Strong Maternal Effects on Gene Expression inArabidopsis lyrataHybrids

Inbreeding Affects Gene Expression Differently in Two Self-IncompatibleArabidopsis lyrataPopulations with Similar Levels of Inbreeding Depression

(2015) Mandy Menzel et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) S. Anders et al.   BIOINFORMATICS

Extensivecis-Regulatory Variation Robust to Environmental Perturbation inArabidopsis

(2014) Francisco A. Cubillos et al.   PLANT CELL

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds

(2011) Peter C McKeown et al.   BMC PLANT BIOLOGY

Design and validation issues in RNA-seq experiments

(2011) Z. Fang et al.   BRIEFINGS IN BIOINFORMATICS

Variation in tolerance to drought among Scandinavian populations of Arabidopsis lyrata

(2011) Nina Sletvold et al.   EVOLUTIONARY ECOLOGY

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm

(2011) Philip Wolff et al.   PLoS Genetics

LOCAL ADAPTATION, PHENOTYPIC DIFFERENTIATION, AND HYBRID FITNESS IN DIVERGED NATURAL POPULATIONS OF ARABIDOPSIS LYRATA

(2010) Päivi H. Leinonen et al.   EVOLUTION

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

Testing population differentiation in plant species - how important are environmental maternal effects

(2010) Armin Bischoff et al.   OIKOS

Patterns of hybridization in plants

(2010) Kenneth D. Whitney et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Geographical variation in postzygotic isolation and its genetic basis within and between two Mimulus species

(2010) N. H. Martin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Paternal effects in Arabidopsis indicate that offspring can influence their own size

(2010) C. House et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2010) Matthew D Young et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Local adaptation in European populations of Arabidopsis lyrata (Brassicaceae)

(2009) P. H. Leinonen et al.   AMERICAN JOURNAL OF BOTANY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Completing the cycle: maternal effects as the missing link in plant life histories

(2009) K. Donohue   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio

(2008) M. J Hegarty et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Developmental plasticity and the evolution of parental effects

(2008) T ULLER   TRENDS IN ECOLOGY & EVOLUTION