LASSO modeling of the Arabidopsis thaliana seed/seedling transcriptome: a model case for detection of novel mucilage and pectin metabolism genes

A Lasso regression model for the construction of microRNA-target regulatory networks

(2011) Yiming Lu et al.   BIOINFORMATICS

HRE-Type Genes are Regulated by Growth-Related Changes in Internal Oxygen Concentrations During the Normal Development of Potato (Solanum tuberosum) Tubers

(2011) Francesco Licausi et al.   PLANT AND CELL PHYSIOLOGY

Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach

(2011) Atsushi Fukushima et al.   Plant Biotechnology

Functional Network Construction inArabidopsisUsing Rule-Based Machine Learning on Large-Scale Data Sets

(2011) George W. Bassel et al.   PLANT CELL

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

Coordinated Gene Networks RegulatingArabidopsisPlant Metabolism in Response to Various Stresses and Nutritional Cues

(2011) Hadar Less et al.   PLANT CELL

The Arabidopsis Transcription Factor LUH/MUM1 Is Required for Extrusion of Seed Coat Mucilage

(2011) J. Huang et al.   PLANT PHYSIOLOGY

The Transcriptional Regulator LEUNIG_HOMOLOG Regulates Mucilage Release from the Arabidopsis Testa

(2011) M. Walker et al.   PLANT PHYSIOLOGY

Computational analysis of tissue-specific gene networks: application to murine retinal functional studies

(2010) Jianfei Hu et al.   BIOINFORMATICS

Algorithm-driven Artifacts in median polish summarization of Microarray data

(2010) Federico M Giorgi et al.   BMC BIOINFORMATICS

Coexpression Analysis Identifies Rice Starch Regulator1, a Rice AP2/EREBP Family Transcription Factor, as a Novel Rice Starch Biosynthesis Regulator

(2010) F.-F. Fu et al.   PLANT PHYSIOLOGY

Network Analysis Identifies ELF3 as a QTL for the Shade Avoidance Response in Arabidopsis

(2010) José M. Jiménez-Gómez et al.   PLoS Genetics

Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions

(2009) Mika Gustafsson et al.   Annals of the New York Academy of Sciences

MUM ENHANCERS are important for seed coat mucilage production and mucilage secretory cell differentiation in Arabidopsis thaliana

(2009) Andrej A. Arsovski et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Arabidopsis MYB5 Transcription Factor Regulates Mucilage Synthesis, Seed Coat Development, and Trichome Morphogenesis

(2009) S. F. Li et al.   PLANT CELL

The Trihelix Transcription Factor GTL1 Regulates Ploidy-Dependent Cell Growth in the Arabidopsis Trichome

(2009) C. Breuer et al.   PLANT CELL

A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize

(2009) BJÖRN USADEL et al.   PLANT CELL AND ENVIRONMENT

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves

(2009) Ling Li et al.   PLANT JOURNAL

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

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

(2009) K. Vandepoele et al.   PLANT PHYSIOLOGY

Discerning static and causal interactions in genome-wide reverse engineering problems

(2008) Mattia Zampieri et al.   BIOINFORMATICS

A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana: Confirmed actors and newcomers

(2008) Muhammad Irshad et al.   BMC PLANT BIOLOGY

TTG1 complex MYBs, MYB5 and TT2, control outer seed coat differentiation

(2008) Antonio Gonzalez et al.   DEVELOPMENTAL BIOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

GeneCAT—novel webtools that combine BLAST and co-expression analyses

(2008) Marek Mutwil et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene-Metabolite Correlations in Arabidopsis

(2008) K. Yonekura-Sakakibara et al.   PLANT CELL

A subtilisin-like serine protease essential for mucilage release from Arabidopsis seed coats

(2008) Carsten Rautengarten et al.   PLANT JOURNAL

Characterization of IRX10 and IRX10-like reveals an essential role in glucuronoxylan biosynthesis in Arabidopsis

(2008) David M. Brown et al.   PLANT JOURNAL

Low duplicability and network fragility of cancer genes

(2008) Davide Rambaldi et al.   TRENDS IN GENETICS