The complex architecture and epigenomic impact of plant T-DNA insertions

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

(2018) Todd P. Michael et al.   Nature Communications

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere

(2017) Henk J. Schouten et al.   PLANT CELL REPORTS

Accurate measurement of transgene copy number in crop plants using droplet digital PCR

(2017) Ray Collier et al.   PLANT JOURNAL

Inactivation of Pol θ and C-NHEJ eliminates off-target integration of exogenous DNA

(2017) Alex N. Zelensky et al.   Nature Communications

T-DNA-genome junctions form early after infection and are influenced by the chromatin state of the host genome

(2017) Shay Shilo et al.   PLoS Genetics

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

The Structural Features of Thousands of T-DNA Insertion Sites Are Consistent with a Double-Strand Break Repair-Based Insertion Mechanism

(2015) Nils Kleinboelting et al.   Molecular Plant

Interpreting the language of histone and DNA modifications

(2014) Scott B. Rothbart et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Poretools: a toolkit for analyzing nanopore sequence data

(2014) N. J. Loman et al.   BIOINFORMATICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Dynamic regulation of Polycomb group activity during plant development

(2012) Marian Bemer et al.   CURRENT OPINION IN PLANT BIOLOGY

Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes

(2012) Devin Coleman-Derr et al.   PLoS Genetics

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Arabidopsis REF6 is a histone H3 lysine 27 demethylase

(2011) Falong Lu et al.   NATURE GENETICS

Gateway Binary Vectors with the Bialaphos Resistance Gene,bar, as a Selection Marker for Plant Transformation

(2010) Shinya NAKAMURA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales

(2010) Seth DeBolt   Genome Biology and Evolution

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

(2010) Kerstin Kaufmann et al.   Nature Protocols

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Linking genotype to phenotype using the Arabidopsis unimutant collection

(2010) Ronan C. O’Malley et al.   PLANT JOURNAL

Chromosomal translocations are a common phenomenon in Arabidopsis thaliana T-DNA insertion lines

(2010) Katie A. Clark et al.   PLANT JOURNAL

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Replication Stress Leads to Genome Instabilities in Arabidopsis DNA Polymerase   Mutants

(2009) D. Schuermann et al.   PLANT CELL

The T-DNA integration pattern in Arabidopsis transformants is highly determined by the transformed target cell

(2009) Sylvie De Buck et al.   PLANT JOURNAL

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Getting the most out of publicly available T-DNA insertion lines

(2008) Bekir Ülker et al.   PLANT JOURNAL

Unexpected silencing effects from T-DNA tags in Arabidopsis

(2008) Lucia Daxinger et al.   TRENDS IN PLANT SCIENCE