidopsis

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(7).

NUBBIN and JAGGED define stamen and carpel shape in Arabidopsis

Dinneny J. R., Weigel D. and Yanofsky M. F.
Development (2006), 133(9) 1645-55.

Potent induction of Arabidopsis thaliana flowering by elevated growth temperature

Balasubramanian S., Sureshkumar S., Lempe J. and Weigel D.
PLoS Genet (2006), 2(7) e106.

Root transformation of Arabidopsis

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(7).

Screening DNA Pools for T-DNA Insertions in Arabidopsis Genes

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(5).

Setting up Arabidopsis crosses

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(5).

Temperature Induced Flowering in Arabidopsis thaliana

Balasubramanian S. and Weigel D.
Plant Signal Behav (2006), 1(5) 227-8.

The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana

Balasubramanian S., Sureshkumar S., Agrawal M., Michael T. P., Wessinger C., Maloof J. N., Clark R., Warthmann N., Chory J. and Weigel D.
Nat Genet (2006), 38(6) 711-5.

Transformation of agrobacterium using electroporation

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(7).

Transformation of agrobacterium using the freeze-thaw method

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(7).

Vectors and agrobacterium hosts for Arabidopsis transformation

Weigel D. and Glazebrook J.
CSH Protoc (2006), 2006(7).

Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis

Levesque M. P., Vernoux T., Busch W., Cui H., Wang J. Y., Blilou I., Hassan H., Nakajima K., Matsumoto N., Lohmann J. U., Scheres B. and Benfey P. N.
PLoS Biol (2006), 4(5) e143.

2005

A gene expression map of Arabidopsis thaliana development

Schmid M., Davison T. S., Henz S. R., Pape U. J., Demar M., Vingron M., Scholkopf B., Weigel D. and Lohmann J. U.
Nat Genet (2005), 37(5) 501-6.

A genetic framework for fruit patterning in Arabidopsis thaliana

Dinneny J. R., Weigel D. and Yanofsky M. F.
Development (2005), 132(21) 4687-96.

Comprehensive interaction map of the Arabidopsis MADS Box transcription factors

de Folter S., Immink R. G., Kieffer M., Parenicova L., Henz S. R., Weigel D., Busscher M., Kooiker M., Colombo L., Kater M. M., Davies B. and Angenent G. C.
Plant Cell (2005), 17(5) 1424-33.

Conservation and divergence of FCA function between Arabidopsis and rice

Lee J. H., Cho Y. S., Yoon H. S., Suh M. C., Moon J., Lee I., Weigel D., Yun C. H. and Kim J. K.
Plant Mol Biol (2005), 58(6) 823-38.

Diversity of flowering responses in wild Arabidopsis thaliana strains

Lempe J., Balasubramanian S., Sureshkumar S., Singh A., Schmid M. and Weigel D.
PLoS Genet (2005), 1(1) 109-18.

FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions

Werner J. D., Borevitz J. O., Uhlenhaut N. H., Ecker J. R., Chory J. and Weigel D.
Genetics (2005), 170(3) 1197-207.

Genetics: hotheaded healer

Weigel D. and Jurgens G.
Nature (2005), 434(7032) 443.

Integration of spatial and temporal information during floral induction in Arabidopsis

Wigge P. A., Kim M. C., Jaeger K. E., Busch W., Schmid M., Lohmann J. U. and Weigel D.
Science (2005), 309(5737) 1056-9.

Natural variation in Arabidopsis. How do we find the causal genes?

Weigel D. and Nordborg M.
Plant Physiol (2005), 138(2) 567-8.

Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation

Werner J. D., Borevitz J. O., Warthmann N., Trainer G. T., Ecker J. R., Chory J. and Weigel D.
Proc Natl Acad Sci U S A (2005), 102(7) 2460-5.

Requirement of homeobox gene STIMPY/WOX9 for Arabidopsis meristem growth and maintenance

Wu X., Dabi T. and Weigel D.
Curr Biol (2005), 15(5) 436-40.

Specific effects of microRNAs on the plant transcriptome

Schwab R., Palatnik J. F., Riester M., Schommer C., Schmid M. and Weigel D.
Dev Cell (2005), 8(4) 517-27.

The 35S promoter used in a selectable marker gene of a plant transformation vector affects the expression of the transgene

Yoo S. Y., Bomblies K., Yoo S. K., Yang J. W., Choi M. S., Lee J. S., Weigel D. and Ahn J. H.
Planta (2005), 221(4) 523-30.

The floral regulator LEAFY evolves by substitutions in the DNA binding domain

Maizel A., Busch M. A., Tanahashi T., Perkovic J., Kato M., Hasebe M. and Weigel D.
Science (2005), 308(5719) 260-3.

WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulators

Leibfried A., To J. P., Busch W., Stehling S., Kehle A., Demar M., Kieber J. J. and Lohmann J. U.
Nature (2005), 438(7071) 1172-5.

2004

Acceleration of flowering by overexpression of MFT (MOTHER OF FT AND TFL1)

Yoo S. Y., Kardailsky I., Lee J. S., Weigel D. and Ahn J. H.
Mol Cells (2004), 17(1) 95-101.

From tough nuts to touch-me-nots

Lohmann J. U. and Weigel D.
Cell (2004), 116(6) 763-4.

Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci

Hagenblad J., Tang C., Molitor J., Werner J., Zhao K., Zheng H., Marjoram P., Weigel D. and Nordborg M.
Genetics (2004), 168(3) 1627-38.

Temporally and spatially controlled induction of gene expression in Arabidopsis thaliana

Maizel A. and Weigel D.
Plant J (2004), 38(1) 164-71.

The role of JAGGED in shaping lateral organs

Dinneny J. R., Yadegari R., Fischer R. L., Yanofsky M. F. and Weigel D.
Development (2004), 131(5) 1101-10.

2003

A thermosensory pathway controlling flowering time in Arabidopsis thaliana

Blazquez M. A., Ahn J. H. and Weigel D.
Nat Genet (2003), 33(2) 168-71.

Control of leaf morphogenesis by microRNAs

Palatnik J. F., Allen E., Wu X., Schommer C., Schwab R., Carrington J. C. and Weigel D.
Nature (2003), 425(6955) 257-63.

Dissection of floral induction pathways using global expression analysis

Schmid M., Uhlenhaut N. H., Godard F., Demar M., Bressan R., Weigel D. and Lohmann J. U.
Development (2003), 130(24) 6001-12.

Genome-wide insertional mutagenesis of Arabidopsis thaliana

Alonso J. M., Stepanova A. N., Leisse T. J., Kim C. J., Chen H., Shinn P., Stevenson D. K., Zimmerman J., Barajas P., Cheuk R., Gadrinab C., Heller C., Jeske A., Koesema E., Meyers C. C., Parker H., Prednis L., Ansari Y., Choy N., Deen H., Geralt M., Hazari N., Hom E., Karnes M., Mulholland C., Ndubaku R., Schmidt I., Guzman P., Aguilar-Henonin L., Schmid M., Weigel D., Carter D. E., Marchand T., Risseeuw E., Brogden D., Zeko A., Crosby W. L., Berry C. C. and Ecker J. R.
Science (2003), 301(5633) 653-7.

Large-scale identification of single-feature polymorphisms in complex genomes

Borevitz J. O., Liang D., Plouffe D., Chang H. S., Zhu T., Weigel D., Berry C. C., Winzeler E. and Chory J.
Genome Res (2003), 13(3) 513-23.

Modes of intercellular transcription factor movement in the Arabidopsis apex

Wu X., Dinneny J. R., Crawford K. M., Rhee Y., Citovsky V., Zambryski P. C. and Weigel D.
Development (2003), 130(16) 3735-45.

Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing

Hong R. L., Hamaguchi L., Busch M. A. and Weigel D.
Plant Cell (2003), 15(6) 1296-309.

The F-box-containing protein UFO and AGAMOUS participate in antagonistic pathways governing early petal development in Arabidopsis

Durfee T., Roe J. L., Sessions R. A., Inouye C., Serikawa K., Feldmann K. A., Weigel D. and Zambryski P. C.
Proc Natl Acad Sci U S A (2003), 100(14) 8571-6.

2002

Building beauty: the genetic control of floral patterning

Lohmann J. U. and Weigel D.
Dev Cell (2002), 2(2) 135-42.

Ectopic expression of SUPERMAN suppresses development of petals and stamens

Yun J. Y., Weigel D. and Lee I.
Plant Cell Physiol (2002), 43(1) 52-7.

High-energy fractures of the tibial plateau. Knee function after longer follow-up

Weigel D. P. and Marsh J. L.
J Bone Joint Surg Am (2002), 84-A(9) 1541-51.

Independent control of gibberellin biosynthesis and flowering time by the circadian clock in Arabidopsis

Blazquez M. A., Trenor M. and Weigel D.
Plant Physiol (2002), 130(4) 1770-5.

Interaction of LEAFY, AGAMOUS and TERMINAL FLOWER1 in maintaining floral meristem identity in Arabidopsis

Parcy F., Bomblies K. and Weigel D.
Development (2002), 129(10) 2519-27.

Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana

Borevitz J. O., Maloof J. N., Lutes J., Dabi T., Redfern J. L., Trainer G. T., Werner J. D., Asami T., Berry C. C., Weigel D. and Chory J.
Genetics (2002), 160(2) 683-96.

Signaling in plants by intercellular RNA and protein movement

Wu X., Weigel D. and Wigge P. A.
Genes Dev (2002), 16(2) 151-8.

Stem cells that make stems

Weigel D. and Jurgens G.
Nature (2002), 415(6873) 751-4.

The extent of linkage disequilibrium in Arabidopsis thaliana

Nordborg M., Borevitz J. O., Bergelson J., Berry C. C., Chory J., Hagenblad J., Kreitman M., Maloof J. N., Noyes T., Oefner P. J., Stahl E. A. and Weigel D.
Nat Genet (2002), 30(2) 190-3.

2001

A molecular link between stem cell regulation and floral patterning in Arabidopsis

Lohmann J. U., Hong R. L., Hobe M., Busch M. A., Parcy F., Simon R. and Weigel D.
Cell (2001), 105(6) 793-803.

A role for flavin monooxygenase-like enzymes in auxin biosynthesis

Zhao Y., Christensen S. K., Fankhauser C., Cashman J. R., Cohen J. D., Weigel D. and Chory J.
Science (2001), 291(5502) 306-9.

Arabidopsis genome: life without notch

Wigge P. A. and Weigel D.
Curr Biol (2001), 11(3) R112-4.

Evolution of floral meristem identity genes. Analysis of Lolium temulentum genes related to APETALA1 and LEAFY of Arabidopsis

Gocal G. F., King R. W., Blundell C. A., Schwartz O. M., Andersen C. H. and Weigel D.
Plant Physiol (2001), 125(4) 1788-801.

Functional divergence of the TFL1-like gene family in Arabidopsis revealed by characterization of a novel homologue

Mimida N., Goto K., Kobayashi Y., Araki T., Ahn J. H., Weigel D., Murata M., Motoyoshi F. and Sakamoto W.
Genes Cells (2001), 6(4) 327-36.

GAMYB-like genes, flowering, and gibberellin signaling in Arabidopsis

Gocal G. F., Sheldon C. C., Gubler F., Moritz T., Bagnall D. J., MacMillan C. P., Li S. F., Parish R. W., Dennis E. S., Weigel D. and King R. W.
Plant Physiol (2001), 127(4) 1682-93.

Natural variation in light sensitivity of Arabidopsis

Maloof J. N., Borevitz J. O., Dabi T., Lutes J., Nehring R. B., Redfern J. L., Trainer G. T., Wilson J. M., Asami T., Berry C. C., Weigel D. and Chory J.
Nat Genet (2001), 29(4) 441-6.

NFL1, a Nicotiana tabacum LEAFY-like gene, controls meristem initiation and floral structure

Ahearn K. P., Johnson H. A., Weigel D. and Wagner D. R.
Plant Cell Physiol (2001), 42(10) 1130-9.

Plant development: from cell fate to organ formation

Bisseling T. and Weigel D.
Plant Cell (2001), 13(2) 221-7.

Transcriptional networks controlling plant development

Benfey P. N. and Weigel D.
Plant Physiol (2001), 125(1) 109-11.

2000

Activation tagging in Arabidopsis

Weigel D., Ahn J. H., Blazquez M. A., Borevitz J. O., Christensen S. K., Fankhauser C., Ferrandiz C., Kardailsky I., Malancharuvil E. J., Neff M. M., Nguyen J. T., Sato S., Wang Z. Y., Xia Y., Dixon R. A., Harrison M. J., Lamb C. J., Yanofsky M. F. and Chory J.
Plant Physiol (2000), 122(4) 1003-13.

Cell-cell signaling and movement by the floral transcription factors LEAFY and APETALA1

Sessions A., Yanofsky M. F. and Weigel D.
Science (2000), 289(5480) 779-82.

Integration of floral inductive signals in Arabidopsis

Blazquez M. A. and Weigel D.
Nature (2000), 404(6780) 889-92.

National Science Foundation-Sponsored Workshop Report: “The 2010 Project” functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them

Chory J., Ecker J. R., Briggs S., Caboche M., Coruzzi G. M., Cook D., Dangl J., Grant S., Guerinot M. L., Henikoff S., Martienssen R., Okada K., Raikhel N. V., Somerville C. R. and Weigel D.
Plant Physiol (2000), 123(2) 423-6.

Natural variation in phytochrome signaling

Maloof J. N., Borevitz J. O., Weigel D. and Chory J.
Semin Cell Dev Biol (2000), 11(6) 523-30.

Regulation of auxin response by the protein kinase PINOID

Christensen S. K., Dagenais N., Chory J. and Weigel D.
Cell (2000), 100(4) 469-78.

Transformation of Medicago truncatula via infiltration of seedlings or flowering plants with Agrobacterium

Trieu A. T., Burleigh S. H., Kardailsky I. V., Maldonado-Mendoza I. E., Versaw W. K., Blaylock L. A., Shin H., Chiou T. J., Katagi H., Dewbre G. R., Weigel D. and Harrison M. J.
Plant J (2000), 22(6) 531-41.

Transformation of rice with the Arabidopsis floral regulator LEAFY causes early heading

He Z., Zhu Q., Dabi T., Li D., Weigel D. and Lamb C.
Transgenic Res (2000), 9(3) 223-7.

1999

Activation of a floral homeotic gene in Arabidopsis

Busch M. A., Bomblies K. and Weigel D.
Science (1999), 285(5427) 585-7.

Activation tagging of the floral inducer FT

Kardailsky I., Shukla V. K., Ahn J. H., Dagenais N., Christensen S. K., Nguyen J. T., Chory J., Harrison M. J. and Weigel D.
Science (1999), 286(5446) 1962-5.

Independent regulation of flowering by phytochrome B and gibberellins in Arabidopsis

Blazquez M. A. and Weigel D.
Plant Physiol (1999), 120(4) 1025-32.

Redundant enhancers mediate transcriptional repression of AGAMOUS by APETALA2

Bomblies K., Dagenais N. and Weigel D.
Dev Biol (1999), 216(1) 260-4.

The Arabidopsis flowering-time gene LUMINIDEPENDENS is expressed primarily in regions of cell proliferation and encodes a nuclear protein that regulates LEAFY expression

Aukerman M. J., Lee I., Weigel D. and Amasino R. M.
Plant J (1999), 18(2) 195-203.

The Arabidopsis thaliana MERISTEM LAYER 1 promoter specifies epidermal expression in meristems and young primordia

Sessions A., Weigel D. and Yanofsky M. F.
Plant J (1999), 20(2) 259-63.

1998

A genetic framework for floral patterning

Parcy F., Nilsson O., Busch M. A., Lee I. and Weigel D.
Nature (1998), 395(6702) 561-6.

Flowering-time genes modulate the response to LEAFY activity

Nilsson O., Lee I., Blazquez M. A. and Weigel D.
Genetics (1998), 150(1) 403-10.

From floral induction to floral shape

Weigel D.
Curr Opin Plant Biol (1998), 1(1) 55-9.

Genetic ablation of flowers in transgenic Arabidopsis

Nilsson O., Wu E., Wolfe D. S. and Weigel D.
Plant J (1998), 15(6) 799-804.

Gibberellins promote flowering of arabidopsis by activating the LEAFY promoter

Blazquez M. A., Green R., Nilsson O., Sussman M. R. and Weigel D.
Plant Cell (1998), 10(5) 791-800.

Patterning the floral meristem

Sessions A., Yanofsky M. F. and Weigel D.
Semin Cell Dev Biol (1998), 9(2) 221-6.

Plant development: the making of a leaf

Christensen S. and Weigel D.
Curr Biol (1998), 8(18) R643-5.

1997

A LEAFY co-regulator encoded by UNUSUAL FLORAL ORGANS

Lee I., Wolfe D. S., Nilsson O. and Weigel D.
Curr Biol (1997), 7(2) 95-104.

Floral determination and expression of floral regulatory genes in Arabidopsis

Hempel F. D., Weigel D., Mandel M. A., Ditta G., Zambryski P. C., Feldman L. J. and Yanofsky M. F.
Development (1997), 124(19) 3845-53.

Flower development: repressing reproduction

Weigel D.
Curr Biol (1997), 7(6) R373-5.

LEAFY expression and flower initiation in Arabidopsis

Blazquez M. A., Soowal L. N., Lee I. and Weigel D.
Development (1997), 124(19) 3835-44.

Modulating the timing of flowering

Nilsson O. and Weigel D.
Curr Opin Biotechnol (1997), 8(2) 195-9.

1996

Cell-cell interactions: taking cues from the neighbors

Weigel D. and Doerner P.
Curr Biol (1996), 6(1) 10-2.

Sizing Up the Floral Meristem

Weigel D. and Clark S. E.
Plant Physiol (1996), 112(1) 5-10.

1995

A developmental switch sufficient for flower initiation in diverse plants

Weigel D. and Nilsson O.
Nature (1995), 377(6549) 495-500.

The APETALA2 domain is related to a novel type of DNA binding domain

Weigel D.
Plant Cell (1995), 7(4) 388-9.

The genetics of flower development: from floral induction to ovule morphogenesis

Weigel D.
Annu Rev Genet (1995), 29 19-39.

1994

Plant development. The SECrets of Arabidopsis embryogenesis

Weigel D.
Curr Biol (1994), 4(11) 1040-2.

Sp1/egr-like zinc-finger protein required for endoderm specification and germ-layer formation in Drosophila

Bronner G., Chu-LaGraff Q., Doe C. Q., Cohen B., Weigel D., Taubert H. and Jackle H.
Nature (1994), 369(6482) 664-8.

The ABCs of floral homeotic genes

Weigel D. and Meyerowitz E. M.
Cell (1994), 78(2) 203-9.

1993

Activation of floral homeotic genes in Arabidopsis

Weigel D. and Meyerowitz E. M.
Science (1993), 261(5129) 1723-6.

Patterning the Arabidopsis embryo

Weigel D.
Curr Biol (1993), 3(7) 443-5.

1992

LEAFY controls floral meristem identity in Arabidopsis

Weigel D., Alvarez J., Smyth D. R., Yanofsky M. F. and Meyerowitz E. M.
Cell (1992), 69(5) 843-59.

Organogenesis in Drosophila melanogaster: embryonic salivary gland determination is controlled by homeotic and dorsoventral patterning genes

Panzer S., Weigel D. and Beckendorf S. K.
Development (1992), 114(1) 49-57.

SUPERMAN, a regulator of floral homeotic genes in Arabidopsis

Bowman J. L., Sakai H., Jack T., Weigel D., Mayer U. and Meyerowitz E. M.
Development (1992), 114(3) 599-615.

1991

A genetic and molecular model for flower development in Arabidopsis thaliana

Meyerowitz E. M., Bowman J. L., Brockman L. L., Drews G. N., Jack T., Sieburth L. E. and Weigel D.
Dev Suppl (1991), 1 157-67.

Floral patterning

Drews G. N., Weigel D. and Meyerowitz E. M.
Curr Opin Genet Dev (1991), 1(2) 174-8.

1990

Regulation of Kruppel expression in the anlage of the Malpighian tubules in the Drosophila embryo

Gaul U. and Weigel D.
Mech Dev (1990), 33(1) 57-67.

Regulatory elements controlling expression of the Drosophila homeotic gene fork head

Weigel D., Seifert E., Reuter D. and Jackle H.
EMBO J (1990), 9(4) 1199-207.

The fork head domain: a novel DNA binding motif of eukaryotic transcription factors?

Weigel D. and Jackle H.
Cell (1990), 63(3) 455-6.

Two gap genes mediate maternal terminal pattern information in Drosophila

Weigel D., Jurgens G., Klingler M. and Jackle H.
Science (1990), 248(4954) 495-8.

1988

Functional interactions of neurogenic genes of Drosophila melanogaster

de-la-Concha A., Dietrich U., Weigel D. and Campos-Ortega J. A.
Genetics (1988), 118(3) 499-508.

1987

EGF homologous sequences encoded in the genome of Drosophila melanogaster, and their relation to neurogenic genes

Knust E., Dietrich U., Tepass U., Bremer K. A., Weigel D., Vassin H. and Campos-Ortega J. A.

EMBO J (1987), 6(3) 761-6.

The Drosophila homolog of the mouse mammary oncogene int-1 is identical to the segment polarity gene wingless

Rijsewijk F., Schuermann M., Wagenaar E., Parren P., Weigel D. and Nusse R.

Cell (1987), 50(4) 649-57.