Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

(2016) Massimo Iorizzo et al.   NATURE GENETICS

Identification of a Chlorophyll Dephytylase Involved in Chlorophyll Turnover in Arabidopsis

(2016) Yao-Pin Lin et al.   PLANT CELL

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

(2016) Zhenzhen Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

(2016) Atsushi Hoshino et al.   Nature Communications

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing

(2015) Kaori Tatsumi et al.   BIOTECHNIQUES

Horizontal gene transfer in parasitic plants

(2015) Charles C Davis et al.   CURRENT OPINION IN PLANT BIOLOGY

Getting ready for host invasion: elevated expression and action of xyloglucan endotransglucosylases/hydrolases in developing haustoria of the holoparasitic angiospermCuscuta

(2015) Stian Olsen et al.   JOURNAL OF EXPERIMENTAL BOTANY

PGSB PlantsDB: updates to the database framework for comparative plant genome research

(2015) Manuel Spannagl et al.   NUCLEIC ACIDS RESEARCH

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

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

De Novo Assembly and Characterization of the Transcriptome of the Parasitic Weed Dodder Identifies Genes Associated with Plant Parasitism

(2014) A. Ranjan et al.   PLANT PHYSIOLOGY

Genomic-scale exchange of mRNA between a parasitic plant and its hosts

(2014) G. Kim et al.   SCIENCE

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

(2014) Pierre-Marc Delaux et al.   PLoS Genetics

Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences

(2013) Lauren A. Eserman et al.   AMERICAN JOURNAL OF BOTANY

Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species

(2013) Yeting Zhang et al.   BMC EVOLUTIONARY BIOLOGY

Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression

(2013) Loren A Honaas et al.   BMC PLANT BIOLOGY

Profiling mRNAs of Two Cuscuta Species Reveals Possible Candidate Transcripts Shared by Parasitic Plants

(2013) Linjian Jiang et al.   PLoS One

Trafficking of molecules between parasitic plants and their hosts

(2013) R Aly   WEED RESEARCH

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

(2013) Michiel Van Bel et al.   GENOME BIOLOGY

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees

(2012) Maureen Stolzer et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Mobilization of retrotransposons in synthetic allotetraploid tobacco

(2010) M. Petit et al.   NEW PHYTOLOGIST

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Horizontal Gene Transfer by the Parasitic Plant Striga hermonthica

(2010) S. Yoshida et al.   SCIENCE

Towards Characterization of the Chloroplast NAD(P)H Dehydrogenase Complex

(2009) Marjaana Suorsa et al.   Molecular Plant

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Exchange of Genetic Material Between Cells in Plant Tissue Grafts

(2009) S. Stegemann et al.   SCIENCE

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS