Genotype–phenotype modeling considering intermediate level of biological variation: a case study involving sensory traits, metabolites and QTLs in ripe tomatoes

A New Method to Infer Causal Phenotype Networks Using QTL and Phenotypic Information

(2014) Huange Wang et al.   PLoS One

Is Structural Equation Modeling Advantageous for the Genetic Improvement of Multiple Traits?

(2013) B. D. Valente et al.   GENETICS

NON-SMOKY GLYCOSYLTRANSFERASE1 Prevents the Release of Smoky Aroma from Tomato Fruit

(2013) Y. M. Tikunov et al.   PLANT CELL

Multi-trait and multi-environment QTL analyses of yield and a set of physiological traits in pepper

(2013) N. A. Alimi et al.   THEORETICAL AND APPLIED GENETICS

Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations

(2013) Xiaodong Cai et al.   PLoS Computational Biology

Alteration of the Interconversion of Pyruvate and Malate in the Plastid or Cytosol of Ripening Tomato Fruit Invokes Diverse Consequences on Sugar But Similar Effects on Cellular Organic Acid, Metabolism, and Transitory Starch Accumulation

(2012) S. Osorio et al.   PLANT PHYSIOLOGY

Genetic analysis of metabolome–phenotype interactions: from model to crop species

(2012) Natalia Carreno-Quintero et al.   TRENDS IN GENETICS

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

(2011) Jan Krumsiek et al.   BMC Systems Biology

Causal graphical models in systems genetics: A unified framework for joint inference of causal network and genetic architecture for correlated phenotypes

(2010) Elias Chaibub Neto et al.   Annals of Applied Statistics

Functional characterization of a carotenoid cleavage dioxygenase 1 and its relation to the carotenoid accumulation and volatile emission during the floral development of Osmanthus fragrans Lour.

(2010) Susanne Baldermann et al.   JOURNAL OF EXPERIMENTAL BOTANY

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Critical reasoning on causal inference in genome-wide linkage and association studies

(2010) Yang Li et al.   TRENDS IN GENETICS

Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations

(2010) Benjamin A. Logsdon et al.   PLoS Computational Biology

Use of network analysis to capture key traits affecting tomato organoleptic quality

(2009) Paola Carli et al.   JOURNAL OF EXPERIMENTAL BOTANY

RNA Interference of LIN5 in Tomato Confirms Its Role in Controlling Brix Content, Uncovers the Influence of Sugars on the Levels of Fruit Hormones, and Demonstrates the Importance of Sucrose Cleavage for Normal Fruit Development and Fertility

(2009) M. I. Zanor et al.   PLANT PHYSIOLOGY

Using genetic markers to orient the edges in quantitative trait networks: The NEO software

(2008) Jason E Aten et al.   BMC Systems Biology

Inferring Causal Phenotype Networks From Segregating Populations

(2008) Elias Chaibub Neto et al.   GENETICS

Flavour compounds in tomato fruits: identification of loci and potential pathways affecting volatile composition

(2008) Sandrine Mathieu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Lycopene Accumulation Affects the Biosynthesis of Some Carotenoid-related Volatiles Independent of Ethylene in Tomato

(2008) Hongyan Gao et al.   Journal of Integrative Plant Biology