Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis

A novel RNA binding protein affects rbcL gene expression and is specific to bundle sheath chloroplasts in C4 plants

(2013) Shaun M Bowman et al.   BMC PLANT BIOLOGY

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4Kranz anatomy

(2013) Peng Wang et al.   PLANT JOURNAL

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Adaptive Evolution of C4 Photosynthesis through Recurrent Lateral Gene Transfer

(2012) Pascal-Antoine Christin et al.   CURRENT BIOLOGY

Exit from Proliferation during Leaf Development in Arabidopsis thaliana: A Not-So-Gradual Process

(2012) Megan Andriankaja et al.   DEVELOPMENTAL CELL

Historical profiling of maize duplicate genes sheds light on the evolution of C4 photosynthesis in grasses

(2012) Yao-Ming Chang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The dicotyledonous NAD malic enzyme C4plant Cleome gynandra displays age-dependent plasticity of C4decarboxylation biochemistry

(2012) M. Sommer et al.   PLANT BIOLOGY

Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis

(2012) Y.-M. Chang et al.   PLANT PHYSIOLOGY

Evolution of GOLDEN2-LIKE gene function in C3 and C4 plants

(2012) Peng Wang et al.   PLANTA

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

C4 eudicots are not younger than C4 monocots

(2011) Pascal-Antoine Christin et al.   JOURNAL OF EXPERIMENTAL BOTANY

Exploiting the engine of C4 photosynthesis

(2011) R. F. Sage et al.   JOURNAL OF EXPERIMENTAL BOTANY

The C4 plant lineages of planet Earth

(2011) R. F. Sage et al.   JOURNAL OF EXPERIMENTAL BOTANY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Systems Analysis of a Maize Leaf Developmental Gradient Redefines the Current C4 Model and Provides Candidates for Regulation

(2011) T. R. Pick et al.   PLANT CELL

Quantitative analysis of venation patterns of Arabidopsis leaves by supervised image analysis

(2011) Stijn Dhondt et al.   PLANT JOURNAL

Multiple Arabidopsis genes primed for recruitment into C4 photosynthesis

(2011) Kaisa Kajala et al.   PLANT JOURNAL

Independent and Parallel Recruitment of Preexisting Mechanisms Underlying C4 Photosynthesis

(2011) N. J. Brown et al.   SCIENCE

The Regulation of Gene Expression Required for C4Photosynthesis

(2010) Julian M. Hibberd et al.   Annual Review of Plant Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

An mRNA Blueprint for C4 Photosynthesis Derived from Comparative Transcriptomics of Closely Related C3 and C4 Species

(2010) A. Brautigam et al.   PLANT PHYSIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Shifts in leaf vein density through accelerated vein formation in C4Flaveria (Asteraceae)

(2009) Athena D. McKown et al.   ANNALS OF BOTANY

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

(2009) Yuling Jiao et al.   NATURE GENETICS

GLK Transcription Factors Coordinate Expression of the Photosynthetic Apparatus in Arabidopsis

(2009) M. T. Waters et al.   PLANT CELL

C4acid decarboxylases required for C4photosynthesis are active in the mid-vein of the C3speciesArabidopsis thaliana, and are important in sugar and amino acid metabolism

(2009) Naomi J. Brown et al.   PLANT JOURNAL

Control of Leaf and Vein Development by Auxin

(2009) E. Scarpella et al.   Cold Spring Harbor Perspectives in Biology

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

(2009) Iain MacCallum et al.   GENOME BIOLOGY

Using C4 photosynthesis to increase the yield of rice—rationale and feasibility

(2008) Julian M Hibberd et al.   CURRENT OPINION IN PLANT BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH