The genetics of plant metabolism

Generalized Linear Models

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Generalized Linear Models

McCullagh, P., & Nelder, J. A. (1989) · doi:10.1007/978-1-4899-3242-6 · Cited by 16,836 · see citing works

Statistical significance for genomewide studies

Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692 · see citing works

Generalized Linear Models

Schuenemeyer, J. H., McCullagh, P. J., & Nelder, J. A. (1992) · Technometrics · doi:10.2307/1269238 · Cited by 2,702 · see citing works

Genetics of gene expression surveyed in maize, mouse and man

Schadt, E., Monks, S. A., Drake, T., Lusis, A., Che, N., Colinayo, V. V., Ruff, T., Milligan, S. B., Lamb, J., Cavet, G., et al. (2003) · Nature · doi:10.1038/nature01434 · Cited by 1,594 · see citing works

Construction of integrated genetic linkage maps by means of a new computer package: Join Map

Stam, P. (1993) · The Plant Journal · doi:10.1111/j.1365-313x.1993.00739.x · Cited by 1,394 · see citing works

Genetic Dissection of Transcriptional Regulation in Budding Yeast

Brem, R. B., Yvert, G., Clinton, R., & Kruglyak, L. (2002) · Science · doi:10.1126/science.1069516 · Cited by 1,392 · see citing works

An integrative genomics approach to infer causal associations between gene expression and disease

Schadt, E. E., Lamb, J., Yang, X., Zhu, J., Edwards, S., GuhaThakurta, D., Sieberts, S. K., Monks, S., Reitman, M., Zhang, C., et al. (2005) · Nature Genetics · doi:10.1038/ng1589 · Cited by 1,043 · see citing works

Genetical genomics: the added value from segregation

Jansen, R. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02310-1 · Cited by 1,010 · see citing works

Interval mapping of multiple quantitative trait loci.

Jansen, R. C. (1993) · Genetics · doi:10.1093/genetics/135.1.205 · Cited by 850 · see citing works

NATURALLY OCCURRING GENETIC VARIATION IN ARABIDOPSIS THALIANA

Koornneef, M., Alonso‐Blanco, C., & Vreugdenhil, D. (2004) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.55.031903.141605 · Cited by 736 · see citing works

Plant breeding: importance of plant secondary metabolites for protection against pathogens and herbivores

Wink, M. (1988) · Theoretical and Applied Genetics · doi:10.1007/bf00303957 · Cited by 677 · see citing works

Genetic Control of Natural Variation in Arabidopsis Glucosinolate Accumulation

Kliebenstein, D. J., Kroymann, J., Brown, P., et al. (2001) · PLANT PHYSIOLOGY · doi:10.1104/pp.126.2.811 · Cited by 672 · see citing works

Phylogenetic Analysis of the UDP-glycosyltransferase Multigene Family of Arabidopsis thaliana

Li, Y., Baldauf, S. L., Lim, E., et al. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m007447200 · Cited by 558 · see citing works

Discovery of meaningful associations in genomic data using partial correlation coefficients

de la Fuente, A., Bing, N., Hoeschele, I., & Mendes, P. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth445 · Cited by 552 · see citing works

Transcriptome and Selected Metabolite Analyses Reveal Multiple Points of Ethylene Control during Tomato Fruit Development

Alba, R., Payton, P., Fei, Z., McQuinn, R. P., Debbie, P., Martin, G. B., Tanksley, S. D., & Giovannoni, J. J. (2005) · The Plant Cell · doi:10.1105/tpc.105.036053 · Cited by 534 · see citing works

A Novel Approach for Nontargeted Data Analysis for Metabolomics. Large-Scale Profiling of Tomato Fruit Volatiles

Tikunov, Y. M., Lommen, A., Vos, C. H. R. D., Verhoeven, H. A., Bino, R. J., Hall, R. D., & Bovy, A. G. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.105.068130 · Cited by 511 · see citing works

Gene Duplication in the Diversification of Secondary Metabolism: Tandem 2-Oxoglutarate–Dependent Dioxygenases Control Glucosinolate Biosynthesis in Arabidopsis

Kliebenstein, D. J., Lambrix, V. M., Reichelt, M., et al. (2001) · The Plant Cell · doi:10.1105/tpc.13.3.681 · Cited by 485 · see citing works

Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population

Alonso‐Blanco, C., Peeters, A. J. M., Koornneef, M., Lister, C., Dean, C., van den Bosch, N., Pot, J., & Kuiper, M. T. R. (1998) · The Plant Journal · doi:10.1046/j.1365-313x.1998.00115.x · Cited by 368 · see citing works

The secondary metabolism of Arabidopsis thaliana: growing like a weed

D’Auria, J. C., & Gershenzon, J. (2005) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2005.03.012 · Cited by 309 · see citing works

Arabidopsis glycosyltransferases as biocatalysts in fermentation for regioselective synthesis of diverse quercetin glucosides

Lim, E., Ashford, D. A., Hou, B., et al. (2004) · Biotechnology and Bioengineering · doi:10.1002/bit.20154 · Cited by 278 · see citing works

Mutants of Arabidopsis thaliana with pleiotropic effects on the expression of the gene for β‐amylase and on the accumulation of anthocyanin that are inducible by sugars

Mita, S., Murano, N., Akaike, M., & Nakamura, K. (1997) · The Plant Journal · doi:10.1046/j.1365-313x.1997.11040841.x · Cited by 261 · see citing works

A Gene Controlling Variation in Arabidopsis Glucosinolate Composition Is Part of the Methionine Chain Elongation Pathway

Kroymann, J., Textor, S., Tokuhisa, J. G., et al. (2001) · PLANT PHYSIOLOGY · doi:10.1104/pp.010416 · Cited by 259 · see citing works

Benzoic acid glucosinolate esters and other glucosinolates from Arabidopsis thaliana

Reichelt, M., Brown, P. D., Schneider, B., et al. (2002) · Phytochemistry · doi:10.1016/s0031-9422(02)00014-6 · Cited by 248 · see citing works

Comparative Quantitative Trait Loci Mapping of Aliphatic, Indolic and Benzylic Glucosinolate Production in Arabidopsis thaliana Leaves and Seeds

Kliebenstein, D. J., Gershenzon, J., & Mitchell‐Olds, T. (2001) · Genetics · doi:10.1093/genetics/159.1.359 · Cited by 247 · see citing works

An integrative genomics approach to the reconstruction of gene networks in segregating populations

Zhu, J., Lum, P. Y., Lamb, J., GuhaThakurta, D., Edwards, S. W., Thieringer, R., Berger, J. P., Wu, M. S., Thompson, J., Sachs, A. B., et al. (2004) · Cytogenetic and Genome Research · doi:10.1159/000078209 · Cited by 221 · see citing works

Genetic Analysis of Seed-Soluble Oligosaccharides in Relation to Seed Storability of Arabidopsis

Bentsink, L., Alonso‐Blanco, C., Vreugdenhil, D., et al. (2000) · PLANT PHYSIOLOGY · doi:10.1104/pp.124.4.1595 · Cited by 220 · see citing works

Integrating genomics and metabolomics for engineering plant metabolic pathways

Oksman‐Caldentey, K., & Saito, K. (2005) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2005.02.007 · Cited by 208 · see citing works

Quantitative Trait Loci Analysis of Nitrogen Use Efficiency in Arabidopsis

Loudet, O., Chaillou, S., Mérigout, P., Talbotec, J., & Daniel‐Vedele, F. (2003) · PLANT PHYSIOLOGY · doi:10.1104/pp.102.010785 · Cited by 204 · see citing works

Studying complex biological systems using multifactorial perturbation

Jansen, R. C. (2003) · Nature Reviews Genetics · doi:10.1038/nrg996 · Cited by 187 · see citing works

Geographic and evolutionary diversification of glucosinolates among near relatives of Arabidopsis thaliana (Brassicaceae)

Windsor, A. J., Reichelt, M., Figuth, A., et al. (2005) · Phytochemistry · doi:10.1016/j.phytochem.2005.04.016 · Cited by 155 · see citing works

Genetic Regulation of Gene Expression During Shoot Development in Arabidopsis

DeCook, R. R., Lall, S., Nettleton, D. S., et al. (2005) · Genetics · doi:10.1534/genetics.105.042275 · Cited by 150 · see citing works

Engineering of plant natural product pathways

Dixon, R. A. (2005) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2005.03.008 · Cited by 146 · see citing works

Genetical genomics in humans and model organisms

de Koning, D., & Haley, C. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.05.004 · Cited by 138 · see citing works

Mapping Quantitative Trait Loci in the Case of a Spike in the Phenotype Distribution

Broman, K. W. (2003) · Genetics · doi:10.1093/genetics/163.3.1169 · Cited by 134 · see citing works

Genetic Control of Storage Oil Synthesis in Seeds of Arabidopsis

Hobbs, D. H., Flintham, J. E., & Hills, M. J. (2004) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.049486 · Cited by 114 · see citing works

Genetical Genomics Analysis of a Yeast Segregant Population for Transcription Network Inference

Bing, N., & Hoeschele, I. (2005) · Genetics · doi:10.1534/genetics.105.041103 · Cited by 107 · see citing works

The Molecular Basis of Quantitative Genetic Variation in Central and Secondary Metabolism in Arabidopsis

Mitchell‐Olds, T., & Pedersen, D. (1998) · Genetics · doi:10.1093/genetics/149.2.739 · Cited by 88 · see citing works

A non-directed approach to the differential analysis of multiple LC–MS-derived metabolic profiles

Vorst, O., Vos, C. H. R. D., Lommen, A., Staps, R. V., Visser, R. G. F., Bino, R. J., & Hall, R. D. (2005) · Metabolomics · doi:10.1007/s11306-005-4432-7 · Cited by 82 · see citing works

Quantitative Trait Loci Associated With Adventitious Shoot Formation in Tissue Culture and the Program of Shoot Development in Arabidopsis

Lall, S., Nettleton, D. S., DeCook, R. R., Che, P., & Howell, S. H. (2004) · Genetics · doi:10.1534/genetics.103.025213 · Cited by 37 · see citing works

Preventing leaf identity theft with hormones

Lumba, S., & McCourt, P. (2005) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2005.07.015 · Cited by 16 · see citing works

Growing like a weed

Johnston, L. (1997) · Cited by 1 · see citing works

Heritability in the genomics era — concepts and misconceptions

Visscher, P. M., Hill, W. G., & Wray, N. R. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2322 · Cited by 1,921 · see citing works

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids

Fu, J., Bonder, M. J., Cenit, M. C., Tigchelaar, E. F., Maatman, A., Dekens, J. A. M., Brandsma, E., Marczynska, J., Imhann, F., Weersma, R. K., et al. (2015) · Circulation Research · doi:10.1161/circresaha.115.306807 · Cited by 748 · see citing works

Data processing for mass spectrometry-based metabolomics

Katajamaa, M., & Orešič, M. (2007) · Journal of Chromatography A · doi:10.1016/j.chroma.2007.04.021 · Cited by 616 · see citing works

Metabolomics-assisted breeding: a viable option for crop improvement?

Fernie, A. R., & Schauer, N. (2009) · Trends in Genetics · doi:10.1016/j.tig.2008.10.010 · Cited by 550 · see citing works

Decoding genes with coexpression networks and metabolomics – ‘majority report by precogs’

Saito, K., Hirai, M. Y., & Yonekura-Sakakibara, K. (2008) · Trends in Plant Science · doi:10.1016/j.tplants.2007.10.006 · Cited by 327 · see citing works

Metabolite annotations based on the integration of mass spectral information

Iijima, Y., Nakamura, Y., Ogata, Y., Tanaka, K., Sakurai, N., Suda, K., Suzuki, T., Suzuki, H., Okazaki, K., Kitayama, M., et al. (2008) · The Plant Journal · doi:10.1111/j.1365-313x.2008.03434.x · Cited by 283 · see citing works

System-wide molecular evidence for phenotypic buffering in Arabidopsis

Fu, J., Keurentjes, J. J. B., Bouwmeester, H., America, T., Verstappen, F. W. A., Ward, J. L., Beale, M. H., de Vos, R. C. H., Dijkstra, M., Scheltema, R. A., et al. (2009) · Nature Genetics · doi:10.1038/ng.308 · Cited by 265 · see citing works

Natural variation for seed dormancy in Arabidopsis is regulated by additive genetic and molecular pathways

Bentsink, L., Hanson, J., Hanhart, C. J., Blankestijn-de Vries, H., Coltrane, C., Keizer, P., El-Lithy, M., Alonso-Blanco, C., de Andrés, M. T., Reymond, M., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000410107 · Cited by 209 · see citing works

Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour ’rules’

Draper, J., Enot, D. P., Parker, D., Beckmann, M., Snowdon, S., Lin, W., & Zubair, H. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-227 · Cited by 169 · see citing works

Genetical metabolomics: closing in on phenotypes

Keurentjes, J. J. (2009) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2008.12.003 · Cited by 139 · see citing works

Integration of multi-omics data for prediction of phenotypic traits using random forest

Acharjee, A., Kloosterman, B., Visser, R. G. F., & Maliepaard, C. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1043-4 · Cited by 109 · see citing works

Editor’s Choice: Evaluating the Potential for Adverse Interactions within Genetically Engineered Breeding Stacks

Steiner, H.-Y., Halpin, C., Jez, J. M., Kough, J., Parrott, W., Underhill, L., Weber, N., & Hannah, L. C. (2013) · Plant Physiology · doi:10.1104/pp.112.209817 · Cited by 46 · see citing works

Metabolism of the neuroleptic agent zetidoline in the rat and the dog.

Assandri, A., Perazzi, A., Fontanella, L., et al. (1984) · Drug Metabolism and Disposition · doi:10.1016/s0090-9556(25)07775-x · Cited by 4 · see citing works

Safety testing of metabolites: Expectations and outcomes.

Pang, K. (2009) · Chemico-Biological Interactions · doi:10.1016/j.cbi.2008.09.013 · Cited by 37 · see citing works

Metabolism of prostaglandin E1in dog kidneys

Nakano, J. (1970) · British Journal of Pharmacology · doi:10.1111/j.1476-5381.1970.tb09924.x · Cited by 26 · see citing works

Drug metabolite concentration‐time profiles: influence of route of drug administration.

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The effects of active metabolites on parameter estimation in linear mixed effect models of concentration–QT analyses

Bonate, P. L. (2013) · Journal of Pharmacokinetics and Pharmacodynamics · doi:10.1007/s10928-012-9292-y · Cited by 11 · see citing works