RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis

OsSPL13 controls grain size in cultivated rice

(2016) Lizhen Si et al.   NATURE GENETICS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids

(2016) Andreas F. Kautt et al.   PLoS Genetics

Clumpak : a program for identifying clustering modes and packaging population structure inferences across K

(2015) Naama M. Kopelman et al.   Molecular Ecology Resources

Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding

(2015) Haijun Liu et al.   Molecular Plant

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Characterization of an activation-tagged mutant uncovers a role of GLABRA2 in anthocyanin biosynthesis in Arabidopsis

(2015) Xiaoyu Wang et al.   PLANT JOURNAL

Transcriptional control of flavonoid biosynthesis by MYB–bHLH–WDR complexes

(2015) Wenjia Xu et al.   TRENDS IN PLANT SCIENCE

Identification of chromosomal translocation hotspots via scan statistics

(2014) Israel T. Silva et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population

(2014) Jia Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Wild Lactuca species, their genetic diversity, resistance to diseases and pests, and exploitation in lettuce breeding

(2013) Aleš Lebeda et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity

(2013) Jianjian Qi et al.   NATURE GENETICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

(2013) Maria José Truco et al.   G3-Genes Genomes Genetics

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Stem cell function during plant vascular development

(2012) Shunsuke Miyashima et al.   EMBO JOURNAL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

QTL analysis reveals the genetic architecture of domestication traits in Crisphead lettuce

(2012) Yorike Hartman et al.   GENETIC RESOURCES AND CROP EVOLUTION

Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels

(2012) Hui Li et al.   NATURE GENETICS

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

ON THE ORIGIN OF CULTIVATED LETTUCE

(2010) K. LINDQVIST   HEREDITAS

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

The VQ motif protein IKU1 regulates endosperm growth and seed size in Arabidopsis

(2010) Aihua Wang et al.   PLANT JOURNAL

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Next generation software for functional trend analysis

(2009) G. F. Berriz et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies

(2009) Priya Duggal et al.   BMC GENOMICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

CPC, a Single-Repeat R3 MYB, Is a Negative Regulator of Anthocyanin Biosynthesis in Arabidopsis

(2009) Hui-Fen Zhu et al.   Molecular Plant

CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL Function Synergistically in the Circadian Clock of Arabidopsis

(2009) S. X. Lu et al.   PLANT PHYSIOLOGY

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

(2009) K. L. McNally et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

ARABIDOPSIS THALIANA HOMEOBOX GENE1 Establishes the Basal Boundaries of Shoot Organs and Controls Stem Growth

(2008) C. Gomez-Mena et al.   PLANT CELL