Comprehensive definition of genome features inSpirodela polyrhizaby high-depth physical mapping and short-read DNA sequencing strategies

Genetic characterization and barcoding of taxa in the genera Landoltia and Spirodela (Lemnaceae) by three plastidic markers and amplified fragment length polymorphism (AFLP)

(2015) Manuela Bog et al.   HYDROBIOLOGIA

A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis

(2015) Michael Freeling et al.   Molecular Plant

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

(2015) Robert VanBuren et al.   NATURE

The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution

(2015) Hieu Xuan Cao et al.   NEW PHYTOLOGIST

A new approach for annotation of transposable elements using small RNA mapping

(2015) Moaine El Baidouri et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes

(2015) Carina F. Mugal et al.   G3-Genes Genomes Genetics

Optical mapping in plant comparative genomics

(2015) Haibao Tang et al.   GigaScience

Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

(2015) Hongzhi Cao et al.   GigaScience

Plant genome size variation: bloating and purging DNA

(2014) T. P. Michael   Briefings in Functional Genomics

NADH-dependent glutamate synthase plays a crucial role in assimilating ammonium in the Arabidopsis root

(2014) Noriyuki Konishi et al.   PHYSIOLOGIA PLANTARUM

Chromatin organisation in duckweed interphase nuclei in relation to the nuclear DNA content

(2014) H. X. Cao et al.   PLANT BIOLOGY

Duckweed in bloom: the 2nd International Conference on Duckweed Research and Applications heralds the return of a plant model for plant biology

(2014) Eric Lam et al.   PLANT MOLECULAR BIOLOGY

Ribosomal RNA gene repeats, their stability and cellular senescence

(2014) Takehiko KOBAYASHI   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation as a system of plant genomic immunity

(2014) M. Yvonne Kim et al.   TRENDS IN PLANT SCIENCE

Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

(2014) Florian Maumus et al.   Nature Communications

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

The clonal dependence of turion formation in the duckweedSpirodela polyrhiza-an ecogeographical approach

(2013) Katja Kuehdorf et al.   PHYSIOLOGIA PLANTARUM

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

(2013) Alex R. Hastie et al.   PLoS One

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Multiple distinct small RNAs originate from the same microRNA precursors

(2010) Weixiong Zhang et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

(2009) C. Johnson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

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

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

The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

(2008) Eric Lyons et al.   Tropical Plant Biology