Extensive genome heterogeneity leads to preferential allele expression and copy number-dependent expression in cultivated potato

Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

(2016) Vasantika Suryawanshi et al.   BMC GENOMICS

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

(2016) Jinghua Yang et al.   NATURE GENETICS

Expression-level support for gene dosage sensitivity in threeGlycinesubgenusGlycinepolyploids and their diploid progenitors

(2016) Jeremy E. Coate et al.   NEW PHYTOLOGIST

Arabidopsis thaliana G2-LIKE FLAVONOID REGULATOR and BRASSINOSTEROID ENHANCED EXPRESSION1 are low-temperature regulators of flavonoid accumulation

(2016) Antonios Petridis et al.   NEW PHYTOLOGIST

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum

(2016) Michael A. Hardigan et al.   PLANT CELL

Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin

(2015) Jan M de Boer et al.   BMC GENOMICS

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance

(2015) James J Crowley et al.   NATURE GENETICS

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

(2015) Zhonghua Zhang et al.   PLANT CELL

Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions

(2015) Lei Gong et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Allele-specific expression and eQTL analysis in mouse adipose tissue

(2014) Yehudit Hasin-Brumshtein et al.   BMC GENOMICS

Extensive Translational Regulation of Gene Expression in an Allopolyploid (Glycine dolichocarpa)

(2014) J. E. Coate et al.   PLANT CELL

Global RNA sequencing reveals that genotype-dependent allele-specific expression contributes to differential expression in rice F1 hybrids

(2013) Gaoyuan Song et al.   BMC PLANT BIOLOGY

RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations

(2013) Graeme D.M. Bell et al.   Genome Biology and Evolution

The bHLH proteins BEE and BIM positively modulate the shade avoidance syndrome in Arabidopsis seedlings

(2013) Nicolás Cifuentes-Esquivel et al.   PLANT JOURNAL

Copy number variation in potato - an asexually propagated autotetraploid species

(2013) Marina Iovene et al.   PLANT JOURNAL

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

(2013) L. G. Maron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retrospective View of North American Potato ( Solanum tuberosum L.) Breeding in the 20 th and 21 st Centuries

(2013) Candice N. Hirsch et al.   G3-Genes Genomes Genetics

Abiotic and Biotic Stress Responses in Group Phureja DM1-3 516 R44 as Measured through Whole Transcriptome Sequencing

(2013) Alicia N. Massa et al.   Plant Genome

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

(2012) Pablo Cingolani et al.   FLY

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Quantitative Allele-Specific Expression and DNA Methylation Analysis of H19, IGF2 and IGF2R in the Human Placenta across Gestation Reveals H19 Imprinting Plasticity

(2012) Sam Buckberry et al.   PLoS One

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Role of the Extensin Superfamily in Primary Cell Wall Architecture

(2011) D. T. A. Lamport et al.   PLANT PHYSIOLOGY

The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44

(2011) Alicia N. Massa et al.   PLoS One

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain

(2010) C. Gregg et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Global Analysis of Allele-Specific Expression in Arabidopsis thaliana

(2009) Xu Zhang et al.   GENETICS

The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water

(2009) Yoko Hattori et al.   NATURE

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Asymmetric allele-specific expression in relation to developmental variation and drought stress in barley hybrids

(2009) Maria von Korff et al.   PLANT JOURNAL

The frequency of polyploid speciation in vascular plants

(2009) T. E. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA